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[3] Step 1 USMLE > Biochem - S > Flashcards

Biochem - S Flashcards

1
Q

What type of bonds stabilize 1° protein structures

A

Peptide Bonds

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2
Q

What type of bonds stabilize 2° protein structures (alpha helix vs. Beta sheets)

A

Hydrogen Bonds

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3
Q

What type of bonds stabilize 3° protein structures (4)

A

Ionic /Hydrophobic /Hydrogen /Disulfide Bonds

Tertiary = overall shape after compact folding of secondary structure

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4
Q

Describe Disulfide Bonds

A

Strong Covalent bonds between 2 cysteine residues within the same polypeptide chain –> prevents denaturation

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5
Q

After 12-18 hours of fasting, ____ becomes the main source for blood glucose. Recall the reaction that ends with Glucose vs. energy.

A

Gluconeogenesis;

Pyruvate —(pyruvate carboxylase)–> Oxaloacetate —(PEP carboxykinase) —> PEP

ActetylCoA upregulates pyruvate carboxylase

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6
Q

What are [Transmembrane Domains] made of and what is their function?

A

[Alpha helices made with Hydrophobic Amino Acids]; anchors Integral proteins to phospholipid bilayer

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7
Q

[Methylmalonic Acidemia] MOD

A

Organic acidemia due to deficiency of methylmalonyl-CoA mutase

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8
Q

[Methylmalonic Acidemia] Labs (3)

A
  1. HyperAmmonemia
  2. Ketotic hypOglycemia
  3. INC Urine Proprionic Acid - metabolic acidosis
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9
Q

[Familial Dysbetalipoproteinemia Type 3] Mode of inheritance

A

auto recessive

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10
Q

[Familial Dysbetalipoproteinemia Type 3] MOD

A

Defects in [ApoE3 and E4]–> DEC clearance of chylomicrons & VLDL remnants

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11
Q

[Familial Dysbetalipoproteinemia Type 3] Clinical Presentation (3)

A
  1. Xanthomas
  2. Atherosclerosis
  3. INC Cholesterol & Triglyceride
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12
Q

Which Vitamin deficiency is [Egg White Avidin] associated with and how does this present (3)?

A

Having No Bio makes me MAD!

[Biotin B7]; [Myalgia(lactic acidosis)] + Anorexia + Dermatitis

(Egg White Avidin Avidly Binds [Biotin B7])

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13
Q

1 gram protein = ___ calories

A

[1 gram protein] = [4 calories]

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14
Q

1 gram fat = ___ calories

A

[1 gram protein] = [9 calories]

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15
Q

Spliceosomes require ____ to Function. What is their function and what are they made by?

A

snRNPs (small nc. ribonucleaic acid - made by RNA Pol 2 in nucleus)

Remove introns containing [GU at 5’] and [AG at 3’] from pre-mRNA –> Forms [Mature mRNA Exons]

snRNPs are targeted by SLE Smith Ab

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16
Q

How is Ca+ associated with Glycogen Degradation in Skeletal m.

A

Sarcoplasmic Retic. releases Ca+ –> Activates [Phosphorylase kinase] –> Stimulates Glycogen phosphorylase —> Glycogenolysis

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17
Q

Where does Vitamin __ hydroxylation of proline and lysine of collagen occur?

A

Vitamin C; Rough ER

Vitamin C deficiency –> Scurvy

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18
Q

Xeroderma Pigmentosum defect

A

defect in DNA excisional repair; exacerbated with UVB radiation

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19
Q

Xeroderma Pigmentosum Clinical Presenatation at:

A: 1 yo (4)

B: Later in life

A

Dry Pigmented Skin

  • 1 yo: Scaling + Erythema + [Lentigo on face] + Hyperpigmentation
  • Later in life: Skin Atrophy + Telangiectasia + CA
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20
Q

Xeroderma Pigmentosum Mode of inheritance

A

auto recessive

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21
Q

What 2 mechanisms regulate the Lac Operon

A
  1. Repressor binding to operator locus = negative regulation
  2. cAMP-CAP binding upstream of promoter = positive regulation
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22
Q

What happens when mutations impair binding of repressor to the operator locus?

A

Constitutive Expression of Lac Operon

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23
Q

Describe Alternative Splicing

A

Exons of a gene are reconnected during post-tx processing – > different mRNA –> different proteins

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24
Q

Is Alternative Splicing a normal function of Eukaryotes? Why or why not?

A

Yes; INC biodiversity of proteins

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25
Q

What is HgbC caused by and how does it manifest?

A

Missense mutation resulting in Glutamate being replaced by Lysine (less negative charge) in beta globin chain –> milder form of sickle cell

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26
Q

[Spinal Muscular Atrophy] MOD

A

SMN1 mutation –> impaired assembly of snRNPs in LMN –> Flaccid paralysis

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27
Q

Transamination occurs between ____ and ____. Which molecule serves as a cofactor for transamination and decarboxylation

A

Transamination occurs between [amino acids] and [a-keto acid]. [Pyridoxine B6] = transamination cofactor

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28
Q

What is the the Wobble Hypothesis

A

First 2 nucleotide positions on mRNA codon require traditional base pairing, but the [third wobble nucleotide] may undergo nontraditional base pairing –> more than 1 codon can code for an AA

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29
Q

How does [Pyruvate Kinase] deficiency cause Hemolytic anemia and Splenomegaly

A

Failure of Glycolysis –> insufficient ATP to maintain RBC structure –> [splenic red pulp hyperplasia] to remove these deformed RBC

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30
Q

[Tetrahydrobiopterin BH4] is a cofactor for the synthesis of what compounds? (3)

A

Tyrosine

Dopapmine

Serotonin

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31
Q

What Dz occurs from [Tetrahydrobiopterin BH4] deficiency? MOD

A

(PKU) Phenylketonuria; Dihydropteridine Reductase becomes deficient w/out cofactor –> Inability to convert Phenylalanine –> Tyrosine

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32
Q

Phenylketonuria tx (2)

A
  1. low phenylalanine diet
  2. BH4 supplementation
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33
Q

Which DNA Polymerase has exonuclease activity and what is the exonuclease function (2)

A

[DNA Pol 1 and 3] has [3 —> 5 exonuclease activity] + [5–>3 Polymerase] activity

Exonuclease removes RNA primer and repairs DNA sequences

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34
Q

What type of relationship does TNFa have with Insulin receptors?

A

TNFa Phosphorylates [serine & threonine AA of insulin receptors and their subtrates] –> Insulin Resistance

Catecholamines/Glucocorticoids/Glucagon also do this

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35
Q

HyperHomocysteinemia is due to mutations in ____ (3)

A

6 / 9 / 12

[Pyridoxine B6] vs. [Folate B9] vs. [B12]

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36
Q

HyperHomocysteinemia Manifestations (3). INC risk for what?

A
  1. Marfanoid Habitus
  2. Ectopia Lentis
  3. Developmental Delay

INC RISK FOR THROMBOEMBOLISM

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37
Q

Describes Homocysteine metabolism

A
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38
Q

[Pyruvate Dehydrogenase Deficiency] causes ____ and ____ clinically. MOD

A

Lactic Acidosis ; Neuro defects

Inability to convert Pyruvate –> AcetylCoA –> shunting of Pyruvate to Lactic Acid during oxidative phosphorylation

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39
Q

[Pyruvate Dehydrogenase Deficiency] Tx

A

[Exclusive Ketogenic Amino Acids (Lysine vs. Leucine)]

since these will provide AcetylCoA w/out INC lactate

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40
Q

Describe the path for Pyruvate –> Energy

A
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41
Q

Describe the path for Pyruvate –> Glucose

A

AcetylCoA upregulates [Pyruvate Carboxylase]

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42
Q

Glycolysis, Fatty Acid Synthesis and Pentose phosphate all occur in what part of the cell?

A

Cytosol

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43
Q

B-oxidation, TCA and Pyruvate Decarboxylation all occur in what part of the cell?

A

Mitochondria

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44
Q

What is Transketolase

A

[Pentose Phosphate pathway] enzyme that uses [Thiamine VitB1] to shuttle 2-carbon fragment between sugar molecules & to convert [Fructose6phosphate] w/the help of TransAldolase

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45
Q

[Aldolase B Deficiency] MOD.

A

Hereditary Fructose intolerancE

  • THIS CAN BE LIFE THREATENING*
  • Surcose –> Fructose & Glucose*
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46
Q

[Fructokinase Deficiency] MOD

A

Fructose from diet is absorbed & secreted into urine due to impairment of Fructose —(Fructokinase)—> Fructose1P

*Detected via Positive Copper Reduction Test*

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47
Q

What is the function of [AcylCoA Dehydrogenase] and how is it related to fasting?

A

Catalyzes first step in B-oxidation of Fatty acids and ironically, the most commonly deficient.

Without it –> hypOglycemia with fasting

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48
Q

NAD+ is required to convert _____ into ____ during glycolysis. What occurs under ANaerobic conditions?

A

NAD+ converts [Glyceradehyde3Phosphate] –> [1-3 Bisphosphoglycerate] during glycolysis

ANAerobic conditions: NADH transfers electrons to pyruvate –> Lactate and More NAD+

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49
Q

[Acute Intermittent Porphyria] tx (2)

A

Glucose vs. Hemin (Both inhibit ALA synthase activity)

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50
Q

Identify

A
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51
Q

How does [Short non-coding RNA sequences] such as ___ and ___ work?

A

microRNA & [small interfering RNA] both induce posttx gene silencing by base-pairing with complementary sequences on target mRNA molecules

52
Q

Where is [Hormone sensitive Lipase] found and what is its function

A

Adipose; Breaks down Stored TAG –> Fatty Acids & Glycerol during starvation. Needed for Hepatic Gluconeogenesis & ketone body formation

53
Q

Galactose is converted to Galactitol by _____ and can cause ___ eye damage if in excess –> _____.

This ultimately occurs from a _____ deficiency which should convert Galactose —> ____. How does Lactose play a role in this?

A

Galactose is converted to Galactitol by Aldose Reductase and can cause Osmotic eye damage if in excess—> Cataracts. This ultimately is from Galactokinase deficiency which should convert Galactose –> Galactose1P.

Lactose is converted –> Galactose by [BGalactoSidase]

54
Q

[RiboFlavin B2] is a precursor for ___ and ___. Which of these participates in the TCA cycle?

A

FMN and FAD.

FAD acts as electron acceptor for [Succinate Dehydrogenase Complex 2] in ETC and converts succinate –> Fumarate in TCA

55
Q

Explain how the [Phospholipase C] 2nd messenger system causes Ca+ release and smooth m. contraction?

A
56
Q

Why is [Total T3 levels] normal in early hypOthyroidism?

A

T3 is converted from T4 in peripheral tissues and so only T4 (made from thyroid) may be initially low

57
Q

What are [P Bodies]

A

Cytoplasmic important molecules for mRNA translation and degradation

58
Q

When is the RAS oncogene normally active?

A

ONLY when bound to GTP

59
Q

Proteins destined for Lysosomes require ______ to ensure proper transit through ______

A

Proteins destined for Lysosomes require [phosphorylation of mannose residues] to ensure proper transit through Golgi

60
Q

[Ehlers Danlos] MOD

A

Heritable Abnormal Collagen formation from [Procollagen Peptidase deficiency (impaired cleavage of N-terminal propeptides)] –>abnormal collagen

61
Q

____ is the most common NON-nuclear DNA in Eukaryotic cells. It codes for what 3 major things?

A

Mitchondria DNA

  • [Oxidative metabolic pathway] proteins
  • rRNA - for mitochondrial proteins
  • tRNA - for mitochondrial proteins
62
Q

Which parameter of O2 does not change with Methemoglobinemia?

A

O2 Partial Pressure (free floating)

Dissolved O2 in plasma is unrelated to HgB function

63
Q

Why is Dysphagia a problem in Demented Elderly?

A

It’s a RF for Aspiration PNA –> Requires Hospitlization

64
Q

Hyperammonemia is common in cirrhotic pts, from inability to metabolize _____ . How does this affect CNS?

A

[Nitrogenous Waste]; Crosses BBB –> Excess Glutamine accumulation within astrocytes–> DEC Glutamine needed for Glutamate neuroexcitatory actions

65
Q

What’s the most abundant amino acid in collagen? How does it play a role in Collagen shape?

A

Glycine; Triple helical conformation of collagen is from reptitive amino acid sequence within each alpha chain. Glycine occupies every 3rd position on that chain (Gly - X - Y)

66
Q

How does 2,3 BPG facilitate O2 release

A

Forms ionic bonds with beta-subunits of DeOxygenated HgBA and facilitates O2 release –> peripheral tissue

67
Q

How is 2,3 BPG related to Fetal HgB

A

When 2,3 BPG is mutated –> [HgB A] starts to resemble [HgB F] since its O2 affinity will be much HIGHER

68
Q

Which enzyme partially compensates for [Fructokinase deficiency: fructosuria]

A

Hexokinase converts excess dietary fructose –> [fructose6Phosphate] but this isn’t sufficient

69
Q

Which Dz are snRNPs attacked in

A

SLE (by Smith Ab)

70
Q

Alkaptonuria MOD

A

Not having [Homogentisic acid Dioxygenase] blocks Tyrosine metabolism –> accumulation of homogentisic acid

71
Q

Alkaptonuria Clinical Presentation (3)

A
  1. Black Urine when exposed to air
  2. Blue connective tissue (sclerae & ear)
  3. Arthropathy
72
Q

Alkaptonuria Mode of Inheritance

A

auto recessive

73
Q

Which hormones utilize [Protein Kinase A] GPCR second messenger? (3)

A

TSH

Glucagon

PTH

74
Q

[Marfan Syndrome MOD].

Where is this protein found normally (3)

A

[Fibrillin1 defect (an extracellular scaffold for elastin)]

  1. Lens
  2. Periosteum
  3. Aortic Media –> Aortic Root Dilation –> Dissection
75
Q

What does Polycistronic mean with Bacterial mRNA

A

1 mRNA codes for several proteins at same time

Regulated by single promoter/operator and regulatory elements

76
Q

Why does Fructose have a more rapid rate of metabolism than Glucose?

A

Dietary fructose –(Liver phosphorylated)–> F1P –> rapidly metabolized because it bypasses PFK1

PFK1 = major rate-limiting enzyme in glycoslysis

77
Q

[Niemann Pick] MOD

A

Sphingomyelinase Deficiency –> accumulation of Sphingomyelin

78
Q

[Niemann Pick] Clinical Presentation (3)

A
  1. Cherry Red Macular Spot
  2. Neuro Regression
  3. Hepatosplenomegaly (differentiates from Tay-Sachs)
79
Q

Tay-Sachs Clinical Presentation (2)

A
  1. Cherry Red Macular Spot
  2. Neuro Regression
80
Q

Tay-Sachs MOD

A

[B-Hexosaminidase A Deficiency] –> GM2 accumulation in neurons

81
Q

How is [Malonyl-CoA] significant in Fatty acid synthesis

A

[Malonyl-CoA] inhibits [mitochondrial carinitine acyltransferase] –> inhibits Beta-oxidation

Malonyl-CoA is formed from acetyl-CoA

82
Q

Name the genetic predisposition to Gout

A

[PRPP synthetase activating mutations] –> INC Risk for Gout due to abnormal purine regulation

Neutrophils are indicated in Gout pathology

83
Q

How does Insulin stimulate glycogen synthesis once it activates Tyrosine Kinase signaling

A

Tyrosine Kinase activates Protein Phosphatase –> Dephosphorylates Glycogen Synthase –> Glycogenesis

84
Q

How do Kidneys excrete Acid in Chronic acidemic states

A

Tubular epithelium metabolize Glutamine –> GlutamATe, generating NH4+ –> excreted in urine while HCO3 is ReAbsorbed

85
Q

What is Southwestern blotting used to detect (3)

A

DNA-binding proteins (transcription factors vs. nucleases vs. histones)

86
Q

[Alpha Glucosidase Acid Maltase] deficiency presents _____ with lysosomal ___ accumulation. Clinical manifestations (3)?

A

early infancy with lysosomal glycogen(PAS+) accumulation;

“Big Heart, Big Tongue, No Muscle”

  • Cardiomegaly
  • Macroglossia
  • Muscular hypOtonia
87
Q

What is the rate-limiting enzyme in the [Pentose Phosphate Pathway] and what does it produce

A

[Glucose - 6 - Phosphate Dehydrogenase] = Major source of Cellular NADPH

If deficient, will resemble [Glutathione Reductase deficiency] = [Hemolytic anemia from oxidative stress]

88
Q

NADPH function (2)

A

Reduces Glutathione (preventing oxidative damage) and [Biosynthesis of Cholesterol/Fatty Acids/Steroids]

[Glutathione Reductase deficiency] may cause similar pathology

89
Q

How is Cortisol related to Epi and NorEpi

A

Cortisol INC conversion of [Epi and NorEpi] in adrenal Medulla by INC expression of [phenylethanolamine methyltransferase]

90
Q

What is Glucokinase and what Dz develops from its mutation?

A

[Pancreatic beta cell: Glucose Sensor] that controls rate of glucose entry into TCA cycle; [Maturity onset Diabetes of the young]

91
Q

[McArdle Glycogen Storage Dz 5] MOD

A

Myophosphorylase Deficiency–> DEC Muscle Glycogenolysis

92
Q

[McArdle Glycogen Storage Dz 5] presentation (3)

A

Myoglobinuria with Exercise

93
Q

Why does HgB-S cause worst sx than HgB-C

A

HgBS has a valine substituted for glutamic acid @ 6th position of B-globin chain –> Hydrophobic interactions between different HgBs–> RBC Sickling

94
Q

Explain the biochemistry for why INC [Fructose 2,6 Bisphosphate] Aids in the treatment of DM

A
95
Q

Lead (poisoning) directly inhibits __ and ____

A

Lead (poisoning) directly inhibits [ALA Dehydratase] and Ferrochelatase

96
Q

Intracellular Receptors that contain [Zinc finger binding domains] interact with which hormones? (3)

A
  1. Steroids
  2. Thyroid Hormone
  3. ADEK Vitamins
97
Q

[Cori Debranching Glycogen Storage Dz 3] presentation (3)

A
  1. Short stature
  2. hypOglycemia
  3. Muscle weakness & hypOtonia
98
Q

[Cori Debranching Glycogen Storage Dz 3] MOD

A

Debranching enzyme deficiency –> accumulation of glycogen with abnormal short outer chains (inability to degrade at alpha1-6 branch points)

99
Q

Base excision repair corrects __base DNA. Describe the process starting with removing defective base (4)

A

Single;

  1. Glycosylases remove defective base
  2. Sugar-phosphate site is cleaved and removed by endonuclease & lyase
  3. DNA Pol replaces missing nucleotide
  4. Ligase seals remaining nick
100
Q

PKU-Phenylketonuria Clinical Manifestation (4)

A
  1. Musty Odor
  2. Seizures (look for upward eye deviation)
  3. Eczema
  4. Retard
101
Q

Orotic Aciduria MOD

A

Defective [5-UMP synthase]–> INC Urinary Orotic Acid –> DEC pyrimidine synthesis. Improved with Uridine supplement

102
Q

What are Amatoxins and what do they inhibit

A

Toxin from Poisonous Mushrooms that inhibit [RNA Pol 2] –> NO mRNA synthesis

103
Q

Which enzyme is impaired in Galactosemia and what do you expect to see in the urine?

A

GALT; [Reducing Substance Unmetabolized Sugar]

104
Q

[Ehlers Danlos] Clinical Presentation (3)

A

Hypermobile Joints

Hyperelastic Skin

Easy Bruising & Hemarhtrosis

105
Q

Glycerol, made from ____ in Fat can be used by ____ in the ____ to make Glucose

A

Glycerol, made from Triglycerides in Fat, can be used by Glycerol Kinase in the Liver& Kidney to make Glucose

This is often the case in DKA pts

106
Q

Ab to Citrullinated proteins are highly associated with what Dz

A

Rheumatoid Arthritis

107
Q

[Beta Glucuronidase] is implicated in what condition

A

Pigment Gallstones

It’s released from injured liver cells and bacteria bilirubin glucuronides –> unconjugated bilirubin

108
Q

What is the recognition sequence for tRNA at its __ end

A

3 end recognition sequence = CCA

109
Q

Homocystinuria is most commonly caused by what

A

Defect in Cystathionine Synthase –> inability to convert Homocysteine to Cysteine. The Homocysteine then accumulates –> Elevated Methionine

Homocysteine is Thrombotic!

110
Q

Carinitine Deficiency MOD

A

Defective Fatty acid transport from cytoplasm into mitochondria –> prevents Beta-oxidation during fasting (No Acetoacetate)

111
Q

All 3 [Prokaryotic DNA Pol] have the abiliy to do what?

A

ALL can remove mismatched nucleotides via [3–>5 exonuclease activity]

Only DNA Pol 1 has [5–>3 exonuclease activity]

112
Q

Which intracellular pathway does GH use

A

JAK-STAT

Cytokines also use this pathway

113
Q

____ converts glucose –>Sorbitol, which is then —> Fructose by _____. Where is this pathway most common? (2)

A

Aldose Reductase converts glucose –>Sorbitol, which is then –> Fructose by Sorbitol Dehydrogenase.

Lens & [Seminal Vesicles]

114
Q

HgB molecules are structurally similar to ____. What does this mean?

A

myoglobin; if separated into alpha & beta monomers, the O2 disassociation curve would resembles myoglobins

115
Q

[Mccune Albright] MOD

A

G Protein activating mutation

116
Q

What is Heteroplasmy

A

Presence of both normal and mutated
mtDNA –> in variable expression in
mitochondrial dz

117
Q

How does Carnitine deficiency affect the body?

A

Carnitine deficiency impairs fatty acid transport from cytplasm –>mitochondria –> Inhibits B-oxidation (formation of Acetoacetate) –> [Myocyte injury from lack of TCA ATP] + [DEC Hepatic ketone production]

Carnitine is a [Mitochondrial acyltransferase]

118
Q

Which compound inhibits Carnitine

A

Malonyl-CoA

119
Q

Arginase is a ____ cycle enzyme that makes __(2)___ from arginine. What’s clinical manifestation of Arginase deficiency? (2)

A

Arginase is an Urea cycle enzyme that makes [Urea & Ornithine] from arginine.

Deficiency = Progressive Spastic Diplegia + growth delay

120
Q

[Biotin B7] is a cofactor for what type of enzymes? (3)

A

Any CARBOXYLATION enzymes!

  1. Pyruvate –> Oxaloacetate
  2. AcetylCoA —> MalonylCoA
  3. PropionylCoA –> MethylMalonylCoA
121
Q

Function of Primase

A

RNA polymerase that incorporates short RNA primers into replicating DNA

122
Q

Where are [Very Long chain fatty acids] & [Fatty acids with branch points at odd # carbons] oxidized?

A

Peroxisomes

123
Q

Function of Lactate Dehydrogenase

A

Pyruvate –> Lactate ; ANEROBIC

124
Q

_____ is the AA that transfers nitrogen to Liver for disposal. How is Nitrogen eliminated? (2)

A

Alanine;

  1. Amino groups are transfered to a-ketoglutarate –> Glutamate –> [Forms Urea in Liver] –> Urinated out
  2. Free Amonia also urinated out

Alanine must transfer Amino group before conversion to Glucose

125
Q

In which parts of the TCA cycle do you get ___(x)___ and how many ATP do they give

A: NADH

B: GTP

C: FADH2

A

Can I Keep Selling Sex For Money, Officer?

A: NADH = 2.5 ATP each = (I-Keep) (Keep-Selling) (Money-Officer)

B: GTP = 1 ATP = (Selling - Sex) - used in Gluconeogenesis by PEP Carboxykinase to convert Oxaloacetate–>PEP

C: FADH2 = 1.5 ATP each = (Sex - For)

[3] Step 1 USMLE (8 decks)

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