Chapter 2- Protein Structure

Question 1

What is a protein?

Answer 1

Polymer of amino acids (peptides) joined by covalent peptide bonds
Amino group and carboxylate group bonded to a alpha carbon

Question 2

AA side chain chemical properties

Answer 2

Hydrophobic Hydrophillic Amphipathic

pKa-pH change b/w charged & uncharged speces

Question 3

What is a disulfide bridge

Answer 3

Covalent bond b/w 2 cysteins

Extracellular proteins

Question 4

Amino acid sequence

Answer 4

N to C terminus

Question 5

Four levels of organization that describe protein structure:

Answer 5

Primary structure
Secondary structure
Tertiary structure
Quarternary structure

Question 6

Primary structure

Answer 6

Amino acid sequence

Question 7

Secondary structure

Answer 7

Regular repeating regions of structure

Polypeptides form regions

Question 8

Tertiary structure

Answer 8

3D structure from folding of polypeptide

Question 9

Quaternary structure

Answer 9

Structure of many folded polypeptides

Question 10

Most common protein structure

Answer 10

Secondary structure alpha helices and beta sheets

Question 11

Decribe an alpha helix

Answer 11

Right handed backbone

Amphipathic helix- Hydrophobic side chains on surface &; polar opposite face

Question 11

Describe a Beta sheet

Answer 11

2 or more polypeptide backbone (beta strands)
Strands either go in same or opposite direction
Parallel or antiparallel beta sheets

Question 13

Example of AA alpha-helices

Answer 13

Leucine, methionine, glutamine, and glutamic acid

Question 14

Example of AA of beta sheets

Answer 14

Valine, isoleucine, and phenylalanine

Question 15

How is a tertiary structure of a protein formed?

Answer 15

When the alpha helices and beta sheets are connected by regular regions of a polypeptide chain
Hydrophobic areas associate together.

Question 16

Protein folding

Answer 16

When the secondary structure folds upon itself to yield more 3D compacted structure

Question 17

Example of protein folds

Answer 17

The Homeodomain-entirely alpha helical (binds DNA)
Immunoglobulin-entirely beta sheets
TIM barrel-mixed alpha/beta helix

Question 18

What is the domain?

Answer 18

Fundamental unit or (distinct region of protein) of tertiary structure
Often associate with specific functions having characteristic fold

Question 19

How can a protein unfold?

Answer 19

Change in solution conditions that destabilize the protein causes unfolding
Heat, pH, chemicals

Question 20

Some polypeptides require assistance of proteins of chaperones, what are they?

Answer 20

Ensure that the folding process proceeds smoothly

Question 21

What is denaturation?

Answer 21

When proteins cannot refold properly

Question 22

What’s the sequence similarity and protein folding

Answer 22

When 2 proteins overlap:
50% of amino acid nearly have identical structure
25% amino acid similar
Therefore predict the occurrence of secondary structure on the basis of primary structure w/ accuracy 75%

Question 23

Whats the evolution of proteins?

Answer 23

When mutations, insertions, and deletions of polypeptide chain may lead to a new protein function

Question 24

Divergent evolution

Answer 24

Process through which variants arise from a single ancestral protein
Lead to proteins new character new funtion

Question 25

Convergent evolution

Answer 25

Not based on ancestry 2 proteins with similar function that evolved independently