biochem 1 - E1

What is not considered a noncovalent interaction?

carbon-carbon bonds, bc the 2 helping me understand my options

What is strongest hydrogen bond here?

a. F and HF

b. N and HF

c. C and HF

d. O and HF

e. Cl and HF

(A) since F is the most electronegative element on the Ptable (making H have a strong partial positive charge)

Humans maintaining a constant level of hemoglobin by continually synthesizing and degrading it is an example of ___________.

dynamic steady state - a condition in an open system where internal components remain constant over time only because energy and matter continuously flow through it

Energy requiring metabolic pathways that yield complex molecules from simpler precursors are ________.

anabolic => big to small

hydrophobic interactions are driven by _________.

Gain in entropy by release of water molecules → bc clustering nonpolar molecules allows ordered water surrounding them to break free and become disordered

The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has _____________.

one million times lower [H+] than the gastric juice

You want to maintain pH = 6.0 for an enzyme-catalyzed reaction that will produce hydrogen ions along with the desired product. At equal concentrations, which weak acid, if any, will serve as the better buffer for the reaction: Acid A, with pKa = 6.5 or Acid B, with pKa = 5.5?

acid b →

define dynamic steady state

reaching an equilibrium with work

Amino acid A has a pI of 3.3

Amino acid B has a pI of 10.7

Amino acid C has a pI of 6

What AA has an ionizable carboxylic acid containing side chain?

A only, bc pI is acidic making is so the AA can be protonated!

For amino acids with neutral R groups, at any pH above the pI (isoelectric point) of the amino acid, the population of amino acids in solution will have:

a net negative charge

In a conjugated protein, a prosthetic group is:

a part of the protein that is not composed of amino acids

In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel- filtration) chromatography?

a part of the protein that is not composed of amino acids

By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:

separate proteins exclusively on the basis of molecular weight

Why are functional groups important?

They determine reactivity of a molecule (or AA in this case).

First law of thermodynamics

energy in the universe is constant; form may change but it cannot be created or destoryed.

catabolism (cat=fat=big)

breaking down large molecules into smaller atoms + energy is released in the process (is exergonic & increases entropy)

anabolism

synthesizing small molecules into larger ones + energy is consumed in the process (is endergonic & descreases entropy)

process of protein digestion

proteins → amino acids → absorbed by our intestinal cells → blood → tissues

What are nucleic acids?

They are the nucleotides of DNA/RNA that contain a 5 carbon sugar, phosphate group, and a nitrogenous base.

What are amino acids?

Organic molecules that are the “building blocks” (chains) for proteins

If diet glucose increases v₁ 2-fold, what happens to v₂?

v₂ also increases 2-fold to maintain blood glucose concentration.

Define polar covalent interaction.

Any compound that has unequally shared electrons (e^-) because a molecule is more electronegative than the rest (ex. H₂O).

Define NON-polar covalent interactions.

Any compound that has electrons shared equally since its molecules have a very small electronegativity difference (ex. O₂ or CH₄).

Define non-covalent interactions.

Primary internal force in ionic compounds → weaker electromagnetic attractions between regions of opposite charge without sharing electrons

Define a dipole moment.

The joining of 2 atoms with 2 different electronegativity values (ex. N-H, O-H)

List “weak” noncovalent interactions in water. (strongest → weakest)

1. ionic interactions

2. ion-dipole

3. hydrogen bonds

4. dipole-dipole

5. hydrophobic interactions

6. van der Waals (London dispersion)

When is hydrogen bonding the strongest?

H being bonded to very electronegative atoms (like N, O, or F) and collinear 180 degree angle.

hydrophobic effect

driven by entropy increase from releasing ordered water; causes micelles, protein folding, ligand binding

How does water act as hydrogen bond donor and acceptor?

It can donate 2 H while oxygen acts as an acceptor that can accept 2 hydrogen bonds.

Which is more soluble in water: sodium benzoate or benzoic acid?

Sodium benzoate → since its a salt that can have ion-dipole interactions with water. [meanwhile acid would form hydrogen bonds]

Benzoic acid is most soluble in which: water, 0.1 M HCl, or 0.1 M NaOH?

NaOH → since it converts the acid into a salt, which is more soluble in water

Define pKa and what its value means.

Refers to how acidic (or not) any given proton is in a molecule.

High => weaker acid

Low => stronger acid [gives up H+ more easily]

Define buffers.

Mixtures of weak acids and their anions (conjugate base); they resist changes in pH.

Why are buffers needed?

Maintenance of intracellular pH is vital; enzyme-catalyzed reactions have optimal pH; solubility of polar molecules depends on H-bond donors/acceptors; CO₂/HCO₃⁻ equilibrium depends on pH.

What makes up all amino acids?

a. amino group (NH₂)

b. carboxyl group (COOH)

c. R group (side chain that varies per AA, except glycine [has 1 more H])

At physiological pH (7.4), what form do most amino acids exist in?

Zwitterion form

What is a Zwitterion?

Where the AA has both a positive and negative charge present but remains with a net charge of 0

Proteins in animals contain almost exclusively which amino acid configuration?

L-amino acids (left)

At low pH (1-6), what is the net charge of a typical amino acid?

+1 (cation) [where NH₂ becomes N⁺H₃ bc amino was protonated]

At high pH (8-14), what is the net charge of a typical amino acid?

-1 (anion) [where COOH becomes COO^- bc CA was deprotonated]

Define Isoelectric point (PI).

The specific pH value where an AA becomes a Zwitterion [has no net charge].

What happens to amino acid solubility at the isoelectric point?

AA is at its LEAST soluable point.

Equation for PI?

pK1+pK2/2

For amino acids with ionizable side chains, how is pI determined?

Average the two pKa values surrounding the zwitterion form

What is the pI of Lysine expected to be relative to glycine?

Much higher because it has a positively ionizable side chain

How do peptide bonds form and what do they look like?

Form when 2 amino acids are joined together and H₂O is excreted. Alpha carbon binds to N of other AA.

Which end of a peptide is written first?

N-terminus (amino on left)

Which end of a peptide is written last?

C-terminus (CA on right)

In SGYAL, what is the N-terminal residue?

Serine

In SGYAL, what is the C-terminal residue?

Leucine

Oligopeptide

10 or fewer amino acids

Polypeptide

More than 10 amino acids

Protein (structure)

A polypeptide with >50 amino acids that folds into a stable 3D structure.

Ion-exchange chromatography separates proteins based on what property?

Charge

Size-exclusion chromatography separates proteins based on what property?

Size/molecular weight

Affinity chromatography separates proteins based on what property?

Binding affinity to a ligand

Which chromatography would separate proteins with identical MW but different pI values?

Ion-exchange chromatography

SDS PAGE

separation based on molecular weight

What does SDS do to proteins?

Denatures proteins and gives them a uniform negative charge

Which proteins move farther in SDS-PAGE?

Smaller proteins, big ones move much less.

Co-factor

A non-amino-acid component required for protein function

Prosthetic group

A permanently attached cofactor that is NOT composed of amino acids (ex. heme)

What are conjugated proteins?

Proteins containing prosthetic groups or other non-protein components.

As protein purity increases, what happens to specific activity?

SA increases

Why is the peptide bond rigid (as in, why wont it rotate)?

Resonance gives the C-N bond partial double-bond character, which makes it planar [most found trend in peptide bonds].

What charges exist within a peptide bond dipole?

Carbonyl oxygen is partially negative; amide nitrogen is partially positive

Which bonds in a polypeptide backbone can rotate?

Bonds connected to the α-carbon

What does φ (phi) represent?

Rotation around the α-carbon to amide nitrogen bond

What does ψ (psi) represent?

Rotation around the α-carbon to carbonyl carbon bond

In a fully extended polypeptide, what are φ and ψ?

Approximately ±180°

Why are many φ and ψ combinations impossible?

Steric hindrance between atoms

What plot displays allowed and forbidden φ/ψ conformations?

Ramachandran plot → shows allowed and disallowed backbone conformations

Describe primary structure of a protein.

singular chain of Amino acid sequence

Describe secondary structure of a protein.

Local folding of polypeptide chain (can be in alpha helixes or beta sheets) due to hydrogen bonding (which causes chain to fold in repeated pattern)

Describe tertiary protein structures.

3D folding patterns of folding due to side chain interactions

Describe quaternary structure of a protein.

Arrangement of multiple amino acid chains folding (ex. Hemoglobin has 2 beta and 2 alpha structures)

Describe alpha helixes.

appears as a coil; is stabilized by hydrogen bonds between closeby residues (n+4)

How are peptide bonds oriented in an α-helix?

Roughly parallel to the helix axis

How are side chains oriented in an α-helix?

Project outward from the helix

Which amino acids strongly favor α-helix formation?

Alanine and leucine (bc of hydrophobic residues)

Which amino acids are α-helix breakers?

Proline and glycine

Why is proline an α-helix breaker?

Restricted geometry and inability to donate backbone H-bonds

Describe beta sheets in proteins.

Are pleated sheet like structures that are stabilized by hydrogen bonds between neighboring strands

What two orientations can β-sheets have?

Parallel and antiparallel

Describe parallel beta sheets.

H-bonded strands run in same direction which results in bent (weaker) H-bonds

Describe antiparallel beta sheets.

Sheets run in opposite direction making them have more linear H-bonds and ultimately stronger

What is the function of a β-turn?

Reverses chain direction by approximately 180 degrees

Which amino acids commonly occur in β-turns?

Proline and glycine

Which residue commonly occupies position 3 in a Type II β-turn?

Glycine

What is the most important driving force for protein folding?

Hydrophobic interactions (GAIN IN ENTROPY)

What is a salt bridge?

Ionic interaction between oppositely charged groups (ex. Aspartame interacting with lysine)

What are van der Waals interactions?

Weak attractions between nonpolar groups (ex. CH3-CH3)

What is the general shape of globular proteins?

Compact and spherical (ex. Myoglobin)

What is the primary function of fibrous proteins?

Structural support and protection.

What characterizes fibrous proteins structurally?

Dominated by one type of secondary structure

Where is α-keratin found and what is its dominant structure?

In hair, wool, nails, etc. → alpha helixes

What structural feature gives keratin strength?

It’s covalent S-S linking between coiled coil dimmers.

What type of structure does collagen form?

Triple helix → each chain is Glycine and proline rich (left handed helixes that have have 3 residues per turn)

What repeating sequence characterizes collagen?

Gly-Pro-Hydroxyproline

Why must glycine appear every third residue?

It is small enough to fit inside the triple helix