BIO101 Study Guide

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Study Guide Structure

In this study guide, the sections in each unit (1a., 1b., etc.) are the learning outcomes of that unit. 

Beneath each learning outcome are:

• questions for you to answer independently;
• a brief summary of the learning outcome topic; and
• and resources related to the learning outcome. 

At the end of each unit, there is also a list of suggested vocabulary words.

How to Use this Study Guide

1. Review the entire course by reading the learning outcome summaries and suggested resources.
2. Test your understanding of the course information by answering questions related to each unit learning outcome and defining and memorizing the vocabulary words at the end of each unit.

By clicking on the gear button on the top right of the screen, you can print the study guide. Then you can make notes, highlight, and underline as you work.

Through reviewing and completing the study guide, you should gain a deeper understanding of each learning outcome in the course and be better prepared for the final exam!

Unit 1: Introduction to Biology

1a. List the basic characteristics of life that are common to all living things

• How does a nonliving thing (such as a rock) differ from a living organism (such as a mouse)?
• What are some examples of nonliving things that have some characteristics of life?
• How does a dead organism differ from a living organism?
• Why is a virus considered nonliving?

Biology studies living things, also known as organisms. We must consider characteristics common to all organisms to determine what makes something alive. Chemistry studies non-living matter, and biochemistry studies non-living chemical processes that occur within living organisms.

All organisms share these characteristics:

• Response to the environment
• Growth and developmental change
• Reproduction of cells
• Energy processing and chemical metabolism
• Regulation and maintenance of homeostasis
• Orderly composition with cellular basis
• Evolutionary adaptation based on the transmission of heritable traits

Some non-living things have some of these characteristics, but to be alive, something must have all of the characteristics. For example, a crystal has a high degree of order and can grow, but it does not maintain homeostasis. A virus can reproduce inside a host but it is not composed of cells and does not perform metabolism.

To review, see:

• Introduction to Biological Systems
• Advanced Characteristics of Life

1b. List the levels of organization of life and characteristics of each level

• What makes each level different from the one below it (or the level above it)?
• What are some examples of each level of organization?
• Where do we find these examples in the human body?
• What types of bonds exist between and among these levels of organization?

The levels of organization in biology are characterized by increasing complexity and order. They are structured in a hierarchical (or nested) arrangement. For example, atoms of different types form more complex structures called molecules. Molecules can form more complex structures called organelles, and so on. You should be able to list the levels of organization – from atoms all the way up to the biosphere.

• Atom – the basic building block of matter
• Element – multiple atoms bonded together; the periodic table shows all known elements
• Molecule – two or more bonded elements of the same type
• Compound – many molecules bond together, essentially a bond between two or more different elements
• Organelle – subcellular structure with specific functions
• Cell – the basic unit of life
• Tissue – a collection of cells
• Organ – multiple tissues packaged for a particular function
• Organ system - a group of functionally related organs
• Organism – a living individual
• Population – a group of individuals of the same species
• Community – different populations living together
• Ecosystem – a community along with the nonliving surroundings
• Biosphere – includes all living things and their surroundings

To review, see:

• Introduction to Biological Systems
• Advanced Characteristics of Life

1c. Describe the steps of the scientific method

• What is science? How does it work?
• What is the scientific method, and what are the steps of the scientific method?

Science is a logical system of inquiry. Consequently, science allows us to learn about ourselves and the universe we live in. A critical aspect of science is that it is based on evidence and is observational. Beyond mere observation, science involves the systematic testing of hypotheses. A hypothesis is an explanation for an observation, which is the process of gaining information. A hypothesis (which may be correct or incorrect) is a prediction. It attempts to explain why something is the way it is. We call hypotheses "educated guesses."

The active part of science is devising experiments to test hypotheses. A hypothesis is supported (although not proven) if an appropriate experiment yields the results the hypothesis predicted. Otherwise, you must modify or reject the hypothesis. This process has helped us learn about the universe. Biology is the corner of science that deals with living things in the universe, but biology is no different from science in general.

As you review the nature and process of science, pay attention to the steps in this flowchart, which demonstrates the process of science. You should understand the distinction between basic and applied science.

To review, see:

• The Science of Biology
• Themes and Concepts of Biology

1d. Describe the importance of using the scientific method in research

• How does scientific writing parallel the scientific method?
• Why is scientific writing important?
• How does scientific writing differ from everyday, "regular" writing?
• What is the goal of scientific writing?

Scientific writing is the action of recording an experiment conducted using the scientific method. The scientific method is a logical and uniform method of sharing the results and outcomes of an experiment or study with the objective of finding common ground and agreement with others in the scientific community.

The parts of a scientific paper parallel the steps of the scientific method. The observation, question, and hypothesis are included in the paper's "introduction" section. The experimentation and how all studies were conducted become the "materials and methods" section. The outcomes and findings, whether qualitative or quantitative, are in the "results" section. Any conclusions and possibilities for future studies are incorporated into the "discussion" section.

To review, see:

• The Science of Biology
• Themes and Concepts of Biology

Unit 1 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• atom
• biochemistry
• biology
• biosphere
• cell
• chemistry
• community
• compound
• ecosystem
• element
• hypothesis
• molecule
• observation
• organ
• organelle
• organism
• organ system 
• population
• science
• scientific method
• scientific writing
• tissue

Unit 2: Basic Chemistry

2a. List the major components of an atom and their relative locations to one another

• What are the three primary subatomic particles?
• What are the major differences between the various subatomic particles?
• Where are the various subatomic particles located within an atom?
• What is an electron shell, a subshell, and an orbital?

The universe is made of matter and energy. Matter (the material in the universe) is composed of almost unimaginably small particles called atoms. As tiny as atoms are, even smaller particles make up each atom. We call them subatomic particles because they are smaller than atoms.

The primary subatomic particles are protons, neutrons, and electrons. Protons and neutrons make up the nucleus of an atom. Electrons are outside the nucleus. A proton has an electrical charge of +1. A neutron is nearly identical in size to a proton, but it has no charge. An electron is much smaller than a proton or neutron. An electron is a charged particle. Despite being much smaller than a proton, the charge of an electron is equal in magnitude to the charge of a proton. However, the charge is opposite, so each electron has a charge of -1.

Electrons occupy spaces around the nucleus. These spaces have a hierarchical arrangement. An orbital is a space that can be occupied by electrons. Each orbital can contain up to two electrons. There are different types and shapes of orbitals: s, p, d, and f. There is only one kind of s orbital, but there are three kinds of p orbital, five d orbitals, and seven f orbitals. A collection of orbitals of the same type makes up a subshell, and a collection of subshells makes up a shell (also called an energy level).

The first shell includes only one subshell (the s subshell), which is made up of only one s orbital. The second shell is made up of two subshells (an s and a p subshell), with the s subshell being made up of one s orbital and the p subshell being made up of three p orbitals. Since different shells contain different numbers of orbitals, each shell has a different maximum number of electrons it can hold.

To review, see:

• More on the Atom
• Protons, Neutrons, and Electrons

2b. Describe how chemical attraction creates bonds of varying strengths

• What are the different types of chemical bonds?
• How is the strength of each bond different from one another?
• How can you relate the strength of a bond to the type of chemical attraction between its parts?
• What type of chemical interaction creates the strongest bonds? …the weakest bonds?

All biological systems rely on chemical bonds of various types. Bond strength is relative to the type of interaction between its parts.

From lowest to highest strength, these bonds are:

1. Van der Waals forces are relatively weak and temporary attractions between molecules, creating temporary dipoles.

2. Dipole-dipole interactions are stronger due to the attraction of negative and positive ends of different molecules.

3. Hydrogen bonds are stronger yet still considered weak bonds; they form between a hydrogen atom (which has one proton) and another negative atom.

4. Metallic bonds are stronger than hydrogen bonds. They form a "sea" of electrons among metal atoms, allowing for the conduction of electricity and heat.

5. Ionic bonds are stronger yet and are created between atoms that transfer electrons among themselves, creating opposite attracting charges.

6. Covalent bonds are the strongest type of bonds, created when atoms share electrons between them, creating a stable bond. The bond can be single (sharing of one pair of electrons), double (sharing two pairs), or triple (sharing three pairs).

To review, see:

• Orbitals
• More on Orbitals and Electron Configuration
• Valence Electrons
• Atoms, Isotopes, Ions, and Molecules: The Building Blocks
• Chemical Notation
• Balancing Chemical Equations
• Writing and Balancing Chemical Equations

2c. List the different types of bonds and how they lead to the formation of molecules and compounds

• What is a compound, and how does a compound differ from a molecule?
• How does a compound differ from an element?
• What hierarchy is involved between atoms, elements, molecules, and compounds?
• How are compounds formed?

Atoms are the building blocks of elements, which are pure substances made of one kind of atom. Although there are just more than 100 elements, there are countless substances in the universe. Most of these substances are compounds, not elements.

A compound is a substance made of two or more different kinds of atoms. This is the fundamental distinction between an element and a compound. Rather than simply being a mixture of two or more kinds of atoms, compounds are formed when different kinds of atoms interact. This interaction gives the compound different properties compared to the properties of the constituent elements.

For example, sodium chloride (table salt) is made of the elements sodium and chlorine, but sodium chloride (the compound) is different from each of these elements. The interactions between atoms in a compound are called chemical bonds. There are three major categories of chemical bonds:

• Ionic bonds form when one or more electrons from one atom are transferred to another atom, creating a positive ion and a negative ion that are attracted to each other because of their opposite charges. Ions are charged elements.

• Covalent bonds form when two different atoms share one or more pairs of electrons, which hold the two atoms together more strongly than an ionic bond.

• Metallic bonds consist of a "sea" of electrons that move about from one metallic atom to another, holding together many metallic atoms.

Molecules are particles bigger than atoms. They are made of multiple atoms (of the same or different elements) held together by covalent bonds. For example, a molecule of water consists of an oxygen atom that is covalently and separately bonded to two hydrogen atoms.

You should appreciate the distinction between atoms, ions, molecules, elements, and compounds.

To review, see:

• Orbitals
• More on Orbitals and Electron Configuration
• Valence Electrons
• Atoms, Isotopes, Ions, and Molecules: The Building Blocks
• Chemical Notation
• Balancing Chemical Equations
• Writing and Balancing Chemical Equations

2d. Describe the primary concepts of thermodynamics as they relate to heat, temperature, energy, and work

• What are energy, heat, temperature, and work?
• Can you name and describe the laws of thermodynamics?

Thermodynamics is the branch of science concerned with energy and energy transfer between objects. Although thermodynamics applies throughout the universe, we study it within biology because organisms are involved in many energy transactions. In other words, organisms are thermodynamic systems.

These are fundamental questions of thermodynamics. We can define energy as the capacity to do work. Work refers to some sort of change. For example, moving an object from one place to another requires work, and energy is required for that work. Heat is energy in the form of movement of particles (atoms, ions, or molecules) within a substance. Heat is energy that is unavailable for performing work. Temperature is a measure of the average speed of the particles in an object. Temperature and heat are not the same thing. Temperature does not depend on how much matter is present, whereas heat does.

For example, a swimming pool has the same temperature as a cup of water from that swimming pool, but the swimming pool contains much more heat than the cup of water because it contains much more matter.

Two of the four laws of thermodynamics are important in biology:

• The First Law of Thermodynamics states that energy cannot be created or destroyed, though it can be transferred and transformed. This is also known as the Law of Conservation of Energy.

• The Second Law of Thermodynamics states that every energy transaction increases the entropy (disorder) of the universe. An implication of this second law is that every energy transaction involves some loss of usable energy as heat, so no energetic process (including those occurring in organisms) can ever be 100 percent efficient.

These thermodynamic concepts are important for understanding the biochemistry of living things.

To review, see:

• Energy and Metabolism
• More on Energy
• The First Law of Thermodynamics
• Gibbs Free Energy

Unit 2 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• chemical bond
• covalent bond
• dipole-dipole interaction
• electron
• energy
• energy level
• entropy
• First Law of Thermodynamics
• heat
• hydrogen bonds
• ion
• ionic bond
• Law of Conservation of Energy
• matter
• metallic bond
• neutron
• orbital
• proton
• Second Law of Thermodynamics
• shell
• subatomic particle
• subshell
• temperature
• thermodynamics
• Van der Waals force
• work

Unit 3: Biological Molecules

3a. List the characteristics of water that make it important to life

• What is special about water?
• What is the electrical charge distribution on a water molecule?
• What does it mean that water is a universal solvent?
• Why does water's polarity make it well suited to its functions in biology?

Water is so indispensable for life that our primary method for searching for life outside Earth is to look for evidence of water.

A water molecule is composed of one oxygen atom that is simultaneously bonded to two hydrogen atoms. The covalent bonds between oxygen and hydrogen are polar because the sharing of electrons between oxygen and hydrogen is not equal. This unequal sharing means the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged. This makes the water molecule polar and gives water several special characteristics:

• Water molecules can form hydrogen bonds with other polar molecules, including other water molecules.

• Water is less dense in the frozen state than in the liquid state. Consequently, bodies of water freeze from the top down and thaw during seasonal warming.

• Water has a high specific heat capacity, requiring more energy than most substances to change its temperature. This stabilizes the temperature of bodies of water more than landmasses.

• Water has a high cohesion. This can create a capillary attraction that can lift water through vessels to the tops of the tallest trees.

• Water is an excellent solvent. The chemistry of life is mostly aqueous solution chemistry.

• Water has high surface tension. This allows small organisms to walk on the surface of water.

• Water has a high latent heat of vaporization. This means it requires a lot of energy to change its state from liquid to gas, allowing for effective evaporative cooling by sweating.

• Water exists in all three states (solid, liquid, and gas) within a comparatively narrow range of temperatures that organisms can tolerate.

Due to these special characteristics, it is no surprise that life evolved in the water of the ocean. We can think of every living cell as a tiny bag of water and biological molecules. Keep these special properties in mind as you study biology. Be sure to review polarity and how it underlies these properties.

To review, see:

• Water
• The Properties of Water

3b. Describe the role of acids, bases, and buffers in biological systems

• What are acids and bases?
• What does the addition of Hydrogen ions (H+) or Hydroxyl ions (OH-) do to the pH of a solution?
• How do buffers work?

In aqueous solutions, the hydrogen atom shifts from one water molecule to another. This creates H+ and OH- ions that are very reactive. These ions are equal in pure water, but an imbalance in concentration occurs when certain solutes are added. Acids increase the H+ concentration; bases decrease the H+ concentration. Different parts of living organisms have different amounts of acids and bases.

For example, the stomach requires high amounts of acid to break down food. The bloodstream is a different environment. Buffers are chemicals that resist the changes that acids and bases make in a solution of the body's environment.

To review, see:

• Acids, Bases, and the pH Scale
• pH, pOH, and pKw
• Electrolytes and pH
• Acid-Base Equilibrium and Acid Strength

3c. Define pH and the role of hydrogen ions in living systems

• What is pH?
• How do acids and bases alter the hydrogen ion concentration in a solution?
• What values are considered acid?
• What values are considered basic?
• What value is neutral?

pH measures the H+ ion concentration in a solution. We define it as the negative log of H+ concentration, which creates an inverse comparison. The pH value is low when the H+ ion concentration increases.

The pH scale is from 0 to 14. Pure water has a pH of 7 because the H+ concentration equals the OH- concentration. Acids increase the H+ ion concentration by tenfold and lower the pH, while bases decrease the H+ concentration. The stomach's pH is 2, while the blood is around 7. Buffers are needed to maintain the pH in these environments.

To review, see:

• Acids, Bases, and the pH Scale
• Electrolytes and pH
• Hydrogen Atoms in Acids and Bases

3d. Describe the structure of the four major biological macromolecules

• What are the four classes of biological macromolecules?
• What are the structural differences between the different classes of biological macromolecules?
• Where can each of the four biological macromolecules be found in the human body?

All organisms feature four major classes of large biological molecules or macromolecules:

1. Lipids are composed of a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them partially non-polar because the covalent bonds in hydrocarbons (between two carbon atoms and between a carbon atom and a hydrogen atom) share electrons equally.

2. Polysaccharides are complex carbohydrates made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio, giving them an empirical formula generalized as (CH₂O)_n.

3. Proteins are enormously diverse in structure and function, yet they all feature the substructure of amino acids. Each amino acid features a central carbon atom simultaneously connected to a hydrogen atom, an amino group, a carboxyl group, and a variable R group.

4. Nucleic acids are informational molecules with a basic structure in which each subunit includes a five-carbon sugar (either ribose or deoxyribose) attached to a phosphate group and a nitrogenous base.

Knowing the chemical structure that underlies these essential biomolecules will help you recognize them. It also explains how they are constructed within cells, interact chemically with each other in metabolism, and form structural components of organisms.

To review, see:

• Biological Polymers
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

3e. Describe the functions of the four major biological macromolecules as they relate to our physical requirements for health

• What are the primary functions of the four classes of biological macromolecules?
• Where is each macromolecule class located in the body?
• Which foods contain each of the four classes of biological macromolecules?
• What amount of each macromolecule is essential for sustaining human life?

Lipids (fats) store energy and provide thermal insulation and protective padding. Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes, oils, and many hormones.

Some polysaccharides, or complex sugars (such as the cellulose in plants and chitin in fungi), are important for their structural strength, whereas other polysaccharides (such as starch, which plants create to store carbohydrates, and glycogen, used for the same function in animals) are important for storing energy. Polysaccharides also serve as identity markers on the surfaces of cells, so they play a role in immunity.

Proteins, composed of chains of amino acids, perform an impressive list of biological functions. They function as enzymes, structural elements, chemical signals, transporters, and receptors. They also play important roles in cell-to-cell adhesion and immunity.

Nucleic acids include various DNA and RNA molecules. They serve informational purposes. DNA stores the genetic code, and various types of RNA help interpret that code to build proteins through transcription and translation. Specific RNAs can also function as catalysts.

To review, see:

• Biological Polymers
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids

3f. Indicate the monomers and polymers of carbohydrates, proteins, and nucleic acids

• Which monomers make up polysaccharides?
• Which monomers make up proteins?
• Which monomers make up nucleic acids?

A polymer is a category of macromolecule that is built by connecting many ("poly" means many) smaller subunits called monomers. Only three of the four biological macromolecules we have been studying are polymers. Lipids are not polymers since they do not contain repeating chains of monomers.

Polysaccharides are macromolecular carbohydrates – polymers made up of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in a linear or branched arrangement.

Carbohydrates include small and large molecules (macromolecules). Put another way, all polysaccharides are carbohydrates, but not all carbohydrates are polysaccharides. As the name implies, polysaccharides are polymers made of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in a linear or branched arrangement.

Proteins are polymers that are made up of monomers called amino acids. Unlike polysaccharides, which may be branched, a protein must be a linear (end-to-end) arrangement of amino acids. Organisms use 20 different kinds of amino acids (in an unlimited number of combinations and orders) to construct their proteins.

We can also call a nucleic acid a polynucleotide. This alternative name indicates it is a polymer made up of many nucleotides. In the case of DNA, the monomers are nucleotides that contain the pentose (five-carbon sugar) called deoxyribose. For RNA, the nucleotides contain ribose instead of deoxyribose. Although there are only four commonly used DNA nucleotides (and four commonly used RNA nucleotides), a typical DNA molecule contains millions of nucleotides. So, there is an unlimited number of sequences of such nucleotides.

Be sure you can match each type of monomer to the type of polymer they can form. In addition to reviewing various monomers, study how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions.

To review, see:

• Biological Polymers
• Proteins
• Nucleic Acids

3g. Describe the four levels of protein structure and how this relates to enzyme function

• What are the four levels of protein structure?
• How is each level distinct?
• Why is an enzyme particular to a certain substrate or class of substrates?
• What happens when a protein is denatured?

As a polymer, a protein is a large and complex molecule. Proteins have the most intricate and variable shapes among the three classes of biological polymers. Each protein has its particular function due to its specific shape (its conformation). This is why proteins have such diverse functions. Some proteins function as enzymes, which are biological catalysts.

We describe protein structure up to four levels:

• Primary structure is the sequence of amino acids (the number and order) for a single polypeptide. A polypeptide is one continuous strand made of a number of amino acids connected end-to-end in a certain order. If a protein is just one polypeptide, the "polypeptide" is a "protein."

• Secondary structure is the repeating pattern found within a polypeptide. The repeating patterns include alpha helices (a singular helix) and beta-pleated sheets.

• Tertiary structure is the three-dimensional structure of a single polypeptide. In other words, the specific shape that a single polypeptide assumes when it bends and folds is called its tertiary structure.

Every protein includes at least one polypeptide, so it features a primary, secondary, and tertiary structure. Only some proteins (called multimeric proteins) are made of more than two polypeptides. There is a fourth level of structure in addition to the other three levels for multimeric proteins.

• Quaternary structure is the way multiple individual polypeptides (each with their own primary, secondary, and tertiary structures) form the overall shape of a multimeric protein. In this case, "polypeptide" and "protein" are not interchangeable terms. The polypeptides are just parts of the overall protein.

Keep in mind that a protein cannot function properly unless it has the correct shape, regardless of its job in the cell.

To review, see:

• Proteins

Unit 3 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• acid
• amino acid
• base
• buffer
• carbohydrate
• DNA
• enzyme
• lipid
• monomer
• monosaccharide
• nucleic acid
• pH
• pH scale
• polymer
• polynucleotide
• polypeptide
• polysaccharide
• primary structure
• protein
• quaternary structure
• RNA
• secondary structure
• tertiary structure
• water

Unit 4: Cells and Cell Membranes

4a. Describe the structure and function of a typical biological membrane

• What is another name for the cell membrane?
• What types of molecules make up a cell membrane?
• Why is it necessary for biological membranes to form a lipid bilayer?
• How does the chemistry of the molecules in a membrane explain why a cell membrane forms?

The cell is the functional unit of life. Every organism has at least one cell, and metabolism (the chemistry of life) occurs within cells. A membrane separates the cell from its surroundings.

Every cell features a cell membrane, also called the plasma membrane. The plasma membrane is a complex arrangement of several different types of molecules. The chief components are phospholipids. Each phospholipid molecule is an amphipathic molecule (polar at one end and non-polar at the other end). This explains why plasma (cell) membranes form.

In the presence of water, phospholipids self-assemble into a phospholipid bilayer, with the non-polar tails in each monolayer pointing toward the non-polar tails of the other monolayer and the polar heads of each monolayer pointing toward the watery solution on its side of the membrane (the water interior of the cell for one monolayer, and the water exterior of the cell for the other monolayer).

In addition to the phospholipid bilayer, the plasma (cell) membrane features various other macromolecules, including proteins, sterols, and polysaccharides.

The plasma (cell) membrane is fundamental to life, so be sure to review its structure (and the structure of an individual phospholipid).

To review, see:

• Parts of the Cell Membrane
• Overview of the Cell Membrane
• Review of the Cell Membrane
• Structure of the Cell Membrane
• The Structure of Lipids
• The Fluid Mosaic Model

4b. Describe the characteristics of a membrane, solutes, and solvents

• What does it mean for a membrane to be semipermeable?
• How does water move through a membrane versus other molecules?
• What is the difference between a solvent and a solute?
• What does it mean to say that water is a "universal solvent"?
• What is the fluid mosaic model, and what part do lipids play?

Membranes are called semipermeable because they allow some substances through, based on size. They are composed of a lipid bilayer with hydrophobic and hydrophilic ends. Pores exist through the membrane that allow water to move via osmosis (down a concentration gradient), and some molecules move through due to their small size. Larger molecules that can not diffuse through the membrane can be transported using embedded integral protein channels through passive transport or facilitated diffusion.

To review, see:

• Overview of the Cell Membrane
• Parts of the Cell Membrane
• Review of the Cell Membrane
• Structure of the Cell Membrane
• The Structure of Lipids
• The Fluid Mosaic Model

4c. Predict where molecules will move and how the mass of a cell may change

• What are the components of a solution?
• What is the difference between a solvent and a solute?
• What happens to cell volume when osmosis occurs?
• What substances are insoluble in water?

A solution is a mixture that includes a solvent and a number of solutes. The solvent is the part of the solution that dissolves the solutes; the solutes are the parts the solvent has dissolved. In an aqueous solution, water is the solvent. A cell's plasma membrane forms a barrier between intracellular fluid and extracellular fluid (which are both aqueous solutions).

The plasma membrane is selectively permeable, which means some particles easily pass through the membrane while other particles cannot get through. Many solutes are effectively (although not perfectly) prevented from passing through the membrane, so we say the membrane is impermeable to these solutes. Water, on the other hand, can pass through to a certain degree.

Water passes through a plasma membrane using a mechanism called osmosis, a special type of passive diffusion process. The direction and rate of osmosis depend on the relative solute concentrations inside and outside the cell. Water always osmoses to the area that is less watery. This means water always moves away from the compartment that has a higher solute concentration. If the solute concentration of the extracellular fluid is higher than the solute concentration of the intracellular fluid, this means the extracellular fluid is less watery, so water will leave the cell by osmosis, and the cell volume will decrease.

If the reverse is true (the gradient is reversed), then water will enter the cell by osmosis, and cell volume will increase. In each case, notice that the water moves toward the less watery compartment (from high concentration to low, or "down" a concentration gradient). Organisms must regulate their osmotic conditions since changes in osmotic gradients can profoundly damage their cells.

To review, see:

• Passive Transport via Simple Diffusion
• Passive Transport and Tonicity
• Passive Transport via Osmosis
• More on Osmosis
• Facilitated Diffusion
• Primary Active, Secondary, and Bulk Transport
• Signaling Molecules and Cellular Receptors

4d. Describe the characteristics of different cell types

• What distinguishes a eukaryotic from a prokaryotic cell?
• Are animal and plant cells eukaryotic or prokaryotic?
• What do eukaryotic and prokaryotic cells have in common?
• What types of cell division are possible for prokaryotic cells but not for eukaryotic cells?

Although all cells share specific characteristics (for example, every cell has a plasma membrane), biologists recognize two fundamentally different categories of cells: prokaryotic cells and eukaryotic cells.

A prokaryotic cell does not feature membrane-bounded organelles; a eukaryotic cell does feature membrane-bounded organelles. A membrane-bounded organelle is an organelle (a tiny organ-like structure within a cell) that is enclosed by its own membrane, separate from the plasma membrane that encloses the entire cell.

Membrane-bounded organelles include diverse structures such as the nucleus, endoplasmic reticulum, lysosomes, mitochondria, chloroplasts, and others. Only eukaryotic cells feature these membrane-bounded organelles, though a eukaryotic cell might feature only some (but not all) of them.

For example, an animal cell (like one in a human body) features most of the membrane-bounded organelles, but it does not feature chloroplasts.

A plant cell, on the other hand, typically includes the membrane-bounded organelles found in an animal cell, plus it also features chloroplasts.

A bacterium, which is a prokaryotic cell, does not feature any of these membrane-bounded organelles. Ensure that you appreciate the differences between these major categories of cell types.

To review, see:

• Cell Structure
• Parts of a Cell
• Studying Cells
• Prokaryotic Cells
• Eukaryotic Cells
• Types of Cells
• The Endomembrane System, Proteins, the Cytoskeleton, and Connections between Cells and Cellular Activities

4e. Classify cells as prokaryotic or eukaryotic, unicellular or multicellular, animal or plant (or other)

• What is the difference between unicellular and multicellular organisms in terms of complexity?
• What do eukaryotes have that prokaryotes lack?
• Which organisms belong in each category: eukaryote or prokaryote?
• What functions of eukaryotes are impossible in prokaryotes?

The term prokaryotic refers to relatively simple cells that lack membrane-bound organelles (including the absence of a nucleus; hence, "pro" means "early", and "eukaryotic" refers to "having a nucleus"). Their DNA is in a simplistic circular form (not in well-defined chromosomes, as seen in eukaryotes) and is located in a "nuclear region" rather than confined and organized in a central location, also seen only in eukaryotes.

Bacteria are prokaryotic, and the rest of the organisms we have studied (plants, fungi, and animals) are eukaryotic ("eu" refers to having a "true" nucleus). Prokaryotes are always unicellular, but they can grow as colonies of individuals. For this reason, they are limited to a rudimentary type of cell division (binary fission or division into two parts) and cannot perform meiosis.

On the other hand, eukaryotic organisms have membrane-bound organelles and a membrane-bound central nucleus. Consequently, biologists consider them more complex. They can perform complex cellular functions, including meiosis. Eukaryotes differ slightly in their organelles due to specialized functions. For example, we only see chloroplasts in some algae and plants, allowing for photosynthesis.

To review, see:

• Cell Structure
• Parts of a Cell
• Studying Cells
• Prokaryotic Cells
• Eukaryotic Cells
• Types of Cells
• The Endomembrane System, Proteins, the Cytoskeleton, and Connections between Cells and Cellular Activities

4f. Indicate the functions of the organelles of different cell types

• What are some examples of organelles?
• Are all organelles membrane-bound?
• What types of cells feature these organelles?
• Which organelles are common to plant and animal cells?
• Do bacteria have organelles?

You should recognize several organelles in this course:

• Ribosome – not membrane-bounded; in prokaryotic and eukaryotic cells
• Plasma (cell) membrane – in prokaryotic and eukaryotic cells
• Cell wall – in most prokaryotic and some eukaryotic cells (although not animal cells)
• Nucleus – membrane-bounded; only in eukaryotic cells
• Mitochondrion – membrane-bounded; only in most eukaryotic cells
• Chloroplasts – membrane-bounded; only in photosynthetic eukaryotic cells (plants and algae)
• Golgi body – membrane-bounded; only in eukaryotic cells
• Central vacuole – membrane-bounded; only in some eukaryotic cells, including plants and some protists
• Rough endoplasmic reticulum – membrane-bounded; only in eukaryotic cells
• Smooth endoplasmic reticulum – membrane-bounded; only in eukaryotic cells
• Lysosome – membrane-bounded; only in eukaryotic cells
• Peroxisome – membrane-bounded; only in eukaryotic cells

Notice that most of these organelles are membrane-bound (wrapped in a membrane). Consequently, they only appear in eukaryotic cells, which are structurally more complex than the prokaryotic cells from which they evolved.

Figure 4.8 These figures show the major organelles and other cell components of (a) a typical animal cell and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central vacuole – structures not in animal cells. Most cells do not have lysosomes or centrosomes.

• What are the primary functions of the various types of organelles?
• What advantage is gained by some organelles being membrane-bound?

One difference between the various organelles is their shapes. However, our primary reason for classifying organelles differently is because they perform different functions, just as different organs in our body perform different functions.

• Ribosome – molecular machines that interpret codes in mRNA to build proteins
• Plasma (cell) membrane – defines the cell and forms the boundary between the contents of the cell and its surroundings
• Cell wall – thicker, more rigid than, and exterior to the plasma membrane; withstands pressure and prevents the cell from bursting
• Nucleus – enclosed by two membranes; houses the DNA
• Mitochondrion – enclosed by two membranes; site for cellular respiration
• Chloroplast – enclosed by two membranes; site for photosynthesis
• Golgi body – receives newly-formed proteins, modifies them, and packages them for transport to the plasma membrane or out of the cell
• Central vacuole – a largely water-filled organelle that can also house pigments and wastes
• Rough endoplasmic reticulum – the site for the synthesis of proteins the Golgi body will package
• Smooth endoplasmic reticulum – the site for the synthesis of lipids and storage of calcium ions
• Lysosome – digests materials by subjecting them to enzymes
• Peroxisome – safely breaks down harmful chemicals in the cell

The organelles that are membrane-bound form sub-compartments so they can perform their functions in isolation from the rest of the cellular contents. Before proceeding, be sure you know which functions each organelle performs.

To review, see:

• Cell Structure
• Parts of a Cell
• Studying Cells
• Prokaryotic Cells
• Eukaryotic Cells
• Types of Cells
• The Endomembrane System, Proteins, the Cytoskeleton, and Connections between Cells and Cellular Activities

4g. Explain how large signal molecules get their signal into the cell

• What are signal modules?
• What are receptors?
• How do signal molecules travel to receptors?
• Where are signal molecules produced in the body?

Signal molecules are examples of ligands because they must bind to other molecules. We call the molecules signal molecules that bind to receptors. When a signal binds to a receptor, that binding causes changes in the cell. These changes are the responses to the signal.

Some signal molecules are small and non-polar, so they pass easily through a cell's plasma membrane and bind to internal receptors. However, most signals are too large or too polar to pass through the plasma membrane and must bind to receptors on the cell's exterior surface. Although they cannot enter the cell, they still cause changes inside using three primary mechanisms – the difference lies in what kind of receptor receives the signals.

• Ion-channel-linked receptors are transmembrane proteins that simultaneously serve as signal receptors and ion channels. When a signal molecule binds to this type of receptor, the ion channel either opens or closes its gate. This leads to changes in the flow of ions, which are charged particles. This redistribution of charge causes various responses.

• G-protein-linked receptors are transmembrane receptors associated with special proteins (G proteins) situated on the part of the protein that is in contact with the interior surface of the membrane. The binding of a signal molecule to the receptor activates (and frees) the G protein, which causes various responses.

• Enzyme-linked receptors are transmembrane proteins that simultaneously serve as signal receptors and enzymes. The binding of a signal molecule to the receptor activates the enzymatic portion of the receptor (which faces the interior of the cell). Once activated, the enzyme catalyzes various reactions, which causes various responses.

Be sure to understand the functional differences between these three classes of receptors; all three operate by binding to a signal molecule at the exterior surface.

To review, see:

• Signaling Molecules and Cellular Receptors

4h. Describe the mechanisms of transport across biological membranes

• What are the primary categories of transmembrane transport?
• What is the fundamental difference between these primary categories?
• What energy source is used for active transport?
• What is the difference between osmosis and diffusion of molecules across a membrane?

Particles pass through biological membranes (including the plasma membrane) using various mechanisms, which we can classify into two categories. Transmembrane transport (transport of a particle through a biological membrane) can be active or passive. The requirement of an external source of energy distinguishes the two.

• Active transport requires an additional (external) source of energy to drive it. ATP is the most common energy source, but other energy sources can be used. Since additional energy is applied, active transport can move particles against their gradient (see definition in next paragraph), which causes gradients to become even steeper.

• Passive transport does not require additional (external) energy to occur. The energy that drives passive transport is in the gradient, a difference in magnitude. The gradient that drives passive transport can be a concentration gradient (the concentration of the particle type is higher on one side of the membrane than the other), an electrical gradient (when the charge distribution is different on one side of the membrane than the other), or both. In all cases of passive transport, the transport occurs down the gradient, from higher to lower concentration. Passive transport never occurs in the direction against the gradient.

There are important subcategories of passive transport:

• Simple diffusion is the passive transport of solute particles down the gradient for that type of solute directly through the phospholipid bilayer of the biological membrane. This can only occur for particles small enough or non-polar enough to pass through the bilayer.

• Facilitated diffusion is also diffusion, but it requires a transport protein's help (facilitation) to get the particle through the membrane. This occurs for particles that are too big or polar to cross the phospholipid bilayer directly.

• Osmosis is the passive transport of solvent particles (not solute particles) down the gradient for solvent particles through a selectively permeable membrane. In biological systems, the solvent is always water, so biological osmosis is the movement of water.

These transmembrane transport processes are fundamental to life because organisms must continuously exchange materials with their surroundings to stay alive.

To review, see:

• Review of the Cell Membrane
• Passive Transport via Simple Diffusion
• Passive Transport and Tonicity
• Passive Transport via Osmosis
• More on Osmosis
• Facilitated Diffusion
• Primary, Secondary, and Bulk Transport

Unit 4 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• active transport
• bacterium
• binary fission
• cell membrane
• cell wall
• central vacuole
• chloroplast
• concentration gradient
• electrical gradient
• enzyme-linked receptor
• eukaryotic cell
• facilitated diffusion
• G-protein-linked receptor
• Golgi body
• ion-channel-linked receptor
• lysosome
• membrane-bound
• metabolism
• mitochondrion
• nucleus
• osmosis
• passive transport
• peroxisome
• phospholipid bilayer
• plant cell
• prokaryotic cell
• receptor
• ribosome
• rough endoplasmic reticulum
• signal molecule
• simple diffusion
• smooth endoplasmic reticulum
• solution
• solvent
• transmembrane transport

Unit 5: Enzymes, Metabolism, and Cellular Respiration

5a. Explain the difference between matter and energy

• What is energy?
• How is energy different from matter?
• Are matter and energy interchangeable?
• What forms of energy and matter exist?

Organisms are open thermodynamic systems because they must exchange matter and energy with their surroundings. Matter, which is made up of atoms, is the material stuff of the universe. As we reviewed in previous units, it occupies space and has mass.

Energy is not material. It does not have mass or occupy space. We often describe energy as the capacity to perform work or bring about some sort of change. There are countless examples. A human performs work by flexing a muscle. A tiny cell within a human performs work by transporting particles into or out of a cell or by oxidizing fuel molecules. There are many different forms of energy (light energy, mechanical energy, heat energy, etc.), and we can broadly classify energy into two categories:

• Potential energy is energy in a stored form. It may be used, but it is not currently being used. The energy in food is an example of chemical potential energy.
• Kinetic energy is energy that is being used at the moment. A falling object, for example, has kinetic energy.

Energy can readily be converted between forms. For example, a book that falls from a shelf converts potential energy into kinetic energy. When someone moves the book back to the shelf, they convert kinetic energy into potential energy. The metabolism of life involves countless interactions between matter and energy and countless conversions between energy forms, so it is important to understand the distinction between matter and energy.

To review, see:

• Energy and Thermodynamics
• Death of a Gummy Bear

5b. Apply the laws of thermodynamics and conservation of matter to metabolism

• What are the laws of thermodynamics?
• How do these laws affect biological processes?
• What does it mean that energy and matter are "conserved"?
• What is the relationship between ADP and ATP in metabolic processes?

Recall that the First Law of Thermodynamics states energy is conserved (it cannot be created or destroyed; it can only be transferred and transformed). In ordinary chemical reactions (like biochemical reactions), matter is also conserved. Therefore, the overall amount of energy and matter entering the processes of glycolysis and cellular respiration is the same as the overall amount of energy and matter exiting these processes. What has changed are the forms of that energy and matter.

Energy enters as the potential chemical energy in the bonds of the glucose molecule. Some of that energy gets released as heat (unavailable for cellular work), and some of that energy ultimately gets stored in the bonds of ATP molecules. ATP is formed when ADP and inorganic phosphate combine. Matter enters as glucose and oxygen, and after many rearrangements of atoms, matter leaves as carbon dioxide and water.

To review, see:

• Energy and Thermodynamics
• Metabolism Part 1
• Metabolism Part 2
• Metabolism Part 3

5c. Describe the role of enzymes and how they function

• What is an enzyme?
• What kind of macromolecule makes up an enzyme?
• What is the function of an enzyme?
• What is a substrate?

Metabolism is the chemistry of life. Thousands of chemical reactions occur in a single cell, most of which rely on enzymes.

An enzyme is a protein that serves as a biological catalyst. A catalyst is a substance that greatly accelerates a chemical reaction without actually being a reactant in that reaction. In other words, a catalyst (and therefore an enzyme) does not get changed into another substance (a product). The enzyme interacts with the reactants to make it more likely for them to chemically react, turning them into products. We call the reactants of catalyzed reactions substrates. An enzyme operates by temporarily binding to substrates.

The rate of a reaction (its speed) when it is catalyzed by an enzyme is usually at least one million times faster than without the help of an enzyme. This is why enzymes are absolutely vital. Without enzymes, biochemical reactions of metabolism would occur much too slowly to support life.

Most importantly, enzymes are reusable since they do not get altered during the reaction – they can continue catalyzing the same sort of reaction until all of the substrate is depleted. To review, see:

• Metabolism: Part 3
• Enzyme Nomenclature

5d. Explain the role of cellular respiration

• What is oxidation and reduction?
• What are the inputs and outputs of cellular respiration?
• How does cellular respiration accomplish its redox reactions?

Any living cell can extract energy from fuel and temporarily store that energy in the form of ATP or a similar energy currency. This primary processing of fuel is called glycolysis. Only specific cells under the right conditions can continue where glycolysis leaves off, allowing much more usable energy to be extracted from the fuel. This additional processing of energy is called cellular respiration. Glycolysis and cellular respiration both extract usable energy from fuel by undergoing oxidation/reduction (or redox) reactions.

Oxidation is the loss of electrons from a particle (like a fuel molecule), whereas reduction is the gain of electrons. Since electrons are not destroyed in chemical reactions, oxidation occurs only if reduction also occurs. When something is oxidized (loses electrons), something else gets reduced (gains electrons). Organisms extract energy from fuel molecules by oxidizing these fuel molecules.

During cellular respiration, there is a substance (external to the process) that ultimately accepts the electrons that have been removed from the fuel. For aerobic organisms, that substance is oxygen, and when oxygen accepts these electrons (along with protons) from the fuel molecules, the oxygen gets reduced into water. Cellular respiration is important because it allows for the maximal oxidation of fuels, which maximizes the amount of energy that can be extracted and stored as ATP.

To review, see:

• Cellular Respiration
• Review of Cellular Respiration

5e. Account for the matter inputs and outputs to glycolysis, pyruvate oxidation (preparatory reaction), the Krebs/Citric Acid cycle, and the electron transport chain

• What are the material inputs and outputs for each of these processes?
• What factors may affect the rate of these processes (faster or slower)?
• What is the role of ADP in these processes?

Each component of the oxidation of glucose contributes to a series of reactions that can be summarized by a reaction equation that lists the inputs (reactants) and the outputs (products) of that process. The component processes that make up the complete oxidation of glucose are glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation (including electron transport and chemiosmosis).

It helps to review illustrations to make sense of these inputs and outputs.

To review, see:

• Introduction to Glycolysis
• Glycolysis
• More on Glycolysis
• The Process of Glycolysis
• The Krebs Cycle (Citric Acid Cycle)
• A Tour of the Citric Acid Cycle
• The Electron Transport Chain
• Energy Accounting
• More on the Electron Transport Chain
• Oxidative Phosphorylation
• Review of Cellular Respiration
• Metabolism Without Oxygen
• Anaerobic Cellular Respiration
• Fermentation and Anaerobic Respiration

5f. Describe the differences in the inputs and outputs in the processes of glycolysis, pyruvate oxidation (preparatory reaction), the Krebs/citric acid cycle, and the electron transport chain

• What are the sources and fates of energy in glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation?

The goal of the oxidation of a fuel (like glucose) is to transfer energy from the fuel into a versatile form of energy storage like ATP (adenosine triphosphate). Many energy transfers occur during the reactions during glycolysis and cellular respiration. These transfers involve the original fuel (glucose), intermediate fuels, energy-carrying coenzymes (NAD and FAD), and ATP. Some energy is lost as heat during each transfer due to the Third Law of Thermodynamics. This lost heat energy becomes unavailable to perform work in the cell.

During glycolysis, energy is first in the original fuel, glucose. By oxidizing glucose, some usable energy gets transferred into ATP and some into NADH. The intermediate fuel (pyruvate) that is left over also contains usable energy. During the oxidation of pyruvate, some of that usable energy gets transferred to more NADH. This leaves only acetyl coenzyme A as the remaining fuel, which still contains usable energy.

The citric acid cycle completes the oxidation of the remaining fuel (acetyl coenzyme A), and the usable energy that is extracted gets transferred to more NADH, to more ATP, and to FADH₂. The carbon dioxide that remains from the fuel contains no usable energy (it is spent fuel). Oxidative phosphorylation collects all of the usable energy that was transferred to NADH and FADH₂ (in the earlier processes), and the usable energy is transferred to more ATP.

The final acceptor of the electron is the molecule oxygen, which subsequently changes to water as the final waste product.

To review, see:

• Introduction to Glycolysis
• Glycolysis
• More on Glycolysis
• The Process of Glycolysis
• The Krebs Cycle (Citric Acid Cycle)
• A Tour of the Citric Acid Cycle
• The Electron Transport Chain
• Energy Accounting
• More on the Electron Transport Chain
• Oxidative Phosphorylation
• Review of Cellular Respiration
• Metabolism Without Oxygen
• Anaerobic Cellular Respiration
• Fermentation and Anaerobic Respiration

Unit 5 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• acetyl coenzyme A
• aerobic organism
• ATP (adenosine triphosphate)
• catalyst
• cellular respiration
• citric acid cycle
• FADH2
• glucose
• glycolysis
• kinetic energy
• NADH
• oxidation
• oxidative phosphorylation
• potential energy
• pyruvate
• pyruvate oxidation
• rate of reaction
• redox
• reduction
• substrate

Unit 6: Photosynthesis

6a. Explain the role of photosynthesis and describe its matter and energy inputs and outputs

• What are the two ecological categories of organisms?
• What type of organism is capable of photosynthesis?
• How does photosynthesis relate to nutrient cycling?
• What is the role of producers in an ecosystem?
• What are the inputs and outputs of photosynthesis?

We can ecologically classify any living organism as an autotroph or a heterotroph. Biologists call autotrophs (self-feeders) producers because they produce organic compounds from inorganic materials. They make their own food. Autotrophs require energy to do so, and most autotrophs use light energy in the process of photosynthesis.

Biologists call heterotrophs (feeders on others) consumers because they feed on organic compounds produced by other organisms. Maximally extracting energy from an organic fuel (food) involves the complete oxidation of the fuel (including glycolysis and cellular respiration); this leaves inorganic carbon dioxide. Heterotrophs can be of different levels or "degrees," such as secondary heterotroph, tertiary heterotroph, and so on, depending on what level they feed on in the food chain.

Photosynthesis reverses these processes by starting with inorganic carbon dioxide and transforming it into organic compounds that can be used as fuel. In this way, photosynthesis is an important part of carbon cycling because photosynthesis has a reciprocal relationship with glycolysis and cellular respiration.

Photosynthesis is of vital importance to organisms because photosynthesis provides food for photosynthetic organisms (the producers) and the consumers of the world. As you review, pay close attention to the summary reaction for photosynthesis. Notice that photosynthesis is the reverse of the summary reaction for glycolysis and cellular respiration.

Figure 8.7 Photosynthesis takes place in two stages: light-dependent reactions and the Calvin cycle. Light-dependent reactions, which take place in the thylakoid membrane, use light energy to make ATP and NADPH. The Calvin cycle, which takes place in the stroma, uses energy derived from these compounds to make G3P from CO2. Credit: Rao, A., Ryan, K., Fletcher, S., Hawkins, A. and Tag, A. Texas A&M University.

Recall that photosynthesis has a reciprocal relationship with the complete oxidation of glucose (glycolysis and cellular respiration). This means the summary reaction for each process is the reverse of the summary reaction for the other process.

As you review the inputs and outputs of photosynthesis, appreciate this reciprocal relationship by noticing that the inputs into photosynthesis are the outputs from the complete oxidation of glucose, and the outputs from photosynthesis are the inputs into the complete oxidation of glucose.

To review, see:

• Overview of Photosynthesis
• The Light-Dependent Reactions of Photosynthesis
• Using Light Energy to Make Organic Molecules
• A Visual Explanation of Photosynthesis
• Photosynthesis

6b. Describe how photosynthesis converts low-energy molecules into energy-rich carbohydrates

• How does photosynthesis transform low-energy, inorganic molecules into high-energy, organic molecules (fuels)?
• What is the name for the process of incorporating inorganic molecules into organic compounds?
• What are the inputs and outputs of photosynthesis?
• Where is the Carbon found for photosynthesis to take place? What form is it in

Although cells use many organic molecules for fuel, carbohydrates (including glucose) are their principal fuel. Carbohydrates make excellent fuels because they contain many C-H bonds. While energy is released by oxidizing an organic fuel molecule into carbon dioxide, it takes energy to reverse the process and reduce carbon dioxide into an organic fuel.

Carbon fixation is the process of incorporating carbon from an inorganic source, such as carbon dioxide, into organic compounds, such as glucose. It is an extremely important function of photosynthesis. Carbon fixation results in products (organic compounds) that contain more chemical energy than the reactants (carbon dioxide molecules), requiring an energy input.

Sunlight provides the energy input for the carbon fixation that occurs during photosynthesis. Powered by light energy, water molecules split into oxygen and hydrogen atoms. The hydrogen atoms bond to the carbon atoms from carbon dioxide molecules to form high-energy carbohydrates. This occurs in the two major pathways of photosynthesis. Light-dependent reactions split the water, while the Calvin Cycle builds the carbohydrate molecules.

To review, see:

• Overview of Photosynthesis
• The Light-Dependent Reactions of Photosynthesis
• Using Light Energy to Make Organic Molecules
• A Visual Explanation of Photosynthesis
• Light and Carbon Reactions
• Photosynthesis
• The Calvin Cycle

6c. Explain the role of the light-dependent phase of photosynthesis

• What is the function of the light-dependent reactions, and what are its inputs and products?
• What is the function of the Calvin cycle, and what are its inputs and products?
• What is the relationship between the Calvin cycle and the light-dependent reactions?
• How is energy transferred from sunlight to carbohydrate molecules, and what energy-carrying compounds are used as intermediates in the process?
• What happens to the products of photosynthesis?
• How can plants store usable energy incorporated during photosynthesis?
• How does photosynthesis contribute to the accumulation of biomass, and what part of photosynthesis produces biomass directly?

Photosynthesis has two major components: the light-dependent reactions and the Calvin cycle. Its purpose is to build carbohydrate molecules. This process requires energy from sunlight, but photosynthetic organisms cannot use sunlight energy directly to build these carbohydrates. Instead, the sunlight energy must be transformed into chemical energy that is temporarily stored as ATP and NADPH molecules. The Calvin cycle uses ATP and NADPH as energy sources to build carbohydrate molecules.

In essence, the main function of the light-dependent reactions is to produce ATP and NADPH. The light-dependent reactions require sunlight, water, NADP⁺, and ADP. The products are heat, oxygen, NADPH, and ATP.

The Calvin Cycle

The Calvin cycle (the light-independent reactions) is the component of photosynthesis where carbon fixation takes place. In other words, during the Calvin cycle, inorganic carbon dioxide is transformed into organic compounds (molecules of glyceraldehyde-3-phosphate, or G3P). This expensive process requires energy in the form of two energy-storing compounds (NADPH and ATP).

Using the energy stored in NADPH and ATP, the Calvin cycle takes in carbon dioxide and (after several rearrangements of atoms, forming several different intermediates) produces a three-carbon compound called G3P. These G3P molecules are chemically transformed into other organic molecules for various uses in the organism.

Light energy indirectly powers the Calvin cycle because the Calvin cycle requires NADPH and ATP, and the light-dependent reactions (using sunlight) produce NADPH and ATP for the Calvin cycle. As you review the particulars of the Calvin cycle, ensure that you understand how the light-dependent reactions must operate first if the Calvin cycle is going to operate at all.

Photosynthesis uses sunlight energy to fix carbon dioxide into carbohydrates. However, the transfer of energy from sunlight to the chemical energy of the carbohydrate product is not direct.

Photosynthetic organisms, such as plants, algae, and cyanobacteria, cannot use sunlight directly to power the fixation of carbon dioxide into carbohydrates. Carbon fixation requires stored energy in the bonds of two important energy-carrying compounds:

• ATP is the general energy currency in cells. It is required in parts of the Calvin cycle of photosynthesis. The light-dependent reactions transform ADP into ATP, storing some of the energy originally in the sunlight.

• NADPH temporarily stores energy for use in the Calvin cycle of photosynthesis, just as the related compound NADH stores energy during cellular respiration. The light-dependent reactions transform NADP⁺ into NADPH, storing some of the energy originally in the sunlight.

As you review the light-dependent reactions and the Calvin Cycle, pay attention to how energy gets transformed from light energy into chemical energy as energy gets transferred from sunlight to ATP and NADPH and finally to the C-H bonds of the carbohydrates produced.

Energy Storage in Plants

The major accomplishment of photosynthesis is carbon fixation, producing organic compounds from inorganic compounds. The direct, organic product of the Calvin cycle is a three-carbon carbohydrate. That organic product can then be used as a precursor to building organic macromolecules, including proteins, lipids, nucleic acids, and polysaccharides, or it can be used to build monosaccharides like glucose.

If a plant needs to store energy in the form of oxidizable fuels, the primary sugar that is produced to store chemical energy is sucrose. Sucrose is a disaccharide consisting of two monosaccharides, glucose and fructose. Sucrose is a significant component of sap that travels through a plant's vessels to deliver that stored energy to different parts of the plant. Plants can also store energy in lipid forms (fats and oils) as occurs, for example, in nuts.

Biomass

Biomass is the matter living organisms produce. Since biomass is the material of living and dead organisms, it is organic material.

Since biomass is organic matter, any biological process that transforms inorganic matter into organic matter – any process that fixes carbon – produces biomass. Carbon fixation occurs in all autotrophs (producers), but the vast majority of autotrophs are photoautotrophs because their method for carbon fixation is photosynthesis.

The Calvin cycle is the component of photosynthesis that fixes the carbon from carbon dioxide into the organic form of carbohydrates produced. So, the Calvin cycle directly contributes to the accumulation of biomass. Recall that organic biomass can be converted back into inorganic carbon dioxide in autotrophs and heterotrophs by oxidizing the organic compounds using glycolysis and cellular respiration. As you review the Calvin cycle, pay attention to the fact that inorganic carbon dioxide enters the process and organic carbohydrate molecules (G3P) exit the process.

To review, see:

• Overview of Photosynthesis
• The Light-Dependent Reactions of Photosynthesis
• Using Light Energy to Make Organic Molecules
• A Visual Explanation of Photosynthesis
• Light and Carbon Reactions
• Photosynthesis
• The Calvin Cycle

6d. Explain how plants have adapted to deal with the problem of photorespiration

• What is photorespiration?
• Why is photorespiration problematic for a plant?
• What kinds of plants can minimize the occurrence of photorespiration?
• How do plants minimize the occurrence of photorespiration?

The fixation step is crucial in the Calvin cycle. It takes in carbon dioxide and joins it with an intermediate compound (ribulose bisphosphate), incorporating inorganic carbon dioxide into an organic compound. Ribulose bisphosphate carboxylase oxygenase (RuBisCO) is the enzyme that catalyzes this step. RuBisCO can operate to join either carbon dioxide or oxygen to ribulose bisphosphate. However, joining oxygen instead of carbon dioxide is counterproductive because no carbon fixation (the purpose of the Calvin cycle) takes place.

We call this counterproductive process (incorporating oxygen instead of carbon dioxide) photorespiration. Two major categories of plant species have evolved ways around this problem:

• C4 plants separate carbon dioxide intake (which occurs in superficial cells called mesophyll cells) from carbon fixation in the Calvin cycle (which occurs in deeper cells called bundle sheath cells).

• CAM plants take in carbon dioxide and store it in the form of organic acids during the night when their stomata are open. During the day, the organic acids get broken down to release the carbon dioxide for the Calvin cycle while the stomata are closed (preventing oxygen from interfering).

These two types of plants operate the Calvin cycle more efficiently because photorespiration is minimized. As you review C4 plants and CAM plants, notice they accomplish the same thing in two different ways.

To review, see:

• Light and Carbon Reactions
• Photophosphorylation
• The Calvin Cycle
• Photorespiration
• C-4 and CAM Photosynthesis

6e. Identify the differences in photosynthesis in CAM and C4 plants

• How does a C4 plant differ from a CAM plant?
• What type of plant has more efficient photosynthesis in a hot, dry environment?
• What type of plant has more efficient photosynthesis in a cool, wet environment?
• When do C4 plants keep their stomata open, as compared to CAM plants?

C4 plants and CAM plants have evolved mechanisms to minimize the costly and wasteful occurrence of photorespiration. Both types of plants avoid photorespiration by separating two processes: the intake of carbon dioxide and the operation of the Calvin cycle.

The major difference between C4 and CAM plants is that C4 plants avoid photorespiration by separating the two processes spatially (they occur in separate spaces). CAM plants avoid photorespiration by separating the two processes temporally (they occur at separate times).

A C4 plant takes carbon dioxide into mesophyll cells, then it transfers that carbon dioxide into bundle sheath cells that are farther away from the atmospheric oxygen. The Calvin cycle then occurs in this separate space (the bundle sheath cells).

A CAM plant opens its stomata only at night, taking in carbon dioxide that gets stored in acid form until the next day. During daylight, the stomata are closed (disallowing oxygen from entering), and the acids are processed to release the carbon dioxide to the Calvin cycle, which occurs at a separate time compared to the intake of carbon dioxide.

As you compare C4 and CAM plants and review how they avoid photorespiration, keep in mind that a typical plant (C3) operates less efficiently because the carbon dioxide intake process and the Calvin-cycle operation do not occur separately.

To review, see:

• C-4 and CAM Photosynthesis

6f. Explain what the carbon cycle is and how it relates to the conservation of matter

• What is the carbon cycle, and why is it a cycle?
• How does the carbon cycle exemplify the conservation of matter?
• Where does the carbon that enters the cycle come from?

The carbon cycle refers to the many chemical transformations that involve compounds containing carbon. It is cyclic because there is a continuous alternation between the carbon of organic compounds and the carbon of inorganic compounds. Inorganic carbon dioxide gets fixed (by autotrophs) into organic compounds. These organic compounds get converted into other organic compounds (including simple organic compounds like monosaccharides, nucleotides, and amino acids, as well as complex macromolecules like polysaccharides, nucleic acids, lipids, and polypeptides).

Carbon in these organic compounds is passed from organism to organism as they feed on each other. Organisms use some of the organic molecules as fuel, and the oxidation of these organic fuels (to provide energy for the organisms) returns the carbon to inorganic form (carbon dioxide) to complete the cycle. In this cycle of transformations, carbon (matter) remains in the ecosystem (it is conserved). It is not destroyed; it is merely transferred and transformed.

To review, see:

• The Carbon Cycle
• Carbon: The Ecosystems View

Unit 6 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• autotroph
• biomass
• C4 plant
• CAM plant
• carbon cycle
• carbon fixation
• glyceraldehyde-3-phosphate (G3P)
• heterotroph
• light-dependent reaction
• NADPH
• photorespiration
• photosynthesis
• ribulose bisphosphate carboxylase oxygenase (RuBisCO)
• stomata
• sucrose

Unit 7: Cellular Reproduction: Mitosis

7a. Differentiate DNA from RNA in terms of structure and function

• How are DNA and RNA chemically different?
• How are DNA and RNA functionally different?
• How are DNA and RNA different in terms of their roles in protein synthesis?
• What organisms have both DNA and RNA?

As their names indicate, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are both nucleic acids. Any nucleic acid is a polymer made up of monomers called nucleotides. Any nucleotide consists of three components:

1. A pentose (five-carbon sugar)
2. A nitrogenous base attached to the pentose
3. A phosphate group also attached to the pentose

For DNA, the specific pentose in each of its nucleotides is deoxyribose, whereas RNA features ribose as the pentose in each of its nucleotides. There are usually four kinds of DNA nucleotides because there are four normal nitrogenous bases used in DNA:

• Adenine
• Guanine
• Cytosine
• Thymine

RNA also features four kinds of nucleotides, and the nitrogenous bases are nearly the same as for DNA, except that RNA uses uracil instead of thymine.

DNA functions for self-replication (before a cell divides into two cells) and for transcription, a process that produces RNA. RNA has different functional categories, including mRNA, tRNA, rRNA, and others.

To review, see:

• DNA and RNA

7b. Describe the different methods of cell division among organisms

• What are the different ways that organisms reproduce?
• Why do organisms go through cell division?
• What is the advantage of cloning versus genetic variation?
• Why is genetic variation an advantage in more complex organisms?

To survive, organisms must pass their traits on to reproduce offspring. Prokaryotic organisms reproduce by binary fission. These unicellular organisms divide to continue the species' existence. Multicellular organisms divide for growth, development, and repair. Eukaryotic organisms reproduce asexually and sexually.

Asexual reproduction involves transferring 100 percent of DNA to their offspring (essentially cloning). For sexual reproduction, the offspring share DNA from two different parents and produce new genetic combinations.

To review, see:

• Cell Division
• The Cell Cycle
• Prokaryotic Cell Division and DNA Replication in Bacteria

7c. Describe the phases of the cell cycle and mitosis

• What is mitosis, and what are the phases of mitosis?
• What types of cells undergo mitosis?
• What are the phases of the cell cycle?
• What occurs between periods of division?
• What are the major events occurring in each phase of the cell cycle?

The Cell Cycle

The cell cycle includes all parts of the normal lifetime of a single eukaryotic cell. The cell cycle begins when a cell is created via the division of a previous cell and ends when the cell undergoes its own cell division to produce two new cells. A single-cell cycle consists of four major phases of unequal length:

1. The G1 phase includes most of the cell's normal lifetime. During G1, the cell uses its DNA as instructions for building proteins that allow the cell to metabolize and function for its specific purpose. During this time, the DNA has not yet been replicated.

2. The S phase is the first step in a cell's preparation for cell division. During the S phase, the DNA is replicated, yielding two identical copies of the DNA (one for each of the two cells that will be created when the cell divides).

3. The G2 phase follows the S phase. Like the G1 phase, the G2 phase features much protein synthesis and metabolism, but most of this activity is concentrated on preparing for cell division.

4. The M phase includes mitosis (the division of the nucleus) and cytokinesis (the division of the cytoplasm). By the end of the M phase, two separate cells have been created from the original cell, and each of these two cells enters its own cell cycle.

Figure 10.5 The cell cycle in multicellular organisms consists of the interphase and the mitotic phase. During interphase, the cell grows, and the nuclear DNA is duplicated. Interphase is followed by the mitotic phase. During the mitotic phase, the duplicated chromosomes (thread-shaped structures in the nucleus that carry genes) are segregated and distributed into daughter nuclei. Following mitosis, the cytoplasm is usually divided as well by cytokinesis, resulting in two genetically identical daughter cells.

Mitosis

Mitosis is the division of a cell nucleus. Since only eukaryotic cells feature a nucleus, only eukaryotic cells undergo mitosis (recall that prokaryotic cells undergo a rudimentary cell division, or "binary fission). Mitosis is part of eukaryotic cell division (the other part is cytokinesis, which is the division of the cytoplasm).

Mitosis (the division of a eukaryotic cell's nucleus) occurs in five phases:

1. Prophase: The first phase of mitosis. The microtubules that make up the mitotic spindle begin forming on the two centrioles, and these centrioles start to move to opposite poles.

2. Prometaphase: Construction of the mitotic spindle is completed, and the nuclear envelope disintegrates, allowing the microtubules of the mitotic spindle to connect to replicated chromosomes.

3. Metaphase: Replicated chromosomes (each consisting of two identical sister chromatids) move along the spindle tubules until all replicated chromosomes are aligned at the metaphase plate, midway between the poles.

4. Anaphase: Each pair of sister chromatids (one pair for each replicated chromosome) separate and move toward opposite poles. At this point, they are no longer called chromatids; rather, each is an unreplicated chromosome.

5. Telophase: The unreplicated chromosomes reach opposite poles. Each pole becomes a new nucleus, as each pole becomes enclosed by a new nuclear envelope.

In most cases, cytokinesis (division of the cytoplasm) occurs near the end of telophase, when the original cell separates into two distinct cells, each with its own nucleus.

To review, see:

• The Cell Cycle
• Mitosis
• What Is Plant Cell Mitosis?
• A Tour of Mitosis

7d. Explain the purpose of mitosis and the relationship between parent and daughter cells

• What cells undergo mitosis in the human body?
• When is mitosis initiated in the body?
• Why is mitosis important?
• Under what conditions does a cell undergo mitosis?

Recall that mitosis is the division of a eukaryotic cell's nucleus. One of the hallmarks of mitosis is that two genetically identical nuclei are produced when the original nucleus divides. The chromosomes in one nucleus are exactly the same as the chromosomes in the other nucleus. Moreover, each nucleus is genetically identical to the nucleus in the original cell (before mitosis). Mitosis creates two nuclei from one, and each of these nuclei can serve as the nucleus of a new cell.

When cytokinesis accompanies mitosis, the cytoplasm divides, forming two distinct cells. Each cell contains its own nucleus (created by mitosis). Cell division that features mitosis allows one parent cell to divide into two genetically identical daughter cells. Creating new cells is important for several reasons:

• Mitosis promotes cell proliferation so a unicellular zygote can develop into a multicellular organism.
• Mitosis promotes cell proliferation to support the growth of a multicellular organism.
• Mitosis creates new cells to replace damaged cells due to injury or infection in a multicellular organism.
• Mitosis is a way for unicellular, eukaryotic organisms to reproduce.

To review, see:

• The Cell Cycle
• Mitosis
• What Is Plant Cell Mitosis?
• A Tour of Mitosis

Unit 7 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• adenine
• anaphase
• asexual reproduction
• cell cycle
• cell division
• chromosome
• cytokinesis
• cytosine
• G1 phase
• G2 phase
• guanine
• metaphase
• mitosis
• M phase
• nitrogenous bases
• prometaphase
• prophase
• sexual reproduction
• S phase
• telophase
• thymine
• uracil

Unit 8: Cellular Reproduction: Meiosis

8a. Identify the different types of daughter cells produced by cell division

• What is the difference between the gamete and somatic cell?
• How do diploid and haploid cells differ?
• Why is a haploid cell unable to undergo meiosis?
• Which types of cells can undergo mitosis?

Organisms that reproduce sexually must create cells that have half of their chromosomes. A gamete is a cell formed by meiosis that is non-identical to the original parent cell. The cells that contain all of the chromosomes are somatic cells, which we also call body cells. Some body cells are in sex organs that reproduce gametes. Somatic cells are diploid (contain two sets of chromosomes), whereas gametes are haploid (have one set of chromosomes).

To review, see:

• The Cellular Basis of Reproduction
• Meiosis
• Mitosis, Meiosis, and Sexual Reproduction

8b. Diagram and label the phases of meiosis given a number of chromosomes or chromosome pairs

• What happens during each phase of meiosis?
• Where in the body does meiosis take place?
• Can prokaryotes undergo meiosis? Why or why not?
• Is there any chance of error inherent in meiosis?

Meiosis allows one diploid cell to become four haploid cells. Each haploid cell is not only genetically different from the original diploid cell, but each haploid cell is also genetically different from the other three haploid cells produced.

Meiosis proceeds in essentially the same way in any eukaryotic cell. The main difference is the number of chromosomes involved. The number of chromosomes depends on the species. The variable N represents the number of different kinds of chromosomes. We also call it the haploid number. This is because a haploid cell contains just one of each type of chromosome. A diploid cell is characterized as 2N because a diploid cell has two of each type of chromosome (one from each sexual parent).

The stages of meiosis are illustrated below for a species with N = 2. The original diploid cell in this example (2N), therefore, has 2 × 2 = 4 overall chromosomes. Each of the four cells produced has N = 2 overall chromosomes (they are haploid). Whatever the value of N, during metaphase of meiosis I, N pairs of homologous, replicated chromosomes line up, and during metaphase of meiosis II, N individual, replicated chromosomes line up.

To review, see:

• Meiosis
• Mitosis, Meiosis, and Sexual Reproduction
• What Are Chromosomes?
• Chromosomes, Chromatids, and Chromatin

8c. Compare mitosis I and meiosis II

• What are the similarities and differences between mitosis and meiosis?
• Why is there only one division in mitosis but two divisions in meiosis?
• How do organisms benefit from being able to perform both mitosis and meiosis?

Mitosis and meiosis are alternative processes in eukaryotic cell division. Here are key similarities:

• Mitosis and meiosis both divide the nucleus of a cell.
• Both processes occur in phases that include prophase, prometaphase, metaphase, anaphase, and telophase.
• Meiosis II is essentially identical to mitosis, but meiosis II occurs in the two cells produced previously in meiosis I.

Here are the key differences:

• Mitosis produces two cells that are genetically identical to the parent cell; meiosis produces four cells that are genetically distinct from each other and the parent cell.
• Mitosis produces duplicate cells to help grow a multicellular organism or replace lost cells; meiosis produces haploid cells out of a diploid cell for the purpose of sexual reproduction.
• Mitosis only involves one round of division; meiosis involves two rounds of division (meiosis I and II).
• In mitosis, chromosomes act individually, and homologous chromosomes do not synapse; in meiosis, homologous chromosomes go through synapsis (come close together), and each homologous pair acts throughout meiosis I as a unit.
• Mitosis does not feature crossing over; meiosis I features crossing over.
• During the metaphase of mitosis, individual, replicated chromosomes line up midway between poles (without pairing of homologs); during the metaphase of meiosis I, homologous pairs of chromosomes line up as tetrads midway between poles.
• During the anaphase of mitosis, sister chromatids separate; during the anaphase of meiosis I, homologs separate.
• Mitosis maintains the ploidy; meiosis cuts the ploidy in half.

To review, see:

• Mitosis, Meiosis, and Sexual Reproduction
• Comparing Mitosis and Meiosis

8d. Compare mitosis and meiosis in terms of their parent and daughter cells

• How does the purpose of meiosis differ from that of mitosis?
• What aspects of meiosis support genetic variation?
• What would happen if there was only one division in meiosis?
• What is the difference in ploidy between somatic cells and gametes?

While mitosis and meiosis share several similarities, some critically important differences allow the two processes to serve different purposes.

The life cycle of any sexual species features fertilization, which is the fusion of unicellular gametes (one male gamete and one female gamete) to produce a unicellular zygote. The unicellular zygote that fertilization produces carries chromosomes from both gametes. Therefore, the ploidy (the number of sets of chromosomes in a cell) of the zygote is double the ploidy of the gametes.

If fertilization were the only process occurring each generation, the ploidy would double each generation (tetraploid, then octoploid, etc.), and the zygote would not be able to contain the DNA.

To prevent the ploidy from doubling each generation, a separate process (meiosis) is needed to cut it in half.

Specifically, the reduction of ploidy occurs in meiosis I, when homologs separate and go to distinct daughter cells. Since a diploid cell that undergoes meiosis will produce haploid cells (gametes), when these haploid gametes fuse (in fertilization), the zygote will be diploid. By alternating meiosis and fertilization each generation, the ploidy simply goes back and forth between haploidy and diploidy (rather than continually increasing).

Another important purpose of meiosis is to drastically increase the genetic variability of the gametes produced. This increase in genetic variability comes in the forms of crossing over (the exchange of genes between homologous chromosomes during prophase of meiosis I) and independent assortment (the random alignment of homologous chromosomes during metaphase of meiosis I).

To review, see:

• Mitosis, Meiosis, and Sexual Reproduction
• Comparing Mitosis and Meiosis

8e. Explain the role of meiosis in adaptation and evolution

• What is survival of the fittest?
• Why is genetic change necessary in today's ecosystems?
• What types of alleles might be disadvantageous to a species?
• How does genetic change occur in a population through meiosis?

Due to the process of crossing over (of homologous chromosomes) in Prophase I, the resulting daughter cells after meiosis are genetically unique. This creates variation and, ultimately, the survival of the fittest. Since offspring have new combinations of alleles, they increase the possibility of their survival until reproductive age and continue their species.

These small genetic changes over time create the variety of species and subspecies we see today. Those with alleles that give them an ecological advantage over others survive to mate. Those that lack them, die off taking their non-adaptable alleles with them and out of the breeding population.

To review, see:

• Meiosis Errors and the Formation of New Species

Unit 8 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• crossing over
• diploid
• fertilization
• gamete
• haploid
• haploid number
• independent assortment
• meiosis
• ploidy
• somatic cell
• survival of the fittest
• synapsis
• zygote

Unit 9: Mendelian Genetics and Chromosomes

9a. Explain how information flows from genotype to phenotype at the molecular level

• What is a genotype and a phenotype?
• How are genotype and phenotype different?
• What is the connection between genotype and phenotype?

We often say our genes give us our traits. This is true, but only indirectly. Genes are sequences of DNA, and these genes provide instructions for how to make corresponding sequences of RNA. These sequences of RNA, in turn, serve as instructions for how to build proteins.

Proteins are the final product of gene expression. The particular proteins built in an organism's cells are what give that organism its traits. The proteins directly determine the traits, but the genes indirectly determine the traits because the genes indirectly instruct the cells on how to build the proteins.

There may be multiple possible traits for any given characteristic, such as black, brown, or red hair color. We call the trait an individual exhibits for a given characteristic, such as the black hair trait for the hair-color characteristic, that individual's phenotype. That phenotype depends on the proteins produced, which depends on the version of the corresponding gene (DNA) that an individual possesses.

An individual's genotype refers to the DNA sequence for a particular gene. Consequently, your genotype indirectly determines your phenotype.

To review, see:

• Mendel's Experiments
• Genetics

9b. Explain how we use the terms genotype, phenotype, homozygous, heterozygous, dominant, recessive, codominant, and sex-linkage

• What do homozygous and heterozygous mean?
• What are dominance and recessivity?
• What is codominance?
• What is sex linkage?

When scientists study organisms genetically, they usually focus on one single gene. A gene is a stretch of DNA coding for a particular protein – a gene controls a particular characteristic. Alternative versions of a gene (with different nucleotide sequences) are called alleles. A diploid cell features two alleles for any particular gene because a diploid cell features two of every kind of chromosome, one from each parent.

An individual's genotype is the sequence of symbols that represent the particular alleles an individual possesses for the gene being studied. Since alleles code for proteins, and proteins give organisms their traits, alleles indirectly determine phenotype. A phenotype is an observable trait an individual exhibits for the characteristic being studied.

Since a diploid cell contains two alleles for a gene, there are two possibilities:

1. Both alleles for the gene under study are the same version (they are identical), so the individual is homozygous.
2. The two alleles for the gene under study are different versions. In this case, the individual is heterozygous.

One allele is typically dominant over another allele, which means the trait gets expressed. The allele that does not have its trait expressed is called recessive. When one or two dominant alleles occur in a cell, the dominant phenotype shows itself. For example, if there is just one dominant allele and the other allele is recessive, the single dominant allele will dominate over the recessive allele. The dominant phenotype is expressed (shows itself), but the recessive phenotype is not expressed. The only way a recessive phenotype is expressed is when both of the alleles are recessive. This individual is homozygous recessive.

A heterozygous individual features one dominant allele and one recessive allele and expresses the dominant phenotype. A homozygous dominant individual (both alleles are dominant) also expresses the dominant phenotype. Codominance describes a special case when two different alleles are both simultaneously expressed. In other words, one allele does not dominate the other. A good example is Type AB blood, which expresses both Type A and Type B phenotypes.

Sex linkage refers to a gene that is part of a sex chromosome. Consequently, the expression is different in males compared to females. For example, in humans, females have two X chromosomes, so they have two alleles for sex-linked genes. Males, on the other hand, have one X chromosome and one Y chromosome, but the Y chromosome does not have all of the genes that an X chromosome has. Therefore, a male has only one allele for a sex-linked gene.

To review, see:

• Mendel's Experiments
• Genetics

9c. Infer whether the trait in a pedigree diagram is dominant or recessive, and indicate individual genotypes when possible

• What is a pedigree?
• How does a pedigree use symbols to indicate phenotypes?
• What can be learned about inherited traits from a pedigree?
• How can traits be traced backward to a source using a pedigree?

A pedigree is merely a symbolic representation (or chart) of the phenotypes and sexes of individuals, with the ancestral relationships between these individuals. Keep the laws of inheritance in mind as you study pedigrees to determine whether a given trait is dominant or recessive.

Once you determine the dominance/recessivity relationship, a pedigree is a useful tool for determining the possible genotypes of individuals based on the phenotypes indicated in the chart.

For example, in this pedigree, the original parents (square and circle at the top) both carry the unaffected phenotype (because their symbols are not filled). They produced some offspring that were unaffected and some that were affected. The only way for this to be possible is if the affected phenotype is the recessive trait. An offspring with the affected (recessive) phenotype must be homozygous recessive; otherwise, that individual would have the unaffected (dominant) trait.

Therefore, each original parent must be heterozygous because each parent must pass on a recessive allele to produce a homozygous recessive offspring. We can make the same inference about the two parents listed rightmost in the generation enclosed by the red dashes because they also produced recessive offspring. A good example of this is when two parents with black hair (dominant) have a child who has red hair (recessive).

To review, see:

• Introduction to Heredity
• Pedigrees

9d. Solve genetic problems involving monohybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• What is a genetic cross?
• How do you use a Punnett square?
• What does it mean to be monohybrid?
• Are recessive alleles expressed in codominant traits?

A genetic cross is an incidence of sexual reproduction that involves a male and female from a particular species. A monohybrid cross is a cross where you are studying only one gene (one characteristic), and the two parents usually differ in their genotypes. For example, one parent might be homozygous dominant (AA), and the other might be homozygous recessive (aa).

Knowing the parents' genotypes allows us to draw a Punnett square to represent the possible fertilization events involving these two parents. Fertilization is the fusion of a male gamete and a female gamete to produce a zygote.

A Punnett square lists (on adjacent sides of the square) all possible gametes that can be produced by each parent. By matching up each possible gamete from one parent with each possible gamete from the other parent, the boxes within a Punnett square list all possible zygotes that can be produced by these parents. Moreover, the ratio of different possible genotypes (the genotypic ratio) and different corresponding phenotypes (the phenotypic ratio) can be computed for the generation created by the particular cross.

To review, see:

• Introduction to Heredity
• Pedigrees

9e. Solve genetic problems involving dihybrid crosses with dominant and recessive traits, codominant traits, and sex-linked traits

• How is a dihybrid cross different from a monohybrid cross?
• How are they similar?
• Are sex-linked traits unique to the X chromosome, the Y chromosome, or both?
• How is a sex-linked trait inherited differently by each gender of offspring?

Once you know the genotypes (for a particular characteristic or gene) of two parents, it is possible to compute the probabilities of various genotypes or phenotypes in the offspring they produce. This is because the genotype of an offspring results from randomly selecting one of the two alleles for the gene in one parent and randomly selecting one of the two alleles in the other parent.

The sperm and egg carry these randomly selected alleles. When the sperm and egg fuse (via fertilization) to produce the zygote of the offspring, the genotype of the offspring is a combination of an allele from the father and an allele from the mother. For example, when a male with genotype Aa mates with a female with genotype aa, we symbolize this mating (or cross) as Aa × aa.

Like a monohybrid cross, a dihybrid cross is a genetic cross. This means it involves the fertilization of a female gamete (from the female parent) by a male gamete (from the male parent) to produce zygotes that can develop into adult offspring. The fundamental difference between a monohybrid cross and a dihybrid cross is that a monohybrid cross tracks only one gene (corresponding to one characteristic), whereas a dihybrid cross simultaneously tracks two different genes (corresponding to two different characteristics).

Since two different genes are studied, the genotypes in a dihybrid cross are longer sequences of symbols (both for the alleles and for the zygotes) because they need to indicate alleles for two genes. Also, because there are more possible combinations of alleles, a dihybrid cross will feature more boxes in its Punnett square compared to a monohybrid cross. These differences are illustrated in the generic examples shown below.

Monohybrid cross: Aa (heterozygous male) × Aa (heterozygous female)

• Number of genes under study: One (Gene A)
• Genotypes of possible male gametes: A, a
• Genotypes of possible female gametes: A, a
• Punnett square:

Dihybrid cross: AaBb (doubly heterozygous male) \times AaBb (doubly heterozygous female)

• Number of genes under study: Two (Gene A and Gene B)
• Possible male gametes: AB, aB, Ab, ab
• Possible female gametes: AB, aB, Ab, ab
• Punnett square:

To review, see:

• Introduction to Heredity

9f. Define mutation and explain how a mutation, such as that in sickle cell, can result in a changed phenotype

• What is a mutation?
• Are mutations considered positive, negative, or both?
• How can mutation affect phenotype?
• How does mutation contribute to genetic diversity and evolution?

A mutation is an accidental change in the DNA sequence of an organism. An organism's DNA is arranged in chromosomes. Each chromosome is a long sequence of DNA nucleotides. A gene is a subsequence of DNA nucleotides within the longer sequence that makes up the chromosome. A mutation arises when the sequence gets changed – either by an error during DNA replication or by some other accident, such as exposure to certain chemicals or forms of radiation. The reason a gene can serve as a code (stored information) is due to its particular sequence of DNA nucleotides.

A mutation changes that sequence. The code is changed, and the RNA will also be altered when the altered code is used to make RNA. Similarly, when the code from the altered (mutated) version of RNA is used to build a protein, the protein may differ from the unmutated version.

Since proteins directly determine phenotypes, a mutant protein (resulting from a mutant form of DNA for the corresponding gene) may alter the phenotype. A mutation is the original source of genetic variation, which is why we have different species and differences among individuals of the same species.

In the case of heterozygote advantage, heterozygous individuals are more fit than both types of homozygous individuals (homozygous dominant and homozygous recessive). For example, a mutant allele for a human hemoglobin gene codes for a mutant form of the hemoglobin protein. This situation is deleterious (causes harm or damage) because it causes sickle cell disease. However, the mutant form of hemoglobin also confers higher resistance to malaria.

A homozygous recessive individual will develop sickle-cell disease, which drastically reduces fitness. A homozygous dominant individual will not develop sickle-cell disease, but that person will not be resistant to malaria. However, a heterozygous individual will not develop sickle-cell disease (because the one normal allele will prevent the disorder), and they will also have increased resistance to malaria (because of the mutant allele).

Therefore, heterozygous individuals have the greatest chance of passing on their alleles to the next generation – this includes the mutant allele. The population maintains the sickle-cell allele by natural selection. To make sense of heterozygote advantage, review the laws of inheritance. Keep in mind that each allele is a code for a particular protein, and therefore, each allele corresponds to a particular trait.

Accidental mutations are the source of differences in genotypes and phenotypes.

To review, see:

• Mutations

Unit 9 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• allele
• code
• codominance
• dihybrid cross
• dominant
• gene
• genetic cross
• genetic variation
• genotype
• heterozygote advantage
• heterozygous
• homozygous dominant
• homozygous recessive
• monohybrid cross
• mutation
• pedigree
• phenotype
• Punnett square
• recessive
• sex linkage
• trait

Unit 10: Gene Expression

10a. Explain the molecular basis of heritable traits and how information in DNA is ultimately expressed as a protein

• What is the central dogma?
• What are the necessary cellular inputs for transcription?
• What is the main output of transcription, and what is its fate after transcription has occurred?
• What are the necessary nucleotides to create mRNA?

DNA indirectly controls traits because the trait is a direct result of the version of protein the individual can produce. The individual's gene (which is made of DNA) determines the type of protein they can produce. The term gene expression refers to the molecular process of building a particular protein using the code that is stored (in DNA form) as a gene. The central dogma is the teaching of the flow of genetic information to the level of the protein. DNA is used as a template to transcribe RNA, and RNA is used to translate proteins.

To review, see:

• DNA
• The Chemical Structure of DNA
• Transcription

10b. Define the roles of DNA and RNA and their means of replication

• What is the structure of DNA, and how does it relate to its function?
• Why and how does DNA self-replicate?
• What are the enzymes involved in DNA replication?
• What starts the process of DNA replication? What terminates DNA replication?

Deoxyribonucleic Acid (DNA) is one of the most celebrated molecules in history. It is a double-helical nucleic acid made up of nucleotides. DNA has two functions:

1. It offers semiconservative replication
2. It provides a template for RNA transcription

DNA nucleotides consist of phosphate, deoxyribose sugar, and four nitrogenous bases (adenine, guanine, cytosine, thymine). You should understand how the structure of DNA represents a code template for gene expression.

DNA replication is a complex process that has different mechanisms and employs a great variety of enzymes. Two new strands are copied. The leading strand is synthesized continuously, while the lagging strand is synthesized as Okazaki fragments. This is because DNA synthesis can only take place in the 5'-3' direction, and the DNA polymerases create the two strands simultaneously.

The main enzymes involved are helicase, primase, DNA Polymerase I and III, and DNA ligase.

• Helicase: unwinds the DNA
• Primase: creates an RNA primer
• DNA Polymerase III: elongates the two strands separately by adding complementary bases
• DNA Polymerase I: removes the RNA primer and replaces it with DNA but leaves a gap between fragments
• DNA Ligase: fills in the gap and joins DNA fragments to create fully joined identical copies of DNA

To review, see:

• DNA
• The Chemical Structure of DNA
• DNA Replication
• Visualizing DNA Replication

10c. Distinguish between the two main phases of gene expression: transcription and translation

• What are the processes involved in gene expression?
• In what order do these processes occur?
• What specifically occurs in these processes?
• How are these processes regulated?

Gene expression consists of two serial processes occurring in the following order:

Transcription is the only part of gene expression that directly involves the gene. The cell "reads" the DNA nucleotide sequence of a gene and uses the sequence as a code to construct a complementary sequence of RNA nucleotides.

That RNA sequence is known as messenger RNA (mRNA) because the mRNA carries the original code, as a message, to a ribosome. DNA's job is done until the gene is read again in a later round of gene expression.

Translation refers to the part of gene expression where the polypeptide (protein) is constructed. A polypeptide is a sequence of amino acids. The code in mRNA (produced earlier by transcription) instructs the cell's ribosomes how to build the polypeptide by conveying how many amino acids to string together, which amino acids to use, and how to order the amino acids in the sequence.

As a ribosome reads each codon (a sequence of three nucleotides) in the mRNA, a type of RNA called transfer RNA (tRNA) delivers the correct type of amino acid to the ribosome. Amino acids are added in this way, one by one, until the polypeptide is complete.

A completed polypeptide (produced by translation) assumes a particular shape depending on its particular sequence of amino acids. Because of that particular shape, that polypeptide will have a particular function, and it will, therefore, give the individual a particular trait.

Gene expression occurs differently in organisms. Transcription and Translation occur simultaneously in prokaryotes. However, in eukaryotes, there are several modifications post-transcriptionally and post-translationally. This allows for more regulation.

To review, see:

• Transcription
• More on Transcription
• Translation and Synthesis
• More on Translation
• Regulation of Gene Expression

10d. Discuss some technological advances in molecular biology

• What is a gene? How is it edited?
• Why are DNA technologies important?
• What diseases can be studied under the context of gene editing?
• What other applications of DNA technologies exist in the public sector?

Biotechnology is the field that uses practical knowledge to solve problems in living organisms. DNA biotechnology incorporates gene modification and other tools to advance certain goals. For example, DNA technology has helped solve problems in the criminal justice system, agriculture, and the medical field.

We know genes reflect specific DNA sequences that help the body produce specific proteins, which in turn express a certain genotype or phenotype. Scientists are learning how to modify problematic genes to alleviate and eradicate disease. For example, they use gene-editing tools to remove and replace harmful genes that cause certain dysfunctions. CRISPR is a specific type of gene editing method.

To review, see:

• Biotechnology
• What Is Gene Editing and How Does It Work?
• CRISPR: A Game-Changing Genetic Engineering Technique
• Genes, Health, and Moving Beyond Race

Unit 10 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

• biotechnology
• central dogma
• codon
• CRISPR
• DNA ligase
• DNA polymerase I
• DNA polymerase III
• gene expression
• helicase
• lagging strand
• leading strand
• messenger RNA (mRNA)
• Okazaki fragment
• primase
• transcription
• translation