Biochem 1 USMLE Flashcards Preview

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Flashcards in Biochem 1 USMLE Deck (210):
1

full-term neonate of uneventful delivery becomes mentally retarded and hyperactive and has a musty odor. What is the d?

PKU

2

Stressed executive comes home from work, consumes 7 or 8 martinis in rapid succession before dinner, and becomes hypoglycemic. What is the mechanism?

NADH increase prevents gluconeogenesis by shunting pyruvate and oxaloacetate to lactate and malate

3

2 y/o girl has an increase in abd girth, failure to thrive and skin and hair depigmentation. What is the dx

kwashiorkor

4

alcoholic develops a rash, diarrhea, and altered mental status. What is the vitamen deficiency

vit B3 (pellagra)

5

51 y/o man has black spots in his sclera and has noted that his urine turns black upon standing. What is the dx

alkaptonuria

6

25 y/o male complains of severe chest pain and has xanthomas on his achilles tendons. What is the dz, and where is the defect?

familial hypercholesterolemia; LDL receptor

7

Condensed by (-) charged DNA looped twice around (+) charged H2A, H2B, H3, & H4 histone octamers (nucleosome bead). H1 ties nucleosmes together on a string (30-mm fiber). In mitosis, DNA condenses to form mitotic chromosomes.

Chromatin sx--image 77

note: Think of beads on a string

8

this type of chromatin is condensed, transcriptionally inactive

heterochromatin

9

this type of chromatin is less condensed, transcriptionally active

euchromatin

eu=true, "truely transcribed."

10

purines are _____ & _____ and have _____ ring/s.
pyramidines are _____,_____, &______

A,G (2 rings)
C,T,U (1 ring)

mneu: PURe As Gold: PURines.
CUT the PY (pie)

11

Guanine has a _______

ketone

12

Thymine has a ______

methyl

mneu: THYmine has a meTHYl

13

Deamination of cytosine makes a _____

uracil

14

uricil is found in this nucleic acid

RNA

15

thymine is found in this nucleic acid

DNA

16

This bond has 3 H bonds and is therefore stronger that this bond which only has 2 H bonds

G-C bond > A-T

17

nucleotides with a higher G-C means a higher this

melting temperature

18

nucleotides are linked by this type of bond

3'-5' phosphodiesterase bond

19

this refers to substituting purine for purine or pyrimidine for pyrimidine

transition

mneu: TransItion=Identical types

20

this refers to substituting purine for a pyrimidine or pyrimidine for purine

Transversion

mneu: TransVersion=conVersion between types

21

this feature of the genetic code refers to the fact that each codon specifies only 1 amino acid

unambiguous

22

this feature of the genetic code refers to the fact that more than 1 codon may code for the same amino acid

degenerate

23

the genetic code is universal (exceptions include mitochondria, archaeobacteria, mycoplasma, and some yeast) T or f

T

24

this mutation in dna often involves the same AA, it is often a base change in the 3rd position of codon (tRNA wobble).

silent

25

this mutation in dna involves a changed AA (conservative-new AA is similar in chemical sx)

missense

26

this mutation in dna often involves a change resulting in an early STOP CODON

nonsense

mneu: stop the nonsense

27

this mutation in dna often involves a change resulting in misreading of all nucleotides downstream, usually resulting in a truncated protein

frame shift

28

Single origin of replication in prokaryotic DNA replication by DNA polymerases refers to ________ DNA synthesis on the leading strand and _______ on the lagging strand

Continuous
Discontinuous (Okazaki fragments)

29

DNA polymerase III has ____ synthesis and proofreads with ______ exonuclease

5'->3'

3'->5'

30

DNA polymerase I excises RNA primer with ____ exonuclease

5'-3'

31

these create a nicks in the helix to relieve supercoils

DNA topoisomerase

32

this makes an RNA primer on which DNA polymerase III can initiate replication

Primase

33

this elongates the chain by adding deoxynucleotides to the 3' end until it reaches primer of preceding fragment. 3' ->5' exonuclease activity "profreads" each added nucleotide.

DNA polymerase III

34

this degrades RNA primer

DNA polymerase I

35

this seals

DNA ligase

36

eukaryotic genome has _____ origins of replications

multiple

37

replication begins at a consensus sequence of ____ base pairs

AT

38

eukaryotes have seperate polymerases ______ for synthesizing RNA primers, leading-strand DNA, mitochondrial DNA, and DNA repair

(αβδγε)

39

describe DNA repair of single strand

single strand, excision repair-specific glycosylase recognizes and removes damaged base. Endonuclease makes a break several bases to the 5' side. Exonuclease removes a short stretch of nucleotides. DNA polymerase fills gap. DNA ligase seals.

40

DNA repair defects regarding skin sensitivity to UV light results in this dz

xeroderma pigmentosum

41

DNA repair defects regarding x-rays results in this dz

ataxia-telangiectasia

42

DNA repair defects regarding radiation results in this dz

Bloom's syndrome

43

DNA repair defects regarding cross-linking agents results in this dz

Fanconi's anemia

44

xeroderma pigmentosum is this inheritance

autosomal recessive

45

XP results in defective excision repair such as uvr ABC endonuclease. It results in inability to repair _____, which form in DNA when exposed to UV light.

thymidine dymers [image p. 79]

46

XP is associated w/ these things

dry skin, melanoma, & other CA

47

DNA & RNA are both synthesized in this direction

5' ->3'

48

The 5' of the incoming nucleotide bears the ______ . The 3' hydroxyl of the nascent chain is the target

triphosphate (energy source for bond

mneu: Imagine the incoming nucleotide bringing a gift (triphosphate) to the 3' host. "BYOP (phosphate) from 5 to 3"

49

Protein synthesis procedes in this direction

5' ->3'

50

amino acids are linked in this way

N to C

51

mRNA is the _____ type of RNA

rRNA is the most _____ type of RNA

tRNA is the ______ type of RNA

massive, Rampant, Tiny

52

In prokaryotes this makes all 3 kinds of RNA

RNA polymerase

53

In eukaryotes, ________ makes rRNA

RNA polymerase I

mneu: I,II, III are numbered as their products are used in protein sythesis

54

In eukaryotes, ________ makes mRNA

RNA polymerase II

mneu: I,II, III are numbered as their products are used in protein sythesis

55

In eukaryotes, ________ makes tRNA

RNA polymerase III

mneu: I,II, III are numbered as their products are used in protein sythesis

56

eukaryotic RNA polymerase has no ________ fx, but can initiate chains

proofreading fx

57

RNA polymerase II opens DNA at _________

promoter site (A-T rich upstream sequence ---TATA and CAAT).

58

this poison is found in death cap mushrooms and works by inhibiting RNA polymerase II

alpha-amantin

59

what is the mRNA initiation codon

AUG (or rarely GUG)

mneu: AUG inAUGurates protien synthesis

60

in eukaryotes AUG codes for this, which may be removed before translation is completed

methionine

61

in prokaryotes the initial AUG codes for ________

formyl-methionine (fmet)

62

Give stop codons

UGA,UAA,UAG

mneu: U Go Awau, U Are Away, U Are Gone

63

In the regulation of gene expression, this is the site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus

promotor

64

promoter mutation commonly results in this

dramatic decrease in amount of gene transcribed

65

In the regulation of gene expression, stretch of DNA that alters gene expression by binding transcription factors. May be located close to, far from, or even within (in an intron) the gene whose expression it regulates

enhancer

66

In the regulation of gene expression, this is the site where negative regulators (repressors) bind.

operator

67

These contain actual genetic information coding for proteins

exons [image p. 80]

mneu: INtrons stay IN the nucleus, whereas EXons EXit and are EXpressed

68

These are intervening noncoding segments of DNA

introns

mneu: INtrons stay IN the nucleus, whereas EXons EXit and are EXpressed

69

Introns are precisely spliced out of primary mRNA transcripts. A lariat-shaped intermediate is formed. ___________ facilitate splicing by binding to primary mRNA transcripts and forming splicosomes.

small nuclear ribonucleoprotein particles (snRNP)

70

RNA processing in eukaryotes occurs in the _______, after transcription.

nucleus

71

only _______ is transported out of the nucleus

processed RNA

72

describe RNA processing in eukaryotes (3 steps)
[image p. 80]

1) capping on 5' end (7-methyl-G)
2) Polyadenylations on 3' end (-200 As)
3) Splicing out of introns

73

what is the initial transcript of RNA processing (eukaryotes) called

heterogeneous nuclear RNA (hnRNA)

74

capped and tailed transcript is called _______

mRNA

75

tRNA sx consists of 75-90 nucleotides, cloverleaf form, anticodon end is opposite 3' aminoacyl end. All tRNAs, both eukaryotic and prokaryotic, have CCA 3' end along w/ a high percentage of chemically modified bases. The amino acid is covalently bound to the ___ end of the tRNA.

3'

76

1 of these is used up per AA, it uses ATP and scrutinizes AA before and after it binds to tRNA. If incorrect, bond is hydrolyzed. The AA-tRNA bond has energy for formation of peptide bond.

Animoacyl-tRNA synthetase

77

A mischarged tRNA reads usual codon but inserts the ______

wrong AA

78

___________ and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection

aminoacyl-tRNA synthetase

79

this describes how accurate base parining is required only in the 1st 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd position may code for the same tRNA/amino acid

tRNA wobble

80

In ribosome protein synthesis Met sits in the ______ site

P site(peptidyl)

81

In ribosome protein synthesis, the incoming amino acid binds to the _____ site, hydrolyzing Met's bond to its tRNA while simulatneously forming a peptidyl bond between 2 amino acids.

A site (aminoacyl)

82

The ribosome shifts 1 codon towards the 3' end of the mRNA, shifting the uncharged tRNA into the __ position and the dipeptidyl tRNA into the __ site

E
P

83

ATP is used for this with tRNA

Activation (charging)

84

GTP is used for this with tRNA

Gripping and Going places (translocation)

85

the lower the Km, the _____ the affinity

higher

86

this type of inhibitor resembles substrate

competitive inhibitor

87

this type of inhibitor can be overcome by increase concentration of substrate

competitive inhibitor

88

this type of inhibitor binds to the active site

competitive inhibitor

89

competitive inhibitors have this effect on Vmax

no effect

90

non0competitive inhibitors have this effect on Vmax

decreased

91

competitive inhibitors have this effect on Km

increased

92

Noncompetitive inhibitors have this effect on Km

no effect

93

enzyme regulation methods:
alter this for increased or decreased synthesis or destricution effects

enzyme concentrations

94

enzyme regulation methods: phosphorylation effects

covalent modification

95

enzyme regulation methods:
proteolytic modification effects

zymogen

96

enzyme regulation methods:
allosteric regulation effects

feedback inhibition

97

enzyme regulation methods:
steroid hormones effects

transcriptional regulation

98

Give the Cell cycle synthesis phases and what they stand for

M (mitosis: prophase-metaphase-anaphase-telophase)
G1 (growth)
S (synthesis of DNA)
G2 (growth)
Go (quiescent G1 phase)

99

these 2 phases are of variable duration

G1 & Go

100

this is usually the shortest phase

M

101

Most cells are in this phase

Go

102

rapidly dividing cells have a shorter ____ phase

G1

103

this is the site of synthesis of secretory (exported proteins and of N-linked oligosaccharide addition to many proteins

Rough endoplasmic reticulum (RER)

104

Mucus-secreting goblet cells of the small intestine and antibody-secreting plasma cells are rich here

RER

105

this is the site of steroid synthesis and detoxification of drugs and poisons

smooth endoplasmic reticulum (SER)

106

Liver hepatocytes and steroid hormone-producing cells of the adrenal cortex are rich in _____

SER

107

Functions of Golgi apparatus

1) distribution center of proteins and lipids from ER to the plasma membrane, lysosomes, and secretory vesicles
2)modifies N-oligosaccharides on asparagine
3) Adds O-oligosaccharides to serine and threonine residues
4) Proteoglycan assembly from proteoglycan core proteins
5) Sulfation of sugars in proteoglycans and of selected tyrosine on proteins
6) Addition of mannose-6 phosphate to specific lysosomal proteins, which targets the protein to the lysosome.

108

I cell disease is caused by the failure of the addition of _________ to lysosome proteins, causing thse enzymes to be secreted outside the cell inside of being targeted to the lysosome. Characterized by coarse facial features and restricted joint movement.

mannose-6-phosphate

109

This is a cylindrical sx 24 nm in diameter and of variable lenght. A helical array of polymerized dimers of alpha and Beta tubulin (13 per circumference). Each dimer has 2 GTP bound. Incorporated into flagella, cilia, mitotic spindles. Grows slowly, collapses quickly.

microtubules

110

this cell sxs are involved in slow axoplasmic transport in neurons

microtubules

111

name 5 drugs that act on microtubules

1) mebendazole/thiabendazole (antihelminthic)
2) taxol (anti Br CA
3) Griseofulvin (antifungal)
4) Vincristine/Vinblastine (anti-cancer)
5) Colchicine (anti gout

112

This syndrome is due to a microtubule polymerization defect resulting in decreased phagocytosis

Chediak-Higashi syndrome

113

this cell sx has 9 + 2 arrangement of microtubules

cilia

114

In cilia, this is an ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets

dynein

115

this syndrome is due to a dynein arm defect, resulting in immotile cilia

Kartagener's syndrome

116

dynein is

retrograde

117

kinesin is

anterograde

118

what are the 2 major components of plasma membranes

cholesterol (-50%)
phospholipids (-50%)

there are also sphingolipids, glycolipids, and proteins.

119

High cholesterol or long saturated fatty acid content results in this

increase melting temp.

120

this side of the membrane contains glycosylated lipids or proteins

noncytoplasmic side

121

T or F. The plasma membrane is an asymmetric, fluid bilater

T

122

This is a major component of RBC membranes, of myelin, of bile, and of surfactant. It is also used in the esterification of cholesteral.

Phosphatidylcholine

123

specific phosphatidylcholine used in esterification of chelesterol

LCAT is lecithin-cholesterol acyltransferase

124

specific phosphatidylcholine used in surfactant

DPPC= dipalmitoyl phosphatidylcholine

125

This is located in the plasma membrane w/ ATP site on the cytoplasmic side.

Na+K+ATPase (sodium pump)

126

For each ATP consumed, ___ Na+ go out and __ K+ come in.

3/2

127

During each cycle of the sodium pump this occurs

phosphorylation

128

This inhibits by blinding to K+ site.

Ouabain

129

These also inhibit the Na+K+ATPase causing increased cardiac contractility

cardiac glycosides (digoxin, digitoxin)

130

This is the most abundant protein in the human body. It fxs to organize and strengthen extracellular matrix.

collagen

131

this type of collagen is 90% of collagen. It makes up BONE, tendon, skin, dentin, fascia, cornia, late wound repair

Type I

mneu: B Cool, Read Books
type I: bONE

132

this type of collagen makes up CARTILAGE (including hyaline), vitreous body, nucleus pulposis

Type II

mneu: B Cool, Read Books
type II: carTWOlage

133

this type of collagen makes up skin, blood vessels, uterus, fetal tissue, granulation tissue

Type III (reticulin)

mneu: B Cool, Read Books

134

this type of collagen makes up basement membrane or basal lamina

Type IV

mneu: B Cool, Read Books
Type IV: under the floor (basement membrane

135

This type of cartilage makes up the epiphyseal plate

Type X

136

collagen alpha chains are called

preprocollagen

137

preprocollagen is translated on this

RER

138

Inside fibroblast, collagen alpha chains or (preprocollagen) is usually this type of polypeptide

Gly-XY (X & Y are proline, hydroxyproline or hydroxylysine)

139

inside the the ER in fibroblasts hydroxylation of specific proline and lysine residues occurs. Hydroxylation requires this vitamen

C

140

Inside fibroblasts the golgi glycosylates the pro alpha chain lysine residues and formation of _______

procollagen (triple helix of 3 collagen chains)

141

these molecules are then exocytosed into into the extracellular space

procollagen

142

outside fibroblasts, procollagen peptidases cleave terminal regions of procollagen, transforming procollagen into insoluble ______

tropocollagen

143

Many staggered tropocollagen molecules are reinforced by covalent lysine-hydroxylysine cross linkage (by lysyl oxidase) to make

collagen fibrils

144

this syndrome results in faulty collagen synthesis causing:
1) hyperextensible skin
2) tendency to bleed (easy bruising)
3) hypermobile joints

ehlers-danlos syndrome

145

Ehlers-Danlos syndrome is associated with this problem

berry aneurysms

146

This dz is a primarily autosomal-dominant d/o caused by a variety of gene defects resulting in abnormal collagen synthesis. It is characterized by :
1) multiple fractures occuring with minimal trauma (brittle bone dz), which may occur during the birth process
2) Blue sclerae due to the translucency of the connective tissue over the choroid
3) hearing loss (abnormal middle ear bones)
4) Dental imperfections due to lack of dentition

osteogenesis imperfecta

147

What can osteogenesis be confused with

child abuse

148

what is the incidence of OI type I

1:10,000

149

what is the incidence of OI type II

0 - death in utero

150

Given the immunohistochemical stain give the cell type it stains for:
Vimentin

Connective tissue

151

Given the immunohistochemical stain give the cell type it stains for:
Desmin

muscle

152

Given the immunohistochemical stain give the cell type it stains for:
Cytokeratin

epithelial cells

153

Glial fibrillary acid proteins (GFAP)

neuroglia

154

Neurofilaments

neurons

155

Give the site of metabolism: Fatty acid oxidation (B-oxidation)

mitochondria

156

Give the site of metabolism: acetyl-CoA production

mitochondria

157

Give the site of metabolism: Krebs cycle

mitochondria

158

Give the site of metabolism: glycolysis

cytoplasm

159

Give the site of metabolism: fatty acid synthesis

cytoplasm

160

Give the site of metabolism: HMP shunt

cytoplasm

161

Give the site of metabolism: protein synthesis (RER)

cytoplasm

162

Give the site of metabolism: steroid synthesis (SER)

cytoplasm

163

Give the site of metabolism: gluconeogenesis

both cytoplasm and mitochondria

164

Give the site of metabolism: urea cycle

both cytoplasm and mitochondria

165

Give the site of metabolism: heme synthesis

both cytoplasm and mitochondria

166

give the enzyme deficiency that would result in MILD galactosemia

galactokinase

167

give the enzyme deficiency that would result in SEVERE galactosemia

galactose-1-phosphate uridyltransferase

168

give the enzyme deficiency that would result in Von Gierke's

glucose-6-phosphatase

169

give the enzyme deficiency that would result in essential fructosuria

fructokinase

170

give the enzyme deficiency that would result in fructose intolerance

aldolase B

171

This is an adenine base + ribose + 3 phosphoryls. 2 phosphoanhydride bonds, 7 kcal/mol each

ATP

172

aerobic metabolism of glucose produces this manny ATP via the malate shuttle and this many ATP via G3P shuttle

38
36

173

Anaerobic glycolysis produces this many ATP per glucose molecule

2

174

How is ATP hydrolysis used

it is coupled to energetically unfavorable rxns

175

Give the activated carrier for each molecule:
ATP

phosphoryl

176

Give the activated carrier for each molecule: NADH, NADPH, FADH2

electrons

177

Give the activated carrier for each molecule: Coenzyme A, lipoamide

Acyl

178

Give the activated carrier for each molecule: biotin

CO2

179

Give the activated carrier for each molecule: tetrahydrofolates

1-carbon units

180

Give the activated carrier for each molecule: SAM

CH3 groups

181

Give the activated carrier for each molecule: TPP

Aldehydes

182

Give the activated carrier for each molecule: UDP-glucose

Glucose

183

Give the activated carrier for each molecule: CDP-choline

Choline

184

ATP + methionine -->

SAM

185

What does SAM do?

SAM transfers methyl units to a wide variety of acceptors (e.g., synthesis of phosphocreatine, a high-energy phosphate active in muscle ATP production).

mneu: SAM the methyl donor man

186

Regeneration of methionine (and thus SAM) is dependent on this vitamen

B12

187

give the signal molecule given its precursor: ATP ->

cAMP via adenylate cyclase

188

give the signal molecule given its precursor: GTP ->

cGMP via guanylate cyclase

189

give the signal molecule given its precursor: Glutamate ->

GABA via glutamate decarboxylase (requires vitamen B6

190

give the signal molecule given its precursor: choline->

ACH via choline acetyltransferase (ChAT)

191

give the signal molecule given its precursor: arachidonate->

prostaglandins, thromboxanes, leukotrienes via cyclooxygenase/ lipoxygenase

192

give the signal molecule given its precursor: fructose-6-P->

fructose 1,6-bis-P via phosphofructokinase (PFK), the rate-limiting enzyme of glycolysis

193

give the signal molecule given its precursor: 1,3BPG->

2,3-BPG via bisphosphoglycerate mutase

194

what are the 2 universal electron acceptors

Nicotinamides (NAD+,NADP+) and flavin nucleotides (FAD+)

195

Describe 1st step of B-oxidation of very long chain FA in Peroxisomes?

1st step of of B-oxidation is catalized by an FAD containing oxidase. e- are transfered from FADH2 to O2 which is then reduced to H2O2

Takes place in peroxisome because H2O2 is produced

196

What are similarities & differences of mitochondrial vs peroxisomal B-oxidation?

Both generate FADH2 & NADH but
Peroxisomal is less efficient because FADH can’t get through peroxisomal membrane (must be oxidized by O2)

197

Why do peroxysomal B-oxidation?

very long chain FA cannot cross mit membrane, must be broken up by peroxysomes

198

Describe oxydation of phytanic acid?

a peroxysomal alpha hydroxylase oxidizes the alpha carbon so that B oxidation can occur.

199

Refsum's disease

alpha oxidase enzyme is defective so we cannot break down phytanic acid

200

w-oxidation of FA

converts FA to dicarboxylic acids. Results in DC urea. Which is diagnostic for problem w/ B oxidation

201

4 steps of B-oxidation

1)Oxidation (ACoA dehyd)
2)Hydration (enol CoA hyd)
3)Oxidation(B hydroxy CoA hyd)
4)Cleavage (B keto thiolase)

202

Metabolism of Monosaturated Fats

2-3 enol-CoA isomerase - converts cis bond to trans

203

Metabolism of Polyunsaturated Fats

2-3 enol-CoA isomerase - converts cis bond to trans
2-4 dienol Co A reductase – reduces one of the double bonds

204

Propynyl Co A pathway

Propionyl CoA to Succinyl CoA. 1st step involves Propionyl CoA carboxylase (ABC enzyme) conversionof Propionyl CoA to methmylmalonyl CoA. Last step involves methyl-Malonyl CoA mutase conversion of Methylmalonyl CoA to Succinyl CoA. This last enzyme requires B12 therefore build up of Methylmalonyl CoA is diagnostic for B12 deficiency.

205

ABC enzymes

ABC
Pyruvate carboxylase -
Acetyl CoA carboxylase -
Propionyl CoA carboxylase -

206

MCAD deficiency

B oxidation in liver tissue in order for gluconeogenesis – if can’t do B-oxidation – hypoglycemic shock;
Feed child, replenished glycogen stores, in night using glycogen stores, next morning feed – child never in hard glucagon world. Never know about deficiency. Using liver glycogen always. When glycogen stores don’t get built up child needs to do gluconeogenis need to do B oxidation – usually dies in middle of night.

207

3 ketone bodies:

1)Acetoacetate can covert to:
2)Acetone (volitile)
3)D-B Hydroxybutyrate (more stable)

208

Why are ketone bodies made in liver cells only?

HMG Co A synthase –makes ketone bodies and found only in liver mitochondria

209

Why are ketone bodies broken down in tissues other than the liver

B-ketoacyl- CoA transferase is found in mitochondria outside liver -allows extrahepatic tissues to break ketone bodies down

210

Fuel for Brain
1) 24 hours
2)day 2-7
3) After 1 week

1)glycogen
2) protein (mostly glucose from gluconeogenesis but some ketone bodies)
3)Fat & small amount of protein-mostly ketone bodies but some glucose from gluconeogenesis