Foundations of Biochemistry - Segment 2

What groups do polar uncharged amino acids have on their side chains?

Hydroxyl groups (-OH) and Amide groups (CONH2)

What groups do polar positively charged amino acids on their side chains?

Amino groups which can gain protons

What groups do polar negatively charged amino acids have on their side chains?

Carboxylic acid groups which can lose protons

What groups do non-polar amino acids have on their side chains?

Alkanes / Aromatic rings

How are polypeptides formed?

Condensation / Dehydration Synthesis

How many amino acids form a peptide bond?

Two

What is lost as a result of the formation of a peptide bond?

a water molecule

In what direction do polypeptides run?

From the “n-terminus” to the “c-terminus”

What is the frequency of phosphorylation?

Very common

What is the frequency of carboxylation?

Less common

What does phosphorylation do to the amino acid?

Makes it larger and polar

In what amino acids is phosphorylation most common?

Serine, Threonine

In what amino acids is phosphorylation less common?

Tyrosine

Why is phosphorylation less common in Tyrosine?

The amino acid has “hydrophobic bulk” because of it’s aromatic ring

Where is carboxylation mainly involved?

Blood clotting factors

What is prenylation?

When a polar protein combines with a non-polar hydrocarbon allowing it to be inserted into a non-polar membrane.

What amino acid makes disulfide bonds?

Cysteine

What protein structure do disulfide bonds help stabilize?

Tertiary structure

Are polar amino acids hydro- philic or phobic?

Hydrophilic

Are non-polar amino acids hydro- philic or phobic?

Hydrophobic

Is the movement of polar amino acids to water favorable or unfavorable ΔG?

Favorable

Is the movement of non-polar amino acids to water favorable or unfavorable ΔG?

Unfavorable

If a protein only has one polypeptide chain - what is it’s highest form of structure?

Tertiary

What bonds does secondary folding involve?

Hydrogen bonds between backbone CO and NH groups.

Where can the protein’s instructions of how it should fold / in what conformation it is thermodynamically stable be found?

The linear chain

What levels of protein structure does Urea disrupt?

Secondary, Tertiary, Quaternary

What does Anfinsen’s experiment prove?

All the information for proper folding of a protein is in it’s linear chain

Why is rotation around the backbone of a peptide bond difficult?

The partial double bond, due to the extended pi cloud.

What are the favorable ranges of Phi and Psi?

Those which provide no steric hindrance.

Are alpha helices all left handed or all right handed?

Right handed

Why are all alpha helices right handed?

All amino acids are L

How are alpha helices stabilized?

The formation of H bonds between the O- of backbone carbonyl group and H- of backbone amino group

What amino acid residues only from 1 hydrogen bond?

Residues 1-4

How is the singular hydrogen bond contained in amino acid residues 1-4 formed?

Oxygen at the carbonyl carbon which is at position i+4

Amino acids at positions >4 form how many H bonds?

2

How many amino acid residues are there in one alpha helical turn?

3.6

Why are all amino acids in L configuration?

In this conformation there is no steric hindrance

What amino acids have low propensities for alpha helices?

Glycine and Proline

Why does Glycine have a low propensity for alpha helices?

It is very flexible, can form right handed and left handed.

Why does Proline have a low propensity for alpha helices?

It can only form 1 H bond, it is very tight and rigid.

Where are prolines present?

In the beginning of alpha helices or linkers

What is the periodicity of beta sheets?

2 amino acids per turn.

When are beta sheets not very stable?

If only occurring between two polypeptide chains.

What type of sheet is more stable? Anti-parallel or parallel?

Anti-parallel

How are two antiparallel beta-sheets connected?

Beta turns

How many alpha helices does Triose Phosphate Isomerase have?

8

How many beta sheets does Triose Phosphate Isomerase have?

8

Are all of the beta sheets in Triose Phosphate Isomerase parallel or antiparallel?

Parallel

What amino acids are have high propensities for beta sheets?

Isoleucine, Phenylalanine, Tyrosine, Valine

What amino acids have low propensities for beta sheets?

Asparagine, Glutamic Acid, Lysine, Proline

Why do polar charged amino acids have a lower propensity to be in beta sheets?

They usually like to be buried.

What structures of protein folding can the hydrophobic effect be found within?

Tertiary and Quaternary

What structures of protein folding can covalent cross-links be found within?

Tertiary and Quaternary

What structures of protein folding can Ionic bonds be found within?

Tertiary and Quaternary

What amino acids have the highest propensities to be in beta-turns?

Proline and Glycine

What is the primary transporter of oxygen in the blood?

Hemoglobin

What is the primary storer of oxygen in the muscles?

Myoglobin

How many oxygen molecules can Hemoglobin bind?

4

What type of binding curve does Hemoglobin have?

Sigmoidal

What type of binding curve does myoglobin have?

Hyperbolic

How many oxygen molecules can Myoglobin bind?

1

What happens to Heme when oxygen binds to it?

Heme flattens

In the absence of O2, what state is Heme in?

Heme bends

Where does hemoglobin have a strong binding affinity curve?

Lungs

Where does hemoglobin have a medium/low binding affinity curve?

Muscles