BIOL 225 > Proteins > Flashcards

Proteins Flashcards

(83 cards)

Study These Flashcards
1
Q

Proteins are named as the most versatile of the macromolecules. Why are the four reasons for this?

A
  1. they carry out most catalytic activities 2. they have chemically reactive functional groups 3. they are very structurally and functionally diverse 4. most of a cell’s functions are mediated by proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the 9 main functions of proteins?

A

Catalytic reactions of enzymes, structural support, movement, regulation, transport, hormones (metabolic control), receptors & signaling, storage of amino acids, defense (antibodies)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is a.a

A

Amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is another word for amino acid

A

residue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is another word for protein

A

polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are R groups

A

Amino acid side chains that determine the properties of amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is a Dalton

A

Molecular weight, unti of mass: MW of a.a = 110g/mol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Define conformation

A

Spatial arrangement of atoms in a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Define Native (gibbs)

A

Lowest energy state of a protein (lowest Gibbs free energy)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the main function of amino acids?

A

Build proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What makes up an amino acid?

A

Hydrogen in the back attached to a central alpha carbon, from which an R-group is attached, as well as an amino and an acid - carboxylate at pH 7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Define enantiomers

A

Mirror images of each other, can’t be superimposed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Define Levrorotatory

A

L isomer, with amino on its left, carboxyl to the right and hydrogen in the back

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Define Dextrorotatory

A

D isomer, with amino on the right, carboxyl on the left, hydrogen in the back

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How can you use CORN to determine if an amino acid is L or D?

A

Leaving the hydrogen in the back, spell out CO-R-N (carboxyl - r group - amino.) Depending on your direction, means L or D. Left goes counter clockwise, D is clockwise.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Ribosomes can only use certain types of isomers. Which are these?

A

L-Isomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Can D-Isomers be used?

A

Yes - just not in humans. Bacteria have them in their shells to protect from host mechanisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How can you determine if an amino acid is hydrophobic or hydrophilic?

A

Hydrophobic amino acids will NOT have ANY charges, no O, OH, SH, or NH2 in their side chains.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

In hydrophilic amino acids, how can you determine if they are uncharged or charged?

A

Every hydrophilic charged amino acid will have a charge on its r group, while uncharged will not.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What makes amino acids polar or non polar?

A

Non polar amino acids are hydrophobic, polar amino acids are hydrophilic.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What makes an atom chiral?

A

four different groups attached

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the 20 amino acids

A

glycine, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, proline, serine, threonine, tyrosine, asparagine, glutamine, cystine, aspartate, glutamate, lysine, arginine, histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Which amino acid is not chiral, and why? Can it have L and D isomers?

A

Glycine b/c two h - no isomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Name the non-polar, hydrophobic amino acids

A

glycine, alanine, valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Which amino acids are identical in mass? Why is this important to know
isoleucine and leucine - can't tell which is which using mass spectrometry
26
Which non polar hydrophobic aas have aromatic groups?
Phenylalanine and tryptophan
27
Why is proline weird?
Side chain connects to amino group
28
name the polar, hydrophilic uncharged aas
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cystine
29
Which polar, hydrophilic uncharged aas are often modified in post-translational modification?
Serine, Threonine, Tyrosine
30
Why is Cystine so unique?
Putting two cystines next to each other under oxidizing conditions forms an S--S disulphide covalent bond
31
Name the polar, hydrophilic, charged amino acids
Aspartate, glutamate, lysine, arginine, histidine
32
Of the polar, hydrophilic, charged amino acids, which two are acidic?
Aspartate and glutamate
33
Of the polar, hydrophilic, charged amino acids, which three are basic
Lysine, arginine, histidine
34
How are aas linked?
Linked covalently via peptide bonds when the arboxyl and amino groups interact with each other, releasing water
35
What is the half-life of peptide bonds? Are they stable?
V stable, half-life of 7 yrs
36
Which bonds in peptides are covalent?
Disulfide bond
37
What is the primary structure of a protein?
The primary structure of a protein includes all the covalent bonds and is defined by amino acid sequence. It is a linear order of aas based on genetic code and linked by peptide bonds to form a polypeptide (protein)
38
Which direction are proteins built?
N to C terminus
39
How are amino acids linked together to form polypeptides?
Peptide bonds
40
What is the secondary structure of a protein?
The secondary structure is a regular repeated arrangement of adjacent aas; patterns of H-bonds between peptide N-H and C=O residues that are near each other in a linear sequence
41
How do secondary protein structures interact with each other? What are they bonded and stabilized by?
They are bonded and stabilized by H-bonds through interactions between different side chains.
42
What are the two different formations of secondary protein structures?
Alpha helix and beta sheet
43
How is an alpha helix secondary structure formed?
Every four residues in a linear stretch, a H-bond is formed.
44
How are the R-groups represented in an alpha helix?
They project outwards from the alpha helix.
45
Alpha helixes are amphipathic/amphiphilic. This means half of them loves water, have of them hates water. How does this happen?
Alpha helixes are two chains in a linear stretch. Protein side chains stick out, and depending on which side group they are, can be hydrophobic or hydrophilic. This leads to half and half.
46
What do beta sheets look like?
They are flat, linear structures that interact with a second stand besides them. Side chains stick out of the flat edge (above and below the plane).
47
beta sheets can be parallel or antiparallel. What is an antiparallel beta sheet?
An antiparallel beta sheet turns back on itself, with its arrows pointing in opposite directions.
48
beta sheets can be parallel or antiparallel. What is an parallel beta sheet?
A parallel beta sheet curls in on itself, with its arrows pointing the same direction.
49
What direction do you draw arrows on a beta sheet?
Always towards c-terminus
50
Beta sheets run in an up-down sequence. Can they be amphipathic? If yes, how?
Yes they can, if all one side pointing up is one hydrophobic and the other pointing down is hydrophilic or vice versa.
51
What is the tertiary structure of a protein?
Tertiary proteins have a spatial relationship among all aas in polypeptides, forming one final folded protein.
52
How are tertiary proteins formed?
Secondary structures group together in a specific way to make them, bending and folding into a 3D shape that can be alterable by environmental changes.
53
How are tertiary proteins stabilized?
By weak bonds.
54
Who was Jane Richardson?
Came up with the spiral ribbon model
55
What is the quaternary structure of a protein?
A protein made up of several polypeptide chains, many interacting structurally.
56
How many proteins make up a protein domain
One polypeptide/one protein strand
57
What are kinase domains?
They add phosphates to the substrate
58
What to Hck and VEGFR2 domains phosphorylate
tyrosines
59
What do p110y domains phosphorylate
lipids
60
Do Hck and VEGFR2 phosphorylate tyrosines the same way?
No
61
How do Hck domains phosphorylate tyrosine?
Hck binds to the substrate within the cell and triggers tyrosine phosphorylation
62
How to VEGFR2 domains phosphorylate tyrosine?
VEGFR2 is located on the outside of the cell and binds to signaling molecules, triggering the phosphorylation of tyrosine inside the cell
63
Protein evolution takes a very long time. What is the benefit of domains for this?
Domains allow the evolution of complex systems in a relatively shot time frame.
64
What is Anfinsen's dogma?
All the info needed to determine the 3D structure of a protein is in the primary structure
65
How did Anfinsen come to the conclusion that proteins fold simultaneously based on the primary sequence? Describe his experiment.
First, he isolated and purified a protein called RNaspA by added urea and BME to denature the protein. Next, he put it into dialysys tubing and into a buffer solution, which allowed the BME and urea to leave over time but not the RNaspA. Over time, the RNaspA refolded itself, leaving purified renatured proteins.
66
How does urea denature proteins?
It is very good a H-bonding
67
How does BME denature proteins?
breaking disulfide bonds
68
What is Anfinsen's thermodynamic hypothesis?
The 3D structure of a native protein is when its free energy is at its lowest.
69
Is there only one way for a protein to fold
No, but they all come to the same result
70
If a protein's native form is its most stable, why don't proteins fold into their native form on their own?
Cells are messy, there are a lot of other molecules around, proteins get distracted. Hydrophobic residues start to stick to all other hydrophobic regions of the cell.
71
How do proteins fold into their native forms?
Via a certain type of enzyme called chaperones
72
What are chaperones?
A type of enzyme also called heat shock proteins that, like catalysts, allow proteins to fold more quickly before other molecules can interfere. They require the input of energy and cannot happen on their own.
73
How are old, damaged, aggregated proteins disposed of?
They use a tagging system: ubiquitin binds to a damaged protein, which tells proteasomes the protein is ready for destruction.
74
What is ubiquitin?
Ubiquitin is a tag that is added to a damaged protein to inform proteasomes that the protein is ready for destruction.
75
Does ubiquitin have any enzymatic activitiy?
No
76
How does ubiquitin bind to the damaged protein?
Ubiquitin carboxyl group forms isopeptide bonds with the side chains of lysine
77
What is a proteosome?
System for destroying damaged proteins
78
How do humans take up all 20 amino acids if we cannot make all of them?
Taken up in diet
79
What is whey and what is it used for
Whey is milk protein that is the waste product of making cheese, used in protein powder for amino acids
80
What are vitamins
Enzyme co factors
81
Why do our bodies need vitamins
Cannot produce all the vitamins required, many proteins require additional functional groups and enzymes can require metals.
82
What is the role of Vitamin K?
Vitamin K permits blood clotting, modifes proteins in the target wound area
83
What would happen to a cut if we didn't have vitamin K
Wound healing wouldn't occur properly
BIOL 225
flashcards
Decks in class (9)
# Cards
Brainscape helps you reach your goals faster, through stronger study habits.
© 2026 Bold Learning Solutions. Terms and Conditions