TJ guide Flashcards
1
Q
What is positive feedback?
A
a system that enhances the disturbance, must be self limited
2
Q
What is considered low gain?
A
gain less than 10
3
Q
What is true about input and output in a steady state situation?
A
input=output
4
Q
What is true about high gain regulation?
A
it tightly regulates a system
5
Q
What will happen to vasopressin concentration if the ECF volume is low?
A
Body releases vasopressin to retain water and decrease urine output
6
Q
What will happen to vasopressin concentration if you infuse a person with saline?
A
It will decrease to increase urine output
7
Q
Which amino acids are prominent in the body?
A
L-amino acids
8
Q
Which conformation is most favorable in amino acids?
A
trans
9
Q
What’s the average weight of an amino acid?
A
110 g/mol
10
Q
What three groups does phosphorylation typically occu on?
A
Ser, Thr, Trp
11
Q
What are three important functions of hydrogen bonds within the cell?
A
DNA, secondary structure in proteins, enzyme binding sites
12
Q
What do micelles aid with?
A
Moving and digesting fats
13
Q
What is the molarity of water?
A
55.5 M
14
Q
How do you increase buffer capacity?
A
Increase the amount of acid and conjugate base in the solution.
15
Q
What is the H-H equation for the bicarbonate buffer system?
A
pH = 6.1 + log [HCO3-]/[0.03PaCO2]
16
Q
Describe hydrogen bonding in an alpha helix
A
carbonyl of group at n, H bonds with the residue n+4 ahead in the primary sequence
17
Q
How many amino acids are typical in a beta turn?
A
4, held together by H bonding C=O to the N-H at N+3,
18
Q
What is the advantage of a protein that has no set tertiary structure?
A
It can bind more ligand and adjust itself to each ligand
19
Q
What types of amino acids most likely form salt bridges?
A
Glu and Asp
20
Q
T or F: protein folding is not mediated by other proteins
A
F
21
Q
What is a protein disulfide isomerase?
A
Breaks and reforms cysteins until lowest energy state is achieved
22
Q
What are Peptidyl propyl isomerases?
A
changes structure from cis to trans at prolines
23
Q
What do molecular chaperones and chaperonins do?
A
- Bind to unfolded regions and prevent hydrophobic regions from clumping
- create bowl for hydrophobic portions to aggregate in safe conformation unitl lowest energy state is achieved
24
Q
Name 3 diseases that are caused by issues in protein folding.
A
Cystic fibrosis, Sickle Cell, Huntington’s
25
Describe the mechanism of Cystic fibrosis
causes a mutation where proteins fold too slowly and are degraded. Sweat, mucus, and digestive fluid proteins never reach the membrane
26
Describe the mechanism of Sickle Cell Anemia
a Glu --> Val change at position 6 causes Val to bind in the hydrophobic pocket in deoxyHb forming polymers
27
Describe the mechanism of Huntington's
excess glutamine reactions in protein that lead to a mutated protein that increases neuron decay rate
28
What is the equation for Kd?
Kd = [Prot.][ligand]/[Prot.]
29
What does a small Kd imply about affinity?
high affinity
30
What does the Langmuir Isotherm indicate?
How much protein is bound at a given ligand concentration
31
What is the Langmuir Isotherm equation?
r = [A]/ (kd + [A])
32
What is r in the Langmuir Isotherm?
r = average number of ligand molecules bound per protein molecule
33
What are the axis in a Langmuir Isotherm?
[A] - ligand concentration = x-axis
| r - average number of ligand molecules bound per protein molecule on the x
34
What equation allows for a straight line to be obtained by the Langmuir Isotherm?
The Scatchard equation
35
What is the Scatchard equation?
r/[A] = n/kd - r/kd
36
What are the x, y axis, slope, and intercept of a scatchard plot?
x axis = r (amount of prot. bound to ligand)
y- axis = r/[A] (bound over free)
Slope = -1/kd
x-int = number of ligand
37
T or F: Hemoglobin binds oxygen most efficiently at high partial pressures?
False, Hb releases O2 at low partial pressure and binds O2 at high partial pressures. This allows for O2 to go into tissues
38
Oxidoreductase
Add or remove hyrdogen
39
Transferases
transfer a functional group from one molecule to another
40
Hydrolases
Add water across a bond hydrolyzing it
41
Lyases
add water, ammonia or CO2 to double bonds or remove these elements to make double bonds
42
Isomerases
Catalyze the conversion of a substrate to an isomer, epimer etc.
43
Ligases
Catalyze reactions where a bond is formed using energy from ATP
44
What is a small non-protein molecule that a protein depends on for catalytic activity?
cofactor
45
What is the difference between a cofactor and a coenzyme?
A coenzyme is an organic molecule where a coefactor can be a metal ion
46
What affect would adding more enzyme to a reaction have on velocity/rate?
Rate will increase in proportion to the amount of enzyme added
47
Will adding more substrate always cause the enzyme to have increased activity?
It will until the binding sites become saturated
48
What is an enzyme assay?
a way to determine the activity of an enzyme
49
What are units of enzyme activity?
one micromole/minute
50
What is the role of isozymes in diagnostic medicine?
In heart attack heterodimer of CK is released into blood which can be differentiated form brain and muscle homodimers
51
What is an isozyme?
proteins that catalyze the same reaction but are different proteins
52
What is the Michaelis-Menten Equation?
v = (Vmax [S]) / (Km + [S])
53
What do each of the variables in the M & M equation stand for?
```
v = reaction velocity
Vmax = maximum velocity at saturation
[S] = substrate concentration
Km = Michaelis constant - indicates 1/2 max activity / half full binding sites
```
54
What does a high Km indicate?
Low enzyme affinity
55
What are the axes of a lineweaver-burk plot?
1/V vs. 1/[S]
56
How can Km and Vmax be found using a lineweaver burk plot?
```
x-intercept = -1/Km
y-intercept = 1/Vmax
```
57
What affect to competitive inhibitors have on Km and Vmax?
Higher Km, Same Vmax
58
What affect to non-competitive inhibitors have on Km and Vmax?
Same Km, Lower Vmax (lower effective enzyme conc.)
59
Allopurinol resembles the transition state for substrate of xanthine oxidase that catalyzes uric acid formation. It binds xanthine oxidase so tightly that it cannot be released. This is an example of....
Suicide inhibtion
60
What is the mixture of protein to DNA in chromatin?
2:1
61
What is an example of genes being silenced via heterochromatin?
Female XX chromosome
62
When do you expect to see more heterochromatin in the cell?
right before mitotic division?
63
When would you expect to see the most euchromatin in the cell?
In S-phase when DNA is being copied
64
Define Telomere
endings of a chromosome
65
Centromere
where mitotic spindle attaches
66
Which would you expect to be more readily transcribed 10 nm Fibers or 30 nm fibers?
10 nm because they are less condensed
67
What is linker DNA?
the DNA between histones
68
What 4 proteins make up histones?
H2A, H2B, H3, H4
69
What is a good example of maternal inheritance in humans?
The mitochondria
70
T or F: Mitochondria have their own genomes?
True
71
What are two disorders resulting from mitochondrial genetics?
MERRF and Leber's optic neuropathy
72
T or F: the initial enzyme substrate reaction is covalent?
False
73
What factors are involved in changing the intracellular concentration of a drug?
inactivation of drug, prevented drug uptake, promotion of drug efflux
74
What factors are involved in changing drug targets?
altering the target, bypassing metabolic requirements, insensitivity to apoptosis
75
How do flexible drugs avoid resistance through active site mutations?
they target multiple areas of the protein and anticipate changes that will occur in response the the drug
76
What are two forms of non-receptor antagonists?
Chemical antagonists, physiologic antagonists
77
What kind of drug depends on your body's ability to metabolize it for activation?
Pro-drug
78
How does DNA replication begin?
Enzyme phosphorylates replication complex at the replication origin and S phase is triggered. (protein quickly degraded to ensure replication happens only once)
79
What is potency?
The amount of drug needed to reach ED50
80
What is the median effective dose (ED50)?
The amount of drug needed for patients to see a specified benefit
81
What is a common cause of drug side effects?
Identical receptors in non-target tissue
82
What are the packing contacts and where are they located?
alpha1, beta1, and alpha2, beta2, these do not move significantly when Hb binds O2
83
What are the sliding contacts and where are they located?
alpha1,beta2 and alpha2,beta1, these move significanly when O2 binds
84
Does 2,3 BPG bind more tightly to oxyHb or deoxyHb?
DeoxyHb because it must stabilize the T state
85
What Hb subunits are present during gestation?
zeta (for alpha) and epsilon (for beta)
86
By birth what are the Hb subunits?
alpha and gamma (for beta)
87
After birth what are the Hb subunits?
alpha and beta
88
What is the homozygous HbS mutation?
sickle cell anemia, heterozygotes = pretty normal
89
Why does dehydration increase the incidence of a sickle cell crisis?
Because it increases the concentration of HbS in the cell (remember polymerization is very conc. dependent)
90
What is the job of RecA and RAD51?
They help with single strand base pairing in double strand breaks using homologous chromosomes
91
What are L1 and Alu?
transposable elements, (Use reverse transcriptase to move in the genome)
92
Does reverse transcriptase proofread?
NO
93
What enters reverse transcribed DNA into the genome?
Integrase
94
Where is rRNA combined with protein?
in the nucleus
95
What aids proteins in cutting rRNAs?
snoRNAs
96
What is the point of the TATA box?
it attracts GTFs
97
What enzyme cleaves a 21-24 nt. region (miRNA) out to make RNAi?
Dicer
98
What does the RISC complex consist of?
Uses the slicer protein (argonaut) to cleave target mRNA strands
99
What is HP1?
protein that recognizes a methylation pattern and binds preventing binding of GTFs.
100
T or F: TFIID works with activators, repressors, and chromatin to start replication?
T
101
T or F: TFIID as a TATA box binding domain?
no its bound to the TBP as one of its factors
102
What is cell memory?
The expression of a reulatory protein with positive feedback control for its own transcription (formation of eye on the leg of the fruit fly)
Could also be caused by altered chromatin structure
103
What is MyoD and example of?
a protein that can set off a cascade to cause cell differentiation
104
What are some proteins that signal position?
HH, SHH, BMP, PAX, HOX
105
T or F: the signal of morphogins acts in a gradient?
T
106
What is a master regulatory gene?
a gene that causes a signal cascade Ey or MyoD
107
What might explain the direct inheritance of which X is expressed in females?
Proteins bound to that particular X may be replicated frequently so there is enough to bind the new X after mitosis
108
What catalyzes the tRNA charging reaction?
aminoacyl-tRNA synthetase
109
What are the steps in the tRNA charging reaction?
ATP bind amino acid to make aminoacyl-AMP, now tRNA binds and bond is transferred to the 3' end of the tRNA
110
What is the Shine-Dalgarno sequence?
30-35 nucleotide long sequence on every 5' portion of prokaryotic mRNA, it helps ensure AUG is on the correct position at the small ribosomal subunit
111
What is an IRES?
secondary structure in the 5' untranslated region of the mRNA (used in cap independent) eIF-4G binds IRES
112
What are the two major differences in prokaryotic and eukaryotic mechanisms of translation?
Eukaryotes have cap dependent and IRES.
| Prokaryotes have no cap depedent and have shine dalgarno sequence instead of IRES
113
What is the action of interferon?
Induces global translation shutdown by activating protein kinase R (PKR)
PKR turns eIF2 to eIF2-GDP (gets trapped in the recycling partner)
(viral so shuts down euks and proks)
114
How does diptheria toxin work?
ADP-ribosylation of eEF-2 (GLOBAL SHUTDOWN) no translocation
115
Poliomyeltis toxicity?
Cleaves eIF-4G shuts down cap dependent but not cap independent because the virus need IRES to replicate
116
Why is the 5' cap of mRNA so important?
mRNA export, stability, splicing, translation enhancement
117
T or F RNA pols II carries the capping, splicing, and polyadenylation factors to enable modification as RNA is transcribed.
True
118
Why is the poly-A tail important?
nuclear transport
119
What would happen if a single nucleotide slipped at a splice point?
Frame shift
120
What is a consensus sequence?
signal binding of snRNPs to the splice site
121
snRNPs are...
Ribozymes
