EXAM 1 REVIEW

STARTING WITH TERMS TO KNOW:

Reductionism reduce a problem/question to smaller things; break something down

into parts to study a whole idea

Glycolysis early anaerobic atmosphere

1. The breakdown of glucose by enzymes, releasing energy and pyruvic acid

Photosynthesis light energy; independence from pre-formed organic molecules

2. Use sunlight to synthesize foods from carbon dioxide and water involves the
green pigment chlorophyll and generates oxygen as a byproduct

Oxidative metabolism oxygen-rich atmosphere, high-efficiency

3. A chemical process in which oxygen is used to make energy from carbohydrates
(sugars). Also called aerobic metabolism, aerobic respiration, and cell respiration.

Viruses an infective agent that typically consists of a nucleic acid molecule in a

protein coat, and is able to multiply only within the living cells of a host

Viroids RNA without protein // infectious RNAs

Prions an infectious protein particle similar to a virus but lacking nucleic acid

MOLECULES VS. COMPOUNDS VS. SALTS

a. Molecules held together by stable covalent actions contrasts with salt
b. Salt held together by ionic actions
c. Compound composed of 1+ element

COVALENT, IONIC, AND HYDROGEN BONDS

a. Covalent bond the sharing of a pair of valence electrons by two atoms
(SHARED)
b. Ionic bonds occurs when atoms have such an unequal attraction for
electrons that one strips an electron completely from the other
(TRANSFERRED)
c. Hydrogen bonds occurs when a hydrogen atom covalently bound to one
electronegative atom is also attracted to another electronegative atom
i. Important for protein structure, protein-protein interactions, properties
of water, etc.

Electronegativity measure of the tendency of an atom to attract a bonding pair of

electrons

Structural and Chemical Complementarity molecules can stick to each other

(interact) with great specificity if they have complementary shapes and complementary
bonding capacities

HYDROPHILIC VS. HYDROPHOBIC

a. Hydrophilic having a tendency to mix with, dissolve in, or be wetted by
water
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b. Hydrophobic tending to repel or fail to mix with water

TYPES OF REACTIONS
a. Synthesis the production of an organic compound in a living thing, aided by
enzymes
ii. The act or process of forming a complex substance by combining or
integrating two or more chemical entities, especially through a
chemical reaction
b. Polymerization a chemical reaction in which two or more small molecules
combine to form larger molecules that contain repeating structural units of the
organic molecules
c. Condensation a chemical reaction in which two molecules combine to form a
larger molecule with the elimination of a small molecule
d. Dehydration chemical reaction that involves the loss of a water molecule
from the reacting molecule
e. Hydrolysis a chemical reaction in which water is used to break down a
compound; this is achieved by breaking a covalent bond in the compound by
inserting a water molecule across the bond. This is the opposite of a
dehydration-condensation reaction

CARBOHYDRATES
a. Simple sugars A monosaccharide
a. Formula: (CH2O)n
b. Key cellular sugars usually have n values from 3-7 carbons
c. Sugars with 5+ carbons can form rings with an a or b configuration
b. Di (2) vs. Oligo vs. Polysaccharides Monosaccharides link to form
disaccharides
a. Oligosaccharides (a carbohydrate whose molecules are composed of a
relatively small number of monosaccharide units) are often attached to
lipids or proteins
b. Monosaccharides can be linked to form polysaccharides
c. Glycosidic bond a bond or Glycosidic linkage is a type of covalent bond that
joins a carbohydrate (sugar) molecule to another group, which could be another
carb

MAJOR POLYSACCHARIDES
a. Glycogen energy storage
b. Starch energy storage
c. Cellulose structural roles
d. Chitin found in the cell walls of fungi and algae

MAJOR LIPIDS
a. Fatty acid carboxylic acid consisting of a hydrocarbon chain and a
terminal carboxyl group, especially any of those occurring as esters in fats
and oils
b. Triglyceride
c. Phospholipid
d. Glycerol phospholipids
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e. Sphingolipids any of a class of compounds that are fatty acid
derivatives of sphingosine and occur chiefly in the cell membranes of the
brain and nervous tissue
f. Glycolipids lipids with a carbohydrate attached by a Glycosidic bond
iii. Their role is to maintain stability of the membrane and to facilitate
cellular recognition
g. Cholesterol

MAJOR NUCLEIC ACIDS

a. Phosphodiester bond a chemical bond of the kind joining successive
sugar molecules in a polynucleotide
b. Purines vs. Pyrimidines
i. Purines: adenine and guanine present in DNA and RNA
ii. Pyrimidines: thymine and cytosine present in DNA
c. Nucleotide vs. Nucleoside
i. Nucleotide: consists of a nitrogenous base, a sugar (ribose or
deoxyribose) and one to three phosphate groups
ii. Nucleoside: consists of a nitrogenous base covalently attached to a
sugar (ribose or deoxyribose) but without the phosphate group

MAJOR PEPTIDE BONDS

a. Peptide Bond
b. Primary, secondary, tertiary, and
quaternary structure
a. Primary the sequence of amino
acids; assembly level, ALPHABET
b. Secondary conformational
relationship between amino acids
leading to a repeating pattern,
folding level, WORDS
c. Tertiary 3D folding based on
properties of R-groups, packing
level, SENTENCES
d. Quaternary associations between
separate polypeptides,
interactions, PARAGRAPHS
c. Helix & Sheet
a. A-helix: protein that turns like a
spiral
b. B-sheet: protein folds back on itself (ribbon)
d. Domains vs. Subunits
a. Domain a distinct region of the tertiary structure produced by a part of a
polypeptide which can fold independently into its own compact, stable
structure
b. Subunits associations between separate polypeptides
EXAM 1 REVIEW
CATABOLISM VS. ANABOLISM
a. Catabolism energy derived from
breakdown of organic molecules
b. Anabolism synthesis of needed cell
components

Activated Carriers source of energy and of

chemical groups for biosynthetic reactions
- Molecules that can be
split (C A + B) to
release energy but only
if there is an excess of C relative to its equilibrium
concentration. (ATP, GTP, NADH, FADH2, and NADPH)

Gluconeogenesis the metabolic process by which organisms produce sugars

(glucose) for catabolic reactions from non-carbohydrate precursors. (three ways to get
glucose: starting material lactate, amino acids, glycerol) Ultimately: conversion of
pyruvate to glucose

Oxidation loss of electrons (addition of O, or removing of H)

Reduction addition of electrons (addition of H)

Free Energy energetics of biochemical reactions are best described in terms of the
thermodynamic parameter (energy available to do work. Usable energy.)

EXERGONIC VS. ENDERGONIC

a. Exergonic reactions lead to the
release of energy doesnt require
energy
b. Endergonic reactions that require
the absorption of energy. The products
being greater free energy than the
reactants.

Activation Energy minimum quantity of

energy that the reacting species must
possess in order to undergo a specified
reaction.
Transition State a particular
configuration along the reaction coordinate. It is defined as the state corresponding to
the highest potential energy along this reaction coordinate.

Competitive Inhibitor a form of enzyme inhibition where binding of the inhibitor to

the active site on the enzyme prevents binding of the substrate and vice versa. Most
function by binding reversibly to the active site of the enzyme.

ALLOSTERIC VS . COVALENT MODIFICATION OF ENZYMES

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a. Allosteric is a little faster the signal (allosteric
effector) works directly on the affected protein
b. Covalent is longer lasting and less prone to fluctuation
lends itself to sustained responses and also to amplification

KINASES VS. PHOSPHATASES

a. Kinase an enzyme that catalyzes the transfer of a phosphate group from ATP to
a specified molecule
b. Phosphatases an enzyme that removes a phosphate group from its substrate by
hydrolyzing phosphoric acid monoesters into a phosphate ion and a molecule with
a free hydroxyl group a common phosphatase in many organisms is alkaline
phosphatase.

Feedback inhibition a cellular control mechanism in which an enzyme that catalyzes

the production of a particular substance in the cell is inhibited when that substance has
accumulated to a certain level, thereby balancing the amount provided with the amount
needed.

Km the concentration of substrate which permits the enzyme to achieve half Vmax
- An enzyme with a high Km has a low affinity for its substrate and requires a
greater concentration of substrate to achieve Vmax.

BASIC FUNCTIONS OF EUKARYOTIC CELL

a. Nucleus: regulate gene expression, controls cellular growth and respiration
b. Lysosomes: waste removal using digestive enzymes membrane bound sacs of
hydrolytic enzymes used to digest macromolecules
c. Endoplasmic Reticulum: folding of protein molecules & transport of synthesized
proteins to the Golgi
d. Golgi Apparatus: modifying, sorting, and packaging of proteins for secretion
transport of lipids, and the production of lysosomes
e. Mitochondria: to produce the energy currency of the cell (ATP) through respiration,
regulate cellular metabolism
f. Chloroplasts: convert light energy of the sun into sugars used by cells.
(Photosynthesis)
g. Peroxisomes: contain oxidative enzymes that oxidize organic substances to make
H2O2, also use H2O2 to oxidize other things (including toxic molecules)
h. Cytoskeleton: framework for the movement of organelles around the cytoplasm
structural
i. Ribosomes: carry out protein synthesis free and bound

OTHER IMPORTANT CELL STRUCTURES

a. Nuclear pores: large complex of proteins that allow small molecules and ions to
freely pass, or diffuse, into or out of the nucleus. They allow necessary proteins to
enter the nucleus from the cytoplasm if they have special sequences that indicate
they belong in the nucleus.
b. Nucleolus: made of proteins and ribonucleic acids (RNA) main function is to
rewrite the ribosomal RNA and combine it with proteins. This results in the
formation of incomplete ribosomes.
c. Endomembrane system: Membranes in the cell related through direct physical
continuity or by transfer of membrane segments (vesicles). These membranes
EXAM 1 REVIEW
divide the cell into functional and structural compartments or organelles. The
organelles included are: the nuclear membrane, the endoplasmic reticulum, Golgi
apparatus, lysosomes, vesicles, endosomes and the cell membrane.
d. Rough vs. Smooth ER:
a. Smooth: roles in a variety of metabolic processes (lipid metabolism,
detoxification of drugs and metabolites)
b. Rough: main role in synthesis of secretory and membrane-bound proteins;
involved in lipid/membrane synthesis
e. Free vs. Bound Ribosomes: Free ribosomes are located in the cytoplasm and the
bound ribosomes are attached to the endoplasmic reticulum. Free ribosomes
produce proteins for the cell, while bound ribosomes
produce proteins that are transported out of the cell.

Fluid Mosaic Model pictured to the right

a. Fluid: Membrane held together mainly by
hydrophobic interactions; lipids and some proteins
can drift laterally
b. Mosaic: Membrane is a collage of different
embedded proteins.

Lipid Rafts subdomains of the

plasma membrane that contain high concentrations of cholesterol
and glycosphingolipids. They exist as distinct liquid-ordered
regions of the membrane that are resistant to extraction with
nonionic detergents.

Peripheral vs. Integral Membrane Proteins

a. Peripheral (Extrinsic) Membrane Proteins adhere only temporarily to the
biological membrane with which they are associated. These proteins attach to
integral membrane proteins or penetrate the peripheral regions of the lipid bilayer.
b. Integral (Intrinsic) Membrane Proteins type of membrane protein that is
permanently attached to the biological membrane. All transmembrane proteins are
IMPs but not all IMPs are transmembrane proteins. IMPs comprise a significant
fraction of the proteins encoded in an organisms genome.

Hydropathy Plot Calculate G needed to transfer segments of

polypeptide from non-polar solvent to water. These plots allow for
the visualization of hydrophobicity over the length of a peptide
sequence. Look at segments of fixed size (10-20 aa). Plot
hydropathy index vs. position in chain. Pictured to the right.

Some Transmembrane Proteins are -Barrels.

(LEFT picture)
-Barrels a large beta-sheet that twists and
coils to form a closed structure in which the first
strand is hydrogen bonded to the last.
Porin class of proteins that forms channels
in the outer membranes of bacteria.
EXAM 1 REVIEW

LEFT TO KNOW:
- Simple Diffusion
- Facilitated Diffusion
- Active Transport
- Channels vs. Carriers vs. Pumps
- Porins
- Aquaporins
- Ion channels

GENERAL INFORMATION ABOUT CELLS AND CELL EVOLUTION REVIEW

QUESTIONS

1. What are the three tenets of cell theory?

All living organisms are composed of one or more cells; the cell is the basic unit of
structure and organization in organisms; cells arise from pre-existing cells.

2. In what order are the mechanisms of metabolism thought to have

evolved? Why?
Glycolysis (because it was the early anaerobic atmosphere) Photosynthesis (because it
had independence from pre-formed organic molecules) Oxidative Metabolism (it had
an oxygen-rich atmosphere and higher efficiency)

3. What is endosymbiosis and what is the evidence for?

Endosymbiosis is one cell living inside another. It was digested, useful, and kept around.
Precursor cell in symbiotic relationship with bacteria that then becomes a chloroplast.

4. How do surface proteins determine host range in viruses?

They determine host ranges in viruses through protein protein interactions.
Protein protein interactions are the physical contacts of high specificity established
between two or more protein molecules as a result of biochemical events steered by
electrostatic forces including the hydrophobic effect.

5. How can a protein be infectious? An RNA that doesnt code for a protein?
ANSWER

BASIC CHEMISTRY REVIEW QUESTIONS

1. What is electronegativity and how does it lead to polar molecules? Why

are polar molecules sticky? What kind of molecules are polar? Non-
polar?
Electronegativity is the measure of the tendency of an atom to attract a bonding pair of
electrons. Polar covalent bonds are important in biology because they allow molecules to
interact through electrical forces.
Polar molecules are sticky and partly ionic bonds: general name weak electrostatic
attractions, also called Hydrogen bonds
EXAM 1 REVIEW
Non-polar molecules = equal sharing of the bond electrons and arise when the electro-
negativities of two atoms are equal

2. What are the two characteristics (complementarities) needed for

molecules to interact with specificity.
Complementarity of - and +; bonding capacities; complementarity of shape and
structure.
(Commonly called structural complementarity and chemical complementarity.

3. Partial charges can explain both the stickiness of molecules for each
other and the shape of complex molecules how?
ANSWER

4. What is the pK of an amino acid? How are acidic vs. basic acids affected?
What is the usual cause of pH sensitivity in proteins (thinking about
moderate changes in pH)?
pK = pH at which half other carboxylic acid and/or amine residues are charged.
Changing the pH level can change the shape of a protein. This process is called
denaturing the protein. When a protein becomes denatured, it does not function
optimally or it does not function at all.

ORGANIC MOLECULES REVIEW QUESTIONS

1. What is the general formula for a simple sugar? Sugar rings exist in two
different forms what are they and how are the different? What is a
practical result of different polysaccharides having different sugar
conformations and different kind of linkages?
The general formula for a simple sugar is (CH 2O)n. Sugar rings exist in two different
forms: A or B configurations.
FINISH ANSWER

2. What are the major functions of carbohydrates? What are mono- and
disaccharides used for? Oligosaccharides? What do the different major
polysaccharides do?
The six major functions of carbohydrates are: providing energy and regulation of blood
glucose, sparing the use of proteins for energy, breakdown of fatty acids and preventing
ketosis. Monosaccharides include glucose,

galactose, and fructose, which are sugars used by organisms for energy. Disaccharides
provide energy to muscles, fuel the central nervous system, metabolize fat and keep
tissues from consuming protein for energy. Oligosaccharides are found as a side chain on
glyco-proteins or glycolipids and are used as chemical markers for cell recognition. Other
major polysaccharides serve as short-term energy stores in plants and animals.

3. What kinds of reactions are used to make and break down the major
organic molecules?
Synthesis is the production of a major organic molecule. Hydrolysis breaks down a major
organic molecule.
EXAM 1 REVIEW

4. What are the 3 main functions of lipids in the cell?

Structure, regulation of movement, and insulation. (as well as signaling)

5. What are the building blocks of fats (fat =

triglyceride)? What is the structure of a triglyceride
(storage form of fatty acids) vs. a
phospholipid (primary component
of cell membranes)?

The building blocks of fat are

molecules are glycerol and fatty
acids.
Triglycerides are chemically tri-esters of fatty acids and glycerol.
They are formed by combining glycerol with three fatty acid
molecules. Alcohols have a hydroxyl (OH-) group. Organic acids
have a carboxyl (-COOH) group. Pictured to the left.
A phospholipid molecule has a phosphate group on one end,
called the head, and two side-by-side chains of fatty acids that make up the lipid
tails.

6. What are the four main phospholipids that make up membranes? Note
that 3 are glycerol phospholipids and one is not.
Phospholipids, sphingolipids, cholesterol, and glycolipids.

7. What are sphingolipids, glycolipids, and cholesterol, and how/where/for

what are they used?
Sphingolipids any class of compounds that are fatty acid derivatives of sphingosine
and occur chiefly in the cell membranes of the brain and nervous tissue.
Glycolipids lipids with a carbohydrate attached by a Glycosidic bond. Their role is to
maintain stability of the membrane and to facilitate cellular recognition. The
carbohydrates are found on the outer surface of all eukaryotic cell membranes.
Cholesterol Insoluble in water; like oil or fat. A type of fat that is made up of four
interlocked rings of carbon called a steroid. They are important for signaling.

8. What are the building blocks of nucleic acids? Proteins?

Nucleic acids nucleotides
Proteins amino acids

9. What are the three roles of NTPs? Nucleoside Triphosphates

Making nucleic acids, making energy (ATP), and signaling (g-proteins).

PROTEIN STRUCTURE REVIEW QUESTIONS

1. What are the four levels of protein structure? What stabilizes each of
them?
a) Primary Structure Assembly Level the sequence of amino acids
EXAM 1 REVIEW
b) Secondary Structure Folding Level conformation relationship between
amino acids leading to a repeating pattern. Folding based on backbone
properties via hydrogen bonds.
c) Tertiary Structure Packing Level 3D folding based on properties of R-groups
(salt bridges, ionic interactions between positively and negatively charged sites
on amino acid side chains help stabilize the tertiary structure of a protein)
d) Quaternary Structure Interactions Associations between separate
polypeptides. (Stabilized by various interactions, including hydrogen-bonding,
disulfide-bridges and salt bridges.)

2. What part of a polypeptide is important for the bonds that create

secondary structure? Tertiary? Quaternary?
a) Secondary a-helix and b-sheets?
b) Tertiary disulfide bridges / salt bridges?
c) Quaternary protein subunits?

3. What is the difference between domains and subunits?

a) A domain is distinct region of the tertiary structure produced by a part of a
polypeptide which can fold independently into its own compact, stable
structure.
b) Subunits are the associations between separate polypeptides.
c) A subunit is one amino acid chain whereas a domain is just a region on the
amino acid chain.

4. What roles do hydrophilic vs. hydrophobic amino acid side chains play in
protein structure?
a) A critical determinant is localization of hydrophobic vs. hydrophilic amino acids.
b) Hydrophilic R-groups of most proteins are oriented outward.
c) Hydrophobic R-groups of most proteins are oriented inwards.

5. How about the role of disulfide bonds?

a) Folded structure of some proteins is then further stabilized by disulfide bonds.
b) Because it is a covalent bond, the disulfide bond can be considered as part of
the primary structure of a protein. They are very important in determining the
quaternary structure of some proteins.

BIOSYNTHESIS REVIEW QUESTIONS

First: a review-
*A major theme is the generation of energy and reducing power by catabolic pathways
and the use of this energy and reducing power by anabolic (biosynthetic) pathways.
*Making macromolecules: hydrolysis is energetically favorable, but biosynthetic reactions
require energy input. For condensation reactions, the OH group to be removed is first
activated (production of high-energy linkage).

The specific intermediates are different for different macromolecules, but the principle is
the same. Note: building blocks and active intermediates are not the same.
EXAM 1 REVIEW
1. What are activated carriers? What are they used for? What is the most
common carrier of energy? Of reducing power? What are examples of
their use?
a) Activated carriers serve as an analogy for the direct oxidation of glucose to CO2
+ water, which produces heat only.
b) They can serve as an analogy for the synthesis of activated carrier molecules.
c) They can serve as the energetically unfavorable reactions that only occurs due
to the activated carrier/couple reaction.
d) Activated carriers couple energy release from spontaneous, energetically
favorable reactions to energetically unfavorable reactions.
e) The most common energy is ATP. The most common carrier of reducing power is
NADH.
f) In order for carriers like ATP to be a stable source of free energy, they must stay
activated when not being used for cellular purposes.

Making Carbohydrates:
1. What are three ways to get glucose? What is the general scheme for making
glucose? Just know the overall idea and how it compares to glycolysis (next
question).
a) Diet, Photosynthesis, and Gluconeogenesis
b) Gluconeogenesis is the general scheme for making glucose the conversion of
pyruvate for glucose

2. Compare/contrast glycolysis and gluconeogenesis. What does

gluconeogenesis cost?
a) Glycolysis: Glucose 2 Pyruvate. Also converts 2 NAD+ to NADH.
b) Gluconeogenesis: 2 Pyruvate Glucose (they are just opposites of each other)
c) Gluconeogenesis costs 4 ATP, 2 GTP, 2 NADH.

3. What is the active intermediate for making polysaccharides (and in

particular, polymers of glucose)?
a) UDP-glucose is the activated intermediate for making polysaccharides.

Making Proteins:
1. What are the three ways to
get nitrogen (and who can do
each of them?)
a) Atmospheric N2
b) Nitrate (NO3)
c) Ammonia (NH3) all
organisms use as a source of
nitrogen
d) Pictured to the right.

2. In general, from what are amino acids derived?

a) Amino acids are derived from intermediates in the central metabolic pathways.

3. What is the active intermediate for making a polypeptide?

a) The active intermediates for making a polypeptide are converted amino acids.
EXAM 1 REVIEW

Making Nucleic Acids:

1. What are three ways to get nucleotides?
a) Diet, breakdown of nucleic acids, or carbs/amino acids broken down.

2. What are the two building blocks used to make nucleotides?

a) DNA and RNA?

3. What is the starting point carbohydrate?

a) Starting point for synthesis: ribose-5-P

4. What is the active intermediate for polymerization of nucleic acids?

a) Nucleoside triphosphates are used as activated precursors (active
intermediates).

Making Lipids:
1. Synthesizing fatty acid chains is essentially the reverse of what?
a) Fatty acids are synthesized from acetyl CoA.
b) Fatty acids are synthesized in the cytosol, membrane, lipids in ER, and Golgi
Apparatus
c) It resembles the reverse of fatty acid oxidation
a. With the reverse of glycolysis, reactions can differ and are often driven by
coupling.

2. Where are fatty acids made? Phospholipids? Sphingomyelin?

a) Fatty acids the creation of fatty acids from acetyl-CoA and NADPH through the
action of enzymes called fatty acid synthases this process takes place in the
CYTOPLASM of the cell!
b) Phospholipids Phospholipids occur with other molecules (proteins, glycolipids,
sterols) in a bilayer such as the CELL MEMBRANE.
c) Sphingomyelin Present in the PLASMA MEMBRANES of animal cells and are
especially prominent in the MYELIN SHEATH.

3. What is the activated intermediate for the linking of fatty acid chains to
glycerol (to make fats)?
ANSWER

BIOENERGETICS REVIEW QUESTIONS

1. What are oxidation and reduction? How can you determine if oxidation or
reduction is occurring in organic molecules?
a) Reduction addition of electrons (addition of H+)
a. C-H increasing: reduction occurring
b) Oxidation loss of electrons (during addition of O- or removing H+)
a. C-H decreasing: oxidation occurring
EXAM 1 REVIEW
2. What is free energy? How does the value of G predict whether a reaction
is energetically favorable? What is G? G?
a) Free Energy is the energy available to do work, or usable energy
b) G is the change in free energy unusable energy, lost during transfer, wasted
in the form of heat

c) To predict whether a reaction is energetically favorable, G takes into account

the changes in enthalpy and the changes in entropy.
d) G under standard conditions, change in free energy. It reflects the nature of
the reactants and products without regard to differences in the concentration.
a. G = G + RT ln [Products]/[Reactants]
e) G same as G but incorporates pH (-pH 7)

3. How can one separate the concentration dependent and independent

parts of G? (Recall that G = G + RTln[X]/[Y]; which part of this
involves concentration?) When is G equal to G? What happens at
equilibrium?
a) Y X involves concentration.
a. Large concentration Y, pushes forward, G being negative
b. Large concentration X, reverse direction, equal amounts need energy
b) G = G when G becomes more negative as ratio of X to Y decreases (more Y
present)
c) When equilibrium occurs, G + RT ln K = 0 or G = -RT ln K

4. What is the G of a combined reaction?

ANSWER

5. What is an advantage to hydrolyzing ATP to AMP + PPi (vs ATP to ADP + Pi)?
ANSWER

6. Energy is needed for many cellular tasks, including performing endergonic

reactions. What are the pathways that lead to production of ATP?
a. How much ATP comes from glycolysis (per glucose molecule)? 4
ATP molecules
b. From the citric acid cycle (again, per glucose molecule)? 2 ATP
molecules
c. From oxidative phosphorylation (aka electron transport chain)? How (what
molecules are produced via other processes and used to make ATP)?
d. Conversion of pyruvate to acetyl CoA does not directly produce ATP what is
produced by this process which ultimately leads to ATP production? Also,
what/how much is produced by glycolysis and the citric acid cycle (other
than ATP)?
e. Why does fatty acid oxidation produce so much energy?

ENZYMES REVIEW QUESTIONS

EXAM 1 REVIEW
1. Enzymes are needed to increase the rate of virtually all chemical
reactions in cells, even though many reactions are energetically
favorable. Why?
a) Enzymes change the rate of a reaction, but not its equilibrium.

2. How enzymes work:

a. 1) Note the importance of shape and charge for binding of substrates at the
active site.
b. 2) Enzymes create a favorable environment for reactions to occur in several
ways. What are they?
3. Enzyme examples chymotrypsin and lysozyme: How is substrate specificity
achieved by chymotrypsin and trypsin (role of shape and charge)? How is
structural specificity achieved by lysozyme?
4. For one of our examples of enzyme activity, what are some key features of
enzymes/active sites/enzyme action that are illustrated (and how)?

5. How do competitive inhibitors work to affect enzyme activity?

a) Competitive inhibition occurs when the substrate and a substance resembling
the substrate are both added to the enzyme. A theory called the lock-key
theory of enzyme catalysts can be used to explain why inhibition occurs.
b) The lock and key theory utilizes the concept of an active site. This concept
holds that one particular portion of the enzyme surface has a strong attraction
for the substrate. The substrate is held in such a way that its conversion to the
reaction products is more favorable.
c) The reaction is slowed down because some of the available enzyme sites are
occupied by the inhibitor. If a dissimilar substance which does not fit the site is
present, the enzyme rejects it, accepts the substrate, and the reaction proceeds
normally.

6. Compare and contrast allosteric and covalent regulation. How does each
work? What is the most common type of covalent regulation of enzymes?
a) Allosteric is a little faster the signal (allosteric effector) works directly on the
affected protein
b) Covalent is longer-lasting and less prone to fluctuation lends itself to sustained
responses and also to amplification
c) Phosphorylation is a very common method of regulating protein function
(covalently)

CELL STRUCTURE REVIEW QUESTIONS

*Key idea: eukaryotic cells utilize compartmentalization to help provide local

environments so that the right reactions/activities can occur in the right times and
places.

1. What is the difference between free and bound ribosomes? Between

smooth and rough ER?
a) Free ribosomes are located in the cytoplasm and the bound ribosomes are
attached to the endoplasmic reticulum. Free ribosomes produce proteins for the
EXAM 1 REVIEW
cell, while bound ribosomes produce proteins that are transported out of the
cell.
b) Smooth ER: roles in a variety of metabolic processes (lipid metabolism,
detoxification of drugs and metabolites)
c) Rough ER: main role in synthesis of secretory and membrane-bound proteins;
involved in lipid/membrane synthesis

2. What is a key feature of the inside of a lysozyme? How is it made possible

and why is it needed?
a) Compartmentalization: Lysosomes provide a space where specific enzymes can
work and not affect the rest of the cell
b) It is made possible through the proton pump. Membrane proteins are actively
pumping ions into it to keep the pH down. It is needed to prevent diseases and
cause any abnormal pH changes.

3. In what way is the Golgi polar? The Golgi is especially extensive in what
sort of cells?
a) Golgi are polar because of their cis and trans faces
a. Cis receiving // trans shipping
b) It is especially extensive in cells doing secretion.

4. In general, know the main features and functions of the parts of the cell
we discussed.
a) Refer to the features in the terms section at the beginning of the study guide.

MEMBRANES REVIEW QUESTIONS

** Side note: The plasma membrane creates a boundary between the cell (cytoplasm)
and its environment, and mediates interactions between the two.

1. Membrane structure (basic outline): What gives membranes their fundamental

structure? What carries out most of the specific functions?
2. Development of fluid mosaic model: What was the evidence for membranes being
made of lipids? Containing proteins? For membranes being bilayers? For
membranes and proteins not being sandwiches (but rather being a fluid mosaic)?
3. In what way are membrane lipids asymmetrical? How does this lead to difference
in charge (in & out)?
4. What is a reason why amounts and types of membrane proteins vary?
5. How were peripheral proteins initially defined? How are they associated with the
membrane?
6. How can integral proteins be released? What is usually used to isolate them?
7. Most integral proteins are of what type? What does a hydropathy plot tell you
about them? Know how to interpret such a plot.
8. What is an example of a non-alpha helix transmembrane protein? What are the
major anchors used for integral proteins which do not pass through the
membrane? What role does charge sometimes play in their targeting?
EXAM 1 REVIEW
MEMBRANE FLUIDITY REVIEW QUESTIONS

1. Membranes have both fluidity and flexibility; what does each of those
mean?
a) Membrane fluidity: the plasma membrane is a fluid combination of
phospholipids, cholesterol, and proteins. The membrane behaves as 2D fluids,
which is crucial for membrane functions. It is important for membrane function
and has to be maintained within a certain limit. Also refers to the viscosity of
the lipid bilayer of a cell membrane or a synthetic lipid membrane.
b) Membrane flexibility: a type of semipermeable material or a material that acts
as a barrier to prevent the transmission of certain substances, yet allows the
passage of others. Provides a long term roof protection solution, has a micro-
porous structure that allows moisture to escape, solvent-free, etc.

2. Fluidity can be studied using synthetic bilayers. What kinds of

movements of lipids are frequent/rare?
a) Lateral diffusion, flexion, and rotation

3. Fluidity depends on temperature and composition. How/why?

a) At low temperatures, cholesterol increases membrane fluidity by preventing
membrane lipids from packing close together. At high temperatures, cholesterol
decreases membrane fluidity.
b) The composition of a membrane can also affect its fluidity. The membrane
phospholipids incorporate fatty acids of varying length and saturation.

4. What is the indirect evidence for mobility of membrane proteins? The

direct evidence?
a) Classic Indirect Evidence that the membrane proteins have and require freedom
of motion within the membrane: create artificial membrane vesicles made of
some pure phospholipid (dimyristoyl phosphatidyl choline) add some specific
players: components of a signaling pathway, specifically,

a receptor and two membrane associated signaling intermediates above 23 C,

this works just fine. But below 23 C, it wont work.
b) Classic Direct Evidence that the Membrane Proteins have freedom of motion
within the membrane: an experiment to demonstrate that proteins are definitely
free to diffuse naturally.
a. The rapid intermixing of cell surface antigens after formation of mouse-
human heterokaryons
b. After some time, the mouse cell and the human cell end up mixed.
Fluorescent tags!

5. What are some examples of things which limit the fluidity of membrane
proteins?
a) Attachment to cytoskeleton
b) Association with other proteins (ECM: Extra-cellular matrix)
EXAM 1 REVIEW
c) Polarized cells with tight junctions
d) Lipid composition / lipid rafts

MEMBRANE TRANSPORT REVIEW QUESTIONS

1. What are the key characteristics of simple diffusion? What determines

the direction of movement?
a) Non-selective, no membrane proteins involved, and direction determined by
relative concentrations
b) Direction of movement is determined by relative concentrations

2. Why is facilitated diffusion necessary? What determines the direction of

movement?
a) A concentration gradient exists that would allow ions and polar molecules to
diffuse into the cell, but these materials are repelled by the hydrophobic parts of
the cell membrane. Facilitated diffusion uses integral membrane proteins to move
polar or charged substances across the hydrophobic regions of the membrane.
b) Carrier proteins are responsible for facilitated diffusion and the direction of
movement.

3. What are the two main classes of proteins involved in facilitated

diffusion? The three kinds of stimuli that regulate ion channels? Ligand-
gated channels are often gated by what kind of ligand?
a) Two main classes of proteins involved: carriers and channels
b) Three kinds of stimuli:
c) Ligand-gated channels: a type of ion channel that opens when a signal molecule
(ligand) binds to an extracellular receptor region of the channel protein.

4. Why is active transport necessary?

a) In active transport, particles move against a concentration gradient and
therefore require energy which must be supplied by the cell. Carrier proteins
that are found in the cell membrane of cells use energy to transport molecules
or ions across the membrane, against the concentration gradient.

5. What are the three main sources of energy for driving active transport?
What are the two major categories of active transport?
a) ATP-driven pumps, coupled transporters, and light-driven pumps
b) 1. Transport Proteins the same as facilitated diffusion, except a molecule goes
from low concentration to high concentration across a cell membrane and it
needs energy to take place
c) 2. Membrane vesicles substances entering the cell become enclosed by an in-
pocketing of the cell membrane to form a vesicle. This process is called
endocytosis.

** You should be able to distinguish situations which would utilize each of the three types
of movement (passive diffusion, active diffusion, and active transport.)
EXAM 1 REVIEW

POSSIBLE DISCUSSION QUESTIONS:

2. Discuss the role of activated carriers in biosynthesis. Why are they needed and
how (in general) are they used? What are some major examples and what do they
carry? What is an example of the use of one of them in biosynthesis?

3. How are enzymes able to catalyze reactions (how do they create environments
conductive to a given reaction)? Give an example using a specific enzyme. Briefly,
what does it do and how does it work; what are some key features of
enzymes/enzyme action which it illustrates? Note: you dont need to be able to
draw the structures of the active site or the substrate, but you do need to be able
to clearly describe the key points.

4. Discuss the development of the fluid mosaic model of membrane structure. What
was the evidence for lipid membranes, the presence of proteins, bilayer structure,
and the actual mosaic part?

5. Describe the experiments providing indirect and direct evidence for the mobility of
membrane proteins.