1A

What is the general structure of an amino acid?

Central α-carbon attached to NH2, COOH, H, and R-group

What is the absolute configuration of most amino acids?

L configuration at the α-carbon (S configuration for all except cysteine).

which amino acid is achiral?

glycine

Which amino acid has R configuration?

cysteine (due to sulfur priority)

Molecule with both positive and negative charges but overall neutral.

zwitterion

What is the form of amino acids at physiological pH?

NH3⁺ and COO⁻ (zwitterionic form)

When are amino acids fully protonated?

At low pH (acidic conditions).

When are amino acids fully deprotonated?

At high pH (basic conditions)

Which amino acids are acidic?

Aspartic acid (Asp, D), Glutamic acid (Glu, E).

What are acidic amino acids charges at physiological pH?

Negative (deprotonated carboxylate)

Which amino acids are basic?

Histidine (H), Arginine (R), Lysine (K)

Which basic amino acid is partially protonated at pH 7.4?

Histidine (pKa ~6), often used in enzyme active sites

List nonpolar amino acids.

gly-g. ala-a. pro-p. leu-L. ile-I. met-M. phe-f. trp-W. val-V

where are hydrophobic residues typically found?

Buried in the interior of proteins.

List polar amino acids.

gln-Q, ser-S, cys-C, ala-A, thr-T, tyr- Y

What enables polar residues to hydrogen bond?

OH, SH, and amide groups.

where are hydrophillic/polar amino acids found

on the outside

What forms a disulfide bond?

Oxidation of two cysteine residues → cystine.

Where do disulfide bonds typically form?

Extracellular proteins (oxidizing environments).

What breaks disulfide bonds?

Reducing agents (ex. β-mercaptoethanol, DTT).

amide bond formed between COOH of one amino acid and NH2 of another.

peptide bond

What type of reaction forms a peptide bond?

dehydration (condensation) reaction

What type of reaction breaks a peptide bond?

hydrolysis-addition of water

What gives the peptide bond partial double-bond character?

Resonance between C=O and C–N.

What is the direction of a polypeptide?

N-terminus → C-terminus.

What conditions cause nonenzymatic hydrolysis?

Strong acid, strong base, or heat.

What enzymes hydrolyze peptide bonds?

proteases (trypsin, chymotrypsin, pepsin).

What is the significance of hydrolysis in the body?

Protein digestion and turnover.

Linear sequence of amino acids held together by peptide bonds.

primary structure

What determines primary structure?

DNA sequence (gene encoding the protein).

What stabilizes secondary structures?

Hydrogen bonding between backbone atoms (C=O and N–H).

Main types of secondary structure?

α-helix and β-sheet.

What amino acid disrupts α-helices?

Proline (rigid ring structure causes kinks).

What stabilizes tertiary structure?

Hydrophobic interactions, ionic bonds, hydrogen bonds, van der Waals interactions, disulfide bonds.

What is the role of cystine in tertiary structure?

Disulfide bonds between cysteine residues stabilize folded proteins.

What drives hydrophobic collapse?

Nonpolar residues move inward to avoid water.

Causes rigid turns or breaks in helices.

proline in tertiary structure

Association of multiple polypeptide chains (subunits).

quaternary structure

What stabilizes quaternary structure?

Same forces as tertiary: hydrophobic interactions, ionic bonds, H-bonds, disulfide bonds

Example of a quaternary protein?

Hemoglobin (tetramer).

what causes protein denaturation?

Heat, pH changes, detergents (SDS), organic solvents, reducing agents.

What structure(s) remain intact after denaturation?

primary structure - peptide bonds

What is protein folding driven by?

Hydrophobic effect + formation of stabilizing interactions.

Help proteins fold correctly and prevent aggregation.

chaperones

Why are hydrophobic interactions important for protein stability?

They reduce disruption of water structure and drive folding inwards

example of hydrophobic residues?

Val, Leu, Ile, Phe, Trp.

Structured shell of water around hydrophobic surfaces.

solvation layer

folding _______ of water

increases entropy

Hydrophobic residues cluster →

water becomes less ordered → entropy increases (favorable).

What thermodynamic force drives folding?

Increase in entropy of water (ΔS > 0), making ΔG negative.

pH where a molecule has no net charge.

isoelectric point (pl)

How do proteins behave at pH < pI?

They are positively charged.

How do proteins behave at pH > pI?

They are negatively charged.

What is pI important for?

Isoelectric focusing.

What does electrophoresis separate molecules by?

charge and size

Which direction do negatively charged proteins migrate?

toward the anode (+).

Separation by size only; ____ denatures proteins and gives uniform negative charge.

SDS

Separates proteins by charge, size, and shape (no denaturation).

native PAGE

Proteins migrate until pH = pI → no movement.

isoelectric focusing

What makes cysteine unique?

Can form disulfide bonds (oxidation).

Where do disulfide bonds form?

Extracellular space (oxidizing)

inside the cytosol =

reducing

What type of bond holds primary structure?

covalent peptide bonds

What type of bond holds secondary structure?

hydrogen bonds

Bind specific molecules to transport, store, or regulate them.

binding proteins

What determines specificity?

Shape, charge, and chemical complementarity of the binding site.

When binding of one ligand influences binding of others (ex: hemoglobin shows positive cooperativity).

cooperativity

examples of binding proteins

Hemoglobin (_____)

myoglobin (____)

albumin (____)

DNA-binding transcription factors.

binds O₂, stores O₂, transports fatty acids,

What is the main nonenzymatic protein involved in immunity?

Antibodies (immunoglobulins).

Structure of an antibody?

Two heavy chains + two light chains linked by disulfide bonds.

What part of the antibody binds antigen?

variable region (Fab region).

What determines antigen specificity?

Amino acid sequence in the variable region.

How do antibodies neutralize pathogens?

Binding and blocking, tagging for destruction, or aggregating antigens.

Proteins that convert chemical energy (ATP) into mechanical work.

motor proteins

Major families of motor proteins?

Myosin, kinesin, dynein

responsible for muscle contraction and actin-based movement.

myosin

Moves cargo toward the + end of microtubules (away from nucleus).

kinesin

Moves cargo toward the – end of microtubules (toward nucleus); also drives cilia and flagella movement.

dynein

What allows motor proteins to move directionally?

Conformational changes driven by ATP binding, hydrolysis, and release.

What type of protein is collagen?

Structural protein (not enzymatic).

Structural protein in hair, nails, skin.

keratin

Motor-related protein (polymer) that interacts with myosin.

actin

Structural motif found in antibodies and many cell surface receptors.

immunoglobulin fold

What do enzymes do in biological reactions?

Increase reaction rate by lowering activation energy (Ea) without being consumed.

Do enzymes change ΔG, ΔH, or Keq?

No. They only affect the reaction rate, not thermodynamic favorability.

oxidation/reduction (ex. dehydrogenases)

Oxidoreductases

transfer functional groups (ex. kinases)

transferases

use water to break bonds (ex. proteases)

hydrolases

break/make bonds without water (ex. aldolase)

lyases

rearrangements (ex. phosphoglucose isomerases

isomerases

bond formation using ATP (ex. DNA ligase)

ligase

Stabilize transition state, bring reactants together, alter local environment, strain substrate bonds.

how enzymes lower activation energy

What part of the energy diagram changes with an enzyme?

Activation energy (peak height) decreases; reactants/products remain the same.

What determines enzyme specificity?

Shape, polarity, charge, and chemical complementarity of the active site.

What is substrate binding based on?

Noncovalent interactions (H-bonding, ionic interactions, hydrophobic forces).

Which model does MCAT emphasize?

induced fit

Enzyme and substrate fit perfectly; rigid model.

aactive Site (Lock-and-Key) Model

Enzyme changes shape when substrate binds; more accurate biological model.

Induced-Fit Model?

Inorganic ions (e.g., Mg²⁺, Zn²⁺) required for enzyme activity.

cofactors

Help stabilize negative charges or assist in substrate binding.

metal ions