BBL Midterm NYU COD 25'

All amino acids with the exception of ______ exhibit chirality

glycine

Amino acids are derived from which cycles?

Glycolysis, pentose phosphate pathway, and TCA

How is selenocysteine formed?

It is formed on a cysteinyl-tRNA where the seleno group is substituted for a sulfur group

Proteins only contain amino acids in what configuration?

L-config

L and D amino acids are ______

enantiomers

Buffer equation

pH=pKa + log [base]/[acid]

Why is proline a unique amino acid?

Proline contains a secondary amine, making it very rigid in structure, meaning it cannot be a hydrogen donor, only a hydrogen bond acceptor

All amino acids are formed by the amination of?

Keto acids

The major metabolic source of amino acid precursors is

TCA

All amino acids have an R group. What is the significance of the R?

Each of the 21 amino acids has a unique R group

At neutral pH, amino acids are dominantly

zwitterions

Branched chain amino acids

Leucine, Isoleucine, Valine

nonpolar aliphatic amino acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

*hydrophobic

hint: GLAMP VIPT

polar uncharged amino acids

Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

* hydrophilic

Hint: STACT G

Acidic amino acids

Aspartate, glutamate (negatively charged)

*salt bridges and electrostatic interactions

basic amino acids

lysine, arginine, histidine (positively charged)

*salt bridges and electrostatic interactions

Abbreviation for: glycine, alanine, valine

Gly

Ala

Val

Abbreviation for: Leucine, Isoleucine, Methionine

Leu

Ile

Met

Abbreviation for: Phenylalanine, Tryptophan, proline

Phe

Trp

Pro

Abbreviation for: Serine, Threonine, Cysteine

Ser

Thr

Cys

Abbreviation for Asparagine, Glutamine, Aspartate, Glutamate

Asn

Gln

Asp

Glu

Abbreviation for Lysine, Arginine, Histidine

Lys

Arg

His

Aromatic amino acids

Phenylalanine

Tryptophan

Tyrosine

What is body pH?

7

Which amino acid is the start signal for translation of mRNA to protein?

Methionine

The use of methionine in methylation is through

Adenylylation of methionine by enzyme to form S'adenosylmethionine

The unique amino acid found in the elastin protein is

Desmosine

The uncommon amino acid ornithine

Is the starting substrate of the Urea Cycle

The carboxylic acid group gets ____ while the amine group gets _____ at physiological pH

deprotonated

protonated

What does pI mean? What does it indicate?

It means isoelectric point

it indicates the region of minimum buffering power

What is pH?

measure of hydrogen ion concentration

What is pKa? What is relevant about it in the context of amino acids?

dissociation constant

pK1 represents the pH where the COOH group is deproto/protonated.

pK2 represents the pH where the NH3 group is deproto/protonated.

pKR represents the pH where the R-group is deproto/protonated.

Which amino acids have R-groups that are ionizable? Around what pH does that happen for each?

Arg: 12.48

Lys: 10.53

Tyr: 10.07

Cys: 8.18

His: 6.00

Glu: 4.25

Asp: 3.25 **** hint: Aggravated Lions Try (CY)Silently Hunting Gluttonous Asps

What is the typical approximate pH that COOH groups are ionized

pH 2 to 2.8

What is the typical approximate pH that NH3 groups are ionized

pH 9 to 10.5

What is the approximate pI of non polar amino acids

5.5 to 6

What is the hydrophobic effect

release of water molecules on the structured salvation layer and around the molecule has the protein folds increasing net entropy

What are hydrogen bonds

Interactions of the NH and CO of the peptide bond lead to regular structures, such as alpha helices and beta sheets.

What are London dispersion?

Medium range, weak attractions between all atoms contributes significantly to the stability in the interior of the protein.

What are electrostatic interactions

Long range, strong interactions between permanently charged groups. And salt bridges, buried in the hydrophobic environment, stabilize the protein in strong ways.

What is a salt bridge?

buried in the hydrophobic environment, stabilizing the protein in strong ways

What is a quaternary structure?

two or more polypeptides (called subunits) held together by noncovalent forces

How are peptide bonds formed? Where are they formed? What kinds of proteins are they found in?

formed between the terminal carboxylic acid of the first amino acid and the amine group of the second amino acid

primary and secondary

What kind of bonds do primary proteins use?

peptide and disulfide

What kind of bonds do secondary proteins use?

hydrogen, peptide, disulfide

What kind of bonds do tertiary proteins use?

hydrophobic, hydrogen, ionic, van der waals, disulfide

What kind of bonds do quaternary proteins use?

hydrophobic, hydrogen, ionic, van der waals, disulfide

What is a homomeric quaternary structure? What about heteromeric?

identical protein sub-units bonded together

different polypeptides bonded together

The three-dimensional structure of a protein depends on

Specific gene codes

What is a motif?

A short, recurring sequence or structural pattern in a protein.

What is a domain?

A larger, independently stable part of a protein that can fold and function on its own. Domains often correlate with specific functions, like binding DNA or catalyzing reactions.

What are the amino acids known as helix breakers?

Proline and glycine

they disrupt the regularity of the helix backbone

Examples of primary structure

amino acid polypeptide chain

Examples of secondary structure

alpha helix: keratin (hair and nails)

beta sheet: silk fibroin (spider silk)

examples of tertiary structure

Myoglobin (single chain globular protein that stores oxygen in muscle)

examples of quaternary structure

Hemoglobin (4 subunits (2a, 2B) that carry O2

DNA polymerase

Tell me about immunoglobin: bond type, structure type, function, key things

bond: disulfide

structure: quaternary

function: antibody that bind antigens

key: modular domain allow recognitions of many antigens

Tell me about myoglobin: bond type, structure type, function

bond: hydrophobic interactions

structure: tertiary

function: stores oxygen in muscle

Tell me about hemoglobin: bond type, structure type, function, key point

bond: salt bridges, hydrogen bonds, hydrophobic affect

structure: quaternary

function: transports oxygen in blood

key: shows cooperative binding

What causes sickle cell anemia? What effect does this have?

cause: mutation in hemoglobin beta chain (Glu to Val mutation at position 6)

effect: hydrophobic valine causes Hb to polymerize which equates to the sickle cell

primary structure change affects quaternary structure change which leads to disease

What type of reaction forms a peptide bond?

A condensation reaction (releases H₂O) between the amino group of one amino acid and the carboxyl group of another.

Which atoms are involved in a peptide bond?

The carbon of the carboxyl group and the nitrogen of the amino group (C-N bond).

Why is rotation restricted around the peptide bond?

The peptide bond has partial double bond character due to resonance, which prevents free rotation.

What is the nature of the peptide bond?

It is planar, rigid, and usually in the trans configuration to reduce steric hindrance.

What is the overall result of peptide bond formation in a polypeptide chain?

Formation of a backbone with repeating N-Cα-C units that determines protein secondary structure.

What is the spatial orientation of amino acids in a peptide, with exception of proline?

Amino acids are trans of each other

What is the native state of a protein?

The properly folded, functional 3D structure of a protein under physiological conditions.

Name 4 common causes of protein denaturation.

Heat, pH changes, heavy metals, and SDS (detergents).

What happens to a protein during denaturation?

It loses its 3D structure and function, unfolding into a nonfunctional state.

What does the folding funnel model show?

Proteins fold stepwise from high-energy, high-entropy states to a low-energy, native state, sometimes passing through intermediate forms.

Interaction of N-H and C=O of the peptide bond leads to local regular structures such as

Alpha helix and beta sheets

Which pair of amino acids are strong alpha-helix formers?

Alanine and leucine

In beta pleated sheet peptide chains, H bonds between parallel strands are

Weaker, 1 Kcal/mol

What is the orientation of the R groups of amino acids in beta sheets?

Perpendicular to the axis and trans to each other

What amino acids are most commonly present in beta turns?

Proline and glycine

The beta turn is composed of four amino acid residues. Where does the H bond form in the beta turn?

Between the CO of the first amino acid residue hydrogen bonds with the NH group of n+3 residues from it

The native configuration of a protein is

The lowest entropy state and lowest energy state when folded

If two proteins share a secondary structural motif, then it can be assumed

Nothing in regards to their secondary structural similarities

What can be said about the enthalpy and entropy of a properly folded protein?

Both entropy and enthalpy decrease

Substrate binds to the active site through

Non-covalent interactions

The binding energy of the enzyme for the substrate

Lowers the energy requirement for the reaction to occur

Which kinetic value is experimentally determined?

Vmax

How many classes of enzymes catalyze reactions in the cell?

6

What determines the specificity of an enzyme-catalyzed reaction?

The enzyme-substrate complex, including energy of activation, transition state, and whether the reaction is endothermic or exothermic.

Define the active site of an enzyme.

The specific region of the enzyme where the substrate binds and the reaction occurs, formed by a unique arrangement of amino acid R groups.

What are binding and catalytic sites in an enzyme?

The binding site holds the substrate, while the catalytic site carries out the chemical reaction.

What is an allosteric site?

A site on the enzyme, distinct from the active site, where molecules can bind to regulate the enzyme's activity.

Explain competitive inhibition. What happens to Km and Vmax?

The inhibitor binds to the active site, competing with the substrate. Vmax remains unchanged, but Km increases.

Explain non-competitive inhibition. What happens to Km and Vmax?

The inhibitor binds to a site other than the active site, reducing Vmax but leaving Km unchanged.

What is Km (Michaelis constant)?

The substrate concentration at which the reaction rate is half of Vmax.

What does a low Km indicate about enzyme-substrate affinity?

High affinity, as the enzyme requires less substrate to reach half of Vmax.

What role do coenzymes play in enzymatic reactions?

They act as carriers of intermediate products, often derived from vitamins.

What is the energy of activation (EA)?

The energy required to form the transition state in a reaction, lowered by enzymes.

How does an enzyme lower the energy of activation?

By stabilizing the transition state through binding energy released during substrate-enzyme interaction.

What is the transition state in an enzyme-catalyzed reaction?

The high-energy intermediate state during the conversion of substrate to product, stabilized by the enzyme.

What is the difference between endothermic and exothermic reactions?

Endothermic absorbs energy (ΔH is positive); exothermic releases energy (ΔH is negative).

How are endothermic and exothermic reactions coupled in biological systems?

The energy released from an exothermic reaction drives an endothermic reaction.

What is the induced fit model of enzyme-substrate interaction?

The enzyme changes conformation upon substrate binding to better fit the substrate, as opposed to the rigid "lock and key" model.

What is the role of Mg²⁺ in substrate-level phosphorylation's?

It shepherds the negatively charged phosphate group during reactions like ATP hydrolysis.

What is the equilibrium constant (Keq)?

The ratio of product to substrate concentrations at equilibrium, unaffected by enzymes.