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BCMB > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

What is the only non-chiral amino acid?

A

Glycine
Gly
G

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2
Q

What are the parts of an amino acid?

A

Amino Group
Carboxylic Group
Hydrogen
Unique side chain

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3
Q

What is the # of possible isomers for a compound?

A

2^n

n= # of asymmetric C atoms

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4
Q

What type of light do amino acids absorb?

A

Infrared
Aromatic amino acids absorb UV light (Trp having the highest absorption)

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4
Q

What is optical activity?

A

The ability to rotate plane polarized light
only Chiral molecules have optical activity

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4
Q

All amino acids in people are in what configuration?
Where does the opposite configuration exist?

A

L- amino acids

D-amino acids exist in antibiotics, and cell walls in plants and bacteria

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5
Q

Alanine

A

Ala
A

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6
Q

Arginine

A

Arg
R

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7
Q

Asparagine

A

Asn
N

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8
Q

Aspartic Acid

A

Asp
D

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9
Q

Cysteine

A

Cys
C

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10
Q

Histidine

A

His
H

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10
Q

Glycine

A

Gly
G
Achiral
Inhibitory neurotransmitter
Most common amino acid of collagen

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11
Q

Glutamine

A

Gln
Q

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11
Q

Glutamic Acid

A

Glu
E

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12
Q

Isoleucine

A

Ile
I

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12
Q

Leucine

A

Leu
L

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12
Q

Lysine

A

Lys
K

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13
Q

Methionine

A

Met
M

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13
Q

Phenylalanine

A

Phe
F

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13
Q

Proline

A

Pro
P

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14
Q

Serine

A

Ser
S

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14
Q

Threonine

A

Thr
T

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15
Q

Tryptophan

A

Trp
W

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16
Q

Tyrosine

A

Tyr
Y

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17
Q

Valine

A

Val
V

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18
Q

What are the amino and carboxylic acid group components when uncharged?

A

NH2 and COOH

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18
Q

What are the amino and carboxylic acid group components when the pH is neutral?

A

NH3+
COO-

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19
Q

What are the amino and carboxylic acid group components when the pH is low?

A

Acidic- amino acid takes up an extra H+
NH3+
COOH

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19
Q

What are the amino and carboxylic acid group components when the pH is high?

A

Basic- amino acid releases some H+
NH2
COO-

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20
Q

What do amino acids do in response to pH change?

A

Resist change in pH

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20
Q

What is pKa?

A

the pH where an ionizable group is 50% ionized

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21
Q

What is the Henderson-Hasselbach equation?

A

pH = pKa + log [base]/[acid]

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22
Q

What are the nonpolar AA’s?

A

Alipathic: G, A, V, L, I, P

Aromatic: F

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22
Q

What is a zwitterion?

A

When the pH is equal to the pI, and there is no net charge

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22
Q

What are the aromatic AA’s

A

F, Y, W

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23
Q

What are the polar uncharged AA’s?

A

N, Q, S, T

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23
Q

What are the sulfur containing AA’s

A

M, C

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24
Q

What are the acidic amino acids? What is their charge?

A

Negatively charged
D, E

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25
Q

What are the basic amino acids? What is their charge?

A

Positive
R, K, H

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25
Q

What is special about proline?

A

It is important for secondary structures
It is an imino acid

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26
Q

Which group of amino acids participate in hydrophobic interactions?

A

Nonpolar, alipathic AA’s

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26
Q

Where do polar and non-polar amino acids cluster on proteins?

A

Non-polar’s cluster together in the interior of globular proteins

Polar’s are found on the outside surface of proteins

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26
Q

Maple Syrup Urine Disease is caused by…

A

A defect in the metabolsim of Nonpolar AA’s

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27
Q

What is the cause of Sickle Cell Disease?

A

Valine substitutes for glutamic acid in hemoglobin
The valine causes abnormal folding

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28
Q

What amino acid is a large component of ferritin subunits?

A

Leucine

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29
Q

What group of AA’s participate in H bonding?

A

Polar uncharged

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30
Q

Which amino acids are important for linking saccharides?

A

Serine and Threonine

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31
Q

What is the special component of the side chain of tryptophan?

A

Indole group

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32
Q

Phe and Tyr are precursors for what?

A

Thyroid hormones
Melanin
Dopamine, Epinephrine and Norepinephrine

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32
Q

What amino acid is very important for signal transduction and enzyme regulation?

A

Tyrosine

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33
Q

Trp is a precursor for….

A

Serotonin- mood
Melatonin- circadian rhythm
Niacin- a deficiency causes pellagra

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33
Q

Which amino acids are proton donors?

A

Acidic amino acids
Found in hydrophilic regions of proteins

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33
Q

What is the most prevalent excitatory neurotransmiter?

A

Glutamate

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34
Q

What is the most prevalent inhibitory neurotransmitter?

A

GABA

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35
Q

What amino acid is a major inflammatory mediator?

A

Histidine

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36
Q

Which amino acid is important for cell division, immune function, hormone release, and ammonia removal?

A

Arg

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36
Q

Which amino acid is important in nitric oxide synthesis, urea synthesis, and creatine synthesis?

A

Arg

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37
Q

Which amino acid is responsible for the buffer action of hemoglobin?

A

His

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37
Q

Which amino acid acid is only essential in children?

A

His

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38
Q

What are the essential amino acids?

A

Arg, His, Ile, Leu, Thr, Lys, Met, Phe, Trp, Val

PVT TIM HALL

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38
Q

What is selenocysteine?

A

A modification of cysteine, found in some redox proteins

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39
Q

Chaperones

A

Proteins that assist in protein folding

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40
Q

What happens when a protein doesn’t fold correctly?

A

It will be covalently marked for destruction by ubiquitin, and then they will be directed to the proteasome for destruction

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41
Q

What happens when 2 cysteine residues combine?

A

It forms a cystine

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41
Q

Primary protein structure

A

Amino acid sequence
Stabilized by covalent bonds: Peptide and disulfide

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42
Q

How are peptide bonds formed?

A

Condensation or dehydration reaction

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43
Q

What are the characteristics of a peptide bond?

A

Partial double bond character
No freedom of rotation
Rigid and planar
Trans bonds usually

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43
Q

AA sequences are read in what direction?

A

N to C
left to right

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44
Q

How can you identify amino acids?
(What methods)

A

Chromatography or Mass Spectrometry

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45
Q

How does N-Terminal sequencing work?

A

Edman degradation
Acid hydrolysis selectively hydrolyzes and then is identified with testing

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45
Q

What are endopeptidases?

A

A molecule that cleaves peptide bonds

46
Q

What stabilizes the protein’s secondary structure?

A

Hydrogen bonds

46
Q

Secondary structure

A

Spatial arrangement of AA’s
Alpha helix, Beta sheets, and beta turns

47
Q

Alpha helix

A

secondary structure
most stable
lowest energy

48
Q

Beta sheets

A

parallel and antiparallel
stabilized by h bonds

49
Q

What caused polypeptide chain kinks?

A

Proline

49
Q

What forms the interior of globular proteins?

A

Motifs

50
Q

What are protein domains?

A

Independently folded, compact units in proteins

51
Q

Tertiary Protein Structure

A

3D arrangment
H-bonds
Ionic Interactions
Hydrophobic Interactions

52
Q

Quaternary Structure

A

Spatial arrangement of a multi-subunit protein

53
Q

What kind of binding does hemoglobin exhibit?

A

Cooperative
Sigmoidal Curve

53
Q

What are the two techniques for protein separation?

A

Chromatography and Electrophoresis

54
Q

Ion Exchange Chromatography
What is it?
What elutes first?

A

Separates based on net charge at a given pH
Proteins with the same charge as the resin elute first

55
Q

Affinity Chromatography
What is it?

A

Purifies protein by using high affinity compunds

56
Q

What separation technique uses an electric field to cause proteins to migrate to the opposite charge?

A

Electrophoresis

57
Q

What are the two methods of protein structure analysis?

A

Electron microscopy
X-ray crystallography

57
Q

Hemoglobin Proteins are examples of what kind of protein structurally?

A

Globular

58
Q

Myoglobin

A

Not found in blood
Binds O2 more tightly

58
Q

Hemoglobin

A

Found in RBCs
Only in blood

58
Q

Collagen, Elastin, and Keratin are examples of what kind of protein structurally?

A

Fibrous

59
Q

What are the 3 domains of life?

A

Bacteria
Archaea
Eukarya

60
Q

What are the componets of the Cell Theory?

A

All living things are made up of cells
All cells came from a preexisting cell
It is the basic functional unit of life

61
Q

Bright field light microscope

A

Light goes directly through sample after being focused with a glass lens

62
Q

Phase contrast microscpe

A

Amplifies in different phases of light
Allows better contrast for denser samples

63
Q

Differential interference contrast/ Nomarski microscopy

A

Used for internal cellular structures

64
Q

Transmission Electron Microscopy

A

A beam of electrons go through the sample

65
Q

What kind of cell does not have a nucleus?

A

Prokaryote

65
Q

Scanning Electron Microscopy

A

The beam scans the surface to create a 3D image

66
Q

What kind of prokaryote is often found in extreme conditions?

A

Archaea

67
Q

What is on the inside of the plasma membrane of a bacterial cell?

A

Cytoplasm
Nucleoid region
Ribosomes

68
Q

What is on the outside of the plasma membrane of a bacterial cell?

A

Cell Wall
Glycocalyx
Appendages

69
Q

After a Gram stain, the bacteria have a red/pink color, what type of bacteria is it?

A

Gram-negative

70
Q

After a Gram stain, the bacteria have a violet color, what type of bacteria is it?

A

Gram-Positive

71
Q

What is another name for the bacterial cell wall?

A

Sacculus

72
Q

What are most bacterial cell walls made up of?

A

Peptidoglycan
Made up of NAG and NAM
Form cross-bridges

73
Q

A bacterium with a thick cell wall is what kind of bacterium?

A

Gram-positive

74
Q

A bacterium with a thin cell wall is what kind of bacterium?

A

Gram-negative

75
Q

What threads the layers of peptidoglycan in gram + bacteria?

A

Teichoic Acid

76
Q

What is the additional crystalline layer of protection found in free living bacteria?

A

S-layer

77
Q

What is on the inward and outward layer of the gram - bacteria membrane?

A

Inward: lipoprotein
Outward: lipopolysaccharides and porins

78
Q

Where is DNA found in bacteria?

A

Nucleoid

79
Q

How many chromosomes do prokaryotes have?

A

One circular chromosome

80
Q

What is the protein complex where prokaryotic DNA is replicated?

A

Replisome

81
Q

What is the dividing partition in cell division?

A

Septum

82
Q

How do bacteria divide?

A

Binary Fission

83
Q

What are the 3 types of protein filaments?

A

Microtubules
Intermediate Filaments
Actin Filaments

84
Q

Where does ribosome assembly occur?

A

Nucleolus

85
Q

Where is the shipping center of the cell?

A

Golgi
(composed of cisternae)

86
Q

What is the recycling of worn out organelles through endocytosis?

A

Autophagy

87
Q

What organelle contains acid hydrolases to break down molecules?

A

Lysosomes

88
Q

What organelle catalyze some reactions by removing H or adding O?

A

Peroxisomes
(H2O2 is a byproduct that is broken down by catalase)

89
Q

What are the functions of the plasma membrane?

A

Transport
Signaling
Adhesion

90
Q

What organelles can reproduce themselves?

A

Mitochondria and chloroplasts
(through binary fission)

91
Q

What is the function of the mitochondria?

A

Make ATP

92
Q

What do plant cells have that animal cells don’t?

A

Cell wall
Central vacuole
Chloroplasts

93
Q

1st law of Thermodynamics

A

Energy cannot be created or destroyed

94
Q

2nd Law of Thermodynamics

A

Entropy always increases

95
Q

What is the total energy in a system?

A

Enthalpy (delta H)

96
Q

Endergonic Reaction

A

Positive Delta G (non-spontaneous)
Require energy
Products have higher energy

97
Q

Exergonic Reaction

A

Negative Delta G (spontaneous)
Release energy
Reactants have higher energy

98
Q

Delta G

A

Free Energy
Predicts a reactions direction

99
Q

What is the main determinant of reaction rate?

A

Activation Energy

100
Q

What do enzymes do?

A

Catalyze reactions by lowering activation energy
Increases reaction rate
Stabilizes transition state

101
Q

Transferase

A

Move a functional group from one molecule to another

102
Q

Hydrolase

A

Use H2O to cleave bonds

103
Q

Lyase

A

Create double bonds, or add molecules to double bonds

104
Q

Isomerase

A

Interconvert isomeric forms

105
Q

Ligase

A

use ATP to form covalent bonds

106
Q

Holoenzyme

A

Apoenzyme + prosthetic group

107
Q

What are the forms of enzyme specificity?

A

Optical
Reaction
Substrate

108
Q

Induced Fit

A

Substrate binding causes a conformational change

109
Q

Coenzymes

A

nonprotein organic molecules
Vitamins

110
Q

Cofactors

A

Metal ions that act as electrophiles

111
Q

Vmax

A

When all on the enzyme is fully saturated
Maximum Reaction Rate

112
Q

Km

A

measure of enzyme affinity for the substrate

High Km: low affinity
Low Km: high affinity

113
Q

Kcat

A

Turnover number

Kcat = Vmax/ [E]

114
Q

What does temperature do to reaction velocity?

A

Temperature will increase reaction velocity

115
Q

What pH do enzymes best work at?

A

Physiological pH (7.4)

116
Q

Reversible inhibitor

A

Non covalent bonds used to bind the inhibitor to the enzyme

117
Q

Irreversible ihibitor

A

Covalent bonds used to bind to the enzyme

118
Q

What are transition state analogs

A

A compound that mimics the transition state
Can be used as an inhibitor to block an activation site of an enzyme

119
Q

Where does a competitive inhibitor bind?

A

The active site

120
Q

Where does a non competitive inhibitor bind

A

Somewhere on the enzyme that is not the active site

121
Q

Where does an uncompetitive inhibitor bind?

A

The enzyme-substrate complex only

122
Q

What does a competitive inhibitor do to Vmax and Km?

A

Vmax is unchanged
Km increases

123
Q

What does a uncompetitive inhibitor do to Vmax and Km?

A

Vmax decreases
Km decreases

124
Q

What does a non-competitive inhibitor do to Vmax and Km?

A

Vmax decreases
Km is unchanged

125
Q

Allosteric Regulation

A

A molecule called an effector is bound to an allosteric site which causes a conformational change (Km and Vmax could change)
Yields a sigmoidal shape

126
Q

Phosphorylation is a type of what kind of enzyme regulation?

A

Covalent modification

127
Q

Amphipathic

A

Contains both hydrophobic and hydrophilic parts

128
Q

Transmembrane protein

A

Goes directly through the membrane

129
Q

Peripheral protein

A

Also called extrinsic protein
Stays on one side of the membrane

130
Q

What makes the membrane MORE fluid, saturated or unsaturated fatty acids?

A

Unsaturated make it more fluid
The double bonds create more space in he membrane

Saturated fatty acids have no double bonds, so it is packed very tightly

131
Q

Flippase

A

A membrane protein that maintains the bidirectional transport of lipids in cells

“Flips” lipid in and out using ATP

132
Q

What is the cholesterol response to increased and decreased temperature?

A

Cholesterol does the opposite of what the membrane does in response to temperature changes

Increase Temp: Cholesterol fluidity is decreased
Decrease Temp: Cholesterol fluidity is increased

133
Q

What does the smooth ER synthesize

A

Lipids

134
Q

How are lipids transported inside of the cell?

A

Vesicles

135
Q

What do snare proteins do

A

They allow the joining of vesicles

136
Q

Forms of passive transport

A

Do not require ATP

Simple diffusion
Facilitated diffusion

137
Q

Distinguish isotonic, hypertonic, and hypotonic

A

Isotonic: [Solute] is equal inside and outside

Hypertonic: [Solute] is higher

Hypotonic: [Solute] is lower

138
Q

Aquaporin

A

A channel that allows for water transport across a membrane

139
Q

Carrier proteins

A

Active transport
Uniporter- one direction
Symporter- two in same direction
Antiporter- two in opposite directions

140
Q

Glucose transporters are what kind of transport?

A

Passive
Facilitated diffusion

141
Q

Channels

A

Form an open passage for ions or molecules

142
Q

Concentration Gradient

A

Ion difference inside and outside of cell

143
Q

Membrane potential

A

Difference in charge inside and outside of cell
Can be determined by the Nernst equation

144
Q

What maintains the Na+ gradient?

A

Na+/K+ ATPase

145
Q

Osmosis is what kind of transport?

A

Passive

BCMB (3 decks)

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