Steele - Lecture 1

Question 0

What is a covalent bond? How does it compare to a noncovalent bond?

Answer 0

Covalent: “permanent” sharing of electrons, require substantial energy to break; results in loss of protein structure.

Noncovalent- partial sharing of electrons or the exclusion of water. Transient, reversible, easily broken.

Question 1

How many genes encoding proteins do humans have?

Answer 1

22,333

Question 2

How atoms are involved in hydrogen bonding?

Answer 2

Hydrogen bound to an N, O (H has partial + profile)

interacts with…

Lone pair on N, O (- charge)

Question 3

Approximately how large is a C-H bond, protein, cell?

Answer 3

C-H bond: 0.1 nm (1.5 Angstroms)
Protein: 1 nm
Cell: 1 micron

Question 4

How much time is required for a simple enzymatic reaction? Conformational change?

Answer 4

Enzymatic reaction- 1 millisecond

Conformational change- 1 microsecond

Question 5

What does primary structure of a protein indicate?

Answer 5

amino acid sequence formed by peptide bonds

Question 6

What does the secondary structure of a protein indicate?

Answer 6

Substructures formed by HYDROGEN BONDING between amino acids

Question 7

What does tertiary structure of a protein involve?

Answer 7

the three-dimensional structure of a protein; formed by combination of 1’ and 2’ structures and additional elements (e.g. loops and disulfide bonds)

Question 8

What does the quaternary structure of a protein indicate?

Answer 8

structure formed to due to the association (not peptide bonding) of multiple polypeptide subunits

Question 9

How many amino acids are used in proteins? What isoform are they found as?

Answer 9

20; L form

Question 10

What are 2 “simply nonpolar” amino acids?

Answer 10

Alanine, glycine

Question 11

Which amino acids have hydrophobic, bulky, aliphatic amino acids?

Answer 11

Leucine, isoleucine, valine, methionine

Question 12

Which amino acids are aromatic and nonpolar?

Answer 12

Phenylalanine, tyrosine (Note hydroxyl group), tryptophan

Question 13

What amino acids are basic?

Answer 13

Lysine, arginine (+ charged at phys pH)

Histidine (sometimes + charged)

Question 14

Which has a polar sulfhydryl group?

Answer 14

Cysteine

Question 15

Which amino acids have a polar hydroxyl group?

Answer 15

serine, threonine

Question 16

Which amino acid has a 5-member ring structure associated with it?

Answer 16

proline (nonpolar)

Question 17

Which amino acids are acidic (carboxyl group?)

Answer 17

aspartic acid, glutamic acid

aspartate, glutamate

Question 18

What are 2 “simply polar” amino acids?

Answer 18

Asparagine, glutamine

Question 19

What are the characteristics of a peptide bond?

Answer 19

Resonance between N-C linkage between amino acids, giving the peptide bond a double peptide bond

• -> Peptide bond has rigid, planar structure (no free rotation)
• -> note that other bonds can rotate (psi and phi), allowing for certain structure like alpha-helices. Certain angle combinations are not allowed and some are faored.

Question 20

Which handed-ness of alpha helices is favored?

Answer 20

Right-handed alpha helices

Question 21

Where do most peptides in nature originate from?

Answer 21

From larger proteins, although some small peptides are assembled without a gene template.

Question 22

How do we sequence proteins nowadays?

Answer 22

We look only at DNA sequences to predict peptide sequences

Question 23

What are three types of secondary structures?

Answer 23

1) helix (alpha helix)
2) Beta-sheet
3) beta turn

Question 24

What is the component of amino acids that lead to alpha helixes?

Answer 24

H-bonds, NOT R groups!

-constrained by phi and psi angles (Ramachandran plot)

Question 25

Where are the R groups located in an alpha helix?

Answer 25

They protrude out, allowing them to interact well with other proteins

Question 26

What are 3 characteristics about alpha helices?

Answer 26

1) N is always the H donor, O is the H accepter (it has to be!)
2) The residues that form the bonds of the helix are four AA apart
3) Commonly found in plasma membranes (exam question involving a mutation of a membrane protein?)

Question 27

What is an alpha coiled coil?

Answer 27

2 polypeptides coiling around one another (found in alpha-keratin), held together with noncovalent interactions. NOT TO BE CONFUSED WITH ALPHA HELICES

Question 28

What are 3 characteristics of beta pleated sheets?

Answer 28

1) Peptide chain is extended, not coiled
2) Stabilized by H bonds
3) Can exist in parallel, anti parallel, and mixed (both) fashion

Question 29

Where are the R groups in a beta pleated sheet?

Answer 29

R groups alternate with respect to the side of the polypeptide chain they protrude from

Question 30

What is special about H bonds in beta sheets?

Answer 30

Each AA is involved in H-bonding with 2 different amino acids on adjoined strand

Question 31

What does a beta turn accomplish?

Answer 31

Allows a polypeptide to reverse direction

Question 32

What are some properties of beta turns?

Answer 32

1) Found on surface of proteins
2) Often sites of glycosylation
3) Important sites of immunological reaction
4) Somewhat predictable from AA sequence

Question 33

How is tertiary structure stabilized?

Answer 33

Stabilized by many weak bonds, major role played by R groups

Question 34

What is denaturing of a protein?

Answer 34

Unfolding of protein without destruction of primary structure

Question 35

How do most non-structural proteins fold?

Answer 35

domains are globular

Question 36

How is folding driven in an aqueous environment?

Answer 36

Hydrophobic interactions drive folding of hydrophobic AA’s to interior of protein

Surface residues are polar/charged

Charged pairs (e.g. lys and glutamate) might be found in a pocket on the inside because they are strong only in the absence of water

Question 37

What other hydrophobic interaction is involved in protein stability?

Answer 37

Pi stacking between aromatic R groups

Question 38

How many energy minimums are there for proteins?

Answer 38

Only one- constrained by primary sequence.

There are folding intermediates (steps of folding) - ex: translation of ribosome

Question 39

What determines tertiary structure? How was this determined?

Answer 39

Primary sequence of protein.

Christian Anfisen demonstrated that RNAses could refold & their activity restored on their own even after denaturation by urea and BME

Question 40

What class of proteins help other proteins fold?

Answer 40

Chaperones; protein folding is not as fool-proof as once thought (mistakes happen), but cells have ways to correct mistakes

Question 41

Does primary sequence determine secondary structure?

Answer 41

NO! Same sequence can be an alpha helix in one protein and a beta sheet in another. Depends on surrounding domain environment.

Question 42

What are 2 diseases associated with protein folding? (not a mutation in AA sequence)

Answer 42

1) Transmissible spongiform encephalopathies (Creuzfeldt-Jakob Disease, mad cow, scrapie)
2) Alzheimer Disease

Question 43

What occurs in scrapie?

Answer 43

A single normal precursor protein becomes misfolded, and it becomes a prion (protein infections particle).

This prion serves as a template to misfold other normal proteins into prions. These prions form aggregated called amyloids, which disrupt normal cellular function.

Question 44

What are the characteristics of protein domains?

Answer 44

-subunit of protein’s tertiary structure

1) folds autonomously
2) formed by secondary structural elements connected by loops
3) has its own hydrophobic core
4) has an independent functional or structural property

Question 45

Describe Src protein-tyrosine kinase

Answer 45

Protein that phosphorylated tyrosine

3 domains: Kinase, SH2, SH3

Inactivated by phosphorylation of tail and subsequent binding of that tyrosine to SH2 domain.