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BISC 312 > Lecture 7 > Flashcards

Lecture 7 Flashcards

1
Q

What structure of proteins specify their function function?

A

3-D structure

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2
Q

What is the primary structure?

A
  • simple sequence of amino acids linked together via peptide bonds
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3
Q

what is the secondary structure ?

A
  • formed by regular folding patterns in specific regions of the protein
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4
Q

What are the different patterns of secondary folding?

A
  • alpha helix
  • beta pleated sheet
  • random coil or loop region
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5
Q

What is the tertiary structure?

A
  • regions of local structure are then coiled into an overall 3-D structure for entire polypeptide sequence
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6
Q

What is Quaternary structure?

A
  • 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
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7
Q

How are changes to amino acid sequence tolerated ?

A
  • it depends on where they occur within the 3-D structure of the protein
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8
Q

What are conservative and non conservative changes ?

A
  • conservative –> preserve chemical properties

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

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9
Q

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

A
  • 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
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10
Q

what determines the protein primary structure?

A

the genetic code

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11
Q

what is the genetic code?

A
  • nucleotide triples, codons, used to code for each amino acid
  • considered to be standard genetic code
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12
Q

what are the possible combinations for codons ?

A

4^3 = 64 possible cominations with 4 nucleotides

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13
Q

What are Pauling’s rules for secondary structure ?

A
  • 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
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14
Q

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

A
  • rotation around these bonds allows protein backbone to fold into secondary and tertiary structures
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15
Q

Around which bonds is rotation allowed around ?

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

think of phi and psi bonds

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16
Q

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

A
  • alpha helix
  • beta pleated sheet
  • most commonly observed secondary structures
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17
Q

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

A
  • 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
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18
Q

Structure of the alpha hellix

A
  • 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
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19
Q

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

A
  • 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
20
Q

Structural features of the alpha helix for H bonding

A
  • 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
21
Q

Structure of beta pleated sheets

A
  • 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
22
Q

structure of polypeptide (polyproline) II helix

A
  • 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
23
Q

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

A
  • 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)

24
Q

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

A

True

25
Q

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

A
  • 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

26
Q

What are Ramachandran plots?

A
  • steric hindrance that excludes phi and psi combinations

- allow us to describe which structures are sterically possible

27
Q

Ranges of allowed psi and phi angles for Beta pleated sheet

A

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

28
Q

Ranges of allowed phi and psi angles for alpha helix?

A

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

29
Q

Ranges of allowed psi and phi angles for 310 helix?

A

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

  • h bonded every 3rd amino acid
30
Q

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

A

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

– H bond between very 5th amino acid

31
Q

Secondary structure function

A
  • help make up proteins to be fibrous (long and extended) or globular (blobs)
32
Q

What type of protein is collagen?

A
  • 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

33
Q

how does hydroxyproline make collagen tougher?

A
  • by cross-linking strands
34
Q

What is hydroxyproline?

A
  • diff version of proline

- has a hydroxyl group

35
Q

What is the relationship between Vitamin C and hydroxyproline?

A
  • enzymes that catalyze the hydroxylation of proline require Vitamin C to function
36
Q

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

A

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

37
Q

Characteristics of weakened collagen (scurvy)

A
  • 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

38
Q

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

A

True

39
Q

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

A

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

40
Q

What types of bonds are included in tertiary structure?

A
  • disulfide bond, hydrogen bond, salt bridges and more
41
Q

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

A

False; proteins are made up of more than one domain

– multiple domains more common in larger proteins

42
Q

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

A

True

43
Q

What is a hairpin turn ?

A
  • 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.
44
Q

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

A

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

45
Q

Even though folding is more ordered why is it favorable?

A
  • 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

46
Q

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

A
  • True

BISC 312 (31 decks)

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