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Biochemistry > Midterm biochem review study guide > Flashcards

Midterm biochem review study guide Flashcards

1
Q

Which amino acids are positively charged (basic) and negatively charged (acidic)?

A

Positively charged: Histidine, Lysine, Arginine
Negatively charged: Aspartic Acid (D) , Glutamic Acid(E)

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2
Q

Which amino acids are hydrophobic?

A

GLAM VIP FW

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3
Q

Which amino acids can be phosphorylated?

A

Serine, Threonine, Tyrosine (OH group on side chain)

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4
Q

Which amino acids have aromatic side chains

A

Phenalanine, Tyrosine, Tryptophan

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5
Q

Which amino acids have S on them

A

Cystine, methionine

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6
Q

Which molecules have a nitrogen ring

A

Proline, Histidine

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7
Q

Which amino acid can form a covalent link with another of the same amino acid

A

Cysteine (S-S bond disulfide). Tertiary structure form

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8
Q

Which amino acid has the smallest side chain

A

Glycine (Just a H)

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9
Q

What is unique about histidine’s side chain compared with the other 4 charged amino acids?

A

Histidine has a charge of 6.04 which is uncharged at 7.4 (physiological ph)
Lysine and Arginine are positively charged at 7.4 because their pKa is above 7.4
Aspartic and glutamic acid are negatively charged at 7.4 bc their pKa is below it

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10
Q

Why are vanderwall interactions stronger in water and not in air

A

In water, hydrophobic interactions are strong because water is polar
in air, there is not a polar medium for the molecules to be pressured on.

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11
Q

3 types of secondary structures

A

A helix, B sheet, turns and loops

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12
Q

What types of interactions are in tertiary structures

A

H bonds, hydrophobic interactions, salt bridges, disulfide bonds

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13
Q

What is a leucine zipper

A

a coiled coil (2 alpha helices that interact because leucine repeats ever 7 residues, they pack to the center since they are nonpolar) Leucines are all on the inside of the zipper bc nonpolar and hydrophobic
Type of a tertiary structure

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14
Q

Describe the cytoplasm environment

A

polar environment, globular proteins are hydrophillic on the outside and hydrophobic on the inside
Membrane is made of lipids- nonpolar (Hydrophobic outside, hydrophibllic inside)

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15
Q

Which amino acids are found in the transmembrane domain?

A

Nonpolar amino acids- GLAM VIP FW

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16
Q

What are some charachteristics of alpha keratin

A

Leucine zipper- coiled coil, cytoskeleton, muscle proteins, heptad repeats, strong and flexible

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17
Q

What are some distinguisihing characteristics of collagen

A

short repeating heptatd sequences, triple coil

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18
Q

What do myoglobin and hemoglobin have in common

A

Myoglobin and hemoglobin both have iron that holds onto oxygen for transport

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19
Q

What are hemoglobin and myoglibin’s structures

A

Myoglobin is a monomer, hemoglobin is a tetramer

20
Q

How do the quaternary structures influence the ability for oxygen to bind in myoglobin and hemoglobin

A

Myoglobin is a monomer and binds to oxygen non cooperatively (releases oxygen when levels are low)
Hemoglobin is a tetromer and binds to oxygen cooperatively, and it has a T/R state with high or low oxygen binding (sigmoidal binding)

21
Q

What is a hyperbolic binder

A

Myoglobin (Binds to oxygen until concentration is 0, then releases)

22
Q

How many oxygens bind to myoglobin vs hemoglobin

A

myoglobin- 1
hemoglobin- 4

23
Q

Which salt bridge is sensitive to the pH change between the lungs and tissues

A

the histidine and aspartic acid salt bridg. histidine is sensitive to pH changes, and when deprotonated, won’t form salt bridges

24
Q

Which amino acid residue enables salt bridge formation when pH drops

A

histidine protonation

25
Q

Why is the pH lower at the surface of tissues compared w the lungs

A

the lungs generate CO2 which is an acid, donating H into blood

26
Q

What stabilizes the T state of hemoglobin

A

2,3, BPG
salt bridges between histidine and aspartic acid

27
Q

Is sickle cell hemoglobin more or less soluble

A

less- protein aggregation makes proteins less soluble

28
Q

What do enzymes change

A

ONLY the kinetics of a reaction- make more product over time by lowering activation energy

29
Q

What is the Km

A

The amount of substrate needed for catalysis

30
Q

What is V max for a reaction

A

the rate of product formation (number of substrate converted into product when fully saturated)

31
Q

Equation for slope

A

Km/Vmax

32
Q

Equation for X intersept

A

-1/km

33
Q

equation for Y intersept

A

1/V max

34
Q

What type of reaction do proteases use

A

nucleophillic substitutions

35
Q

What does a protease have on its active site

A

a nucleophile

36
Q

What amino acid does chymotrypsin recognize

A

large, nonpolar, bulkey side chains
Alanine, Leucine, Methionine, Valine (GLAM VIP FW)

37
Q

What amino acids does trypsin recognize

A

Lysine and arganine

38
Q

Why are trypsin and chemotrypsin serine proteases

A

they use serine at their active site to cleave

39
Q
A

Competitive inhibition

40
Q
A

Uncompetitive inhibition

41
Q
A

noncompetitive inhibition

42
Q

Why is competitive inhibition the only inhibition that can be reversed by increasing substrate concentration

A

the substrate can increase to the point that it out competes the competitor because of its concentration

43
Q

What is the charge on the amide group of an amino acid at physiological pH?

A

Positive (protonated)

44
Q

What is the charge on the carboxyl group of an amino acid at physiological pH?

A

negative (deprotonated)

45
Q

Are you protonated or deprotonated in an acidic environment

A

protonated

46
Q

are you protonated or deprotonated in a basic environment

A

deprotonated

Biochemistry (7 decks)

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