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Biochemistry > Lecture 1 - Quiz 1 > Flashcards

Lecture 1 - Quiz 1 Flashcards

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1
Q

What are the substituents on an amino acid?

A

Amino group - NH3
Carboxyl group - COO
H
R side chain

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2
Q

What is the most common amino acid steroisomer?

A

L isomer

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3
Q

What are stereoisomers?

A

mirror image conformations of AAs

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4
Q

What absorbs at 280 nm? at which is the highest and which is the lowest?

A

aromatic rings - tryptophan is highest, tyrosine middle and phenylalanine lowest

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5
Q

What is capable of forming a disulfide bond?

A

Cysteine to form cystine

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6
Q

Why do we measure protein at 280?

A

Many other molecules absorb at lower ranges including S-S bonds

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7
Q

What is the pH of a neutral molecule in respect to charge?

A

2.4 - 9.6 (COO- and NH3+)

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8
Q

What demonstrates a pH higher than 9.6?

A

negative charge on carboxyl group COO- (and NH2)

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9
Q

What demonstrates a pH lower than 2.4

A

A positive charge on the amino group NH3+ (and COOH)

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10
Q

Are the aromatic groups most hydrophobic or hydrophilic?

A

Hydrophobic

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11
Q

What gets lost in the process of forming a peptide bond?

A

H20 - condensation reaction COO- on one and NH3+ on other forming CONH bond

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12
Q

Monosaccharides bind together by what kind of linkage to form a polysaccharide? what do they lose?

A

glycosidic, H20

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13
Q

What is the term for the point at which a protein has no charge?

A

Zwitterion

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14
Q

What is the primary structure of AA? and what is an example of this?

A

linear sequence of amino acids - polypeptide hormones like proinsulin

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15
Q

What holds pro insulin together in its primary structure? What happens to form insulin?

A

Intra chain disulfide bonds - undergoes proteolytic cleavage to to give inter-chain disulfide bonds instead

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16
Q

What is the secondary structure of a protein? and what are some of these forms called?

A

The local folding of the polypetide backbone stabilized by H bonds, alpha helix, beta sheet, turns

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17
Q

What stabilizes an alpha helix?

A

H bonds formed by C=O…H-N-C every 4th residue

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18
Q

What points outward on an alpha helix?

A

R groups

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19
Q

What are some examples of alpha helices? and how many residues/turn does it have?

A

tropomyosin, alpha keratin, intermediate filaments, 3.6

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20
Q

How are coiled coils formed? what is an example?

A

Tropomyosin - hydrophobic groups can interact with other hydrophobic groups of another chain

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21
Q

What characteristics do beta sheets lead to?

A

Usually insolubility

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22
Q

What is an example of a beta sheet?

A

Silk, h bonding resists tension, has flexibility due to van der waals forces between alternating glycine and alanine side chains

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23
Q

How many turns per residue does a polyproline II helix have?

A

3/turn

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24
Q

What is collagens secondary structure?

A

polyproline II helix, collagen made up of a coiled coil of triple helix, and has a repeating glycine residue every third AA because it is so small

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25
What modified amino acids are made in collagen?
hydroxylated prolines - forming ring structure = imino acid now
26
What are turns (secondary structure)?
Consist of 3-4 amino acids, usually contain glycine and proline, allow compaction of large proteins, found on surface of proteins
27
How can secondary structures be determined?
X ray crystallography, NMR, spectroscopy (like circular dichroism or ORD), computer predictions
28
What is tertiary structure in proteins?
Overall 3D conformation of polypeptide chain
29
What stabilizes tertiary structure?
hydrophobic interactions b/w nonpolar side chains, hydrogen bonding between polar side chains, ionic interactions between charged side chain and disulfide and peptide bonds
30
What is a helix-loop-helix?
A ca+2 blinding motif = EF hand
31
What is a zinc finger motif?
two antiparallel beta strands bound to an alpha helix through a zinc ion - common in RNA and binding proteins
32
What is a coiled coil motif?
Helical segments are formed with heptad repeats having a hydrophobic and hydrophilic side
33
How large are domains?
larger than 15,000 MW
34
How can domains be recognized? and what do they form
x ray crystallography or electron microscopy, molecular mosaics
35
What is the quaternary structure for a protein? and what holds them together? what are some examples?
the number and relative position of subunits in multimeric proteins, held together by non-covalent, ionic or covalent (S-S) interactions, hemoglobin has a quaternary structure
36
How many possible confirmations do proteins have?
8^n with n = the number of residues
37
What is the most stable state of proteins? and what can disrupt it?
Native state, denaturation
38
What is the general protein folding mechanism?
Chaperones help to becomes partially folded by utilizing ATP and binding to hydrophobic patches, hydrolisis of the ATP to ADP helps it fold properly
39
What is a chaperonin?
A ring structure that helps fold protein by ATP hydrolysis
40
What conditions can change protein conformation?
pH, ionic strength, heat, dilution, vigorous movement
41
What does the denaturation of collagen cause?
It creates gelatin when heated to 45dC the three chains of triple helix come apart - becomes more flexible and has lower viscosity - but is also sensitive to protease as individual chains
42
What are some protein modifications?
chemical (phosphate, acetyl), glycosylation (targeting), proteolysis (proinsulin), ubiquitin (targets for degradation)
43
What are some of the modifications in collagen?
H bonds to stabilize triple helix, o linkage for sugars and x links and x link formation
44
What is formed when the glutamate side chain is modified with the addition of a second carboxyl group? and what carries out the process?
gamma carboxyglutamic acid (Gla), vitamin K
45
What does the formation of gamma carboxyglutamic acid allow interaction with?
Calcium
46
Where are Gla residues found?
In osteocalcin in bone and blood clotting proteins like prothrombin
47
What drugs inhibit vitamin K activity?
Coumarin drugs - dicumarol
48
What is the family of enzymes that phosphorylate proteins and that remove phosphates called?
kinases phosphorylate and phosphatases remove
49
Which residues can be phosphorylated?
Serine, threonine or tyrosine
50
What does phosphorylation do to charge?
It makes it negative, and allows positive charges to come closer
51
What does phosphorylation of glycogen synthase and glycogen phosphorylase do in hepatocytes in response to epinephrine?
Synthase - inhibits activity, phosphorylase - increases activity - event together lead to increased hepatic glucose delivery to blood q
52
Where can phosphorylation be important in regulation?
Signaling pathways -- changes activity of transcription factors that can inhibit or express genes
53
What is being used as anti-cancer therapeutics in regard to phosphorylation modifications?
Using kinase inhibitiors
54
What are some ways proteolytic processing occurs?
signal peptide cleavage, intracellular polypeptide cleavage, extracellular polypeptide cleavage, proenzyme activation
55
What is a signal peptide?
15-30AA long on proteins synthesize by RER, with a hydrophobic core and positive N- polar C-term
56
How are signal peptides cleaved?
Signal peptide binds to signal recognition particle (SRP), this complex then binds to SRP receptor on ER membrane - ribosome is transferred to a translocon and GTP is hydrolyzed to release SRP - chain then transits emmbrane and signal peptide excised by aspartyl signal peptidase at ER lumen
57
How is mature insulin processed?
Intracellular proteolytic processing - pro insulin synthesize in ER lumen and disulfide bonds are formed - then transported to golgi where it is processed by protease cleavage to liberate C-peptide - and carboxypeptidase E produces mature insulin - increased blood glucose
58
How is collagen processed by proteolytic processing?
Extracellular proteolytic processing - after secretion from the cell the procollagen molecule is cleaved by N- and C-peptidases to form the triple helical tropocollagen molecule - individual tropocollagen molecules can now assemble into collagen fibrils
59
What are some examples of protelytic proenzyme activation (zymogen)?
Pepsinogen --> pepsin by autoactivation HCl Trypsinogen --> trypsin by enteropeptidase Chymotrypsingoen --> chymotrypsin Prothrombin --> thrombin Procollagenase MMP-1 --> collagenase (plasminogen activator)
60
How does protein glycosylation occur?
There is no template --> addition requires an activated sugar like UDP glucose and a glycosyl transferase, and an acceptor protein, sugars are covalently linked through O-linkage to serine or threonine or N-linked through asparagine
61
Where does the protein glycosylation occur?
ER and transferred to Golgi for further trimming and addition of monosaccharides
62
What are two major classes of N linked saccharides and what is their glycosylation important for?
high-mannose oligos and complex oligos - correct folding of some eukaryotic proteins during their biosynthesis
63
What are proteasomes and where are they found?
Complex structure composed of seven individual proteins that catalyze the six major protease activities - sites located onthe interior surface of the rings - proteins must enter central pore to be degraded - found in the cytosol and the nucleus
64
Why is ubiquitin added?
Tags with degredation - adds 8.5 kDa - proteins must be about 100 kDa to be degraded
65
What enzymes are needed for ubiquitination?
Ubiquitin activating enzyme binds ubiq. to enzyme via ATP, ubiquitin conjugating enzymes - transfer to the substrate protein and ubiquitin protein ligases carry out final step to covalent attachment of ubiquitin to lysine - tagged proteins then degraded by proteasome complex - ubiquitin release and recycled
66
What can defective ubiquitination lead to?
defective degradation of growth promoting proteins --> myc, src, can lead to cancer or cause neurodegenerative diseases

Biochemistry (19 decks)

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