Exam 1 Flashcards
(179 cards)
1
Q
What is the only non-chiral amino acid?
A
Glycine
Gly
G
2
Q
What are the parts of an amino acid?
A
Amino Group
Carboxylic Group
Hydrogen
Unique side chain
3
Q
What is the # of possible isomers for a compound?
A
2^n
n= # of asymmetric C atoms
4
Q
What type of light do amino acids absorb?
A
Infrared
Aromatic amino acids absorb UV light (Trp having the highest absorption)
4
Q
What is optical activity?
A
The ability to rotate plane polarized light
only Chiral molecules have optical activity
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
5
Q
Alanine
A
Ala
A
6
Q
Arginine
A
Arg
R
7
Q
Asparagine
A
Asn
N
8
Q
Aspartic Acid
A
Asp
D
9
Q
Cysteine
A
Cys
C
10
Q
Histidine
A
His
H
10
Q
Glycine
A
Gly
G
Achiral
Inhibitory neurotransmitter
Most common amino acid of collagen
11
Q
Glutamine
A
Gln
Q
11
Q
Glutamic Acid
A
Glu
E
12
Q
Isoleucine
A
Ile
I
12
Q
Leucine
A
Leu
L
12
Q
Lysine
A
Lys
K
13
Q
Methionine
A
Met
M
13
Q
Phenylalanine
A
Phe
F
13
Q
Proline
A
Pro
P
14
Q
Serine
A
Ser
S
14
Q
Threonine
A
Thr
T
15
Q
Tryptophan
A
Trp
W
16
Tyrosine
Tyr
Y
17
Valine
Val
V
18
What are the amino and carboxylic acid group components when uncharged?
NH2 and COOH
18
What are the amino and carboxylic acid group components when the pH is neutral?
NH3+
COO-
19
What are the amino and carboxylic acid group components when the pH is low?
Acidic- amino acid takes up an extra H+
NH3+
COOH
19
What are the amino and carboxylic acid group components when the pH is high?
Basic- amino acid releases some H+
NH2
COO-
20
What do amino acids do in response to pH change?
Resist change in pH
20
What is pKa?
the pH where an ionizable group is 50% ionized
21
What is the Henderson-Hasselbach equation?
pH = pKa + log [base]/[acid]
22
What are the nonpolar AA's?
Alipathic: G, A, V, L, I, P
Aromatic: F
22
What is a zwitterion?
When the pH is equal to the pI, and there is no net charge
22
What are the aromatic AA's
F, Y, W
23
What are the polar uncharged AA's?
N, Q, S, T
23
What are the sulfur containing AA's
M, C
24
What are the acidic amino acids? What is their charge?
Negatively charged
D, E
25
What are the basic amino acids? What is their charge?
Positive
R, K, H
25
What is special about proline?
It is important for secondary structures
It is an imino acid
26
Which group of amino acids participate in hydrophobic interactions?
Nonpolar, alipathic AA's
26
Where do polar and non-polar amino acids cluster on proteins?
Non-polar's cluster together in the interior of globular proteins
Polar's are found on the outside surface of proteins
26
Maple Syrup Urine Disease is caused by...
A defect in the metabolsim of Nonpolar AA's
27
What is the cause of Sickle Cell Disease?
Valine substitutes for glutamic acid in hemoglobin
The valine causes abnormal folding
28
What amino acid is a large component of ferritin subunits?
Leucine
29
What group of AA's participate in H bonding?
Polar uncharged
30
Which amino acids are important for linking saccharides?
Serine and Threonine
31
What is the special component of the side chain of tryptophan?
Indole group
32
Phe and Tyr are precursors for what?
Thyroid hormones
Melanin
Dopamine, Epinephrine and Norepinephrine
32
What amino acid is very important for signal transduction and enzyme regulation?
Tyrosine
33
Trp is a precursor for....
Serotonin- mood
Melatonin- circadian rhythm
Niacin- a deficiency causes pellagra
33
Which amino acids are proton donors?
Acidic amino acids
Found in hydrophilic regions of proteins
33
What is the most prevalent excitatory neurotransmiter?
Glutamate
34
What is the most prevalent inhibitory neurotransmitter?
GABA
35
What amino acid is a major inflammatory mediator?
Histidine
36
Which amino acid is important for cell division, immune function, hormone release, and ammonia removal?
Arg
36
Which amino acid is important in nitric oxide synthesis, urea synthesis, and creatine synthesis?
Arg
37
Which amino acid is responsible for the buffer action of hemoglobin?
His
37
Which amino acid acid is only essential in children?
His
38
What are the essential amino acids?
Arg, His, Ile, Leu, Thr, Lys, Met, Phe, Trp, Val
PVT TIM HALL
38
What is selenocysteine?
A modification of cysteine, found in some redox proteins
39
Chaperones
Proteins that assist in protein folding
40
What happens when a protein doesn't fold correctly?
It will be covalently marked for destruction by ubiquitin, and then they will be directed to the proteasome for destruction
41
What happens when 2 cysteine residues combine?
It forms a cystine
41
Primary protein structure
Amino acid sequence
Stabilized by covalent bonds: Peptide and disulfide
42
How are peptide bonds formed?
Condensation or dehydration reaction
43
What are the characteristics of a peptide bond?
Partial double bond character
No freedom of rotation
Rigid and planar
Trans bonds usually
43
AA sequences are read in what direction?
N to C
left to right
44
How can you identify amino acids?
(What methods)
Chromatography or Mass Spectrometry
45
How does N-Terminal sequencing work?
Edman degradation
Acid hydrolysis selectively hydrolyzes and then is identified with testing
45
What are endopeptidases?
A molecule that cleaves peptide bonds
46
What stabilizes the protein's secondary structure?
Hydrogen bonds
46
Secondary structure
Spatial arrangement of AA's
Alpha helix, Beta sheets, and beta turns
47
Alpha helix
secondary structure
most stable
lowest energy
48
Beta sheets
parallel and antiparallel
stabilized by h bonds
49
What caused polypeptide chain kinks?
Proline
49
What forms the interior of globular proteins?
Motifs
50
What are protein domains?
Independently folded, compact units in proteins
51
Tertiary Protein Structure
3D arrangment
H-bonds
Ionic Interactions
Hydrophobic Interactions
52
Quaternary Structure
Spatial arrangement of a multi-subunit protein
53
What kind of binding does hemoglobin exhibit?
Cooperative
Sigmoidal Curve
53
What are the two techniques for protein separation?
Chromatography and Electrophoresis
54
Ion Exchange Chromatography
What is it?
What elutes first?
Separates based on net charge at a given pH
Proteins with the same charge as the resin elute first
55
Affinity Chromatography
What is it?
Purifies protein by using high affinity compunds
56
What separation technique uses an electric field to cause proteins to migrate to the opposite charge?
Electrophoresis
57
What are the two methods of protein structure analysis?
Electron microscopy
X-ray crystallography
57
Hemoglobin Proteins are examples of what kind of protein structurally?
Globular
58
Myoglobin
Not found in blood
Binds O2 more tightly
58
Hemoglobin
Found in RBCs
Only in blood
58
Collagen, Elastin, and Keratin are examples of what kind of protein structurally?
Fibrous
59
What are the 3 domains of life?
Bacteria
Archaea
Eukarya
60
What are the componets of the Cell Theory?
All living things are made up of cells
All cells came from a preexisting cell
It is the basic functional unit of life
61
Bright field light microscope
Light goes directly through sample after being focused with a glass lens
62
Phase contrast microscpe
Amplifies in different phases of light
Allows better contrast for denser samples
63
Differential interference contrast/ Nomarski microscopy
Used for internal cellular structures
64
Transmission Electron Microscopy
A beam of electrons go through the sample
65
What kind of cell does not have a nucleus?
Prokaryote
65
Scanning Electron Microscopy
The beam scans the surface to create a 3D image
66
What kind of prokaryote is often found in extreme conditions?
Archaea
67
What is on the inside of the plasma membrane of a bacterial cell?
Cytoplasm
Nucleoid region
Ribosomes
68
What is on the outside of the plasma membrane of a bacterial cell?
Cell Wall
Glycocalyx
Appendages
69
After a Gram stain, the bacteria have a red/pink color, what type of bacteria is it?
Gram-negative
70
After a Gram stain, the bacteria have a violet color, what type of bacteria is it?
Gram-Positive
71
What is another name for the bacterial cell wall?
Sacculus
72
What are most bacterial cell walls made up of?
Peptidoglycan
Made up of NAG and NAM
Form cross-bridges
73
A bacterium with a thick cell wall is what kind of bacterium?
Gram-positive
74
A bacterium with a thin cell wall is what kind of bacterium?
Gram-negative
75
What threads the layers of peptidoglycan in gram + bacteria?
Teichoic Acid
76
What is the additional crystalline layer of protection found in free living bacteria?
S-layer
77
What is on the inward and outward layer of the gram - bacteria membrane?
Inward: lipoprotein
Outward: lipopolysaccharides and porins
78
Where is DNA found in bacteria?
Nucleoid
79
How many chromosomes do prokaryotes have?
One circular chromosome
80
What is the protein complex where prokaryotic DNA is replicated?
Replisome
81
What is the dividing partition in cell division?
Septum
82
How do bacteria divide?
Binary Fission
83
What are the 3 types of protein filaments?
Microtubules
Intermediate Filaments
Actin Filaments
84
Where does ribosome assembly occur?
Nucleolus
85
Where is the shipping center of the cell?
Golgi
(composed of cisternae)
86
What is the recycling of worn out organelles through endocytosis?
Autophagy
87
What organelle contains acid hydrolases to break down molecules?
Lysosomes
88
What organelle catalyze some reactions by removing H or adding O?
Peroxisomes
(H2O2 is a byproduct that is broken down by catalase)
89
What are the functions of the plasma membrane?
Transport
Signaling
Adhesion
90
What organelles can reproduce themselves?
Mitochondria and chloroplasts
(through binary fission)
91
What is the function of the mitochondria?
Make ATP
92
What do plant cells have that animal cells don't?
Cell wall
Central vacuole
Chloroplasts
93
1st law of Thermodynamics
Energy cannot be created or destroyed
94
2nd Law of Thermodynamics
Entropy always increases
95
What is the total energy in a system?
Enthalpy (delta H)
96
Endergonic Reaction
Positive Delta G (non-spontaneous)
Require energy
Products have higher energy
97
Exergonic Reaction
Negative Delta G (spontaneous)
Release energy
Reactants have higher energy
98
Delta G
Free Energy
Predicts a reactions direction
99
What is the main determinant of reaction rate?
Activation Energy
100
What do enzymes do?
Catalyze reactions by lowering activation energy
Increases reaction rate
Stabilizes transition state
101
Transferase
Move a functional group from one molecule to another
102
Hydrolase
Use H2O to cleave bonds
103
Lyase
Create double bonds, or add molecules to double bonds
104
Isomerase
Interconvert isomeric forms
105
Ligase
use ATP to form covalent bonds
106
Holoenzyme
Apoenzyme + prosthetic group
107
What are the forms of enzyme specificity?
Optical
Reaction
Substrate
108
Induced Fit
Substrate binding causes a conformational change
109
Coenzymes
nonprotein organic molecules
Vitamins
110
Cofactors
Metal ions that act as electrophiles
111
Vmax
When all on the enzyme is fully saturated
Maximum Reaction Rate
112
Km
measure of enzyme affinity for the substrate
High Km: low affinity
Low Km: high affinity
113
Kcat
Turnover number
Kcat = Vmax/ [E]
114
What does temperature do to reaction velocity?
Temperature will increase reaction velocity
115
What pH do enzymes best work at?
Physiological pH (7.4)
116
Reversible inhibitor
Non covalent bonds used to bind the inhibitor to the enzyme
117
Irreversible ihibitor
Covalent bonds used to bind to the enzyme
118
What are transition state analogs
A compound that mimics the transition state
Can be used as an inhibitor to block an activation site of an enzyme
119
Where does a competitive inhibitor bind?
The active site
120
Where does a non competitive inhibitor bind
Somewhere on the enzyme that is not the active site
121
Where does an uncompetitive inhibitor bind?
The enzyme-substrate complex only
122
What does a competitive inhibitor do to Vmax and Km?
Vmax is unchanged
Km increases
123
What does a uncompetitive inhibitor do to Vmax and Km?
Vmax decreases
Km decreases
124
What does a non-competitive inhibitor do to Vmax and Km?
Vmax decreases
Km is unchanged
125
Allosteric Regulation
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
Phosphorylation is a type of what kind of enzyme regulation?
Covalent modification
127
Amphipathic
Contains both hydrophobic and hydrophilic parts
128
Transmembrane protein
Goes directly through the membrane
129
Peripheral protein
Also called extrinsic protein
Stays on one side of the membrane
130
What makes the membrane MORE fluid, saturated or unsaturated fatty acids?
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
Flippase
A membrane protein that maintains the bidirectional transport of lipids in cells
"Flips" lipid in and out using ATP
132
What is the cholesterol response to increased and decreased temperature?
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
What does the smooth ER synthesize
Lipids
134
How are lipids transported inside of the cell?
Vesicles
135
What do snare proteins do
They allow the joining of vesicles
136
Forms of passive transport
Do not require ATP
Simple diffusion
Facilitated diffusion
137
Distinguish isotonic, hypertonic, and hypotonic
Isotonic: [Solute] is equal inside and outside
Hypertonic: [Solute] is higher
Hypotonic: [Solute] is lower
138
Aquaporin
A channel that allows for water transport across a membrane
139
Carrier proteins
Active transport
Uniporter- one direction
Symporter- two in same direction
Antiporter- two in opposite directions
140
Glucose transporters are what kind of transport?
Passive
Facilitated diffusion
141
Channels
Form an open passage for ions or molecules
142
Concentration Gradient
Ion difference inside and outside of cell
143
Membrane potential
Difference in charge inside and outside of cell
Can be determined by the Nernst equation
144
What maintains the Na+ gradient?
Na+/K+ ATPase
145
Osmosis is what kind of transport?
Passive
