MCAT Biochemistry (Kaplan)

Amino acids have four groups attached to a central (α) carbon:

an amino group, a carboxylic acid group, a hydrogen atom and a R group

The R group determines

chemistry and function of that amino acid.

Twenty amino acids appear in the proteins of eukaryotic organisms

The stereochemistry of the α-carbon is`

1 for all chiral amino acids in Eurkaryotes

D-amino acids can exist in

prokaryotes

All chiral amino acids expect______ have an (S) configuration

Cysteine

All amino acids are chiral expect

glycine, which has a hydrogen atom as its R group

Side chains can be

polar or nonpolar, aromatic or nonaromatic, charged or uncharged

Nonpolar nonaromatic amino acids

glycine, alanine, valine, leucine, isoleucine, methionine, proline

Aromatic

Tryptophan, phenylalanine, tyrosine

Polar

Serine, threonine, asparagine, glutamine, cysteine

Negatively charged (acidic)

aspartate, glutamate

Positively charged (basic)

Lysine, arginine, histidine

Amino acids with _____alkyl chains are ______ and those with charges are _____; many others fall somewhere in between

long; hydrophobic; hydrophilic

Amino acids are

amphoteric; that is, they can accept or donate protons

The pKa of a group is the 

pH at which half of the species are deprotonated; [HA] = [A^-]

At low (acidic) pH, the amino acid is

fully protonated

At pH near the pI of the amino acid, the amino acide is

a neutral zwitterion

At high (alkaline) pH, the amino acid

is fully deprotonated

The titration curve is nearly _____ at the pKa values of the amino acid

flat

The titration curve is nearly_______ vertical at the pI of the amino acid

Vertical

Amino acids with charged side chains have an additional pKa value, and their pI is calculated

by averaging the two pKa values that correspond to protonation and deprotonation of the zwitterion

Amino acids without charged side chains have a pI around

6

Acidic amino acids have a pI

well below 6

Basic amino acids have a pI

well above 6

Dipeptides

have two amino acid residues

tripeptides

have three amino acid residues

Oligopeptides

have a “few” amino acid residues (<20)

Polypeptides

have “many” (>20)

Forming a peptide bond is a

condensation or dehydration reaction (releasing one molecule of water)

The nucleophilic amino group of one amino acid attacks the

electrophilic carbonyl group of another amino acid

Amide bonds are

rigid because of resonance

Breaking a peptide bone is a 

Hydrolysis reaction

Primary structure

is the linear sequence of amino acids in a peptide and is stabilized by peptide bonds

Secondary structure

is the the local structure of neighboring amino acids, and is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups

α-helices

are clockwise coils around a central axis

β-pleated sheets

are rippled strands that can be parallel or antiparallel

Proline can interrupt

secondary structure because of its rigid cyclic structure

Tertiary structure

is the three-dimensional shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-baser interactions (salt-bridges), hydrogen bonding, and disulfide bonds

Hydrophobic interactions

push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy

Disulfide bonds

occur when two cysteine molecules are oxidized and create a covalent bond to form cysteine

Quaternary structure

is the interaction between peptides in proteins that contain multiple subunits

Proteins with covalently attached molecules are termed

conjugated proteins. The attached molecule is a prosthetic group and may be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid

Denaturation

Both heat and increasing solute concentration can lead to loss of three-dimensional protein structure

Heat denatures proteins by increasing their average

kinetic energy, this disrupting hydrophobic interactions

Solutes denature proteins by

disrupting elements of secondary, tertiary, and quaternary structure

Isoelectric point of a neutral amino acid

Isoelectric point of an acidic amino acid

Isoelectric point of a basic amino acid

Enzymes

are biological catalysts that are unchanged by the reactions they catalyze and are reusable

Each enzyme catalyzes a

single reaction or type of reaction with high specificity

Oxidoreductases

catalyze oxidation-reduction reactions that involve the transfer of electrons

Transferases

move a functional group from one molecule to another molecule

Hydrolases

catalyze cleavage with the addition of water

Lyases

catalyze cleavage without the addition of water and without the transfer of electrons. The reverse reaction (synthesis) is often more important biologically

Isomerases

catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers

Ligases

are responsible for joining two large biomolecules, often of the same type

Exergonic reactions

release energy; ΔG is negative

Enzymes lower the

activation energy necessary for biological reactions

Enzymes do not alter the

free energy (ΔG) or enthalpy (ΔH) change that accompanies the reaction nor the final equilibrium position; rather, they change the rate (kinetics) at which equilibrium is reached

Enzymes act by stabilizing

the transition state, providing a favorable microenvironment, or bonding with the substrate molecules

Enzymes have an

active site, which is the site of catalysis

Binding to the active site is explained by the 

lock and key theory of the induced fit model

The lock and key theory hypothesizes that the

enzyme and substrate are exactly complementary

The induced fit model hypothesizes that the

enzyme and substrate undergo conformational changes to interact fully.

Some enzymes require

metal cation cofactors or small organic coenzymes to be active

Enzymes experience saturation kinetics

as substrate concentration increases, the reaction rate does as well until a maximum value is reached

Michaelis-Menten and Lineweaver-Burk plots represent

this relationship as a hyperbola and line respectively

Enzymes can be compared on a basis of their

K_m and v_max values

Cooperative enzymes display a

sigmoidal curve because of the change in activity with substrate binding

Temperature and pH affect an enzyme’s activity

in vivo

changes in temperature and pH can result in

denaturing of the enzyme and loss of activity due to loss of secondary, tertiary, or, if present, quaternary structure

In vitro

salinity can impact the action of enzymes

Enzyme pathways are highly

regulated and subject to inhibition and activation

Feedback inhibition

is a regulatory mechanism where by the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway

Reversible inhibition

is characterizes by the ability to replace the inhibitor with a compound of greater affinity or to remove it using mild laboratory treatment

Competitive inhibition

results when the inhibitor is similar to the substrate and binds at the active site.

Competitive inhibition can be overcome by adding more substrate. V_max is unchanged, K_m increases.

Noncompetitive inhibition

results when the inhibitor binds with equal affinity to the enzyme and the enzyme–substrate complex. vmax is decreased, Km is unchanged.

Uncompetitive inhibition

results when the inhibitor binds only with the enzyme-substrate complex. K_m and V_max both decreases

Mixed inhibition

results when the inhibitor binds with unequal affinity to the enzyme and the enzyme-substrate complex. Vmax is decreased, Km is increased or decreased depending on if the inhibitor has higher affinity for the enzyme or enzyme-substrate complex

Irreversible inhibition

alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently; new enzyme molecules must by synthesized for the reaction to occur again

Regulatory enzymes can experience

activation as well as inhibition

Allosteric sites

can occupied by activators, which increase either affinity or enzymatic turnover

Phosphorylation (covalent modification with phosphate) or glycosylation (covalent modification with carbohydrate)

can alter the activity or selectivity of enzymes

Zymogens

are secreted in an inactive form and are activated by cleavage

Michaelis-Menten rates

Michaelis-Menten equation

Turnover number (K_cat)

Structural proteins

compose the cytoskeleton, anchoring proteins, and much of the extracellular matrix

The most common structural proteins are

collagen, elastin, keratin, actin, and tubulin

They are generally fibrous in natur

Motor proteins

have one or more heads capable of force generation through a conformational change.

They have catalytic activity, acting as ATPases to power movement.

Muscle contraction, vesicle movement within cells, and cell motility are the 

most common applications of motor proteins.

Common examples include myosin, kinesin, and dynein

Binding proteins

binds a specific substrate, either to sequester it in the body of hold its concentration at steady state

Cell adhesion molecules (CAM)

allow cells to bind to other cells or surfaces

Cadherins

are calcium-dependent glycoproteins that hold similar cells together

Integrins

have two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix. Some also have signaling capabilities

Selectins

allow cells to adhere to carbohydrates on the surfaces of other cells and are commonly used in the immune system

Antibodies (or immunoglobulins,Ig)

are used by the immune system to target a specific antigen, which may be a protein on the surface of a pathogen (invading organism) or a toxin

Immunoglobulin contain

a constant region and a variable region; the variable region is responsible for antigen binding

Two identical heavy chains and two identical light chains form a

single antibody; they are held together by disulfide linkages and noncovalent interactions

Ion channels

can be used for regulating ion flow into or out of a cell. There are three main types of ion channels