Lecture 7

Question 1

Primary protein structure:

Answer 1

represented as a simple line and is simply the order amino acids are linked together (amino acid sequence)

Question 2

Secondary protein structure:

Answer 2

the polypeptide backbone exists in different section of a protein either as an alpha helix, beta sheet, or random coil

Question 3

Tertiary protein structure:

Answer 3

the secondary structures are folded into the compact globular protein, 3D structures

Question 4

Quaternary protein structure:

Answer 4

protein molecules known as subunits assemble into a multimeric protein held together by weak forces (multiple subunits)

Question 6

Properties of the primary structure:

Answer 6

• proteins are long
• proteins are similar but not identical
• changes are tolerated depending on where they occur within the 3-D structure of the protein

Question 7

Conservative protein changes:

Answer 7

preserve chemical properties or size of the side chain

Question 8

Nonconservative protein changes:

Answer 8

changes that result completely different side chains type or size

Question 9

What determines primary protein structure:

Answer 9

the genetic code

Question 10

Codon:

Answer 10

nucleotide triplets are used to code for each amino acid

Question 11

Number of amino acid combinations vs. number of amino acids:

Answer 11

64 possible combinations code for 20 amino acids

Question 12

Linus Pauling’s rules for secondary structure:

Answer 12

1. bond lengths and nalges of amino acids and peptides must stay fairly consistent to those observed by diffraction studies
2. no atoms should approach more closely than their Van de Waals radii. steric restrictions make up the peptide backbone
3. six atoms in the peptide-amide should be coplanar. Rotation is possible around bonds and adjacent to alpha carbon. remain in trans configuration
4. noncovalent bonding is necessary to stabilize structure, usually hydrogen bonding between amide protons and carbonyl oxygen

Question 13

Rotations about single bonds in a polypeptide:

Answer 13

peptide bonds cannot rotate, but their adjacent carbon/nitrogens can: allows unique folding of proteins into many different 3D structures

Question 14

Phi bond:

Answer 14

bond between N amide and alpha C

Question 15

Psi bond:

Answer 15

bond between the alpha C and carbonyl C

Question 16

Most frequent forms of secondary structures:

Answer 16

alpha-helix and beta-sheet, in each structure the amide group is planar and all amide protons and carbonyl carbons are involved in H-bondings

Question 17

Properties of alpha helix:

Answer 17

• rod-like in structure
• inner backbone with R group extending outward
• C-O and N-H, H-bonding hold 2o structures in place
• Right-handed most
• Side chains project outwards

Question 18

H-bonding pattern of alpha helix:

Answer 18

C=O — H-N via

Question 19

Structure features of alpha helix:

Answer 19

• Right handed helix: 3.6 residues
• H-bond between every 4th aa between the oxygen of the carboxyl group and the hydrogen of the amino group (before and after)
• R groups project out from helix, generally towards the N terminal end of the helix
• H-bonds (orange) are parallel to axis of the helix
• the sturcture can be in hydrophobic or hydrophilic environments

Question 20

Properties of beta strands and beta sheets:

Answer 20

• strand + strand = sheet (from same polypeptide)
• fully extended. often in hydrophobic core of a protein
• distance between adjacent a.a. is 3.5 A
• parallel and anti-parallel sheets are possible

Question 21

What leads to parallel and anti-parallel configurations:

Answer 21

• unique H-bonding properties
• antiparallel arrangement can arise by “hairpin folding” of a single strand

Question 22

Properties of polypeptide (polyproline) II helix:

Answer 22

• does not satisfy H-bond requirements
• left-handed
• these structures tend to have many prolines that kink
• glycine are often found as well because they are smaller

Question 23

Positions of alpha-helix and beta sheets:

Answer 23

can have amphipathic characteristics so one face is hydrophobic and one is hydrophilic (i.e. an alpha helix will have side chains of similar polarity every 3-4 residues, whereas a standard B-strand will have alternative polar and nonpolar side-chains)

Question 24

Side chains on alpha helix:

Answer 24

radiate away from the helical axis

Question 25

Side chains on beta sheet:

Answer 25

located on opposite faces of the sheet

Question 26

Determination of peptide bond conformations:

Answer 26

some combination of phi and psi angles are now allowed due to steric intereactions. in the alpha-helix (b), the backbone atoms are already closely packed and R groups project out

Question 27

Ramachandran Plots:

Answer 27

* white regions correspond totheoretically allowable conformations * grey dots represent the areas of angles * each amino acid has its own Ramachandram Plot

Question 28

Avaliable secondary structure based on Ramachandran plots:

Answer 28

* beta strand * alpha helix * 310 helix * polypeptide II helix

Question 29

Types of proteins:

Answer 29

fibrous (long and extended) and globular (blobs)

Question 30

Fibrous proteins:

Answer 30

each tends to be enriched with 3-4 particular amino acids, which stabilize their particular structure

Question 31

Amino acid composition of collagen:

Answer 31

glycine, alanine, and proline

Question 32

Amino acid composition of most proteins:

Answer 32

glycine, alanine, and leucine

Question 33

Properties of collagen:

Answer 33

* each polypeptide is a left-handed helical structure with glycine, and proline * Gly-Proline or Hydroxy-Proline repeats * Tropocollagen: 3-left handed helices favored by Proline joine to form a right-handed tripple helix * Cross-links between lysine residues form between helices to form a collagen fibril

Question 34

What links collagen:

Answer 34

hydrogen bonding between amide protons and carbonyl carbons, but hydroxyproline also links the triple helices

Question 35

Secondary and tertiary structure of collagen:

Answer 35

the same as each other

Question 36

Primary structure found in collagen:

Answer 36

quatenary structure

Question 37

Function of hydroxyproline:

Answer 37

makes collagen tougher by cross-linking strands by acting as a hydrogen donor and acceptor

Question 38

How are hydroxyproline composed:

Answer 38

an addition to proline after translation

Question 39

Vitamin C and hydroxyproline:

Answer 39

enzymes that catalyze hydroxyprolation of proline require Vitamin C to function. less vitamin C reduces hydroxyproline that keeps collagen together, weakening

Question 40

Symptoms of Scurvy:

Answer 40

* anemia (small-cell type) * atherosclerotic plaques * pinpoint hemorrahages under the skin, bone fragility, joint pain * poor wound healing, frequent infections, bleeding gums, loosened teeth * muscle degeneration and pain, hysteria, depression, rough skin, blotchy brusies

Question 41

How are tertiary structures stabilized:

Answer 41

by noncovalent bonds and sometimes covalent disulfide bonds between Cysteines

Question 42

Tertiary structures of globular proteins:

Answer 42

* myoglobin with heme group pocket. 8 alpha-helices form a pocket * alpha/beta barrel encloses hydrophobic side chains * pyruvate kinase with 3 domains: cap covering catalytic site, catalytic domain, and regulatory domain

Question 43

Protein domains:

Answer 43

* compact globular units that are connected by flexible regions * make up regions of a protein * can be large * stable; can be associated with specific function(s) of protein

Question 44

Supersecondary structures:

Answer 44

repeated secondary structure motifs within a tertiary structure (domain)

Question 45

Abrupt chages in polypeptide chain direction:

Answer 45

hairpin turns stabilized by H-bonds

Question 46

Free Energy of folding of a protein:

Answer 46

spontaneous reaction driven by a low Delta H because bonds formed between folded proteins replaced those formed between surroundings

Question 47

Entropy of protein folding:

Answer 47

folding is more ordered; however, in an unfolded state the water molecules are more ordered around the structure, thus it is usually more favorable to fold the molecule

Question 48

Stability of protein folding:

Answer 48

highly unstable, can be unfolded with slight increases in temperature