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4th Year Fall > H2001 Midterm 1 > Flashcards

H2001 Midterm 1 Flashcards

1
Q

Where is all the information required to fold a protein into its tertiary structure contained?

A

Primary sequence

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2
Q

What do proteins need to include to bind oxygen?

A

A prosthetic group

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3
Q

What is a crucial role of IDPs (2)

A

1) binding to multiple partners
2) high-specificity / low affinity interactions

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4
Q

What is important to note about the hydrogen bond that stabilizes a-helices?

A

It STARTS from a carbonyl oxygen and GOES to the amino NH

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5
Q

What groups are attached to the alpha carbon in an amino acid

A

alpha-carboxyl and alpha-amino

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6
Q

Buffers

A

pH doesn’t change much as you add acid or base.

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7
Q

p53

A

famous tumour suppressor protein with IDP regions

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8
Q

What stabilizes the T state?

A

greater number of ionic interactions at the interfaces between subunits

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9
Q

What happens if there are two deep wells in the E landscape? One corresponding to the right fold, and the other the wrong fold.

A

Mad cows disease

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10
Q

What causes the twist in a coiled coil?

A

The two helices must twist around each other to match up their hydrophobic faces

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11
Q

True or False: glycine does not have to be every third residue.

A

False

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12
Q

How long are typical domains in terms of residues?

A

100-200 residues

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13
Q

Polarity

A

distribution of e- clouds around covalent bond

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14
Q

How are prions formed

A

PrP converted to an infectious, high B-sheet conformation called PrP^SC (scrapie); acts as a template to refold

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15
Q

What conditions can denature proteins? (5)

A

1) High temperatures
2) extreme pH
3) Organic solvents
4) chemicals like urea and guanidinium hydrochloride
5) detergents like SDS

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16
Q

Which point mutation listed below is least likely to wreck protein function?
Leu - Tyr
Leu - Ser
Leu - Phe
Leu - Trp

A

Leu - Phe

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17
Q

List the cellular macromolecules and their building blocks

A

Proteins - amino acids
Sugars - polysaccharides
Fatty acids - lipids
Nucleic acids - nucleotides

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18
Q

What does NOT stabilize silk fibroins?

A

Disfulfide bonds

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19
Q

What are the names of the next 6 of the monomer naming convention?

A

dimer, trimer, tetramer, pentamer, hexamer

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20
Q

Repeating unit of silk fibroin

A

G-S-G-A-G-A

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21
Q

Cavity where BPG binds is lined with positive or negative amino acids that interact with the negative groups n BPG?

A

Positive

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22
Q

Is CO2 soluble in aqueous solution?

A

Not very

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23
Q

What special bonds can cysteine form?

A

Disulphide bonds

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24
Q

Myoglobin History

A

binds O2; first atomic resolution protein structure ever solved with X-ray crystallography; earned nobel prize in 1962

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25
Q

What part of globular proteins allow them to carry out a wider range of biological functions than fibrous proteins?

A

Their tertiary structure

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26
Q

2 traditional methods to determine protein structures

A

1) X-Ray crystallography
2) Nuclear Magnetic Resonance (NMR)

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27
Q

When would a specific R group be negatively charged (general)?

A

pH > pKa

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28
Q

What do IDPs do to carry out their functions?

A

Fold

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29
Q

What side chain is likely to bind H+ in hemoglobin?

A

Histidine; forms ion pairs to asp that helps stabilize deoxyhemoglobin, which promotes deoxygenation by favouring transition to T state

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30
Q

When does enthalpy favour a process

A

when dH < 0

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31
Q

Review EDI info

A
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32
Q

At pH 7, what is the charge on this peptide:
AEGK

A

0

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33
Q

Dihedral Angles

A

Rotation can occur around the alpha carbons, only by two angles per residue

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34
Q

At neutral pH, do the charged on the C- and N- terminal groups of hemoglobin matter?

A

Yes, they help to form ionic interactions that stabilize deoxyhemoglobin

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35
Q

Review iClicker Qs in lecture 11

A
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36
Q

Apoprotein

A

protein without its prosthetic group

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37
Q

What stabilizes the structure of fibrous proteins? silk fibroin

A

Secondary: H bonds
Quaternary: van de waals

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38
Q

*Review how to explain the hydrophobic effect and hydrophobic interactions

A
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39
Q

Ionic interaction

A

attraction (or repulsion) of charged species (ions, dipoles, charged groups)

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40
Q

Allosteric activation

A

promotes O2 binding (CO)

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41
Q

Sickle-Cell Anemia is caused by mutation in B subunit of hemoglobin; glu6-val6.

a) hydrophobic residue - hydrophobic residue
b) charged residue - hydrophobic residue
c) hydrophobic - polar

A

B

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42
Q

2 major types of secondary structure

A

1) alpha-helices
2) beta-sheets

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43
Q

What are important buffer systems in biochem?

A

Phosphate (cytoplasm) and bicarbonate (blood plasma)

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44
Q

Which of the following is not a characteristic of peptide bonds?
a) Polar
b) planar
c) cis
d) formed by condensation of L amino acids

A

C

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45
Q

What is another type of secondary structure?

A

Beta Turns

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46
Q

Phi Dihedral Angle

A

toward N-terminus

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47
Q

Gibbs Free Energy Formula

A

dG = dH - TdS

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48
Q

Is myoglobin a tetramer like hemoglobin?

A

No, monomer

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49
Q

Why is the oxygen binding site buried deep in the protein?

A

When one O2 molecule reacts with 2 heme molecules, the result can be conversion of Fe2+ to Fe3+; burying the heme prevents this.

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50
Q

Carbon Monoxide poisoning

A

CO coordinates to heme
CO is colorless odorless, can build up in enclosed spaces, responsible for more than half of poisonings yearly.
250 fold greater affinity for hemoglobin than O2.

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51
Q

Bronsted Acid / Base Def

A

Acid: lose a proton
Base: gain a proton

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52
Q

What is another helix breaker and why?

A

Glycine; it has high conformational flexibility, making it entropically expensive to adopt the constrained a-helical structure

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53
Q

Intrinsically Disordered Proteins (IDPs)

A

lack stable tertiary and/or secondary structures under physiological conditions; exist as dynamic ensembles of interconverting structures

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54
Q

Endergonic

A

dG > 0
Will not occur spontaneously

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55
Q

Why do we need proteins for oxygen storage / transport?

A

O2 is poorly soluble in H2O; can’t be carried in tissues. Also doesn’t diffuse effectively

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56
Q

Hydrogen Bonding

A

occurs btwn an electronegative atom (O, N, F) and a H atom bonded to another electronegative atom

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57
Q

Are most a-helices right or left handed?

A

Right-handed

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58
Q

What stabilizes the structure of fibrous proteins? a-keratin

A

Secondary: H bonds
Quaternary: disulphide bonds

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59
Q

Enthalpy

A

changes are related to formation, breaking, or distortion of bonds (internal energy)

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60
Q

Where might proline fit well in a peptide?

A

In the first turn of an a-helix

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61
Q

Why do we use heme as opposed to free Fe as our binding group?

A

Free Fe is dangerous; promotes formation of highly reactive oxygen species that damage DNA (one of most common causes of death in children)

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62
Q

Why do cats spit up fur-balls?

A

a-keratin in fur is indigestible, insoluble due to S-S bonds

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63
Q

What range does a buffer work best for?

A

within +- 1 pH unit around the pKa value

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64
Q

Amyloids

A

misfolded proteins form insoluble fibrous protein aggregations formed largely of B-sheet structures

Amyloid plaques destroy nerve cells and lead to loss of thought and memory

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65
Q

Summary of collagen structure levels

A

Primary: Gly-Pro-Hyp-Gly-X-Y

Secondary: left-handed polypro helix

Tertiary: none

quaternary: right-handed triple helix, heterotrimer

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66
Q

Direction of collagen helix

A

left-handed

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67
Q

Summary of a-keratin structure levels

A

Secondary: a-helix

Tertiary: none

Quaternary: coiled coil

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68
Q

BPG

A

interacts with hemoglobin and modulates its O2 affinity

BPG binds at a site distant from O2 binding site, decreases the affinity of hemoglobin for O2

Allosteric inhibitor

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69
Q

Alpha-helix

A

secondary structure where the polypeptide chain winds tightly around; side chains stick out from the helical axis like branches

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70
Q

Carboxyl terminal residue

A

amino acid at the end with a free carboxyl group

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71
Q

Do we expect chunky sidechains to fit better with a-helices or b-sheets?

A

B-sheets

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72
Q

Fibrous proteins all possess structural features that give them:
a) frailty
b) delicacy
c) flimsiness
d) strength

A

d

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73
Q

What stereoisomer label is used for the only amino acids that occur in proteins?

A

L-amino acids (not D)

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74
Q

True or false: myoglobin and hemoglobin are conjugated proteins, but only myoglobin is a hemoprotein.

A

False; both are hemoproteins

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75
Q

Which amino acid sidechain is capable of participating in Hydrogen bonds?
Leucine
Tyrosine
Phenylalanine

A

Tyrosine

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76
Q

Phi values around -60 degrees and psi values around -50 degrees are in what handed helices?

A

Right-handed

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77
Q

dG vs. Keq formula

A

dG = - RT ln Keq

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78
Q

How does having small sidechains make silk fibroin strong?

A

close packing of B-sheets and an interlocking arrangement of R groups

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79
Q

Which of these point mutants (all n-p) is least likely to wreck a protein?
L - I
L - A
L - G
L - F

A

L - I

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80
Q

Tm - midpoint / inflection point

A

50% of protein is denatured

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81
Q

holoprotein

A

protein with its prosthetic group

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82
Q

True or False: H bonds are formed between two B-strands to make a B-sheet

A

True

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83
Q

Tertiary Structure

A

overall 3D arrangement of the atoms in a globular protein; how secondary structure pack together

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84
Q

Van der Waals

A

occur between transient partial charges / dipoles formed in e- clouds; weak

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85
Q

What holds helices together in coiled coils?

A

Hydrophobic interactions between hydrophobic residues

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86
Q

What orientation makes H bonding the strongest?

A

Linear

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87
Q

Thermodynamics

A

Tells you if a process is spontaneous or not

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88
Q

Tripeptide

A

3 amino acids, 2 peptide bonds

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89
Q

Review and draw / sketch a Ramachandram plot and indicate the regions for beta-sheets and right handed alpha helices

A

General: B-sheets above right-handed alpha-helices

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90
Q

What structural mechanisms are behind hemoglobin’s sensitive response to O2?

A

Hemoglobin has 4 myoglobin-like chains; fewer than half amino acid residues are identical, although they fold similar to myoglobin

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91
Q

What direction is the helical path of the supertwists

A

Left-handed

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92
Q

Separation of Oil and Water is caused by changes in what?

A

Entropy

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93
Q

Quaternary structure

A

spacial arrangement of a protein’s individual polypeptide chains; exhibited only by proteins which contain two or more polypeptide chains

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94
Q

What terminal end defines where peptides start being named?

A

The amino terminal, always placed at the left

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95
Q

Considering 3.6 residues per turn in an a-helix, which two residues in MEQALKRN would wind up on the same face of the helix?

A

M and A

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96
Q

What does the binding of O2 to one hemoglobin subunit in the T state trigger?

A

A change in conformation to the R state (high O2 affinity)

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97
Q

Chaperones

A

proteins present in cells that help other proteins fold

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98
Q

Would the presence of two Lys residues near the amino terminus stabilize or destabilize the a-helix?

A

Destabilize

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99
Q

A better view of protein folding

A

E landscape is funnel-shaped, so the protein is biased to fold towards the native state, with many different intermediate conformations leading to the same native state

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100
Q

In active tissues, there are more protons around, so the pH is _____ and hemoglobin has ____ affinity for O2 compared to in the lungs.

A

Lower, lower

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101
Q

What insect can eat wool and how?

A

Moths; they have high conc of mercaptans so they can reduce S-S bonds to eat wool from clothing

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102
Q

Entropy

A

Changes related to change in order or randomness of a system

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103
Q

At pH 1, what is the charge on this peptide:
AEGK

A

+2

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104
Q

2 major conformations of hemoglobin

A

“R State”: relaxed; stabilized by O2 binding (oxyhemoglobin)

“T State”: tense; more stable and dominant conformation if O2 isn’t bound (deoxyhemoglobin)

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105
Q
A
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106
Q

Conjugated proteins

A

contain permanently associated chemical components (known as the prosthetic group) in addition to amino acids

107
Q

What COHb levels does a healthy person have? What about a smoker / chain smoker?

A

1% or less
3-8% for smokers
15% chain smokers

108
Q

How is the a-helix structure stabilized?

A

By H bonds forming between one alpha-carbonyl and the N-H group 4 residues further along the chain

109
Q

What is the structure of alpha-keratin?

A

Built up from a-helices in a coiled coil; 2 helices wrap around each other to give a “supertwisted” coiled coil. Helices are parallel.

110
Q

Are free amino and carboxyl groups ionizable?

A

Yes

111
Q

Try to identify phi and psi from a drawing

A
112
Q

What amino acids can bind oxygen?

A

None!

113
Q

Zwitterion

A

spatially separated positive and negative charges; overall charge is 0.

114
Q

Protein that prions are made from

A

PrP (Prion related protein), found in healthy people and animals

115
Q

Protein Data Bank

A

contains all experimentally determined structures

116
Q

Explain how entropy causes the separation of oil and water

A

lipid molecules become ordered around water; however when there are clusters of molecules, the entropy is increased

117
Q

True or False? Multi-domain proteins have domains with all the same function.

A

False

118
Q

Integrated transport by hemoglobin (Bohr effect)

A

Lungs carry O2 to tissues, tissues send H+ and CO2 back to lungs to increase affinity for O2 binding (?)

119
Q

How many amino acids

A

20

120
Q

What is tertiary structure stabilized by?

A

Many noncovalent interactions

121
Q

What is likely to happen if we switch a polar amino acid for a non-polar one in a protein?

A

It will wreck the protein

122
Q

How do proteins know what tertiary structure to fold into, and who discovered this?

A

Christian Anfinsen: started with ribonuclease, denatured by exposure to concentrated urea – loss of all catalytic activity. He then removed urea, and ribonuclease regained its catalytic activity (refolded into native structure), all by itself (no cell components involved)

123
Q

What do amino acid groups help us predict?

A

The consequences of mutations

124
Q

Which is the strongest “weak” interaction in biomolecules?

A

Hydrogen bond

125
Q

Secondary structure of collagen

A

stabilized by steric repulsion of Pro and hy-Pro rings

Not an a-helix, sometimes called the collagen helix

126
Q

How many residues / turn in collagen helix

A

3

127
Q

What stabilizes protofibril and protofilaments?

A

Disulfide bonds

128
Q

In which direction does the dipole moment of an a-helix orient?

A

Large net dipole moment with - towards C-terminus, + toward N-term

129
Q

Amino terminal residue

A

amino acid at the end with a free amino group

130
Q

Globin fold

A

Myoglobin’s domain fold
Typically 8 a-helices
stabilized by H bonds and non-covalent interactions btwn sidechains

131
Q

What catalyzes the acid dissociation of CO2 in tissues?

A

Carbonic anhydrase

132
Q

Protein Folding

A

conversion of an irregular, flexible arrangement of the protein chain to a regular, relatively rigid, well defined 3D structure

133
Q

What enzyme is required for hydroxylation and what symptoms could arise from a lack of this?

A

Vit C
Scurvy

134
Q

B-strands and B-sheets

A

Secondary structure with a much more extended conformation

135
Q

Which type of forces are NOT responsible for stabilizing tertiary structure of globular proteins?

A

Peptide bonds

136
Q

How many oxygen groups can hemoglobin bind?

A

4; 1 at each site

137
Q

How does biochem explain changing hair from curly to straight or straight to curly?

A

Breaks the strong disulfide bonds with a reducing agent, put hair in the shape, then oxidize to re-form the disulfides

138
Q

Which amino acid side chains are positively charged at pH 7?

A

Lys, Arg

139
Q

Prions

A

proteins that can misfold and cause infectious disease.

The infectious agent is resistant to denaturation by protease, heat, and radiation.

The prions can refold abnormally into a structure which is able to convert normal molecules of the protein into a form that forms amyloid plaques.

140
Q

Solution to Levinthal paradox, not supported by experimental evidence

A

A protein takes on specific intermediate conformations en route to the folded state

141
Q

Second Law interpretation by VB

A

Systems tend to proceed from low entropy states to high entropy states

142
Q

What is the central carbon in an amino acid called

A

Alpha carbon

143
Q

As CO binds to one or two subunits of a hemoglobin tetrameter, the affinity for O2 is ____ , i.e. CO is an _____ of hemoglobin.

A

increased, allosteric activator

144
Q

Would the interactions btwn neighboring D and R residues stabilize or destabilize an a-helix?

A

Stablize

145
Q

What is protein primary structure?

A

Amino acid residues and peptide bonds

146
Q

At pH 3, what is the charge on this peptide:
KITTEN

A

+1

147
Q

Where does hair get its strength?

A

alpha-keratin

148
Q

Would you expect glycines amino and carboxyl groups to be neutral or charged at pH 7?

A

Charged

149
Q

Hair

A

an array of many a-keratin filaments

150
Q

Protein misfolding diseases examples

A

Alzheimers, BSE/CJD, mad cows

151
Q

True or false: subunits and domains are not the same thing.

A

True

152
Q

Isoelectric point

A

pH at which a solute has no net electric charge ; pI

153
Q

What happens to the pH as CO2 dissolves?

A

Decreases

154
Q

Are most proteins globular or fibrous?

A

Globular

155
Q

What are the approximate pKa values for the 5 main ionizable groups?

A

alpha carboxyl = 2
alpha amino = 9.5
asp, glu R groups = 4
lys, arg R groups = 11.5
Hist = 6 - 6.5

156
Q

Residue

A

an amino acid unit within a protein / peptide

157
Q

How to break a disulfide bond?

A

Use a reducing agent (such as mercaptoethanol)

158
Q

Denatured state

A

the partially or completely unfolded form of a biological macromolecule; it is incapable of carrying out its functions

159
Q

What is the fundamental units of tertiary structure?

A

Domains

160
Q

Enzymes

A

protein catalysts that reduce the activation E and increase the rate of rxn

161
Q

Collagen primary sequence

A

GXY repeats, usually with one of X or Y being Proline or hydroxyproline
No Cys, Trp, little Tyr

162
Q

Post-translational modification

A

Chemical modification of protein after its translation

163
Q

What do vdw forces depend on?

A

Size and shape of molecules interacting

164
Q

When would a specific R group be positively charged (general)?

A

pH < pKa

165
Q

Which of the following is false about IDP sequences?

a) IDPs have more hydrophobic amino acids than globular

b) IDPs have more polar/charged residues

c) IDPs have more glycine and proline residues

A

A

166
Q

Protofilaments and protofibrils

A

Combined two-chain coiled coils in higher order structures

167
Q

What does lower cysteine percentage correlate with practically?

A

Soft, stretchable and flexible materials; i.e. used for warmth, waterproofing

168
Q

When does entropy favour a process

A

TdS > 0

169
Q

T or F? At low pH, there is more H3O+ than OH-

A

T

170
Q

Where might negatively charged ligands prefer to proteins (think of dipoles)?

A

The N-terminus

171
Q

Which amino acids are prevalent in the regions of proteins that contact DNA (negatively charged)?

A

K, R

172
Q

Do we expect long skinny sidechains to fit better with a-helices or b-sheets?

A

A-helices

173
Q

Collagen

A

most abundant protein in the body (25%).
Bones, teeth, cartilage, tendons, cornea
GLue, gelatin
Insoluble, strong
30 different types

174
Q

What does the sickle-cell anemia mutation cause?

A

Hydrophobic patch on surface of B-subunit, causes hemoglobin tetramers to polymerize long fibrils, distorting the shape of red blood cells. These don’t fit through capillaries, block and interrupt delivery of O2 to tissues

175
Q

How can you learn about the oligomeric structure of multisubunit proteins?

A

Treat them with B-mercaptoethanol (breaks disulfides) and/or urea (disrupts non-covalent interactions)

176
Q

How many hydrogen bonds can water make?

A

4; donor of H to 2 and acceptor of H from 2

177
Q

What is the difference between the N-terminus and the N-terminal residue?

A

The N-terminus is the amino terminal end (just the amino group), whereas the residue is the entire amino acid group at this end of the peptide

178
Q

Why do hemoglobin and myoglobin differ in structure?

A

Because they differ in function

179
Q

What are the dihedral angles expected in B-sheets?

A

Phi around -135 and psi around 135

180
Q

True or False: there is no pH at which the alpha-amino and alpha-carboxyl groups of a free amino acid in an aqueous solution are both un-ionized.

A

True

181
Q

Protein

A

Polymer of L-amino acids; capable of completing a variety of biological tasks

182
Q

Protein Folding Energetics

A

difference in free E between folded and unfolded states is only about 10kcal/mol; proteins only barely fold

183
Q

If you have a protein made up of D-amino acids instead of L, what do you think will happen if you treat it with a protease?

A

Nothing!
This is one strategy for stabilizing small protein drugs

184
Q

Two types of common structural patterns in proteins (list ex of each)

A

1) Motifs: small; B-a-B loop
2) Domain folds: bigger; a/B Barrel

185
Q

First Law Interpretation by VB

A

Energy can’t be created or destroyed, but it can change form

186
Q

What is the backbone of a peptide?

A

N-C-C-N-C-C-N-C-C

187
Q

New Protein structure identification method

A

Cryoelectron microscopy and artificial intelligence (AlphaFold)

188
Q

What is a second determinant to check if a point mutation will wreck a protien?

A

Size; if the size is very different it’s more likely to wreck the protein

189
Q

Does a-keratin have tertiary structure?

A

Not really; secondary structure is helix and quaternary structure is coiled coil

190
Q

Native conformation (protein)

A

biologically relevant, folded protein conformation; denoted N

191
Q

Shape of hemoglobin binding curve vs. myoglobin

A

Myoglobin: hyperbolic
Hemoglobin: sigmoidal (S shaped) because it permits a more sensitive response to ligand concentration

192
Q

Energy landscapes

A

visual representations of E of protein conformations; the folded conformation is the minimum of E, the deep well

193
Q

What happens to CO2?

A

some is carried away by hemoglobin, but most is hydrated to form bicarbonate

194
Q

Which force is responsible for the slight spontaneity of protein folding, considering ionic, vdw, and hbond have dG values around 0?

A

Hydrophobic

195
Q

Why is wool stretchier than silk?

A

Silk is stabilized by weak and numerous non-covalent interactions, whereas a-keratin is stabilized by strong but few covalent interactions (disulfide bonds), meaning silk cannot stretch, although it is flexible

196
Q

Three major types of proteins

A

1) Globular
2) Fibrous
3) Integral membrane

197
Q

What amino acid is the only case where the alpha carbon is not a chiral centre?

A

Glycine

198
Q

Heme binds to Fe in what state? How many coordination bonds are possible?

A

Fe2+
6 coord bonds; 4 to N atoms in porphyrin ring and 2 perpendicular to porphyrin ring (one to N atom of the protein, other to O molecule)

199
Q

What is the only interactions that favours folding

A

Hydrophobic

200
Q

The overall 3D arrangement of secondary structure elements that characterizes a single domain is called a what?

A

Fold

201
Q

True or False? there is a specific 3-base genetic code for the amino acid hydroxyproline so that it is incorporated into the protein during translation of mRNA

A

False

202
Q

Peptide prefixes above tri

A

Tetra, penta, hexa, hepta, octa, nona, deca, oligo, poly

203
Q

What prosthetic groups are good at binding oxygen?

A

Transition metals, including Fe and Cu

204
Q

Why does binding of O2 make the affinity for O2 greater?

A

Causes the heme group to become planar, leading to a change in conformation of the whole protein

205
Q

What type of reaction forms a protein?

A

Condensation reaction; endergonic
This means water is eliminated in formation

206
Q

Allosteric protein

A

Conformation is changed when it binds a ligand; the new conformation changes the protein’s ability to react to a second molecule

207
Q

Where do peptide bonds form?

A

Between the amino group of one amino acid and the carboxyl group of another (both alpha)

208
Q

Psi dihedral angle

A

toward C-terminus

209
Q

Are van der Waals ever repulsive?

A

No, they always induce the opposite charge

210
Q

Where does H bonding happen in quat structure of collagen?

A

from NH of Gly to carbonyl O of adjacent strand; no H bond for pro

211
Q

Which of the following is true about protein domains?
a) a protein must have more than one domain to be functional.
b) protein domains lose their 3D structure when separated from the polypeptide chain.
c) protein domains lose their function when separated from the polypeptide chain.
d) protein domains often fold into stable globular units.

A

d

212
Q

Henderson-Hasselbalch Equation

A

pH = pKa + log [conjugate base] / [conjugate acid]

213
Q

What is protein secondary structure?

A

The local conformation of some part of the polypeptide

214
Q

The protein folding problem / Levinthal paradox

A

many different conformations for proteins with many amino acids. A topic of active research.

215
Q

List the 4 non-covalent, weak interactions

A

Ionic
Van der Waals
Hydrogen bonds
Hydrophobic

216
Q

Dipeptide

A

2 amino acids, 1 peptide bond

217
Q

Take some time to review the amino acids

A
218
Q

Which amino acid can form disulfide bonds?

A

Cysteine

219
Q

What are the 2 possible directions of B-sheets?

A

1) Antiparallel: N-term of one aligned with C-term of next
2) Parallel: N-terms of adjacent peptides aligned

220
Q

How many residues are in each turn in an alpha-helix?

A

3.6

221
Q

What does higher cysteine percentage correlate with practically?

A

Harder, rigid, and inflexible materials; i.e. used for protection and defense

222
Q

What is the primary sequence of a-keratin?

A

A repeat of 7 residues (abcdefg) with hydrophobic residues at positions a and d, on the same face

223
Q

Fetal Hemoglobin

A

a fetus must extract O2 from its mothers blood, so fetal hemoglobin must have higher affinity for O2 than the mother does.

224
Q

The amino acid composition of spider silk (more flexible) and silk from cocoons (less flexible) is different. Which combo belongs to spiders?
A) 45% G
30% A
12% S
no C

B) 37% G
21% A
4.5% S
no C

A

B

225
Q

What amino acid is called a helix-breaker and why?

A

Proline, because it has no backbone NH to participate in H bonds

226
Q

Domain Fold

A

the particular topographical arrangement of secondary structure elements that characterizes a single domain

227
Q

Allosteric inhibition

A

inhibits O2 binding (H+ and CO2)

228
Q

What type of mer is hemoglobin?

A

Heterotetramer

229
Q

Standard Conditions in Biochemistry

A

[H+] = 10^-7M (pH 7)

230
Q

How strong are disulfide bonds?

A

About 100 times stronger than H bonds

231
Q

Unfolded conformation (protein)

A

denoted U

232
Q

Polypeptide

A

2 or more amino acids joined by peptide bonds

233
Q

Silk fibroin

A

Protein produced by spiders and insects; very strong and waterproof

234
Q

What determines a protein’s function?

A

Its structure!

235
Q

Hydrophobic Effect

A

The only of the forces due to entropy.

236
Q

Cooperative binding

A

A little bit of binding initially leads to a lot more binding; gives sigmoidal shaped binding curves

237
Q

Summary of fibroin structure levels

A

Secondary: antiparallel B-strands

Tertiary: none

Quaternary: stacked B-strands

238
Q

Do parallel or anti-parallel B-sheets have stronger H bonds?

A

Antiparallel, because the bonds are linear

239
Q

At low pH, things will tend to be more or less protonated than at high pH?

A

More

240
Q

Metamorphic proteins

A

2 conformations in equilibrium with different activity for each conformation

241
Q

What are Beta turns?

A

found in regions where polypeptide chain reverses direction, within a span of 4 residues, stabilized by H bonds between first and fourth resiudes

242
Q

General rule for globular protein organization

A

Most hydrophobic residues are on the inside, most hydrophilic residues are on the outside

243
Q

What differences in amino acid composition make IDPs less structured than globular proteins?

A

Less hydrophobic core

244
Q

Are the CO and NH groups that connect one amino acid to the next ionizable in a peptide?

A

No

245
Q

What is fetal hemoglobin composed of?

A

Gamma subunits (not as many K/R residues) instead of B subunits; this has a lower affinity for BPG = higher affinity for O2

246
Q

What is dG at eq

A

0

247
Q

Exergonic

A

dG < 0
Occurs Spontaneously

248
Q

Domain

A

a compact unit of protein structure that is usually capable of folding stably as an independent entity in solution

249
Q

How does oxygen get to the buried binding site?

A

Dynamics; the proteins are always rearranging and are only marginally stable. This opens cavities that momentarily open / close, big enough to hold O2

250
Q

What holds the quaternary structure of hemoglobin together?

A

Hydrophobic and ionic interactions

251
Q

Ramachandran plot

A

plot of psi vs. phi; blue areas show ‘allowed’ options

252
Q

What is responsible for biological function of a protein?

A

Folded structure

253
Q

What does BPG play an important role in?

A

Physiological adaptation to high altitude and the reduced O2 available there

BPG conc in blood rises, leading to more O2 being released into tissues

254
Q

Monomor / subunit

A

one polypeptide chain in a protein with more than 1 chain

255
Q

Can hemoglobin bind to H+?

A

Yes, but at a different site from O2 binding site

256
Q

What is the function of fibrous proteins?

A

Structural support

257
Q

Myoglobin and hemoglobin

A

related proteins that store and transport oxygen

258
Q

What is the secondary structure of silk fibroin?

A

Antiparallel B-pleated sheet, stabilized by H bonding. Sheets stack with glycines facing each other, and ala/ser facing each other, stabilized by noncovalent interactions

259
Q

3 characteristics of the peptide bond

A

1) Planar
2) Polar
3) Trans

260
Q

How do disulfides form properly in tertiary structure?

A

Non-covalent interactions ensure that cysteines are positioned to form disulfide bonds correctly

261
Q

Which of the 20 amino acids have ionizable sidechains? (5)

A

R, K, E, D, H

262
Q

Collagen quaternary structure

A

heterotrimer, right-handed triple helix, glycine residues in the centre, R groups face out, sided gelix

263
Q

Coupled Process

A

an unfavourable process can be coupled with a highly favourable one to drive the overall process

264
Q

What is one of the biggest things to remember when finding pH of peptides?

A

Don’t forget to account for the charge of the terminal groups

4th Year Fall (2 decks)

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