Exam 1 study guide mistakes

Draw and label a tripeptide with the N-terminal the C-terminal each peptide bond

and R1, R2 and R3.

Answer

Review catalytic triad

(on iPad)

Why are the R and T states important for hemoglobin’s function?

R state: high affinity for oxygen → BINDS/TAKES oxygen in HIGH oxygen concentration areas (ex. lung)

T state: low affinity for oxygen → (binds less tightly to oxygen), RELEASES oxygen in LOW oxygen concentration areas (ex. tissues)

An amino acid that is a good phosphomimetic has:

Negatively charged side chains (ex. aspartate, glutamate)

Aromatic

Ring shaped structure in amino acid side chains

What are the common characteristics of hydrophobic side chains?

Nonpolar, uncharged

What is immunohistochemistry?

Used to study in-situ observations

1. cut cells thin and attach to a microscope slide

2. primary antibody finds target protein in sample

3. secondary antibody finds primary antibody based on its constant (Fc) region

4. makes a brown color where antibody is bound (due to color changing enzyme)

How can an antibody that recognizes protein on a Western blot not recognize it in immunohistochemistry?

In immunohistochemistry, the proteins are native. in western blot, the proteins are denatured. so the antibody may not recognize the folding.

Which amino acids are targets for phosphorylation?

serine, threonine, tyrosine

Which amino acids absorb UV?

Tyrosine, Tryptophan, Phenylalanine

Review Lysozyme mechanism

(on iPad)

substitution mutation

one nucleotide (letter) is replaced with another in a codon

frameshift mutation

When a single nucleotide (letter) is added or deleted, which shifts the whole reading frame (sequence of codons)

What happens when you add a solute to: vapor pressure, boiling point, freezing point, melting point, and osmotic pressure?

Colligative property	What happens when solute is added?	Example
Vapor pressure	⬇ Decreases	Salt water evaporates less readily than pure water
Boiling point	⬆ Increases	Salt water boils at a slightly higher temperature
Freezing/melting point	⬇ Decreases	Salt on roads prevents water from freezing
Osmotic pressure	⬆ Increases	Water moves toward the more concentrated solution

Practice

The reading frame can only be read starting with AUG because it is the universal start codon

so, to solve this problem:

1. identify AUG in the sequence (you don’t have to read in threes for this part)

2. then solve the problem

3. Arg → Arg (CGC → CGA), so silent mutation

What does it mean if an alpha-helix has a metadipole?

the individual peptide-bond dipoles within the α-helix add together because they’re oriented in the same direction → The overall charge at the n-terminal domain or C-terminal domain have a net charge (Like a big charged finger)

What is BLAST and what does it do?

Compares peptide sequences to a database and aligns them to find the identity of your unknown protein

What enzymatic activity does the proteasome have in its barrel?

Trypsin, chymotrypsin

What classification of an enzyme would a kinase be?

Transferase

Why do we want trypsin in our bodies?

To break down old or broken peptide bonds, or digestion

How does heath enthalpy (H) correlate to reaction energy?

The formation of bonds and breaking of bonds can be measured by energy

What does Keq tells us differently than standards Gibbs free energy?

	ΔG°	Keq
	ΔG° < 0 → favorable forward reaction	Keq > 1 → products favored
	ΔG° > 0 → unfavorable forward reaction	Keq < 1 → reactants favored
	ΔG° = 0 → equilibrium	Keq = 1 → neither side strongly favored

How to determine if a reaction is favorable?

What you're comparing	Result	Meaning
Q < Keq	Forward direction	Forward reaction is favorable
Q > Keq	Reverse direction	Reverse reaction is favorable
Q = Keq	At equilibrium	No net movement, no change in reactants or products