Lecture 7

Question 1

What structure of proteins specify their function function?

Answer 1

3-D structure

Question 2

What is the primary structure?

Answer 2

• simple sequence of amino acids linked together via peptide bonds

Question 3

what is the secondary structure ?

Answer 3

• formed by regular folding patterns in specific regions of the protein

Question 4

What are the different patterns of secondary folding?

Answer 4

• alpha helix
• beta pleated sheet
• random coil or loop region

Question 5

What is the tertiary structure?

Answer 5

• regions of local structure are then coiled into an overall 3-D structure for entire polypeptide sequence

Question 6

What is Quaternary structure?

Answer 6

• not every protein has this structure
• protein molecules known as subunits assemble into a multimeric protein held together by weak forces
• structures are only present if a protein has multiple subunits associated together in its final form

Question 7

How are changes to amino acid sequence tolerated ?

Answer 7

• it depends on where they occur within the 3-D structure of the protein

Question 8

What are conservative and non conservative changes ?

Answer 8

• conservative –> preserve chemical properties

- nonconservative –> result in completely different side chain type or size

Question 9

What are the comparisons of the primary structure of sperm whale myoglobin vs. human myoglobin ?

Answer 9

• both 153 amino acids long
• similar in primary sequence but not identical, but still manage to have same function
• evolution has resulted in changes to amino acid sequences between the proteins

Question 10

what determines the protein primary structure?

Answer 10

the genetic code

Question 11

what is the genetic code?

Answer 11

• nucleotide triples, codons, used to code for each amino acid
• considered to be standard genetic code

Question 12

what are the possible combinations for codons ?

Answer 12

4^3 = 64 possible cominations with 4 nucleotides

Question 13

What are Pauling’s rules for secondary structure ?

Answer 13

• bond lengths and angles of aa and peptides must stay fairly consistent to those observed by diffraction studies
• no atoms should approach more closely than their Van de Waals radii
• six atoms in peptide-amid should be coplanar –> rotation is possible around bonds adjacent to alpha carbon
• some kind of noncovalent bonding is necessary to stabilize structure, usually hydrogen bonding

Question 14

What is the importance of rotation about single bonds in a polypeptide?

Answer 14

• rotation around these bonds allows protein backbone to fold into secondary and tertiary structures

Question 15

Around which bonds is rotation allowed around ?

Answer 15

• N amide – C alpha –> phi
• C alpha – C carbonyl –> psi

think of phi and psi bonds

Question 16

What are the most frequent forms of secondary structure that satisfy Pauling’s criteria? (Hint: most commonly observed)

Answer 16

• alpha helix
• beta pleated sheet
• most commonly observed secondary structures

Question 17

What are structures like for the alpha helix and beta pleated sheet ?

Answer 17

• in each structure the amide group is planar –> think of Pauling’s rules for secondary structure
• all amide protons and carbonyl carbons are involved in H bonding

Question 18

Structure of the alpha hellix

Answer 18

• Rod-like in structure
• R groups extend outwards
• C–O & N–H hydrogen bonding hold 2^0 structures in place
• right hand are the most common of helices

Question 19

What is the H-bonding patter of the alpha helix ?

Answer 19

• each of the carbonyls are bonded to an amide that is 4 residues removed
• Example: (1) C=O — H-N (5)
  (2) C=O — H-N (6)
  and so forth

Question 20

Structural features of the alpha helix for H bonding

Answer 20

• for the right handed helix 3.6 a.a –> meaning hydrogen bonds that form between amino acids is not exactly 4
• H-bond between every 3.6 (4) between the oxygen of the carboxyl group and the hydrogen of the amino group
• H bonds are parallel to axis of helix
• can be in hydrophobic or hydrophilic environments
• can even be amphipathic

Question 21

Structure of beta pleated sheets

Answer 21

• held together by hydrogen bonds
• fully extended; often in hydrophobic core of a protein
• can have amphipathic sheet where R groups point on inside and also outside
• distance between adjacent a.a. is 3.5
• parallel and anti-parallel beta sheets are possible
• -> unique H bonding properties
• -> antiparallel arrangement can arise by “hairpin folding” of a single strand

Question 22

structure of polypeptide (polyproline) II helix

Answer 22

• highly made up proline residues
• does not satisfy H bond requirements –> this is because helical nature is created by Proline kinks themselves
• left handed
• glycine are often found as well –> non polar, very small –> bc its so small it allows for all these kinks

Question 23

What are the positions of side chains in alpha helix and beta sheets ?

Answer 23

• can have amphipathic charateristics:

–> one face is hydrophobic and one is hydrophilic

Ex: an amphipathic alpha helix will have side chains of similar polarity every 3-4 residues ; whereas B-strand will have alternating polar and nonpolar side chains (2 hydrophilic, and 2 hydrophobic)

Question 24

T or F; Beta pleated sheets are usually twisted or wrapped into barrel structures

Answer 24

True

Question 25

T or F; at phi = 0 degrees and psi = 0 degrees is a sterically allowed conformation

Answer 25

• False; it is a sterically nonallowed conformation

– this is due to steric crowding: congestion caused by physical presence of surrounding ligands which may slow down or prevent reactions

Question 26

What are Ramachandran plots?

Answer 26

• steric hindrance that excludes phi and psi combinations

- allow us to describe which structures are sterically possible

Question 27

Ranges of allowed psi and phi angles for Beta pleated sheet

Answer 27

phi: -150 to -100
psi: 120 to 160

phi bond: between amino group and alpha carbon

psi bond: between alpha carbon and carboxylic acid group

Question 28

Ranges of allowed phi and psi angles for alpha helix?

Answer 28

phi: -70 to -60 degrees
psi: -50 to -40 degrees
- h bonding between every 4th amino acid right handed

Question 29

Ranges of allowed psi and phi angles for 310 helix?

Answer 29

phi: -70 to -60 degrees
psi: -30 to -10 degrees

• h bonded every 3rd amino acid

Question 30

Ranges of allowed psi and phi angles for polypeptide ii helix ?

Answer 30

phi: -80 to -60 degrees
psi: 130 to 160 degrees

– H bond between very 5th amino acid

Question 31

Secondary structure function

Answer 31

• help make up proteins to be fibrous (long and extended) or globular (blobs)

Question 32

What type of protein is collagen?

Answer 32

• fibrous protein
• most plentiful protein in the vertebrates made up of proline and glycine
• each polypeptide is a left-handed helical structure which is Gly (every 3rd aa) Proline and Hydroxyproline

– any other amino acid other than Gly would be too buly

– cross-links between lysine residues form between helices to form a collagen fibril

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

Question 33

how does hydroxyproline make collagen tougher?

Answer 33

• by cross-linking strands

Question 34

What is hydroxyproline?

Answer 34

• diff version of proline

- has a hydroxyl group

Question 35

What is the relationship between Vitamin C and hydroxyproline?

Answer 35

• enzymes that catalyze the hydroxylation of proline require Vitamin C to function

Question 36

T or F; excessive vitamin C leads to scurvy, weaking collagen

Answer 36

False; it is extreme vitamin C deficiency, called scurvy, weakens collagen fibers because of reduced hydrogen bonding between collagen fiber chains; proline in this case cannot be hydroxylased

Question 37

Characteristics of weakened collagen (scurvy)

Answer 37

• all of the following happen due to weak connective tissue:

–> deficiency disease: scurvy

–> deficiency symptoms: anemia, atherosclerotic plaques, pinpoint hemorrhages under skin, bone fragility, joint pain;

–> poor wound healing, frequent infections, bleeding gums, loosened teeth

–> muscle degeneration and pain, hysteria, depression, rough skin, blotch bruises

Question 38

T or F; Tertiary structure shows conformation of the whole polypeptide in 3 dimensions?

Answer 38

True

Question 39

T or F; tertiary structure is stabilized by majority covalent disulfide bonds between Cysteines

Answer 39

False; stabilized by noncovalent bonds and sometimes by covalent disulfied bonds between Cysteines

Question 40

What types of bonds are included in tertiary structure?

Answer 40

• disulfide bond, hydrogen bond, salt bridges and more

Question 41

True or False; proteins cannot be made up of more than one domain

Answer 41

False; proteins are made up of more than one domain

– multiple domains more common in larger proteins

Question 42

True or False; hairpin turns allow abrupt changes in polypeptide chain direction

Answer 42

True

Question 43

What is a hairpin turn ?

Answer 43

• A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact.

Question 44

T or F, It is energetically unfavorable to adopt a protein structure

Answer 44

False; it is favorable –> folding of a protein is a chemical reaction with a negative change in free energy if folding is to be spontaneous

Question 45

Even though folding is more ordered why is it favorable?

Answer 45

• in an unfolded state water molecules are more ordered around structure –> causing folding to be more favorable

– however the folding is not that stable and takes little to denature or unfold protein

Question 46

True or False; protein structure is usually unstable and can be unfolded with slight increases in temperature

Answer 46

• True