Biochemistry Day 1

Front 1

Which histones form the nucleosome octamers that DNA loops around?

Back 1

H2A, H2B, H3, H4

Front 2

H1 ties nucleosomes together in a ___-nm string.

Back 2

30 nm

Front 3

Heterochromatin is ___ and transcriptionally ___.

Back 3

condensed, inactive

Front 4

Euchromatin is ___ and transcriptionally ___.

Back 4

loose, active

Front 5

Purines consist of ___ & ___, and have ___ ring(s)

Back 5

Adenine & Guanine; 2 rings

Front 6

Pyridimidines consist of ___, ___, & ___ and have ___ ring(s).

Back 6

Cytosine, Uracil, Thymine; 1 ring

Front 7

Guanine has a ___ group.

Back 7

ketone

Front 8

Thymine has a ___ group.

Back 8

methyl

Front 9

Nucleotides are linked by ___'-___' ___ bonds.

Back 9

3'-5' phosphodiesterase bond

Front 10

Silent mutation =

Back 10

same AA, often base change in 3rd position of codon

Front 11

Missense mutation =

Back 11

changed AA (new AA is similar in chemical structure)

Front 12

Nonsense mutation =

Back 12

early STOP codon

Front 13

Frame shift mutation =

Back 13

misreading of all downstream nucleotides, result in truncated protein (WORST damage!)

Front 14

DNA topoisomerases =

Back 14

create nick in helix to relieve supercoils

Front 15

Primase =

Back 15

makes RNA primer for DNA Pol III to start replication

Front 16

DNA Pol III =

Back 16

elongates DNA chain by adding nucleotides to 3' end; has 3'-5' exonuclease proofreading activity

Front 17

DNA Pol I =

Back 17

degrades RNA primer

Front 18

DNA ligase =

Back 18

seals

Front 19

DNA repair: ___ locates damaged base, ___ makes a break upstream, ___ removes the chunk of nucleotides, ___ fills gap, ___ seals.

Back 19

excision repair-specific glycosylase, endonuclease, exonuclease, DNA pol, DNA ligase

Front 20

DNA repair defects:
Xeroderma pigmentosum ~ ___
Ataxia-telangiectasia ~ ___
Bloom's syndrome ~ ___
Fanconi's anemia ~ ___

Back 20

XP ~ UV light
AT ~ xray
BS ~ radiation
FA ~ crosslinking agents

Front 21

Xeroderma pigmentosum is where you can't repair ___ ___ which form in DNA when exposed to UV light. Associated with ___ & ___.

Back 21

thymine dimers
dry skin, melanoma

Front 22

mRNA is the ___ type of RNA.
rRNA is the ___ type of RNA.
tRNA is the ___ type of RNA.

Back 22

largest
most abundant
smallest

Front 23

RNA Pol I makes ___.
RNa Pol II makes ___.
RNA Pol III makes ___.

Back 23

rRNA
mRNA
tRNA

Front 24

alpha-amanitin (from mushrooms) inhibits RNA Pol ___.

Back 24

RNA Pol II --> cannot open DNA to start transcription

Front 25

Prokaryotic RNA Pol makes ___.

Back 25

all 3 kinds of RNA.

Front 26

Stop codons =

Back 26

UGA
UAA
UAG

Front 27

Promoter =

Back 27

site where RNA Pol and TFs bind DNA upstream from gene locus

Front 28

Enhancer =

Back 28

piece of DNA that alters a gene expression by binding TFs

Front 29

Operator =

Back 29

where gene repressors bind

Front 30

Exons =

Back 30

encode the actual genetic info

Front 31

After mRNA transcription, 3 processes:

Back 31

1) capping 5'end (7-methyl-G)
2) polyAAA tail
3) splice out introns
* then transport out of nucleus

Front 32

All tRNAs have _ _ _ at the 3' end which binds AA.

Back 32

CCA

Front 33

What is the enzyme that links an AA to the 3'end of tRNA?

Back 33

aminoacyl-tRNA synthase - 1 per AA, uses ATP

Front 34

What is tRNA wobble?

Back 34

mRNA codons differing in 3rd base position may still code for same tRNA/AA

Front 35

Methionine sits in the ___ site on the ribosome, the incoming AA lands in the ___ site.

Back 35

P site, A site

Front 36

How is GTP used in protein synthesis?

Back 36

"tRNA gripping & going places" - translocation along the ribosome

Front 37

___ Km = higher affinity

Back 37

lower

Front 38

Km =

Back 38

[S] at 1/2 Vmax

Front 39

Competitive inhibitors:
effect on Vmax =
effect on Km =

Back 39

unchanged
increase

Front 40

Noncompetitive inhibitors:
effect on Vmax =
effect on Km =

Back 40

lower
unchanged

Front 41

Most cells are in which phase?

Back 41

G0

Front 42

Rapidly dividing cells have a short ___ phase.

Back 42

G1

Front 43

How can enzymes be regulated?

Back 43

1) synthesis/destruction
2) zymogen cleavage
3) phosphorylation
4) feedback inhibition
5) transcriptional regulation

Front 44

What happens in the RER?

Back 44

1) make secretory proteins
2) add N-linked oligosaccharide to proteins

Front 45

What are Nissl bodies?

Back 45

neuronal RER that make enzymes and NTs (not found in axon hillock or axon)

Front 46

What happens in the SER?

Back 46

1) steroid synthesis
2) detox of drugs/poisons

Front 47

Which cells have a lot of RER?

Back 47

goblet cells, plasma cells

Front 48

Which cells have a lot of SER?

Back 48

hepatocytes, adrenal cortex

Front 49

I-cell Disease =

Back 49

Caused by failure to add mannose-6-phosphate to lysosome proteins --> enzymes secreted out of cell instead of going to lysosome. Have coarse facial features and restricted joint movement.

Front 50

What are the 6 functions of Golgi?

Back 50

1) distribute proteins/lipids
2) modify N-oligosaccharides
3) add O-oligosaccharides
4) assemble proteoglycans
5) sulfation of sugars
6) add mannose-6-phosphate to lysosomal proteins which targets protein to lysosome

Front 51

Drugs that act on microtubules:

Back 51

1) mebendazole/thiabendazole for worms
2) griseofulvin for fungi
3) taxols for breast cancer
4) vinca alkaloids for cancer
5) colchicine for gout

Front 52

Chediak-Higashi syndrome =

Back 52

microtubule polymerization defect --> dec. phagocytosis

Front 53

Cilia structure =

Back 53

9 + 2 arrangement microtubules, dynein for retrograde axon transport, kinesin for anterograde axon transport

Front 54

Microtubules are found in what cell structures?

Back 54

flagella, cilia, mitotic spindles

Front 55

Kartagener's syndrome =

Back 55

dynein arm defect --> immotile cilia (infertility, chronic respiratory infection)

Front 56

What is the function of cholesterol in plasma membrane?

Back 56

promote stability, makes up ~ 50% of membrane

Front 57

Phosphatidylcholine =

Back 57

aka lecithin; component of RBC membrane, myelin, bile, surfactant (dipalmitoyl phosphatidylcholine); helps esterify cholesterol

Front 58

Na/K pump =

Back 58

3 Na out: 2 K in (1 ATP used)

Front 59

Oubain inhibits Na/K pump by:

Back 59

binding to K site

Front 60

Digoxin and digitoxin inhibit Na/K pump -->

Back 60

inc. heart contractility

Front 61

Gq goes to which receptors to activate phospholipase C?

Back 61

H1, a1, V1, M1, M3

Front 62

IP3 -->
DAG -->

Back 62

inc. intracellular calcium
protein kinase C

Front 63

Gs subunit goes to which receptors to activiate adenylyl cyclase?

Back 63

B1, B2, D1, H2, V2

Front 64

Gi subunit goes to which receptor to inhibit adenylyl cyclase?

Back 64

M2, a2, D2

Front 65

Type 1 collagen found in:

Back 65

BONE, tendon, skin, fascia, teeth, cornea, late wound repair

Front 66

Type 2 collagen found in:

Back 66

CARTILAGE, vitreous body, nucleus pulposus

Front 67

Type 3 collagen found in:

Back 67

skin, vessels, uterus, fetal tissue, granulation tissue (early wound repair)

Front 68

Type 4 collagen found in:

Back 68

basement membrane

Front 69

Type 10 collagen found in:

Back 69

epiphyseal plate

Front 70

Preprocollagen =

Back 70

collagen alpha chains, Gly-X-Y (proline, lysine)

Front 71

Scurvy =

Back 71

VitC deficiency, cannot hydroxylate preprocollagen in ER

Front 72

Procollagen =

Back 72

triple helix of 3 alpha chains, made in Golgi

Front 73

Osteogenesis imperfecta =

Back 73

AD disorder, abnormal collagen synthesis at triple helix step --> multiple fractures, blue sclera, bad teeth, hearing loss

Front 74

Once triple helix procollagen get outside fibroblast:

Back 74

procollagen peptidases cleave terminal ends --> insoluble tropocollagen

Front 75

Ehlers-Danlos syndrome =

Back 75

faulty collagen synthesis at terminal cleavage step --> hyperextensible skin, hypermobile joints, easy bruising, associated with BERRY ANEURYSMS!

Front 76

Tropocollagen is crosslinked by ___ to make collagen fibrils.

Back 76

lysyl oxidase

Front 77

IHC stains:
vimentin
desmin
cytokeratin
GFAP
neurofilaments

Back 77

connective tissue
muscle
epithelial cells
neuroglia
neurons

Front 78

Metabolism sites: mitochondria

Back 78

1) fatty acid oxidation
2) acetyl CoA production
3) TCA cycle

Front 79

Metabolism sites: cytoplasm

Back 79

1) glycolysis
2) fatty acid synthesis
3) HMP shunt
4) protein synthesis (RER)
5) steroid synthesis (SER)

Front 80

Metabolism sites: both mito and cyto

Back 80

1) gluconeogenesis
2) urea cycle
3) heme synthesis

Front 81

Aerobic metabolism of glucose yields ___ ATP via malate shuttle, ___ ATP via G3P shuttle.

Back 81

38, 36

Front 82

Anaerobic glycolysis yields ___ ATP per glucose.

Back 82

2

Front 83

Activated carriers: ready?
phosphoryl
electrons
acyl
CO2
1-carbon units
methyl groups
aldehydes
glucose
choline

Back 83

ATP
NADH/NADPH/FADH2
coenzyme A, lipoamide
biotin
tetrahydrofolates
SAM
TPP
UDP glucose
CDP choline

Front 84

ATP + methinonine =

Back 84

S-adenosyl methionine (methyl donor)

Front 85

Regeneration of methionine and SAM requires Vit__.

Back 85

B12

Front 86

Signal molecule precursors:
ATP -->
GTP -->
glutamate -->
choline -->
arachidonate -->
fructose 6P -->
1,3 BPG -->

Back 86

cAMP
cGMP
GABA
Ach
PGs, LTs, TX
fructose 1,6 BP (via PFK)
2,3 BPG

Front 87

NAD+ is generally used in catabolic or anabolic processes?

Back 87

catabolic, H+ away as NADH

Front 88

NADPH is used in ___ processes as a supply of reducing equivalents. It is a product of which pathway that takes place in cytoplasm?

Back 88

anabolic, HMP shunt

Front 89

NADPH needed for 3 things:

Back 89

1) anabolic processes
2) respiratory burst
3) P-450

Front 90

NADPH oxidase deficiency -->

Back 90

chronic granulomatous disease, cannot do first step in respiratory burst!

Front 91

Superoxide dismutase =

Back 91

turns O2- into H2O2

Front 92

Myeloperoxidase =

Back 92

turns H2O2 into HOCl (bleach), lyses phagocytosed bacteria!

Front 93

Catalase =

Back 93

converts H2O2 into water, and oxidizes GSH to GSSH

Front 94

Glutathione reductase =

Back 94

Duh. Reduces glutathione by oxidizing NADPH

Front 95

Glucose 6 phosphate dehydrogenase =

Back 95

makes NADPH, first step in HMP shunt (G6P to 6PG)

Front 96

Hexokinase is found ___.
Glucokinase is found ___.

Back 96

throughout body
in Liver

Front 97

Glycolysis, irreversible enzymes (4):

Back 97

1) hexokinase/glucokinase
2) phosphofructokinase
3) pyruvate kinase
4) pyruvate dehydrogenase

Front 98

Glycolytic enzyme deficiency -->

Back 98

hemolytic anemia, because RBC only use glucose anaerobically (no mito)

Front 99

Pyruvate dehydrogenase complex requires which 5 cofactors?

Back 99

1) pyrophosphate (B1/thiamine; TPP)
2) FAD (B2, riboflavin)
3) NAD (B3, niacin)
4) CoA (B5, pantothenate)
5) lipoic acid

Front 100

What other complex uses the same cofactors as pyruvate dehydrogenase?

Back 100

a-ketoglutarate dehydrogenase

Front 101

Pyruvate dehydrogenase is activated by exercise which inc. 3 things:

Back 101

1) inc. NAD/NADH ratio
2) inc. ADP
3) inc. calcium

Front 102

Reaction catalyzed by pyruvate dehydrogenase:

Back 102

pyruvate + NAD + CoA --> acetyl CoA + CO2 + NADH

Front 103

What happens in pyruvate dehydrogenase deficiency (vitamin def, alcoholism)?

Back 103

backup of pyruvate & ala --> lactic acidosis, neurologic defects!
* TX ~ eat ketogenic nutrients like fat or lys & leu

Front 104

Which AA serves as a carrier of amino groups from muscle to liver?

Back 104

alanine

Front 105

2 functions of Oxaloacetate:

Back 105

1) TCA cycle (mito)
2) gluconeogenesis (mito & cytoplasm)

Front 106

What catalyzes reaction of pyruvate --> lactate?

Back 106

Lactate Dehydrogenase (LDH)

Front 107

Which enzyme converts pyruvate --> Oxaloacetate?

Back 107

pyruvate carboxylase

Front 108

Which enzyme converts oxaloacetate --> PEP for gluconeogenesis?

Back 108

PEP carboxykinase

Front 109

What is the purpose of the Cori cycle?

Back 109

allows muscle to function anaerobically (net 2 ATP); muscle glucose --> pyruvate --> lactate which goes to Liver and is made into glucose again

Front 110

TCA cycle produces:
___ NADH
___ FADH2
___ CO2
___ GTP
= ___ ATP

Back 110

3 NADH
1 FADH2
2 CO2
1 GTP
= 12 ATP per acetyl CoA

Front 111

What are the elements (in order) of the TCA cycle? Start after pyruvate --> acetyl CoA.

Back 111

acetyl CoA + oxaloacetate --> citrate --> isocitrate --> a-KG --> succinyl CoA --> succinate --> fumarate --> malate --> oxaloacetate

Front 112

Which ETC inhibitors directly inhibit electron transport, causing dec. proton gradient and block of ATP synthesis?

Back 112

rotenone, antimycin A, CN, CO

Front 113

Which is the ATPase inhibitor that directly inhibits mito ATPase, causing inc. proton gradient but no ATP production?

Back 113

oligomycin

Front 114

What is the uncoupling agent that inc. mito membrane permeability causing dec. proton gradient, continued O2 consumption, and no ATP production?

Back 114

2,4-dinitrophenol

Front 115

Gluconeogenesis, irreversible enzymes (w/o which leads to hypoglycemia):

Back 115

1) pyruvate carboxylase
2) PEP carboxykinase
3) fructose 1,6-BPase
4) glucose 6 phosphatase

Front 116

Which organs can do gluconeogenesis?

Back 116

liver, kidney, intestine
* muscle cannot!!

Front 117

What are the 2 functions of the HMP shunt (in cytoplasm)?

Back 117

1) make ribose-5P from glucose-6P for nucleotide synthesis
2) generate NADPH for FA synthesis, steroid synthesis, reducing glutathione

Front 118

G6PD deficiency:
- what kind of anemia?
- inheritance?
- epidemiology?
- intracellular body?

Back 118

- hemolytic anemia due to low NADPH in oxidative situations
- XR
- blacks more
- Heinz body (Hb precipitate)

Front 119

Which oxidizing agents can precipitate a G6PD deficiency attack?

Back 119

- fava beans
- anti-TB drugs
- sulfonamides
- primaquine

Front 120

What is the missing enzyme in fructose intolerance (AR dz)?

Back 120

aldolase B - accumulate fructose 1P causing dec. in available P and inhibit glycogenolysis & gluconeogenesis

Front 121

What is the defective enzyme in essential fructosuria?

Back 121

fructokinase - benign, asymptomatic, just fructose appears in blood/pee

Front 122

What is the absent enzyme in galactosemia (AR disease)?

Back 122

galactose-1P uridyltransferase - accumulate toxic substances causing mental retardation, hepatomegaly, cataracts!
* TX ~ don't eat lactose or galactose

Front 123

Who gets lactase deficiency?

Back 123

blacks, Asians

Front 124

Essential AA:
ketogenic (2)=
glucogenic (5)=
both (3)=

Back 124

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

Front 125

What are the si/sx of fructose intolerance?

Back 125

hypoglycemia, jaundice, cirrhosis, vomiting
* TX ~ don't eat fructose or sucrose!

Front 126

Which 2 essential AA are required during periods of growth?

Back 126

Arg, His

Front 127

Which 2 basic, positively charged AA are found in histones because they bind to negatively charged DNA?

Back 127

Arg, Lys

Front 128

At body pH 7.4, acidic AA glutamate and aspartate are ___ charged.

Back 128

negatively

Front 129

Urea cycle:
CO2 + NH4 --> carbamoyl P... then what?

Back 129

carbamoyl P + ornithine --> citrulline, + aspartate --> argininosuccinate, - fumarate (join TCA cycle) --> arginine, + H2O --> UREA!

Front 130

AA derivatives:
Phe -->

Back 130

tyrosine --> thyroxine, Dopa --> melanin, dopamine --> NE --> Epi

Front 131

AA derivatives:
Trp -->

Back 131

niacin --> NAD/NADP
serotonin
melatonin

Front 132

AA derivatives:
His -->

Back 132

histamine (easy peasy)

Front 133

AA derivatives:
Gly -->

Back 133

porphyrin --> heme

Front 134

AA derivatives:
Arg -->

Back 134

creatine
urea
nitric oxide

Front 135

AA derivatives:
Glu -->

Back 135

GABA

Front 136

What is missing in Phenylketonuria?

Back 136

either low phenylalanine hydroxylase, or low tetrahydrobiopterin cofactor - can't make Tyrosine

Front 137

How does PKU present?

Back 137

mental retardation, growth retardation, musty odor, fair skin, eczema
* AR disease, 1:10 000
* TX ~ lower Phe and raise Tyr in diet

Front 138

What disease makes urine turn black on standing and makes connective tissue dark? May have arthralgias but otherwise benign condition.

Back 138

Alkaptonuria, deficiency of homogentisic acid oxidase in degradative pathway of Tyrosine

Front 139

What are the causes of albinism?

Back 139

1) no tyrosinase - can't make melanin from Tyr
2) defective Tyr transporters

Front 140

What are 3 forms of homocystinuria?

Back 140

1) cystathionine sythase def.
2) dec. affinity of cystathionine synthase for B6
3) methionine synthase def.

Front 141

What are the si/sx of homocystinuria?

Back 141

mental retardation, tall stature, osteoporosis, kyphosis, lens subluxation, atherosclerosis

Front 142

Which AA transporters are missing from kidney tubules in the disease Cystinuria?

Back 142

COLA - cysteine, ornithine, lysine, arginine

Front 143

What is a result of cystinuria?

Back 143

Cystine kidney stones, TX acetazolamide to alkalinize urine

Front 144

What is the disease where you can't degrade branched AA (Ile, Leu, Val)?

Back 144

Maple Syrup Urine disease - deficient a-ketoacid dehydrogenase lead to inc. Leu in blood

Front 145

How can Maple Syrup Urine disease present?

Back 145

severe CNS defects, mental retardation, death

Front 146

What happens if there is deficient Adenosine deaminase?

Back 146

Build up ATP and dATP --> inhibit ribonucleotide reductase --> prevent DNA synthesis and lymphocyte production --> SCID!!

Front 147

What is the enzyme missing in Lesch-Nyan syndrome?

Back 147

HGPRTase, which converts hypoxanthine to IMP and guanine to GMP

Front 148

What are some manifestations of Lesch-Nyan syndrome?

Back 148

- hyperuricemia, gout
- retardation
- self-mutilation, aggression

Front 149

In fasted state, Liver glycogen will eventually become ___ and ___.

Back 149

glucose (via G6P --> glu), ketones (via G6P --> pyruvate --> acetyl CoA)

Front 150

Insulin is needed for glucose uptake in ___ and ___.

Back 150

skeletal muscle, adipose

Front 151

GLUT 2 receptors are found:

Back 151

beta cells

Front 152

GLUT 4 receptors are found:

Back 152

muscle and fat

Front 153

5 anabolic effects of insulin:

Back 153

1) glucose uptake
2) glycogen synthesis
3) TG synthesis
4) Na retention in kidney
5) protein synthesis in muscle

Front 154

Glucagon turns glycogen synthase ___, glycogen phosphorylase ___.

Back 154

OFF, ON

Front 155

Insulin turns glycogen synthase ___, glycogen phosphorylase ___.

Back 155

ON, OFF

Front 156

Von Gierke's disease =

Back 156

glucose 6-phosphatase deficiency; hypoglycemia, hepatomegaly, inc. blood lactate

Front 157

Pompe's disease =

Back 157

lysosomal a-1,4 glucosidase deficiency; cardiomegaly, hepatomegaly, lack muscle tone or weakness (ie exercise intolerance, difficulty breathing)

Front 158

Cori's disease =

Back 158

lysosomal a-1,6 glucosidase; mild hypoglycemia, normal lactate

Front 159

McArdle's disease =

Back 159

skeletal muscle glycogen phosphorylase deficiency; can't break down glycogen; get cramps and myoglobinuria upon exercising

Front 160

Tay-Sach's disease:
inheritance
enzyme
accumulated substrate
findings

Back 160

AR
hexosaminidase A
GM2 ganglioside
progressive neurodegeneration, developmental delay, cherry red spot, onion skin lysosomes

Front 161

Fabry's disease:
inheritance
enzyme
accumulated substrate
findings

Back 161

XR
a-galactosidase A
ceremide trihexoside
peripheral neuropathy of hands/feet, angiokeratomas, CV/renal disease

Front 162

Gaucher's disease:
inheritance
enzyme
accumulated substrate
findings

Back 162

AR
beta-glucocerebrosidase
glucocerebroside
hepatosplenomegaly, aseptic necrosis of femur, bone crises, Gauchers cells (macs)

Front 163

Niemann-Pick disease:
inheritance
enzyme
accumulated substrate
findings

Back 163

AR
sphingomyelinase
sphingomyelin
progressive neurodegeneration, hepatosplenomegaly, cherry red spot

Front 164

Krabbe's disease:
inheritance
enzyme
accumulated substrate
findings

Back 164

AR
beta-galactosidase
galactocerebroside
peripheral neuropathy, developmental delay, optic atropy

Front 165

Metachromatic Leukodystrophy:
inheritance
enzyme
accumulated substrate
findings

Back 165

AR
arylsulfatase A
cerebroside sulfate
central and peripheral demyelination w/ataxia, dementia

Front 166

Hurler's syndrome:
inheritance
enzyme
accumulated substrate
findings

Back 166

AR
a-L-iduronidase
heparan sulfate, dermatan sulfate
developmental delay, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly

Front 167

Hunter's syndrome:
inheritance
enzyme
accumulated substrate
findings

Back 167

XR
iduronate sulfatase
heparan sulfate, dermatan sulfate
mild Hurler's + aggressive behavior, no corneal clouding

Front 168

What are si/sx of Fanconi's anemia?

Back 168

AR disease of DNA repair defect, pancytopenia, cafe au lait spots, short stature, radial arm deformities (no thumbs), small testicles, small head, mental retardation, small kidneys