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CHEM271: BIOCHEM 1 > Lecture 2 > Flashcards

Lecture 2 Flashcards

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1
Q

what defines the secondary and tertiary structure?

A

the amino acid (primary ) sequence

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2
Q

What is a secondary structure?

A

Regular repeating structure stabilized by H-bonding within polypeptide backbone

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3
Q

What is the most common type of helix?

A

a-helix

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4
Q

the alpha helix is a coiled structure stabilized by:

A

intrachain hydrogen bonds
i.e. hydrogen bonds between the NH and CO groups of the main chain

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5
Q

In alpha helixes, the CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated:

A

four residues ahead in the sequence

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6
Q

In biochemistry, a residue refers to

A

a single unit within a polymer, such as an amino acid in a protein or a nucleotide in a nucleic acid

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7
Q

In the A-helix, all the main chain CO and NH groups are hydrogen bonded except for:

A

amino acids near the ends of an a helix

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8
Q

How many residues are there per turn in the a-helix?

A

3.6 amino acid residues per turn

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9
Q

In a -helix: Residues separated by a rise (or translation) of

A

1.5 Å along the helix axis and a 100° rotation

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10
Q

pitch cue card

A
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11
Q

Most α-helices found in proteins
are

A

right-handed

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12
Q

why are right-handed helices more energetically favorable?

A

fewer steric clashes between R
groups and the peptide
backbone

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13
Q

Why do valine (V), threonine (T) and isoleucine (I) destabilize the alpha helix?

A

bulky groups at the β-carbon tend to destabilize
α-helices because of steric clashes

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14
Q

bulky groups at the β-carbon tend to destabilize
α-helices because of steric clashes

A

Valine (V), threonine (T), and isoleucine (I)

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15
Q

Why do serine (S), aspartate, (D) and asparagine (N) destabilize a-helixes?

A

side chains contain hydrogen-bond donors or
acceptors that are close to the main chain can
compete for main-chain NH and CO groups

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16
Q

proline is a helix breaker because:

A

the ring structure of its side chain blocks the NH group and does not allow the phi bond value required to fit into an a-helix

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17
Q

Phi, φ

A

describe the rotations of the polypeptide backbone around the bonds between N-Cα

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18
Q

Psi, ψ

A

describe the rotations of the polypeptide backbone around the bonds between Cα-C

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19
Q

distance between adjacent amino acids along a β
strand =

A

~3.5 A

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20
Q

In B sheets, Side chains of adjacent amino
acids point in:

A

opposite directions.

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21
Q

B-sheets can be

A

flat or twisted

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22
Q

Comparison: a-helix vs. b-sheet

A
  • β-sheet: hydrogen bonds between strands, amino acids far apart in
    primary sequence
  • α-helix: hydrogen bonds between amino acids close in sequence
  • Both: hydrogen bonds between –NH and C=O in peptide backbone
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23
Q

Some proteins contain

A

domains that are mainly -helical and others mainly -sheets!

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24
Q

Secondary structure: B-turn: also called:

A

“hairpin turn or “reverse turn”

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25
In many reverse turns, the C=O group
of residue i is hydrogen bonded to the NH group of residue i + 3
26
Usually on surface of protein
Loops
27
No regular structure, variable lengths
Loops
28
Often involved in interactions with other proteins
Loops
29
example of a globular protein
myoglobin
30
Tertiary structure:
the overall course of the polypeptide chain
31
Myoglobin
a highly compact, globular, mainly α helical protein with a heme prosthetic group
32
Globular proteins are characterized by:
-a highly compact structure. * a lack of symmetry * solubility in water * protein surface has many charged amino acids * Protein interior (core) is tightly packed with mostly non-polar residues.
33
porins
Membrane proteins
34
* Amphipathic structures
35
Membrane proteins have:
many hydrophobic amino acids in contact with the hydrophobic membrane. * many polar and charged amino acids surrounding a water-filled channe
36
Motifs are
specific combinations of secondary structures e.g. helix-turn-helix
37
Motifs frequently exhibit
similar functions
38
Domains:
independently folding regions within a polypeptide that may be connected by a short, flexible linker segment
39
cell-surface protein CD4 (shown) has
four domains.
40
fibrous protein examples:
α-keratin, collagen
41
fibrous proteins from :
long, extended
42
* α-keratin:
: two right-handed α-helices intertwined to form a left-handed super helix
43
* α-keratin:member of
a superfamily of structural proteins called coiledcoil proteins
44
α-keratin: two helices are stabilized by
ionic and van der Waals interactions
45
* Coiled-coil proteins:
central region of 300 amino acids that contains a heptad repeat (imperfect repeats of a sequence of seven amino acids Every seventh residue in each helix is leucine
46
Collagen:
the main fibrous component of skin, bone, tendon, cartilage, and teeth
47
Fibrous proteins: collagen: __ appears at every third residue
glycine
48
Fibrous proteins: collagen: the sequence _ reccurs frequently
glycine-prolinehydroxyproline
49
with collagen helix, there are no:
hydrogen bonds
50
osteogenesis imperfecta (“brittle bone disease”)
results when other amino acids replace the internal glycine residue. Results in improper folding and accumulation of defective collagen
51
Tertiary structure can vary:
globular proteins, membrane proteins, fibrous proteins
52
* Secondary structures are stabilized by
hydrogen bonds between backbone N-H and C=O groups: A-helices, B-sheets, B-turns
53
What are the three types of tertiary structure:
(1) globular proteins (2) membrane proteins (3) fibrous proteins
54
Cro protein of bacteriophage is an example of which quaternary structure?
Homodimer
55
THe simplest form of quaternary structure is:
a homodimer
56
A homodimer consists of :
two identical subunits
57
human hemoglobin consists of what type of quaternary structure
a2B2 tetramer
58
Ribonuclease:
A very stable, secreted pancreatic enzyme (protein) that degrades RNA
59
Ribonuclease is a single polypeptide chain consisting of:
124 amino acid residues cross-linked by four disulfide bonds
60
Anfinsen's plan was to:
destroy the three dimensional structure of the enzyme and to then determine what conditions were required to restore the structure
61
Christian Andinsen placed the ribonuclease in a solution containing:
Urea and B-mercaptoethanol
62
Anfinsen's experiment yielded:
a denatured protein, a randomly coiled polypetide chain devoid of enzymatic activity
63
In Anfinsen's experiment: Urea
disrupted all noncovalent bonds
64
In Anfinsen's experiment: B-mercaptoethanol fully reduced:
disulfide bonds
65
What do we mean when we say a protein is denatured?
When a protein is converted into a randomly coiled peptide without its normal activity
66
Anfinson's experiment showed (1) :
(1) it is possible to destroy the structure (denature the protein) (2) It is possible to regain structure and activity after denaturation (but this doesnt work on all proteins)
67
Anfinsen experiment: what happens if the experiment conditions are altered? e.g. reoxidation of ribonuclease while urea is present
The product is a "scrambled" protein"
68
Why do we get "scrambled proteins" in urea?
Wrong disulfides formed pairs in urea There are 105 different ways of pairing 8 cysteine molecules to form four disulfides -->104 wrong pairings have been termed "scrambled" ribonuclease
69
Is it possible to refold the scrambled protein into its native, fully active structure?
Yes: remove urea: a trace of B-mercaptoethanol must be present this allows the slow formatioon and breakage of disulfide bonds ovver the course of several hours until the lowest energy, most stable active form is finally regenerated
70
protein folding is a __ process
cooperative
71
The folding funnel depicts:
the thermodynamics of protein folding
72
The top of the funnel represents:
all possible denatured conformations
73
protein folding: folding funnel : the protein has maximum entropy at:
the top fo the funnel
74
protein folding : folding funnel: the folded protein exisAts at:
the bottom of the funnel
75
A common feature of diseases associated with improperly folded proteins:
normally soluble proteins are converted into insoluble fibrils rich in B sheets
76
Amyloid fibrils / amyloid plaques
Protein aggregates composed of insoluble fibers rich in B sheets that are found in the brains of patients with certain neurological diseases, inclluding alzheimers disease and parkinson disease
77
What are four examples of covalent modification of proteins?
(1) Hydroxyproline (2)y- Carboxyglutamate (3) Carbohydrate-asparagine adduct (4) Phosphoserine
78
homology:
two molecules are said to behomologous if they are derived from a common ancestor
79
homologous molecules or homologs can be divided into two classes:
(1) orthologs (2) paralogs
80
orthologs are:
homologs that are present within different species and have very similar or identical functions
81
paralogs are:
homologs that are present within one species, paralogs often differ in their detailed biochemical functions
82
example of orthologs:
bovine ribonuclease and human ribonuclease
83
example of paralogs:
human ribonuclease human angiogenin
84
homologs are derived from:
a common ancestor
85
sequence alignment to detect:
homologs
86
significatnt sequence similarities imply that:
two proteins have the same evolutionary origin
87
sequence alignment:
process of systematically aligning two sequences to identify regions of significant overlap
88
α-hemoglobin and myoglobin: the best alignment reveals
23 sequence identities.
89
Alignment: gap insertion and scoring:Scoring system:
-each identity between aligned sequences is counted as +10 point -each gap introduced (regardless of size) counts for −25 points.
90
Shuffling
The significance of an alignment can be assessed by randomly rearranging one sequence and determining a new alignment score If the original score is appreciably higher than the shuffled alignment scores, it is unlikely to have occurred by chance alone.
91
The blossum 62 method accounts for:
residue similarity, which leads to better seperation of authentic vs shuffled sequences
92
For sequences longer than 100 amino acids, sequenced identities greater than 25% are:
almost certainly not the result of chance alone (such sequences are probably homologous
93
For sequences longer than 100 amino acids, sequence identities less than 15% identical are:
unlikely to indicate statistically significant similarity
94
For sequences longer than 100 amino acids, sequence identities between 15% and 25% identical :
further analysis is necessary to determine the statistical significance of the alignment
95
We can use 3D structure to:
understand evolutionary relationships
96
tertiary structure is more closely associated with __ and is more __ than is primary structure
tertiarty structure is more closely associated with function and more evolutionarily conserved than is primary structure
97
3D structures can be similar despite a small sequence identity due to:
their three dimensional structures
98
convergent evolution:
very different evolutionary pathways lead to the same solution
99
divergent evolution:
proteins derived from a common ancestor accumulate differences over time, potentially acquiring new functions

CHEM271: BIOCHEM 1 (3 decks)

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