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Biochemistry > Exam Two > Flashcards

Exam Two Flashcards

1
Q

Where does numbering start for peptide bonds?

A

Starts from the amino terminus

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2
Q

What are the functions of peptides?

A

Hormones and pheromones
Neuropeptides
Antibiotics
Protection

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3
Q

What do polypeptides have in addition to amino acids?

A

Cofactors
Coenzymes
Prosthetic groups

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4
Q

What are cofactors?

A

Functional non-amino acid component

Typically metal ions or organic molecules

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5
Q

What are coenzymes?

A

Designate an organic cofactor

NAD+ in lactate dehydrogenase

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6
Q

What are prosthetic groups?

A

Covalently attached cofactors

Heme in myoglobin

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7
Q

What is an inclusion body?

A

Misfolded proteins that do not have a 3D structure

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8
Q

What are the different ways to estimate protein concentration?

A

UV spectroscopy
Bradford assay
BCA assay

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9
Q

What does UV spectroscopy detect?

A

Not very sensitive
Detects aromatic amino acids only
Reads at wavelength of 280nm

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10
Q

What does Bradford Assay detect?

A

Highly sensitive
Will detect any protein present
Depends on types of side chains

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11
Q

What does BCA Assay detect?

A

Highly sensitive
Depends on backbone of protein
Reduces Cu2+ to Cu+ to yield a purple color
Best one

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12
Q

What is the function of ELISA?

A

Allows you to determine if something is present and it’s concentration

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13
Q

What are the steps to ELISA?

A
  1. Immobolize antibody on solid support
  2. Incubate with protein containing surface, if the desired protein is present then it will bind
  3. Add a second antibody that is covalently linked to an assayable enzyme
  4. Wash and assay enzyme.
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14
Q

How can you tell how much of a protein is present with ELISA?

A

Amount of substrate converted to product indicates amount of protein present

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15
Q

How do you separate proteins based on their solubility?

A

Salting out

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16
Q

How do you separate proteins based on their ionic charge?

A

Ion exchange chromatography
Electrophoresis
Isoelectric focusing

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17
Q

How do you separate proteins based on their polarity?

A

Hydrophobic interaction chromatography

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18
Q

How do you separate proteins based on their size?

A

Gel filtration

SDS-PAGE

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19
Q

How do you separate proteins based on their binding specificity?

A

Affinity chromatography

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20
Q

How does salting out work?

A

As the amount of salt is added to a solution, the salt will compete with the dissolved solutes for the solvent, solutes will precipitate based on their solubility, then centrifuge to remove

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21
Q

When are proteins the most soluble?

A

At their isoelectric point

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22
Q

What is a cation exchange column?

A

Column lined with anions

Cations will bind

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23
Q

How do you remove proteins that have bound to a cation exchange column?

A

Proteins can be eluted off by increasing the salt levels

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24
Q

What charge will a protein have if the pH is higher than it’s PI?

A

The protein will be negatively charged

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25
Q

How does gel filtration work?

A

Two proteins are added to a column full of beads, the larger beads will travel through quicker and will come out first

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26
Q

How does affinity chromatography work?

A

Have a mimic substrate or antibody that our protein of interest will bind to, rest will flow through
Proteins with highest affinity will bind

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27
Q

How does SDS-PAGE work?

A

Unfolds and gives all proteins a negative charge
Separates by mass
Smaller mass will travel farther

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28
Q

What does a native PAGE separate by?

A

Separation by tertiary shape

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29
Q

What does a 2D-Page do?

A

Separates by mass and PI

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30
Q

What blocks disulfide formation?

A

Iodoacetate

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31
Q

What cleaves disulfide bonds?

A

2-mercaptoethanol

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32
Q

What id edman degradation?

A

Protein sequencing technique

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33
Q

What are the favorable interactions that occur in proteins?

A

Hydrophobic effect
Hydrogen bonds
London dispersion
Electrostatic interactions

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34
Q

What does the resonance of peptide bonds cause?

A

Less reactivity
Causes to be rigid and planar
Exhibit large dipole moment

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35
Q

Can rotation around a peptide bond occur?

A

No

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36
Q

What are phi angles?

A

Angle around the alpha carbon-amide nitrogen bond

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37
Q

What are psi angles?

A

Angle around the alpha carbon-carbonyl carbon bond

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38
Q

Why are some phi psi angle combinations more favorable than others?

A

Some conformations would form steric crowding while others allow the formation of favorable H-bonding interactions

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39
Q

What does a ramachandran plot show?

A

Shows the distribution of phi and psi angles that are found in a protein
Shows common secondary structure elements

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40
Q

What is the alpha helix backbone held together by?

A

Hydrogen bonds

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41
Q

What amino acids are strong helix formers?

A

Small hydrophobic residues

Ala and Leu

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42
Q

What amino acids are helix breakers?

A

Gly and Pro

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43
Q

What are the charges that are on the different ends of an alpha helix?

A

Carbonyl end has a negative charge

Amide end has a positive charge

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44
Q

What size structures do parallel and antiparallel beta sheets form?

A

Parallel forms large structures (more than 5 strands)

Antiparallel forms small strucutres ( two strands)

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45
Q

Where are hydrophobic residues arranged on parallel and antiparallel beta sheets?

A

Parallel - hydrophobic residues on both sides of sheet

Antiparallel - hydrophobic residues on one side of sheet

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46
Q

What do antiparallel beta sheets require?

A

Alternation of hydrophobic and hydrophilic residues in the primary amino acid sequence

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47
Q

What kind of proteins do cross linked alpha helixes form?

A

Tough, rigid, hard
Nails and horns
Alpha-keratin

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48
Q

What kind of proteins do cross linked triple-helixes form?

A

Tensile strength, non-strectching
Tendons and cartilage
Collagen

49
Q

What kind of proteins do Non-covalently held beta sheets form?

A

Soft, flexible non-stretchy
Egg sac, nest, and web
Silk fibroin

50
Q

What do you need to make collagen cross links without cystine?

A

Vitamin C (ascorbate)

51
Q

What are the two major classes of tertiary proteins?

A

Fibrous

Globular

52
Q

What are the characteristics of fibrous proteins?

A

Typically insoluble

Made from a single secondary structure

53
Q

What are the characteristics of globular proteins?

A

Water-soluble globular proteins

Lipid-soluble membraneous proteins

54
Q

What do electron density maps do?

A

Show the electron field of a protein

Lower the resolution the more accurate the electron field is

55
Q

What is NOESY spectrum of a a protein?

A

Protein NMR
Gives the backbone of the protein
May give insight to some R chains

56
Q

What holds quaternary structure together?

A

R-chain interactions and hydrophobic effect

57
Q

How can proteins be denatured?

A

Heat or cold
pH extremes
Organic solvents
Chaotropic agents

58
Q

What is the ribonuclease refolding experiment?

A

2-mercaptoethanol and urea were added to ribonuclease
Ribonuclease was then denatured fully
When 2-mercaptoethanol and urea were removed from the solution, ribonuclease refolded with the correct disulfide bonds

59
Q

What is levinthal’s paradox?

A

Proteins fold to the lowest energy state within seconds, however if proteins were to try every possible conformation it would take longer than the earth has been around

60
Q

What allows proteins to fold to the correct arrangement so quickly?

A

Hydrophobic collapse
Hydrogen bonds
Electrostatic interactions

61
Q

What catalyses disulfide bond interchange so the correct disulfide bonds can be formed?

A

Protein disulfide isomerase

62
Q

What is used to refold misfolded proteins?

A

GroEL/ES chaperonin

63
Q

How does the GroEL/ES chaperonin work?

A

Misfolded proteins will have their hydrophobic areas exposed, these areas will bind to GroEL
GroES binds to GroEL with a proteins inside the pocket
Protein folds inside the structure and is then released because the hydrophobic areas will no longer be exposed

64
Q

What are the functions of globular proteins?

A 
Storage
Transport
Muscle contraction
Defense against pathogens
Biological catalysis
65
Q

What is a ligand?

A

A molecule that binds

66
Q

What is a binding site?

A

A region in the protein where a ligand binds

67
Q

What is ka?

A

Association rate constant

68
Q

What is kd?

A

Disassociation rate constant

69
Q

What is Ka?

A

Equillibrium constant

ka/kd

70
Q

Where is calcium released from in muscle contraction?

A

Sarcoplasmic reticulum

71
Q

What are the thick filaments involved in muscle contraction?

A

Myosin

72
Q

What are the thin filaments involved in muscle contraction?

A

Actin

73
Q

What is the Z disk?

A

Anchor for thin filaments

74
Q

What is the M disk?

A

Anchor for thick filaments

75
Q

What does the ATPase activity on the heads of myosin allow?

A

The hydrolysis of ATP to ADP

76
Q

What is the contraction cycle?

A
  1. ATP binds to myosin head, myosin head releases actin
  2. Active site closure followed by ATP hydrolysis causing cocking of myosin head
  3. Weak binding of myosin head to actin
  4. Phosphate release, causes strong binding of myosin head to actin
  5. Power stroke
  6. ADP release
77
Q

Why does ATP cause the myosin head to release actin?

A

ATP decreases the affinity of myosin for actin

78
Q

How does calcium allow muscle contraction to occur?

A

Calcium binds to troponin which changes shape and moves tropomyosin, allowing mysoin to bind

79
Q

What kind of cells make antibodies?

A

B cells

80
Q

How do antibodies get rid of unwanted cells?

A

Antibodies coat the outside of an infected cell, they then bind to Fc receptor on macrophage, allowing phagocytosis to occur

81
Q

What are antigens?

A

Substances that stimulate production of antibodies
Coat proteins of bacteria and viruses
Recognized as foreign by the immune system

82
Q

Where does an antibody bind on an antigen?

A

Epitope

83
Q

What is the general formula for carbohydrates?

A

Cn(H2O)n

84
Q

What are the functions of carbohydrates?

A

Energy source and energy storage
Structural component of cell walls and exoskeletons
Informational molecules in cell-cell signaling

85
Q

What is an aldose?

A

A carbohydrate that contains an aldehyde

86
Q

What is a ketose?

A

A carbohydrate that contains a ketone

87
Q

How do you recognize a d-form carbohydrate?

A

Look at the farthest chiral carbon from the alpha carbon, if it is facing right then it is in d-form

88
Q

What are enatiomers?

A

Stereoisomers that are non-superimposable mirror images

89
Q

What are diastereomers?

A

Stereoisomers that are not mirror images

90
Q

What is an epimer?

A

Diastereomers that only differ by one carbon

91
Q

What is formed when an alcohol attacks an aldehyde?

A

Hemiacetal

92
Q

What is formed when an alcohol attacks a ketone?

A

Hemiketal

93
Q

What is a pyranose?

A

Six-membered oxygen containing ring

94
Q

What is a furanose?

A

Five-membered oxygen containing ring

95
Q

How is the Kd and amount of ligands bound related?

A

Higher the Kd, lower the binding

96
Q

What is Kd equal to?

A

kd/ka

97
Q

How are ligands and binding sites complementary?

A

Size
Shape
Charge
Hydrophobic/hydrophilic character

98
Q

What is the lock and key model?

A

Assumes that complementary surfaces are performed and fit together without any change

99
Q

What is induced fit specificity?

A

Conformational changes may occur upon ligand binding so that they will fit together
Both the ligand and the protein can change conformation

100
Q

What are the benefits to induced fit specificity?

A

Allows for tigher binding

Can increase the affinity of the protein for a second ligand

101
Q

What is the main oxygen storage protein in mammals?

A

Myoglobin

102
Q

Why does carbon monoxide have such a higher binding affinity than oxygen?

A

CO has a filled lone electron pair that can be donated to vacant d-orbitals on the Fe2+

103
Q

Why is myoglobin not a strong O2 transporter?

A

The YO2 difference between the lungs and tissue is not larg enough to cause good release

104
Q

What is cooperativity?

A

Multiple binding sits interact with each other

105
Q

How does the structure of hemoglobin change when oxygen binds?

A

Oxygen binds to Fe2+ which causes transition to Fe3+
Ionic radius shrinks, electrons are pulled closer because of the additional positive charge
The Iron ion now fits in the protoporphyin ring, pulling the His and F helix with it

106
Q

Which subunits are more stable in the T state?

A

deoxyhemoglobin

107
Q

What effect does pH have on hemoglobin binding to oxygen?

A

Oxygen binds well at higher pH (lungs)

Oxygen releases well at a lower pH (tissues)

108
Q

What is the Bohr effect?

A

Increasing pH (removing protons) stiumlates hemoglovin to bind more O2

109
Q

What converts CO2 to HCO3+?

A

Carbonic anhydrase

110
Q

What is the amino acid change that produces sickle-cell?

A

Glu changes to Val

111
Q

How does BPG decrease the binding affinity of oxygen to hemoglobin?

A

BPG binds to deoxyhemoglobin and stabilizes the T-state

112
Q

Why does high elevation affect oxygen delivery ability?

A

When at higher altitudes there is more BPG produced, this shifts the curve to the right, which decreases oxygen delivery
More BPG = More stable T-state
Long stays at high altitudes results in a decrease in O2 binding in lungs but an increase in O2 release in tissue

113
Q

What adaptation does fetal hemoglobin have?

A

Fetal hemoglobin has a higher affinity for oxygen at lower pressures (shift graph to the left)
This allows the fetus to rip oxygen away from the parent

114
Q

Why does fetal hemoglobin have a higher affinity for hemoglobin than adult hemoglobin?

A

Fetal hemoglobin has a serine rather than a histidine
This removes a positive amino acid and replaces it with a neutral one
Less of a positive charge means the T-state is not as favored

115
Q

What are the two theories describing cooperative binding?

A

Symmetry or concerted model

Sequential model

116
Q

What is the symmetry or concerted model of cooperative binding?

A

An oligomer contains either R or T state conformational states
Never has both R and T state

117
Q

What is the sequential model of cooperative binding?

A

Conformational changes occur sequentially as more binding sites are occupied
Supported by the binding curve of hemoglobin, change in affinity throughout

118
Q

What happens in sickle cell anemia?

A

Deoxy hemoglobin forms are insoluble

119
Q

How is the bohr effect applicable in the human body?

A

pH difference between lungs and metabolic tissues incrases the O2 transfer efficieny

Biochemistry (4 decks)

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