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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

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2
Q

Warfarin

A

blood thinner to stop clots

does this by stopping thrombin from cutting fibrinogen

therefore, there is no fibrin

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3
Q

Hydropathy index

A

the more positive, the more hydrophobic the molecule is

the less positive, the less hydrophobic the molecule is

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4
Q

The Isoelectric point

A

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

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5
Q

What happens at pH below the isoelectric point?

A

the molecule has a positive charge

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6
Q

What happens at pH above the isoelectric point?

A

the molecule has a negative charge

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7
Q

What happens to proteins at their pI point?

A

they may be insoluble due to the lack of charge

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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

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9
Q

Cysteine reduced form

A

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

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10
Q

Cysteine oxidized form

A

Is in disulfide bridge which removes the negative charge/electrons

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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

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12
Q

Proline

A

R side chain attaches itself to the amino group

Has a constricted ring like structure

Ability to break secondary structures

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13
Q

What is peptide bond formation catalyzed by?

A

ribosomes

ribosomes bring amino acids together and make a polypeptide sequence

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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

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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

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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

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17
Q

Type I B-turn

A

proline used to add a kink

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18
Q

Type II B-turn

A

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

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19
Q

Are there only 20 amino acids?

A

No! There are many more less common ones

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20
Q

What type of stereoisomers are L and D configurations?

A

they are enantiomers

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21
Q

What stereochemistry do biological amino acids have?

A

exclusively the L conformation

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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

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23
Q

What wavelength do proteins absorb light at?

A

280 nm

use this in lab

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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

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25
What is the only amino acid with a pKa near neutral?
histidine
26
y-carboxyglutamate
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
27
Zwitterion
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
28
positive electrode
called the anode at pH greater than pI, the amino acid will be negatively charged and migrate towards the positive anode
29
negative electrode
the cathode at pH less than pI, the amino acid will be positively charged and migrate towards the negative cathode
30
peptide bond textbook definition
two amino acid molecules can be covalently joined through a substituted amide linkage
31
How does peptide bond happen even though thermondynamically unfavorable?
the carboxyl group must be chemically activated or modified so that the hydroxyl group is more easily eliminated in dehydration synthesis
32
Why does hydrolysis of peptide bond not occur even though energetically favorable?
the activation energy barrier is too high kinetically unfavored
33
simple proteins
contain only amino acid residues and no other chemical constituents
34
conjugated proteins
contain permanently associated chemical components other than amino acids this other components are known as prosthetic group ex: lipoproteins have lipids, glycoproteins have sugar
35
Edman degradation
labels and removes only the amino-terminal residue from a peptide, leaving all other peptides in tact
36
proteases
catalyze the hydrolytic cleavage of peptide bonds can be down in a predictable and controllable way
37
conformation
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
native proteins
functional, folded conformation
39
stability
the tendency to maintain a native conformation of proteins
40
How do proteins fold energetically?
most of the free energy is derived from weak interactions within a protein and the increased entropy in the surrounding aqueous solution
41
Are there normally lots of unpaired hydrogen-bonding and ionic groups?
No! These are highly destabilizing Proteins maximize hydrogen bonds and ionic interactions
42
Phi angle
between the N-Ca bond
43
Psi angle
between the Ca-Carbonyl bond
44
What values can phi and psi be?
anything between -180 and +180
45
secondary structure
refers to any chosen segment of a polypeptide chain and describes the local spatial arrangement of its main chain atoms
46
Most prominent secondary structures?
a-helicies, b-turn, and b-conformations
47
A-helix
the simplest arrangement the polypeptide chain can assume that maximizes the use of internal hydrogen bonding
48
Where are the R-groups in A-helix?
they protrude outwards from the backbone
49
Why does the a-helix occur so frequently (roughly 25% of all amino acid residues)?
it maximizes the amount of hydrogen bonding
50
Hydrogen bonds in A-helix?
occur between the hydrogen atom attached to the electronegative nitrogen atom and the electronegative carbonyl oxygen atom on every fourth amino acid
51
Amino acid with greatest tendency to form alpha helix
Alanine
52
Why do long strains of Glu not make an alpha helix?
the negative charged carboxyl groups repel each other this is the same with positively charged R-groups
53
Why does Gly not make an alpha helix?
too much flexibility
54
Why does Pro not make an alpha helix?
introduces a kink in the helix
55
B sheet
more of a zig zag structure than the alpha helix
56
where are beta turns normally found?
near the surface of the protein since the turn needs hydrogen bonds from the aqueous environment to stabilize it
57
Where is B sheet and A helix in a Ramachandran plot?
B sheet is above near the +120-180 A helix is below near the 0- -60
58
Ion exchange chromatography
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
Size exclusion chromatography
separates proteins according to size large proteins emerge quicker than smaller proteins
60
Why do large proteins emerge quicker than smaller proteins in the size exlcusion chromatography?
the smaller proteins get stuck in little pores in the matrix that the larger proteins cannot
61
Affinity chromatography
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
Sodiym dodecyl sulfate (SDS)
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
Catalytic effect of enzyme
the increase in the rate at which substrate is converted to reaction products when the enzyme is present
64
activity
the total units of enzyme in a solution
65
specific activity
the number of enzyme units per miligram of total protein increases during purification
66
A-Helix dipole
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
Difference between cystine and cysteine?
Cystine is when 2 cysteine molecules are in a disulfide bridge
68
How can you measure UV light absorption?
with aromatic rings
69
When can amino acids without ionizable R groups act as zwitterions?
in neutral conditions will have +NH3 and -COO
70
When looking at a titration curve of an amino acid how do you know if it has an ionizable R group?
There are 3 buffering regions
71
Hydrogen bonds in alpha helix
are roughly parallel to the backbone axis
72
Why are antiparallel B sheets more stable than parallel B sheets?
antiparallel B sheets can line hydrogen bonds up more directly and therefore, have stronger H-bonds
73
Right handed alpha helix
Goes in clockwise spiral
74
What does a buffer zone between 2-3 indicate on a titration curve?
the carboxyl group is ionizing
75
What does a buffer zone between 9-10 indicate on a titration curve?
the amino group is ionizing
76
Gel filtration column
another name for size exclusion chromatography
77
The first protein to elute from the gel filtration column will be the ____ protein in an SDS page
slowest since it is the largest
78
How would you isolate a molecule of interest from cation-exchange chromatography?
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
Intramolecular
within the molecule A-helicies have intramolecular bonds
80
Intermolecular
between the molecule B-pleated sheets have intermolecular bonds
81
What is a problem with Edman degradation?
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
CORN rule
counterclockise = L clockwise = D make sure H group is in the back
83
R versus S configuration
counterclockwise = S | clocwise =R
84
Heterodimer with no cysteines on the SDS-page
Will see 2 bands on the gel
85
Homodimer with no cysteines on the SDS-page
1 band on the gel
86
Multimeric protein made of 3 differently sized polypeptides, 2 of which are connected by disulfide bonds?
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)

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