Exam questions for Exam 1 biochem

Hydrogen bonding in water gives rise to water's unique properties. Where else is hydrogen bonding important in biochemistry?

Dissolving sugars, stabilizing protein secondary structure, and DNA base pairing

An amphipathic molecule is one that has what?

A polar region and a nonpolar region

Colligative properties, such as melting point changes, depend on what?

Number of dissolved particles

What false claim about the lifetime of individual hydrogen bonds in water appeared on the past exam?

That they persist for seconds or minutes

What is the equilibrium constant for the relationship between protons and hydroxide in water?

K_w = 1 × 10⁻¹⁴

What is the buffering range of a weak acid?

pKₐ ± 1 pH unit

When a buffer's pKa is above its solution pH, what is true?

Base form is less abundant than acid form

If [OH-] = 4.3 × 10^-10 M, what is the pH?

pOH = −log₁₀(4.3 × 10⁻¹⁰) = 9.37; pH = 14 − 9.37 = 4.63

The common protein amino acids are L-amino acids. What does L refer to?

Alpha-carbon stereochemistry compared with glyceraldehyde

Aspartate has pK1 = 1.88, pK2 = 9.60, pKR = 3.65. What is its pI?

pI = (1.88 + 3.65)/2 = 2.765 ≈ 2.77 (average the two pKₐ values around the neutral form)

On an amino-acid titration curve with carboxyl pKa near 2, which pH range buffers the carboxylic acid group?

pKₐ ± 1 = 2 ± 1 → pH 1–3

At histidine's pI of 7.59, what are the dominant ionization states of its carboxyl, amino, and side-chain groups?

Carboxyl and side chain deprotonated; amino protonated

How can cystine residues stabilize protein structure?

Disulfide bridges

For peptide EVIQH, when can anion exchange bind the negatively charged peptide? E side-chain pKa 4.3, H side-chain pKa 6.0.

pI ≈ (4.3 + 6.0)/2 = 5.15; above pI the peptide is net negative → pH > 5.2

All 20 common amino acids have an R group attached to which atom?

Alpha carbon

An amino acid without an ionizable side chain has a pKa near 9.5. Which reaction does it describe?

Deprotonation of the charged amino group

What is the simplest way to obtain a protein's amino-acid sequence?

Deduce it from the gene sequence

Which methods directly sequence proteins?

Edman degradation and MS/MS peptide analysis

After which residues does V8 protease cut?

After Asp or Glu

What primarily drives protein folding?

Hydrophobic effect

Free rotation in a peptide backbone is largely limited to which bonds?

N–Cα (phi) and Cα–carbonyl C (psi)

A beta turn is an example of which protein-structure level?

Secondary structure

Roughly how many amino acids make an alpha helix 27 Å long?

27 Å ÷ (1.5 Å/residue) = 18 residues

Approximately how long is an antiparallel beta strand with 36 residues?

36 residues ÷ (2 residues/turn) = 18 turns; 18 × 7 Å/turn = 126 Å

Vitamin C deficiency causes connective-tissue failure through inability to form what?

4-hydroxyproline in collagen

Two extended peptide strands have nearly straight interstrand hydrogen bonds and run in opposite directions. What structure is this?

Antiparallel beta sheet

What is the major thermodynamic driving force for protein folding?

Burying hydrophobic residues

Which statement about spontaneous protein folding is FALSE?

That spontaneous protein folding is essentially random

What is the role of chaperone proteins such as Hsp40?

Assist folding to the native state

Parkinson disease, mad cow disease, and chronic wasting disease are associated with what?

Accumulation of misfolded proteins

What can comparing protein sequences across species reveal?

Evolutionary relationships

What is the role of the proximal histidine in myoglobin/hemoglobin?

Occupies one axial coordination site on heme iron

How are hemoglobin subunits related to myoglobin?

Divergent sequence but similar three-dimensional fold

Which property characterizes the R conformation of hemoglobin?

High oxygen affinity

What is allostery?

Binding at one site alters another site

What does a heterotropic modulator do when it binds?

Changes binding of a different ligand at another site

What is the Bohr effect?

Hemoglobin oxygen affinity depends on pH

What major heterotropic modulator of hemoglobin oxygen affinity was emphasized in the course?

2,3-BPG

How many antigen-binding sites does a basic IgG antibody have?

Two antigen-binding sites

What does tropomyosin do in muscle regulation?

Covers myosin-binding sites on actin

Why is water a good solvent for ions?

Ion–dipole interactions and a high dielectric constant

What type of molecule is free phenylalanine?

Amphipathic

Colligative properties, such as melting-point changes, depend on what?

Number of dissolved particles

What is the main thermodynamic driving force for clustering nonpolar molecules in water?

Release of ordered water around hydrophobic molecules

In aqueous solution, free H+ mainly exists as what?

Hydronium, H₃O⁺

What is a weak acid's buffering range?

pKₐ ± 1 pH unit

If a buffer's pKa is above the pH, what is true?

Base form is less abundant than acid form

What is [H+] at pH 6.2?

[H⁺] = 10⁻ᵖᴴ = 10⁻⁶·² M = 6.31 × 10⁻⁷ M = 0.631 μM

What does L mean in an L-amino acid?

Alpha-carbon stereochemistry compared with glyceraldehyde

Glycine has pI 5.97. What does that mean?

No net charge at pH 5.97

On an amino-acid titration curve with carboxyl pKa near 2, which pH range buffers the carboxyl group?

pKₐ ± 1 = 2 ± 1 → pH 1–3

Which amino acids cause characteristic protein UV absorbance?

Phenylalanine, tryptophan, and tyrosine

How do cystine residues stabilize proteins?

Disulfide bridges

For peptide EVIQH, when can anion exchange bind the negatively charged peptide? E pKa 4.3, H pKa 6.0.

pI ≈ (4.3 + 6.0)/2 = 5.15; above pI the peptide is net negative → pH > 5.2

What is the name of the side-chain carbon directly beside an amino acid's alpha carbon?

Beta carbon

A pKa near 9.5 for an amino acid without ionizable R group describes what?

Deprotonation of the charged amino group

What is the simplest way to get a protein's sequence?

Deduce it from the gene sequence

Which methods directly sequence protein?

Edman degradation and MS/MS peptide analysis

Where do trypsin and V8 protease cut?

Trypsin after Lys/Arg; V8 after Glu/Asp

In water, after backbone H-bond formation, what other major factor determines protein conformation?

Bury hydrophobic residues inside

Which backbone bonds permit most peptide rotation?

N–Cα (phi) and Cα–carbonyl C (psi)

An alpha helix belongs to which structural level?

Secondary structure

How many residues are needed for an alpha helix 27 Å long?

27 Å ÷ (1.5 Å/residue) = 18 residues

How many residues make one turn of a beta strand?

Two residues per turn

Vitamin C deficiency causes scurvy partly because of failed formation of what?

4-hydroxyproline in collagen

Two beta strands run in opposite directions and form interstrand hydrogen bonds. What structure is this?

Antiparallel beta sheet

What is the main thermodynamic driving force for protein folding?

Buried hydrophobic residues

If two proteins have little sequence similarity, what best predicts shared function?

Similar three-dimensional shape

What do chaperones such as Hsp40 do?

Assist folding to the native state

What causes disorders such as Parkinson disease and prion diseases in this context?

Accumulation of misfolded proteins

Why compare related protein sequences from different species?

Evolutionary relationships

What is hemoglobin's biological role?

Transport oxygen to tissues

How do hemoglobin monomers compare with myoglobin?

Divergent sequence but similar three-dimensional fold

What is Kd for a simple binding protein?

Ligand concentration at 50% occupancy

What is allostery?

Binding at one site changes another site

What does a homotropic modulator change?

Changes binding of the same ligand at other sites

What is the Bohr effect?

Hemoglobin oxygen affinity depends on pH

What is the major heterotropic regulator of hemoglobin O2 affinity?

2,3-BPG

In immunochemistry, what is an antigen?

A molecule capable of causing an immune response

What does ATP binding do during muscle contraction?

Myosin detaches from actin

A peptide hormone from Gila monster has a predicted monomer near 3,335 Da but possible gene duplication. Purified protein MS has +5 m/z 668.1459 and +6 m/z 556.9549. Is the purified peptide monomer or dimer?

M = z[(m/z) − 1.0073]; +5: 5(668.1459 − 1.0073) = 3335.693 Da; +6: 6(556.9549 − 1.0073) = 3335.686 Da → monomer ≈ 3335.7 Da

Given FDNB identifies N-terminal histidine plus overlapping V8, chymotrypsin, trypsin and CNBr fragments, how do you determine the peptide sequence?

Starts with histidine (H); complete sequence requires checking the fragment overlaps on the original exam image

Make 100 mL of 60 mM HEPES buffer at pH 7.3. pKa = 7.5; acid MW 238.3 g/mol; base MW 260.29 g/mol. How many grams of each form?

[base]/[acid] = 10^(7.3 − 7.5) = 0.631; total = 0.060 mol/L × 0.100 L = 0.00600 mol; acid = 0.00600/(1 + 0.631) = 0.00368 mol × 238.3 = 0.877 g; base = 0.00600 − 0.00368 = 0.00232 mol × 260.29 = 0.604 g

Myoglobin P50 = 0.26 kPa; tissue pO2 = 4 kPa. What fraction is oxygen-bound?

Y = pO₂/(P₅₀ + pO₂) = 4/(0.26 + 4) = 0.939 → 93.9% bound

Myoglobin P50 = 0.26 kPa. At what pO2 is 90% unbound?

90% unbound → Y = 0.10; pO₂ = P₅₀ × Y/(1 − Y) = 0.26 × 0.10/0.90 = 0.0289 kPa

Hemoglobin P50 = 4 kPa and Hill coefficient n = 3. What pO2 leaves 80% of hemoglobin unbound?

80% unbound → Y = 0.20; pO₂ = P₅₀[Y/(1 − Y)]^(1/n) = 4(0.20/0.80)^(1/3) = 2.52 kPa

Hemoglobin P50 = 4 kPa, n = 3, and lung pO2 = 13 kPa. What fraction is O2-bound?

Y = (pO₂)ⁿ/[(P₅₀)ⁿ + (pO₂)ⁿ] = 13³/(4³ + 13³) = 2197/2261 = 0.972 → 97.2% bound

In COPD, lung pO2 falls to about 7 kPa. How should 2,3-BPG change during adaptation, and what happens to hemoglobin's oxygen affinity?

2,3-BPG increases; hemoglobin oxygen affinity decreases

How can the immune system produce an antibody specific to a pathogen it has not previously encountered?

Preexisting B-cell diversity and antigen-driven clonal selection