Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochem > Quiz 3: Lecture/Reading Info > Flashcards

Quiz 3: Lecture/Reading Info Flashcards

1
Q

Fibrinogen protein

A

Fibrinogen floats around our blood inactively

Thrombin has to cut fibrinogen to make fibrin

Fibrin interacts with other fibrin molecules to form long complexes

These long complexes catch platlettes and form blood clots

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

Warfarin

A

blood thinner to stop clots

does this by stopping thrombin from cutting fibrinogen

therefore, there is no fibrin

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

Hydropathy index

A

the more positive, the more hydrophobic the molecule is

the less positive, the less hydrophobic the molecule is

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

The Isoelectric point

A

the point at which a molecule has a net charge of zero

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

What happens at pH below the isoelectric point?

A

the molecule has a positive charge

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

What happens at pH above the isoelectric point?

A

the molecule has a negative charge

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

What happens to proteins at their pI point?

A

they may be insoluble due to the lack of charge

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

Cysteine and the disulfide bridge

A

Cysteine can ionize and this negatively charged sulfur will interact with another cysteine to form a disulfide bridge

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

Cysteine reduced form

A

Is not in a disulfide bridge and has negative charge on separate cysteines

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

Cysteine oxidized form

A

Is in disulfide bridge which removes the negative charge/electrons

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

Are disulfide bonds normally found in intracellular proteins?

A

the cytosol is a reducing environment, so disulfide bridges are often broken down within the cell and not found there

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

Proline

A

R side chain attaches itself to the amino group

Has a constricted ring like structure

Ability to break secondary structures

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

What is peptide bond formation catalyzed by?

A

ribosomes

ribosomes bring amino acids together and make a polypeptide sequence

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

How are amino acid residues different from amino acids?

A

Amino acid residues are found within the polypeptide and this can modify them chemically

they have lost a water molecule through dehydration synthesis when being added to the polypeptide

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

what molecular weight do we use for amino acids?

A

110 g/mol

can divide total weight of protein by 110 to figure out roughly how many amino acids are in the protein

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

Peptide bond rigidity

A

The C=O and the N-H in the peptide have some resonance

This makes the peptide bond have double bond like qualities and is rigid / planar

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

Type I B-turn

A

proline used to add a kink

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

Type II B-turn

A

glycine used since it doesn’t have a R-group and is easier to turn

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

Are there only 20 amino acids?

A

No! There are many more less common ones

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

What type of stereoisomers are L and D configurations?

A

they are enantiomers

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

What stereochemistry do biological amino acids have?

A

exclusively the L conformation

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

What are aromatic side chains?

A

relatively nonpolar

however, tryptophan and tyrosine are slightly more polar due to their nitrogen and hydroxyl group respectively

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

What wavelength do proteins absorb light at?

A

280 nm

use this in lab

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

Cysteine is what type of molecule

A

a weak acid due to it’s ability to make weak hydrogen bonds with oxygen or nitrogen

sulfhydryl group is quite modestly polar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the only amino acid with a pKa near neutral?

A

histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

y-carboxyglutamate

A

occurs from carboxylation of glutamic acid

this transition from GLU to GLA is essential for the functioning of thrombin and warfarin prevents this transformation from occuring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Zwitterion

A

amino acids that can act as either an acid or a base

amphoteric

normally, have a positive amino group and a negative carboxyl group and a non-ionizable R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

positive electrode

A

called the anode

at pH greater than pI, the amino acid will be negatively charged and migrate towards the positive anode

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

negative electrode

A

the cathode

at pH less than pI, the amino acid will be positively charged and migrate towards the negative cathode

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

peptide bond textbook definition

A

two amino acid molecules can be covalently joined through a substituted amide linkage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

How does peptide bond happen even though thermondynamically unfavorable?

A

the carboxyl group must be chemically activated or modified so that the hydroxyl group is more easily eliminated in dehydration synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Why does hydrolysis of peptide bond not occur even though energetically favorable?

A

the activation energy barrier is too high

kinetically unfavored

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

simple proteins

A

contain only amino acid residues and no other chemical constituents

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

conjugated proteins

A

contain permanently associated chemical components other than amino acids

this other components are known as prosthetic group

ex: lipoproteins have lipids, glycoproteins have sugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Edman degradation

A

labels and removes only the amino-terminal residue from a peptide, leaving all other peptides in tact

36
Q

proteases

A

catalyze the hydrolytic cleavage of peptide bonds

can be down in a predictable and controllable way

37
Q

conformation

A

the spatial arrangement of atoms in a protein or any part of a protein

conformations that naturally occur are normally the most thermodynamically stable

38
Q

native proteins

A

functional, folded conformation

39
Q

stability

A

the tendency to maintain a native conformation of proteins

40
Q

How do proteins fold energetically?

A

most of the free energy is derived from weak interactions within a protein and the increased entropy in the surrounding aqueous solution

41
Q

Are there normally lots of unpaired hydrogen-bonding and ionic groups?

A

No! These are highly destabilizing

Proteins maximize hydrogen bonds and ionic interactions

42
Q

Phi angle

A

between the N-Ca bond

43
Q

Psi angle

A

between the Ca-Carbonyl bond

44
Q

What values can phi and psi be?

A

anything between -180 and +180

45
Q

secondary structure

A

refers to any chosen segment of a polypeptide chain and describes the local spatial arrangement of its main chain atoms

46
Q

Most prominent secondary structures?

A

a-helicies, b-turn, and b-conformations

47
Q

A-helix

A

the simplest arrangement the polypeptide chain can assume that maximizes the use of internal hydrogen bonding

48
Q

Where are the R-groups in A-helix?

A

they protrude outwards from the backbone

49
Q

Why does the a-helix occur so frequently (roughly 25% of all amino acid residues)?

A

it maximizes the amount of hydrogen bonding

50
Q

Hydrogen bonds in A-helix?

A

occur between the hydrogen atom attached to the electronegative nitrogen atom and the electronegative carbonyl oxygen atom on every fourth amino acid

51
Q

Amino acid with greatest tendency to form alpha helix

A

Alanine

52
Q

Why do long strains of Glu not make an alpha helix?

A

the negative charged carboxyl groups repel each other

this is the same with positively charged R-groups

53
Q

Why does Gly not make an alpha helix?

A

too much flexibility

54
Q

Why does Pro not make an alpha helix?

A

introduces a kink in the helix

55
Q

B sheet

A

more of a zig zag structure than the alpha helix

56
Q

where are beta turns normally found?

A

near the surface of the protein since the turn needs hydrogen bonds from the aqueous environment to stabilize it

57
Q

Where is B sheet and A helix in a Ramachandran plot?

A

B sheet is above near the +120-180

A helix is below near the 0- -60

58
Q

Ion exchange chromatography

A

exploits differences in the sign and magnitude of the net electric charge

for example, in cation exchange chromatography, the solid matrix has negatively charged groups, so proteins with more positive charge take longer to migrate

59
Q

Size exclusion chromatography

A

separates proteins according to size

large proteins emerge quicker than smaller proteins

60
Q

Why do large proteins emerge quicker than smaller proteins in the size exlcusion chromatography?

A

the smaller proteins get stuck in little pores in the matrix that the larger proteins cannot

61
Q

Affinity chromatography

A

based on the binding affinity

the beads in the column have a covalently attached ligand and proteins with an affinity for this ligand bind to the beads

62
Q

Sodiym dodecyl sulfate (SDS)

A

SDS binds to amino acids and gives them a negative charge and similar rod-like shape

Since amino acids now have a similar charge:mass ratio and shape, electrophoresis separates them strictly by size

63
Q

Catalytic effect of enzyme

A

the increase in the rate at which substrate is converted to reaction products when the enzyme is present

64
Q

activity

A

the total units of enzyme in a solution

65
Q

specific activity

A

the number of enzyme units per miligram of total protein

increases during purification

66
Q

A-Helix dipole

A

Tend to have more a negative charge near the carboxyl group and a positive charge near the amino group (this creates a dipole)

therefore, to stabilize want negatively charged amino acids near the positive amino end and want positively charged amino acids near the negative carboxyl end

67
Q

Difference between cystine and cysteine?

A

Cystine is when 2 cysteine molecules are in a disulfide bridge

68
Q

How can you measure UV light absorption?

A

with aromatic rings

69
Q

When can amino acids without ionizable R groups act as zwitterions?

A

in neutral conditions

will have +NH3 and -COO

70
Q

When looking at a titration curve of an amino acid how do you know if it has an ionizable R group?

A

There are 3 buffering regions

71
Q

Hydrogen bonds in alpha helix

A

are roughly parallel to the backbone axis

72
Q

Why are antiparallel B sheets more stable than parallel B sheets?

A

antiparallel B sheets can line hydrogen bonds up more directly and therefore, have stronger H-bonds

73
Q

Right handed alpha helix

A

Goes in clockwise spiral

74
Q

What does a buffer zone between 2-3 indicate on a titration curve?

A

the carboxyl group is ionizing

75
Q

What does a buffer zone between 9-10 indicate on a titration curve?

A

the amino group is ionizing

76
Q

Gel filtration column

A

another name for size exclusion chromatography

77
Q

The first protein to elute from the gel filtration column will be the ____ protein in an SDS page

A

slowest since it is the largest

78
Q

How would you isolate a molecule of interest from cation-exchange chromatography?

A

in this case, we want the cations

cations are currently attached to negatively charged beads

so we raise the pH above the pI

Now the cations will be more negative and elute

79
Q

Intramolecular

A

within the molecule

A-helicies have intramolecular bonds

80
Q

Intermolecular

A

between the molecule

B-pleated sheets have intermolecular bonds

81
Q

What is a problem with Edman degradation?

A

5% does not react

We will have 95% of the protein of interest and 5% of the protein before it

This builds up overtime

Can only use Edman degradation for small proteins

82
Q

CORN rule

A

counterclockise = L

clockwise = D

make sure H group is in the back

83
Q

R versus S configuration

A

counterclockwise = S

clocwise =R

84
Q

Heterodimer with no cysteines on the SDS-page

A

Will see 2 bands on the gel

85
Q

Homodimer with no cysteines on the SDS-page

A

1 band on the gel

86
Q

Multimeric protein made of 3 differently sized polypeptides, 2 of which are connected by disulfide bonds?

A

See 2 bands on the gel

Had 3 peptides, but 2 are now connected as 1. So have a total of 2 separate bands on the page

Biochem (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions