Lecture 5 (Protein Structure)

Question 1

Macromolecules account for what percent of the dry weight of bacterial cells?

Answer 1

87% This includes proteins, fatty acids, nucleic acids

Question 2

Condensation reaction between two amino acids takes place between what groups?

Answer 2

The carbonyl group of one amino acid and the amino group of the other amino acid. The condensation reaction causes water to be lost.

Question 3

Zwitterion

Answer 3

At physiological pH of 7. amino acids are zwitterions. Molecules that contain both a positive and a negative charge.

Question 4

Methionine and Cysteine

Answer 4

Sulfur bearing amino acids. These two amino acids are considered to be non-polar

Question 5

What are some of the modifications that can be done to Lysine?

Answer 5

Methylation, acetylation, ubiquination, sumosylation

Question 6

What are some of the modifications that can be done to Asp, blu, his, arg?

Answer 6

Ligand binding & catalysis

Question 7

What are some of the modifications that can be performed on Tyrosine, threonine, serene

Answer 7

Phosphorylation and glycosylation

Question 8

The non-polar amino acids serve what function in the cell?

Answer 8

Conformational support/stability

Question 9

True or False.

A protein can fold into more than one single conformation.

Answer 9

False. Although allosteric binding causes some sort of conformational alteration, the protein cannot just adopt a different conformation

Question 10

Protein conformation is stabilized by _______ bonds.

Answer 10

Non-covalent. These includes van der waals interactions, hydrophobic interactions, hydrogen bonding, as well as electrostatic interactions

Question 11

The strength of Van der Waasl attraction in water and in vacuum

Answer 11

Are the same. This is because Van der Waals interactions deal with atomic attraction caused by close proximity between atoms and electrostatic fluctuations when two atoms are positioned near one another

Question 12

The hydrophobic Effect

Answer 12

Entropically driven exclusion of non-polar compounds in polar media. When they aggregate together is more thermodynamically favored due to less disruption of the hydrogen bonds and less surface area that is exposed to the polar solvent

Question 13

Hydrophobic Effect on proteins

Answer 13

Most proteins have a hydrophobic core. This are typically situated in the core of the protein to diminish their exposure to the aqueous media.

Question 14

Studies into protein folding and denaturation reveal what?

Answer 14

That the protein is able to adopt its native conformation after being denatured. This means that all the information required to direct proper protein folding is recorded in the primary protein sequence

Question 15

non-Adjacent Amino acids

Answer 15

Proper protein folding allows an active site where substrate binding occurs. The active site brings non-adjacent amino acids to participate in reaction.

Question 16

Chaperone Proteins

Answer 16

These proteins bind to nonpolar chains of partially folded proteins and prevent misfolding of proteins to occur

Question 17

Protein Primary Structure

Answer 17

The amino acid sequence

Question 18

Protein Secondary Structure

Answer 18

Structural elements like beta sheets and alpha helices

Question 19

Protein Tertiary Structure

Answer 19

Domains (functional/structural)

Question 20

Protein Quaternary structure

Answer 20

Multimeric complexes

Question 21

What are some elements of secondary structure?

Answer 21

Alpha helices
Beta Sheets
Loops
Turns
Disulfide Bridges

Question 22

The Alpha Helix and beta sheet account for what percent of protein secondary structure`

Answer 22

60%

Question 23

The alpha Helix

Answer 23

3.6 residues per turn
Amino acids chains directed outward
Stabilized by hydrogen bonds (between amide HN and carbonyl CO)
Can have amphipathic character

Question 24

How many amino acids are sufficient to traverse the plasma membrane?

Answer 24

18-22 amino acids

Question 25

The Beta Sheet

Answer 25

Composed of Beta strands arranged in either parallel of anti-parallel orientation. Strands are stabilized by hydrogen bonds. Amino acids project towards alternate faces of the sheet

Question 26

Which of the two major secondary structures can have amphipathic character?

Answer 26

Both the alpha helix and the beta sheet can have non-polar and polar regions

Question 27

Beta Sheet Stacking

Answer 27

Beta Sheets composed largely of hydrophobic amino acid side chains can form large aggregates that are difficult to degrade, tend to accumulate in tissue, and are toxic to the tissue in which the are located

Question 28

Coiled Coil

Answer 28

Associations of TWO alpha helices bound together by hydrophobic interactions between non-polar amino acids present along one side of each helix

Question 29

What does a coiled coil do?

Answer 29

Stabilizes protein-protein interactions

Question 30

Leucine Zipper

Answer 30

Also the name for a coiled coil. A non polar amino acid must repeat every three and every two.
L A**LV**L

Question 31

Domains

Answer 31

Stable regions of a protein consisting of groups of secondary structural elements

Question 32

What occurs as a nascent polypeptide emerges from the ribosome?

Answer 32

1) Secondary elements form
2) Domains fold
Protein begins folding while it is still being translated in the ribosome. It finishes flooding entirely once it is out of the ribosome

Question 33

What are protein Modules

Answer 33

Domains that appear in many different proteins. A result of protein evolution that involves recombination of modules and yields proteins with new functionality

Question 34

Modular Mix and Match

Answer 34

Gives rise to proteins with new combinations of properties

Question 35

Is tertiary structure preserved?

Answer 35

Tertiary structure is preserved within protein families

Question 36

Immunoglobulin is comprised of

Answer 36

both heavy and light chains

Question 37

The inside of the cell is a _______ environment

Answer 37

Reducing. Since most cellular compartments are reducing environment, in general, disulfide bonds are unstable in the cytosol.

Question 38

Immunoglubulin

Answer 38

Antibody. The Ig Y shaped domain that consists of four polypeptide chains: two identical heavy chains and two identical light chains that are connected by disulfide bonds

Question 39

Hemoglobin

Answer 39

Heterotetrameric complex (2 alpha and 2 beta). An assembly of four globular protein complexes.

Question 40

Neuraminidase

Answer 40

Used in viral antigen against influenza virus. Cleaves glycosidic linkages of neruraminic acids. Used in the prevention of spread of influenza virus. Composed of a homotetrameric protein complex. The tetramers are held together always by the same two domains. Like a snake circle. “Blue and orange domains bind.”