Biochem miscellaneous Flashcards
1
Q
exceptions to degeneracy of genetic code
A
methionine + tryptophan (each encoded by only 1 codon)
2
Q
codon for methionine
A
AUG
3
Q
codon for tryptophan
A
UGG
4
Q
nucleotides methylated in replication
A
cytosine + adenine
5
Q
how is uracil derived?
A
deamination of cytosine
6
Q
what makes thymine unique?
A
Has a methyl grow.
7
Q
when does NER occur?
A
G1
8
Q
sequence of events in base excision repair
A
glycosylase removes altered base and creates AP site –> AP endonuclease cleaves 5’ end –> lyase cleaves 3’ end –> pol fills gap –> ligase seals it
9
Q
significance of N-formylmethionine (fMET)
A
- initiates protein synthesis in bacteria.
- Nucleic acid coded by start codon.
- Stimulates neutrophil chemotaxis.
10
Q
polyadenylation signal
A
AAUAAA
11
Q
describe mRNA quality control
A
Occurs at cytoplasmic processing bodies (P-bodies), which contain exonucleases, decapping enzymes, and microRNAs. mRNAs may be stored in P-bodies for future translation.
12
Q
what initiates protein synthesis?
A
GTP hydrolysis
13
Q
describe trimming
A
removal of N- or C-terminal propeptides from zymogen to generate mature protein (eg trypsinogen –> trypsin).
14
Q
labile cell types
A
bone marrow + gut epithelium + skin + hair follicles + germ cells
15
Q
stable cell types
A
hepatocytes + lymphocytes
16
Q
golgi functions
A
1) protein distribution
2) modifies N-oligosaccharides on asparagine
3) adds O-oligosaccharides on serine and threonine.
4) adds mannose-6-phosphate
17
Q
Signal recognition particle (SRP)
A
abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER. Absent or dysfunctional SRP leads to protein accumulation in the cytosol.
18
Q
examples of intermediate filaments
A
vimentin + desmin + cytokeratin + lamins + glial fibrillary acid proteins (GFAP) + neurofilaments
19
Q
Vimentin
A
stains for mesenchymal tissue (eg., fibroblasts, endothelial cells, macrophages).
20
Q
microvilli
A
microfilament
21
Q
cilia structure
A
9+2 arrangement of microtubule doublets. Base (basal body) consists of 9 microtubule triplets with no central microtubules.
22
Q
axonemal dynein
A
ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets.
23
Q
frequency of an x-linked recessive disease in males
A
q
24
Q
frequency of an x-linked recessive disease in females
A
q squared
25
what is wrong in prader willi vs. angelmans
codebook
26
2 rules for inheritance chart
1) look for recessive/dominance
| 2) who's passing it down (only moms --> mitochondrial inheritance)
27
gene mutated in myotonic dystrophy type 1
DMPK
28
myotonia
Delayed relaxation of skeletal muscles after voluntary contraction or electrical stimulation. Feature of myotonic dystrophy.
29
medical word for night blindness
nyctalopia
30
medical word for dry, scaly skin
xerosis cutis
31
medical word for corneal degeneration
keratomalacia
32
significance of flavins (FMN, FAD)
used as cofactors in redox reactions
33
relationship between isoniazid and pyridoxine deficiency
Pyroxidine’s active form is the cofactor for gamma-aminolevulinate synthase, the enzyme that catalyzes the rate-limiting step of heme synthesis
34
vitamins required for niacin synthesis
B2 + B6
35
pyridoxine used in synthesis of...
cystathionine, heme, niacin, histamine, serotonin, epinephrine, norepinephrine, dopamine, GABA
36
storage form of vitamin D
25-OH D3
37
active form of vitamin D
calcitriol, 1,25-(OH)2D3
38
ergocalciferol
D2, ingested from plants
39
cholecalciferol
D3, consumed in milk, formed in sun-exposed skin.
40
location of D3 synthesis
stratum basale
41
biochemistry of folate deficiency
Deficiency inhibits the formation of deoxythymidine monophosphate (dTMP), which limits DNA synthesis and promotes megaloblastosis and erythroid precursor cell apoptosis. Since thymidine supplementation can moderately increase dTMP levels, it can reduce erythroid precursor cell apoptosis, so need to give thymidine with folate deficiency.
42
other names for vitamin K
phytomenadione, phylloquinone, phytonadione
43
enzyme that metabolizes ethanol in microsome
CYP2E1
44
biochem explanation for hepatosteatosis in alcoholism
dihydroxyacetone phosphate --> glycerol-3-phosphate, which combines with fatty acids to make triglycerides leading to hepatosteatosis.
45
dehydrogenase action
catalyze oxidation-reduction reaction
46
ATP production
32 net ATP via malate-aspartate shuttle, 30 net ATP via glycerol-3-phosphate shuttle
47
glycerol-3-phosphate shuttle
ATP shuttle in muscle
48
malate-aspartate shuttle
ATP shuttle in heart and liver
49
what does CoA carry?
acyl groups
50
what does lipoamide carry?
acyl groups
51
What does TPP cary (thiamine pyrophosphate)?
aldehydes
52
glycolysis equation
FA pg 99
53
enzymes requiring ATP
1) hexokinase/glucokinase 2) PFK-1
54
where is ATP produced in glycolysis?
1) 1,3 BP --> 3-phosphoglycerate
| 2) PEP --> pyruvate
55
where is GTP produced
succinyl-CoA --> succinate
56
regulation by F-2-6-bisphosphate
FBP-ase (fructose bisphosphatase-2) and PFK-2 (phosphofrutokinase-2) are the same bifunctional enzyme whose function is reversed by phosphorylation by PKA.
57
regulation by F-2-6-bisphosphate in fasting state
increased glucagon --> increased cAMP --> increased PKA --> inceased FBPase-2 --> decreased PFK-2 --> less glycolysis, more gluconeogenesis
58
regulation by F-2-6-bisphosphate in fed state
increased insulin --> increased cAMP --> increased PKA --> decreased FBPase-2 --> increased PFK-2 --> more glycolysis + less gluconeogenesis
59
pyruvate dehydrogenase reaction
pyruvate + NAD+ + CoA --> acetyl-CoA + CO2 + NADH
60
positive regulation of pyruvate dehydrogenase complex
elevated NAD+/NADH, elevated ADP, elevated Ca2+
61
vitamins required by pyruvate dehydrogenase complex
B1-B5, except B4
62
tissues that rely on anaerobic glycolysis
RBCs, WBCs, kidney, medulla, lens, testes, and cornea
63
products of pyruvate --> acetyl-CoA
acetyl-CoA + 1 NADH + 1 CO2
64
products of TCA cycle
3 NADH + 1 FADH2 + 2CO2 + 1 GTP per acetyl-CoA. Thus 10 ATP/acetyl-CoA.
65
Where is NADH generated in TCA cycle?
1) isocitrate --> alpha-KG
2) alpha-KG --> succinyl-CoA
3) Malate --> oxaloacetate
66
Where is FADH2 generated in TCA cycle?
succinate --> fumarate
67
Where is GTP generated in TCA cycle?
succinyl-CoA --> succinate
68
irreversible enzymes in TCA cycle
1) PDH 2) citrate synthase 3) isocitrate dehydrogenase 4) a-KG dehydrogenase
69
ATP produced via ATP synthase
1 NADH --> 2.5 ATP
| 1 FADH2 --> 1.5 ATP
70
site of gluconeogenesis
primarily liver, enzymes also in kidney + intestinal epithelium.
71
nonoxidative reaction in HMP shunt --> enzymes required + cofactors + products
ribulose-5-P --> ribose-5-p + glyceraldehyde-3-phosphate + fructose-6-p
- via phosphopentose isomerase + transketolases
- requires B1
72
sucrose
glucose + fructose
73
treatment for hereditary fructose intolerance
decrease intake of both fructose + sucrose
74
triose kinase
Fructose pathway: enzyme that metabolizes glyceraldehyde --> glyceraldehyde-3-P
75
aldose reductase 1) action 2) where its expressed
1) galactose --> galactitol
| 2) glucose --> sorbitol (using NADPH)
76
4 epimerase
galactose metabolism: interconverts UDP-gal to UDP-Glu
77
sorbitol dehydrogenase
sorbitol --> sorbitol dehydrogenase (using NAD+)
78
pathophys of osmotic damage (cataracts, retinopathy, peripheral neuropathy) in diabetics
glucose converted to sorbitol
79
tissues that have both aldose reductase + sorbitol dehydrogenase
liver + ovaries + seminal vesicles
80
tissues that have only aldose reductase
schwann cells + retina + kidneys + lens (primarily)
81
essential amino acids
all amino acids coded as glucogenic + glucogenic/ketogenic + ketogenic
82
location of synthesis of norepinephrine, dopamine, epinephrine
NE + dopamine are produced in the CNS + PNS. Epinephrine produced predominately in the adrenal medulla.
83
phenylketones (detected in urine of PKU kids)
phenylacetate, phenyllactate, phenylpyruvate
84
describe biochem of homocystinuria
...
85
limit dextrin
1-4 residues remaining on a branch after glycogen phosphorlase has already shortened it.
86
deficiency vs. accumulated substrate in gaucher's
glucocerebrosidASE deficiency; glucocerebroside accumulation
87
explain why ketone bodies build up in DKA and prolonged starvation
oxaloacetate is depleted for gluconeogenesis. This causes a build-up of acetyl-CoA, which shunts glucose and FFA toward the production of ketone bodies.
88
explain why ketone bodies build up in alcoholism
excess NADH shunts oxaloacetate to malate. This causes a buildup of acetyl-CoA, which shunts glucose and FFA toward the production of ketone bodies.
89
energy source during fasting state
Glycogenolysis is the primary source; also gluconeogenesis + adipose release of FFA.
90
LCAT
lecithin-cholesterol acyltransferase. Esterifies 2/3 of plasma cholesterol into cholesteryl ester (more hydrophobic form that is then sequested into the core of a lipoprotein particle). This forces newly synthesized HDL spherical and forcing reaction to become unidrectional.
91
exonucleases vs. endonucleases
Exonucleases remove base pairs, endonucleases cleave phosphodiester bonds within polynucleotide chains.
92
Folate deficiency labs
Methmalonic acid normal + homocysteine elevated.
93
Mucopolysaccharidoses
Hurler's + hunters
94
Location of heme synthesis
1st 2 steps in mitochondria, 4 steps in cytosol, final 3 steps in mitochondria
95
heme synthesis pathway
succinyl-CoA + glycine --> delta-aminolevulinic acid --> porphobilinogen --> hydroxymethylbilane --> uroporphyrinogen --> coproporphyrinegen --> protoporphyrinogen --> protoporphyrin --> heme
96
polyadenylation vs. capping
5' end is capped, 3' end is cleaved off, then polyadenylated
97
ketogenesis.
Think of DKA. Body breaks down fatty acids to produce ketone bodies. This process supplies energy to certain organs (particularly the brain) under circumstances like fasting.
98
DM1 HLA association
DR3 and DR4
99
Insulin sensitivity in DM1
High
100
glucose intolerance in DM1
Severe
101
serum insulin level in DM1
low
102
Genetic predisposition in DM1
Relatively weak (50% concordance in identical twins), polygenic.
103
genetic predisposition of DM2 vs. DM1
DM2 relatively much stronger than DM1
104
genetic predisposition of DM2
Relatively strong (90% concordance in identical twins), polygenic.
105
HLA type DM association
None
106
Glucose intolerance in Type 2DM
Mild to moderate
107
Labs in DKA
Hyperglycemia + increased hydrogen ions + decreased HCO3 + increased blood ketone + leukocytosis + HYPERKALEMIA.
108
DKA treatment
IV fluids + IV insulin + K+ + glucose if necessary to prevent hypoglycemia.
109
Amino acids necessary for purine synthesis:
o Code: Spartin gagging out peter strand + fat sailor masturbating /GAG glycine + aspartate + glutamine. Massive wooden cat overhead/purine synthesis.
o Location: entrance to pool area
110
Basic positively charged amino acids
o Code: giant cat + pirate with terrible head + Edward Norton on the couch/arginine + lysine + histidine. Huge pirate in middle/arginine is most basic. Cat floating in pool of water in front of TV/histidine has no charge at body pH.
o Location: TV area
111
Acidic negatively charged amino acids:
Code: Spartin doing acid + fat sailor doing acid/aspartic acid + glutamic acid. Electrical wires from ceiling zapping them/negatively charged at body pH.
Location: His bedroom
112
Hydrophobic amino acids
o Coded character: Alan in corner + val in middle around stripper pole + Lucy in a block of ice + methhead in right corner + mike O’connell /hydrophobic amino acids = valine, alanine, isoleucine, methionine, and phenylalanine. /these amino acids compose the transmembrane domains of signaling proteins.
o Location: Hottub
113
glycogenic and ketogenic amino acids
o Code: lucy in a block of ice + pale and pasty Mike O’connell on top + a big turkey + theon greyjoy feasting on the turkey/isoleucine + phenylalanine + threonine + tryptophan.
o Location: Area between ketogenic and glucogenic area
114
glycogenic amino acids
o Code: Cuppola made of candy/glucogenic amino acids. Val stripping around pole + meth head + cat dancing/methionine (Met) + valine (Val) + histidine (his).
o Location: Patio
115
Describe G protein mechanism
Ligand activates the receptor ---> inducing conformational change --> GDP exchanged for GTP --> Galpha subunit dissociates --> Galpha has downstream effects.
Termination --> Ga subunit hydrolyzes GTP to GDP, allowing it to re-associate with Gby and start a new cycle.
116
GTPase
hydrolase that binds and hydrolyzes GTP
117
G protein regulation
When they are bound to GTP, they are activated, and when bound to GDP, they are 'off.' Thus,
118
Amino acid type found in proteins...
Only L
119
Vimentin staining tumors?
Mesenchymal tumors + endometrial carcinoma + renal cell carcinoma + meningiomas.
120
Fuel use in exercise -- when do you deplete ATP by? creatine phosphate? anaerobic metabolism?
Stored ATP depleted in 2 seconds.
Creatine phosphate rises and is depleted by 10 secs.
Anaerobic metabolism depleted by 1 min.
121
Myotonic type 1 Muscular dystrophy pathophys
CTG trinucleotide repeat expansion in the DMPK gene leads to abnormal expression of myotonia protein kinase.
122
Permanent cell types
Neurons
Skeletal and cardiac muscles
*RBCs
123
stable vs permanent vs labile cell types
FA 58
