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Biochem Final Exam (Ahn) > MCAT information > Flashcards

MCAT information Flashcards

1
Q

all amino acids have what terminus

A

All amino acids have a N-terminus and a C-terminus

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2
Q

peptide bonds and what direction are they formed in?

A

Peptide bonds are dehydration reactions (and produce water and the chain of amino acids) and are formed in the N-C direction
The resulting covalent bond is called an amide bond
cysteine can form additional covalent bonds (aka disulfide bridge)

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3
Q

what determines an amino acid’s properties?

A

their R-group side chain

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4
Q

what are 3 side chain properties?

A

aromatic
aliphatic
charged

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5
Q

aromatic side chain property definition and 2 examples

A

aromatic compounds: organic compounds that have a cyclic structure with alternating single and double bonds (aka conjugated double bonds)
- aromatic compounds are often more stable than aliphatic compounds

ie. phenylalanine, tryptophan

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6
Q

aliphatic side chain property definition and 2 examples

A

aliphatic: organic compounds that do NOT contain aromatic rings and instead consists of carbon chains or branched structures
- can be saturated (alkanes) or unsaturated (alkenes, alkynes)

ie. valine, leucine

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7
Q

charged side chain property

A

has either a positive or negative charge (result of an unequal number of protons and electrons)

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8
Q

what are the components of a general amino acid?

A

amino group (NH2)
carboxyl group (COOH)
R group side chain
alpha carbon (aka central carbon)
hydrogen atom (H): a single hydrogen atom bonded to the central carbon)

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9
Q

Amino acid sequences are listed in what direction?

A

Amino acid sequences are listed in the N-terminus to the C-terminus direction

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10
Q

Kinases

A

the enzymes that transfers phosphate groups onto amino acids (addition of phosphate groups PO4 3-)

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11
Q

what type of amino acids can MIMIC phosphorylation?

A

Amino acids with a net negative charge can MIMIC phosphorylation

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12
Q

any amino acid with ____ can be phosphorylated

A

Any amino acid with an R-group possessing a hydroxyl OH group can be phosphorylated

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13
Q

The phosphate groups on phosphorylated proteins/amino acids are negatively or positively charged?

A

The phosphate groups on phosphorylated proteins/amino acids are negatively charged

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14
Q

relation between any R group being charged and the entire amino acid?

A

Any R-group with a net charge will give the amino acid a net charge

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15
Q

3 examples of positively charged amino acids

A

Arginine (R), Lysine (K), and Histidine (H)

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16
Q

2 examples of negatively charged amino acids

A

Glutamate (E) and Aspartate (D)

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17
Q

5 examples of hydrophobic amino acids

A

A, I, L V, F

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18
Q

7 examples of hydrophilic amino acids

A

H, R, K, D, E, N, Q

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19
Q

what type of side chains do hydrophobic amino acids have?

A

nonpolar, long alkyl side chains

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20
Q

what type of side chains do hydrophilic amino acids have?

A

polar, charged side chains

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21
Q

where are hydrophobic regions/residues found in the protein’s structure?

A

Hydrophobic residues will be found in the protein’s INTERIOR since this conformation is entropically favorable

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22
Q

secondary structure consists of what?

A

Consists of alpha-helices and beta-pleated sheets stabilized by hydrogen bonds between amides

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23
Q

which 2 amino acids can disrupt a protein’s secondary structure of alpha helices and beta-pleated sheets?

A

Proline (P) can disrupt these structures due to its sterically hindered ring Gly (G) due to its very small methyl R group that allows for increased flexibility

P and G are usually found at ends of alpha-helices or within creases of beta-pleated sheets

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24
Q

how is tertiary structure formed and what breaks tertiary structure?

A

Tertiary structure is formed by side chain interactions: salt bridges, disulfide bonds, and hydrogen bonds

Denaturation breaks tertiary structure

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25
Q

3 types of side chain interactions

A

salt bridges (a noncovalent interaction between 2 OPPOSITELY charged chemical groups/atoms that combines hydrogen bonding and ionic bonding
disulfide bonds
hydrogen bonds

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26
Q

disulfide bonds

A

a type of side chain interactions (COVALENT BOND) and are formed by oxidation of the thiol (SH) side chains of 2 cysteine (C) residues
aka cystines

2Cysteine(–SH) –(oxidation) –> Cystine(–S–S–) + 2H+ + 2e-

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27
Q

Quaternary structure consists of what?

A

Quaternary structure consists of multiple subunits or polypeptides sometimes with a prosthetic groupe (ie. heme in hemoglobin)

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28
Q

isoelectric focusing

A

a lab technique used to separate proteins based on their isoelectric point (pI) - the pH at which a molecule has no net electric charge (aka the number of positively charged groups = number of negatively charged groups)

a protein is applied to the gel that contains a continuous pH gradient and the protein will migrate through the pH gradient due to an electric field until it finds its isoelectric point where the molecule has no net charge (aka reach the point where their pH = pI)
- At pH values below its pI, the molecule has a positive charge and moves toward the negative electrode
- At pH values above its pI, the molecule has a negative charge and moves toward the positive electrode
- At its isoelectric point (pI), the molecule has no net charge and will stop migrating because it is no longer influenced by the electric field

Basic amino acids (RKH) have a higher pI; acidic amino acids (ED) have a lower pI

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29
Q

isoelectric point (pI)

A

pI: average of all pKa values of functional groups
also the pH at which a molecule has no net electric charge (aka the number of positively charged groups = number of negatively charged groups) ==> aka zwitterion

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30
Q

basic amino acids have higher or lower pI; acidic amino acids have higher or lower pI

A

Basic amino acids (RKH) have a higher pI; acidic amino acids (ED) have a lower pI

31
Q

SDS page: what does SDS stand for and PAGE stand for?

A

SDS page: a lab technique to separate proteins based on their MOLECULAR WEIGHT only (shape does not matter)

PAGE stands for polyacrylamide gel electrophoresis: essentially a spongy network that blocks protein fragments based on SIZE and CHARGE

SDS stands for sodium dodecyl sulfate: a chemical that essentially coats everything with a NEGATIVE charge and DENATURES proteins
→ once a protein is denatured, their movement through the gel is not affected by their SHAPE and now only depends on their MASS

32
Q

what does a reducing agent do in SDS page?

A

A reducing agent (ie. tBME) adds hydrogens (to the protein)
- results in the reduction of disulfide bonds (S-S) which results in SH and HS → efficiently breaks the disulfide bond

33
Q

what are the 3 types of SDS page?

A

native page
nonreducing SDS page
reducing SDS page

34
Q

native page

A

no SDS, no reducing agent
→ protein is not denatured & the disulfide bond S-S remains → protein will stay together and the movement of proteins through the polyacrylamide gel depends on both their size and shape → will see one single band

35
Q

nonreducing SDS page

A

yes SDS, no reducing agent
–> coats everything with a negative charge and disrupts the electrostatic interactions → the 50kDa component is no longer attached to the protein → will see two separate bands in the gel

36
Q

what does SDS do to the protein?
what does the reducing agent do to the protein?

A

SDS breaks up the electrostatic interactions of the protein since it coats everything with a negative charge

reducing agent breaks the covalent disulfide bond (S-S)

37
Q

reducing SDS page

A

yes SDS, yes reducing agent
→ everything is coated with a negative charge and there’s a reducing agent → electrostatic interactions and S-S bond are disrupted → protein separates into 3 different components → will see 3 separate bands in the gel

Allows researchers to determine how many SUBUNITS there are in a protein and what their connections are

38
Q

blotting technique mnemonic SNOW DROP

A

Southern blot detects DNA
Northern blot detects RNA
O stands for nothing
Western blot detects proteins

39
Q

what are the 6 types of chromatography?

A

Column chromatography
Size-exclusion chromatography
Ion-exchange chromatography
Affinity chromatography
Gas chromatography
Thin layer chromatography (TLC)

40
Q

chromatography techniques are used for what?

A

A method of separating and identifying proteins of interest from a sample (ie. a mixture of substances)

41
Q

Stationary phase (adsorbent)
Mobile phase (eluent)

A

Stationary phase (adsorbent): the solid medium (that remains fixed in place and provides a medium/surface with which the components of the mixture can interact)
Mobile phase (eluent): the fluid medium (that carries the components of the mixture with it)

42
Q

Retention time
Retention factor (Rf)

A

Retention time: the amount of time a given protein spends on the adsorbent
Retention factor (Rf): the distance moved by the protein / the distance moved by the solvent front

43
Q

relationship between a protein’s affinity for the stationary phase and the speed at which it migrates at in chromatography

A

Proteins with greater affinity for the stationary phase will migrate slower

44
Q

column chromatography

A

separate by polarity (more polar, migrate slower)

45
Q

size-exclusion chromatography

A

separate by size (smaller proteins migrate slower)

46
Q

Ion-exchange chromatography

A

separate by charge (more charged migrate slower)
- subcategories: Cation-exchange & anion-exchange

47
Q

Affinity chromatography

A

separate by affinity (higher affinity migrate slower)

48
Q

Gas chromatography

A

separate by boiling point (higher boiling point migrate slower)

The mobile phase is a gas, NOT a liquid in this case

49
Q

Thin layer chromatography (TLC)

A

glass plate, separate by polarity (usually adsorbent is more polar, but for reverse phase TLC, the eluent is more polar)

The simplest chromatography; the glass plate acts as the stationary phase
–> add a small quantity of sample to the stationary phase and then observe upon the addition of the mobile phase how fast does the sample migrate along the stationary phase

50
Q

we can analyze what 4 things about a protein?

A

We can analyze protein structure, activity, amino acid composition, and concentration

51
Q

what do we use to analyze a protein’s structure?

A

NMR or X-ray crystallography

52
Q

NMR

A

a powerful analytical technique used to determine the structure of molecules, particularly organic compounds
- NMR exploits the magnetic properties of atomic nuclei and their interactions with an external magnetic field to provide detailed information about the chemical environment and arrangement of atoms within a molecule

ie. proton NMR, carbon-13 NMR

53
Q

X-ray crystallography

A

X-ray crystallography: crystallize protein → irradiate with X-rays to produce diffraction pattern → convert diffraction pattern to electron density map which is interpreted to reveal the molecule’s 3D structure

54
Q

how do we analyze a protein’s activity?

A

monitor a known reaction with a given concentration of substrate and compare to a standard
–> gives a relative measurement of protein activity

55
Q

what do we use to analyze a protein’s amino acid composition?

A

Edman degradation and mass spectrometry if sequence is less than 70 amino acids
otherwise, digest with trypsin or cyanogen bromide first and then run it again

56
Q

Edman degradation

A

a way to remove amino acids from the N-terminus of a protein
→ once they are removed, use mass spectrometry to identify them

57
Q

Mass spectrometry

A

ionize the compound of interest with a high energy electron beam → accelerate these ions to all have the same kinetic energy → deflect them with a magnetic field → these ions hit a detector and different levels of deflection can be converted into a mass spectrum

58
Q

what do we use to analyze a protein’s concentration?

A

UV spectroscopy or colorimetric assay

59
Q

UV spectroscopy

A

shine light onto your sample and vary the wavelength of the light → measure how much light is absorbed at the different wavelengths: more absorption of one sample compared to another sample at the same wavelength ⇒ tells us that sample is more concentrated with the molecule of interest

However, a problem with UV spectroscopy is that it is quite susceptible to sample contamination

60
Q

colorimetric assay

A

uses color changes to measure the concentration of a substance in a sample
–> The assay typically involves a chemical reaction that results in the formation of a colored product, with the intensity of the color being directly related to the concentration of the substance being measured
–> The color change can be detected using a spectrophotometer, which measures the absorbance of light at specific wavelengths

ie. BCA assay, Lowry reagent essay, Bradford protein assay - green dye turns blue after nucleophilic attack by amino acid

61
Q

what is a way to break proteins down so that we can analyze them at a smaller resolution?

A

use hydrolytic agents which cleave peptide bonds via the addition of water

62
Q

3 examples of hydrolytic agents

A

trypsin
chymotrypsin
cyanogen bromide

63
Q

which hydrolytic agents are biologics and which are synthetic compounds: trypsin, chymotrypsin, cyanogen bromide

A

Trypsin and chymotrypsin are biologics; cyanogen bromide is a synthetic compound

64
Q

trypsin cleaves what

A

Trypsin cleaves at C-terminal side of Lys and Arg residues

65
Q

chymotrypsin cleaves what

A

Chymotrypsin cleaves at N-terminal side of Trp, Phe, and Tyr (aromatic residues)

66
Q

cyanogen bromide cleaves what

A

Cyanogen bromide cleaves at C-terminal side of Met

67
Q

michaelis menten kinetics definition and Vmax, Km, Kcat

A

Provides a model for how enzyme reaction rate changes as a function of substrate concentration

Vmax = max velocity of enzyme’s reaction rate
Km = substrate concentration at which the enzyme’s reaction rate is half of its maximum value (Vmax)
- lower Km ==> higher enzyme affinity
Kcat = turnover number (the number of substrate molecules that a single enzyme molecule can convert into product per unit of time when the enzyme is fully saturated with substrate)
- a measure of enzyme’s catalytic efficiency under optimal conditions

Enzyme + substrate –> enzyme-substrate complex –> enzyme + product

68
Q

lineweaver-burke plot: x-axis, y-axis, x-intercept, y-intercept, slope

A

a linearization of MM kinetics plot and can change in the presence of different inhibitors

x-axis: 1/[S]
y-axis: 1/v
x-intercept: -1/Km
y-intercept: 1/Vmax
slope = Km/Vmax

69
Q

michaelis-menten kinetics 4 assumptions

A

assumptions
1. Only measuring initial velocity
2. Concentration of enzyme-substrate complex is constant
3. Substrate concentration is much higher than enzyme concentration
4. Forward reaction rate is much higher than reverse reaction rate

70
Q

3 different types of inhibitors

A

competitive
uncompetitive
noncompetitive

71
Q

competitive inhibitor: Km and Vmax

A

Km increases; Vmax does not change
- the two lines intercept at y-axis on lineweaver-burke plot

72
Q

uncompetitive inhibitor: Km and Vmax

A

Km decreases; Vmax decreases

Uncompetitive inhibitor binds the the enzyme-substrate COMPLEX

73
Q

noncompetitive inhibitor: Km and Vmax

A

Km unaffected; Vmax decreases
Binds to allosteric site on enzyme
- the two lines intercept at x-axis on lineweaver-burke plot

Biochem Final Exam (Ahn) (8 decks)

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