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BioChem Flashcards

1
Q

Tuberous Sclerosis
What kind of inheritance?
Manifestations?

A

Autosomal Dominant w/ incomplete penetrance
Harmatomas of CNS and Retina, Adenoma Sebaceum (cutaneous angiofibroma), Mitral Reg, Ash-Leaf Spots on skin, Cardiac Rhabdomyomas, Mental Retardation, Renal Angiomyolipomas and Renal Cysts, Seizures, Increased incidence of astrocytomas

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2
Q 
Histones?
Charge
Amino Acids
What do they form?
What ties it together?
A

Positively charged
Lysine and Arginine
Octamer tied together by H1

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3
Q 
DNA methylation 
Which Nucleotides 
When in cell cycle?
Function 
What organisms
A

C and A
Template strand is methylated during DNA replication which allows mismatch repair enzymes to distinguish between old and new strands
Prokaryotes

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4
Q

What does Histone Methylation do?

A

Inactivates DNA

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5
Q

What does Histone Acetylation do?

A

Relaxes DNA coiling allowing for transcription

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6
Q

Purines
Names
Rings
What is it made from?

A

“PURe As Gold”
Adenine, Guanine
2 rings
Glycine, Aspartate, Glutamine

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7
Q

Pyrimidines

Names

A

“CUT the PY”

Cytosine, Uracil, Thymine

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8
Q

Molecular group on Guanine

A

Ketone

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9
Q

Molecular group on Thymine

A

MeTHYl

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10
Q

How is Uracil made?

A

Cytosine gets Deaminated

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11
Q

RNA Nucleotides?

A

G-C, A-U

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12
Q

DNA Nucleotides

A

G-C, A-T

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13
Q

Which nucleotide bond is strongest

A

G-C has 3 hydrogen bonds

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14
Q

How is DNA melting point affected

A

↑ GC content –> ↑ melting temperature

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15
Q

Nucleoside

A

Base + Ribose

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16
Q

Nucleotide

A

Base + Ribose + Phosphate linked by 3’5’ phosphodiester bond

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17
Q

What makes up Pyrimidines

A

Aspartate and Carbamoyl Phosphate

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18
Q

Basic schematic of de novo purine synthesis

A

Start with sugar + phosphate (PRPP)

Then add base

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19
Q

Basic schematic of de novo pyrimidine synthesis

A

Make temporary base (orotic acid)
Add sugar + phosphate (PRPP)
Modify base

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20
Q

Purine synthesis pathway

A

Ribose 5-P –> PRPP ->->-> IMP –> AMP and GMP

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21
Q

Inhibition of de novo purine synthesis

A

6-mercaptopurine blocks de novo purine synthesis

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22
Q

Production of deoxyribonucleotides

A

Ribonucleotide reductase converts ribonucleotides into deoxyribonucleotides

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23
Q

CTP synthesis

A

Ribose 5-P –> PRPP

PRPP + Orotic Acid –> UMP –> UDP –> CTP

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24
Q

dTMP synthesis

A

Ribose 5-P –> PRPP

PRPP + Orotic Acid –> UMP –> UDP –> [Ribonucleotide reductase] –> dUDP –> dUMP –> [Thymidylate Synthase] –> dTMP

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25
Q

What pathways is Carbamoyl Phosphate involved with?

A

de novo pyrimidine synthesis and urea cycle

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26
Q

Ornithine transcarbamoylase deficiency
What is it?
Findings

A

OTC is a key enzyme in the urea cycle
Deficiency leads to accumulation of carbamoyl phosphate which is then converted into orotic acid
↑ Orotic acid with hyperammonemia

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27
Q

What inhibits Ribonucleotide reductase

A

Hydroxy Urea

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28
Q

What inhibits Thymidylate Synthase?

A

5-Fluorouracil

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29
Q

What inhibits human Dihydrofolate reductase

Net result?

A

Methotrexate

↓ dTMP

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30
Q

What inhibits bacterial Dihydrofolate reductase

Net result?

A

Trimethoprim

↓ dTMP

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31
Q

THF and dTMP synthesis

A

THF –> N5N10 methylene THF –> [Thymidylate Synthase] –> DHF –> [Dihydrofolate reductase] –> THF

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32
Q 
Orotic Aciduria 
What is it?
Pathway involved?
Where is the defect?
Genetics 
Findings 
Treatment
A 
Inability to convert orotic acid to UMP
de novo pyrimidine synthesis pathway 
UMP synthase 
Autosomal Recessive 
↑ orotic acid in urine, Megaloblastic anemia (does not improve with B12 or folic acid), Failure to thrive, No hyperammonemia 
Oral uridine administration
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33
Q

Adenine salvage pathway

A

Adenine + PRPP –> [APRT] –> AMP

AMP can become Nucleic acids, Adenosine, or IMP

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34
Q

Fate of Adenosine in salvage pathway

A

Adenosine can become AMP or Adenosine deaminase (ADA) can turn it into Inosine

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35
Q

Fate of IMP in purine salvage pathway

A

Hypoxanthine + PRPP –> [HGPRT] –> IMP

IMP can become inosine, AMP, or GMP

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36
Q

Fate of Inosine in Purine salvage pathway

A

Adenosine –> Inosine

Inosine –> Hypoxanthine

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37
Q

Fate of Hypoxanthine in Purine salvage pathway

A

Hypoxanthine can become IMP, Inosine, or Xanthine

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38
Q

Fate of Guanine in Purine salvage pathway

A

Guanine +PRPP –> [HGPRT] –> GMP
Guanine –> Guanosine
Guanine –> Xanthine

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39
Q

Fate of Guanosine in Purine salvage pathway

A

GMP –> Guanosine

Guanine ↔ Guanosine

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40
Q

Fate of GMP in Purine salvage pathway

A

GMP can be come Nucleic Acids, IMP or Guanosine

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41
Q 
Adenosine Deaminase Deficiency 
PathoPhys
Genetics
What does it lead to
Treatment
A

Excess ATP and dATP leads to an imbalance in nucleotide pool via feedback inhibition of ribonucleotide reductase thus preventing DNA synthesis thus ↓ Lymphocyte count
Autosomal recessive
SCID
1st disease to be treated by experimental human gene therapy

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42
Q 
Lesch-Nyhan Syndrome 
Deficiency 
Metabolic result
Genetics 
Findings
A

“He’s Got Purine Recovery Trouble”
HGPRT mutation which converts hypxanthine into IMP and Guanine into GMP
Excessive uric acid production and de novo purine synthesis
X linked recessive
Retardation, Self-Mutilation, Aggression, Hyperuricemia, Gout, Choreoathetosis

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43
Q 
Genetic Code Features 
Unambiguous 
Degenerate 
Commaless
Universal
A

Each codon = 1 AA
Most AA are coded by multiple codons except for Methionine (AUG) and Tryptophan (UGG)
Nonoverlapping: fixed starting point at a continuous sequence of bases except in some viruses
Conserved throughout evolution except in human mitochondria

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44
Q

Silent mutation

A

Same AA usually at 3rd position of condon (tRNA wobble)

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45
Q

Missense mutation

A

Changed AA to a similar AA

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46
Q

Nonsense mutation

A

Early stop codon

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47
Q

Frameshift

A

Misreading of all downstream nucleotides resulting in truncated, nonfunctional protein

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48
Q

DNA topoisomerases
Function
What inhibits it

A

Creates a nick in the helix to relieve supercoil created during replication
Fluoroquinolones inhibit prokaryotic topoisomerase II

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49
Q

DNA pol III
What organisms?
Direction of synthesis
Other functions?

A

Prokaryotic only
5’ –> 3’
Proofreads 3’ to 5’

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50
Q

DNA pol I
What organisms
Function
Functions with directions

A 
Prokaryotic only
Degrades RNA primer and replaces it with DNA 
Synthesis 5' --> 3'
Proofreading 3' --> 5'
Exonuclease 5' --> 3'
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51
Q

DNA ligase

A

Catalyzes the formation of phosphodiesterase bonds within strand of dsDNA. Joins Okazaki fragments

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52
Q

Telomerase

A

Adds DNA to 3’ end of chromosome to avoid loss of genetic material with every duplication

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53
Q

Nucleotide Excision repair
Process
What kind of lesions does it repair
Disease involving this pathway

A

Specific endonucleases release the oligonucleotide-containing damaged bases. Then DNA pol and Ligase fill and reseal the gap
Repairs bulky helix distorting lesions
Xeroderma pigmentosum: Prevents repair of pyrimidine dimers because of UV light

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54
Q

Base Excision repair
Process
What kind of lesions does it repair?

A

Specific glycosylases recognize and remove damaged bases. Apurinic/Apyrimidinic endonucleases cut DNA at both sites. Empty sugar is removed. Gap is filled in and resealed
Important in reapir of spontaneous/toxic deamination

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55
Q

Mismatch Repair
Process
Disease

A

Newly synthesized strand is recognized, mismatched nucleotides are removed and gap is filled and resealed
Mutated in Hereditary NonPolyposis Colorectal Cancer (HNPCC)

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56
Q

Nonhomologous end joining
Process
Requirements
Disease

A

Brings together 2 ends of DNA fragments to repair double stranded breaks
No requirement for homology
Mutated in ataxia telangiectasia

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57
Q

Direction of DNA and RNA synthesis?

Energy source?

A

5’ –> 3’

5’ end of dNTP

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58
Q

In which direction is mRNA read?

A

5’ –> 3’

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59
Q

Direction of Protein Synthesis

A

N to C

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60
Q

Most abundant type of RNA

61
Q

Ways to remember types of RNA?

A

“Rampant, Massive, Tiny”

62
Q

Eukaryotic start codon

A

“AUG inAUGurates protein synthesis”

AUG (rarely GUG) which codes for Methionine

63
Q

Prokaryotic start codon

A

AUG which codes for formylmethionine

64
Q

mRNA stop codons

A

UGA: U Go Away
UAA: U Are Away
UAG: U Are Gone

65
Q

Promoter code

A

TATA Box

TATAAT and CAAT

66
Q

Start of transcription numbering

67
Q

Termination signal

68
Q

Eukaryotic RNA pol
I, II, III
Functions

A

Numbered in order that they are used in protein synthesis
I: rRNA
II: mRNA - can open DNA at promoter site
III: tRNA
No proofreading function but can initate chains

69
Q

Prokaryotic RNA pol

A

1 RNA pol (multisubunit complex) makes all 3 kinds of RNA

70
Q

What inhibits RNA pol II

What does it lead to

A

α-amanitin (from mushroom)

Hepatotoxicity if ingested

71
Q

RNA processing in eukaryotes
What is initial transcript called?
What is it called if destined for transcription?
Where does processing occur?

A

Heterogenous nuclear RNA
pre-mRNA
Processing occurs in the nucleus

72
Q

RNA processing in eukaryotes

A

Capping on 5’ end with 7-methylguanosine
Polyadenylation an 3’ end
Splicing out of introns

73
Q

What is required for RNA to be transported out of the nucleus

A

Only processed RNA can be transported out of the nucleus

74
Q

Polyadenylation
What enzyme does it?
Template?
Signal

A

Poly-A polymerase
Does not require a template
AAUAAA

75
Q

Steps of Splicing pre-mRNA

A 
Primary transcript combines with snRNPs (small nuclear ribonucleoproteins) and other proteins to form a spliceosome 
Lariat shaped (looped) intermediate is generated 
Lariat is released to remove intron precisely and join 2 exons
76
Q

Disease involving snRNPs

A

Lupus: autoAbs to spliceosomal snRNPs

77
Q 
tRNA
Length 
Secondary structure 
What is on end?
Which end binds AAs
A

75-90 NTs
Cloverleaf form
On 3’ end is 5’ CCA 3’ along with a high percentage of chemically modified bases
3’ is bound to AA

78
Q

tRNA Charging
Enzyme
Proofreading
Energy

A

Aminoacyl-tRNA synthetase
Scrutinizes AA before and after it binds tRNA
If incorrect, bond is hydrolyzed
AA-tRNA bond has energy for formation of peptide bond

79
Q

Tetracyclines

A

Bind 30S subunit and prevents attachment of aminoacyl tRNA to A site

80
Q

Eukaryote Ribosomes

A

Even #s

40S and 60S

81
Q

PrOkaryote Ribosomes

A

Odd #s

30S and 50S

82
Q

Protein synthesis initiation

A

Activated by GTP hydrolysis

Initiation Factors help assemble 40S ribsomal subunit with the initiator tRNA and are then released

83
Q

Protein synthesis Elongation

A

“Going APE”

  1. Aminoacyl-tRNA binds A site (except initiator methionine)
  2. rRNA catalyzes peptide bond formation transferring polypeptide into A site
  3. Peptidyl tRNA moved into P site and empty tRNA moves to E site
84
Q

Protein synthesis Termination

A

Stop codon recognized by release factors and complete protein is released from ribosome

85
Q

Aminoglycosides

A

Bind 30S and inhibit formation of initiation complex and cause misreading of mRNA

86
Q

Chloramphenicol

A

Binds 50S and inhibits peptidyl transferase

87
Q

Macrolides

A

Bind 50S and prevent release of uncharged tRNA after it has donated its AA

88
Q

Process of Proteasomal degradation

A

Attachment of Ubiquitin tags them for breakdown

89
Q

Stages of cell cycle

A

G1 –> [Rb, p53] –> S –> G2 –> Mitosis

90
Q

Interphase

A

G1, S, and G2

91
Q

Stages of mitosis

A

Prophase, Metaphase, Anaphase, Telophase

92
Q

Regulation of Cell Cycle
CDKs
Cylcins
Cyclin-CDK complexes

A

CDKs are constitutively present and inactive
Cyclins are regulatory and are produced in a phase specific manner
Cyclin-CKD complexes activate and the inactivate for cell cycle to progress

93
Q

Tumor Suppressors
Names
Function

A

p53 and Hypophosphorylated Rb

Normally inhibit G1 to S progression

94
Q

Permanent cell type
Phase
What do they form
Examples

A

Remain in G0
Regenerate from stem cells
Neurons, Skeletal muscle, Cardiac muscle, RBCs

95
Q

Stable cell types
Name
Phase
Examples

A

Quiescent
Enter G1 from G0 when stimulated
Hepatocytes and Lymphocytes

96
Q

Labile cells
Phase
Examples

A

Never go to G0. Divide rapidly with a short G1

Bone marrow, Gut epithelium, Skin, Hair follicles, Germ cells

97
Q

Rough Endoplasmic Reticulum
What kind of proteins are synthesized here?
Protein modifications

A

Site of synthesis of secretory (exported) proteins

N linked oligosaccharide addition to many proteins

98
Q

Nissl Bodies

A 
RER in neurons 
Synthesizes ChAT (choline acetyltransferase) to make ACh and peptide NTs
99
Q

What do free ribosomes produce

A

Cytosolic and organellar proteins

100
Q

Which kind of cells are rich in RER?

A

Mucus-secreting goblet cells of SI and Ab secreting plasma cells

101
Q

Smooth Endoplasmic Reticulum
What is synthesized here?
Which cells are rich in it?

A

Site of steroid synthesis and detoxification of drugs and poisons
Liver hepatocytes and steroid hormone-producing cells of adrenal cortex are rich in SER

102
Q

Modifications that take place in Golgi?

A

Modifies N-oligosaccharides on Asparagine

Adds O-oligosaccharides on Serine and Threonine

103
Q

What directs proteins to lysosomes

A

Mannose-6-Phosphate added in lysosomes

104
Q

I cell disease
Genetics
PathoPhys
Presentation

A

Inherited lysosomal storage disorder
Failure of addition of mannose-6-phosphate in golgi means enzyme are directed outside of cell instead of lysosomes
Coarse facial hair, Clouded corneas, Restricted joint movement, High plasma levels of lysosomal enzymes. Often fatal in childhood

105
Q

Vesicle trafficking proteins
COPI
COPII
Clathrin

A

COPI: Retrograde (Golgi –> Golgi, Golgi –> ER)
COPII: Anterograde (Golgi –> Golgi, ER –> Golgi)
Clathrin: trans-Golgi –> lysosomes, Plasma membrane –> Endosomes (receptor mediated endocytosis)

106
Q

Peroxisomes

A

Membrane enclosed organelle involved in catabolism of very long fatty acids and AA

107
Q

Proteasomes

A

Barrel shaped protein complex that degrades damaged or unnecessary proteins tagged for destruction by ubiquitin

108
Q 
Microtubules 
Composition 
What is each dimer bound to?
What cellular structures does it make up? What functions are they involved with?
How does it grow and collapse?
A

α and β subunits
Each dimer has 2 GTPs bound to it
Flagella, Cilia, Mitotic spindles, Centrioles
Slow Axonal Transport and Cell Movement
Grows slowly, collapses quickly
Involved in slow axoplasmic transport in neurons

109
Q

Molecular motor proteins

A

Dynein: retrograde in MTs (+ –> -)
Kinesin: anterograde in MTs (- –> +)

110
Q

Drugs that act on MTs

A

Mebendazole/Thiabendazole: antihelminthic (prevents polymerization)
Griseofulvin: antifungal (prevents polymerization)
Vincristine/Vinblastine: anticancer (prevents polymerization)
Paclitaxel: anti-breast cancer (Stabilizes MTs)
Colchicine: antigout (prevents polymerization)

111
Q

Chediak-Higashi Syndrome
Where is the mutation?
PathoPhys
Presentation

A

Mutation in lysosomal trafficking regulator gene (LYST)
LYST required for MT dependent sorting of endosomal proteins into late multivesicular endosomes
Recurrent pyogenic infections, Partial albinism, Peripheral neuropathy

112
Q

Cilia
Structure
Motor proteins
Disease

A

9+2 arrangement of MTs. 9 doublets of MTs + 2 individual MT in middle
Dynein links peripheral 9 doublets
Kartagener’s Syndrome

113
Q

Kartagener’s Syndrome
PathoPhys
Presentation
Associated with what developmental defect

A

Immotile cilia due to dynein arm defect
Male infertility, ↓ female fertility, Bronchiectasis, Recurrent sinusitis
Associated with sinus inversus

114
Q

Actin and Myosin functions

A

Microvilli, Muscle contraction, Cytokinesis, Adherens junctions

115
Q

Intermediate filament names and stains

A 
Vimentin: Connective tissue
Desmin: Muscle 
Cytokeratin: Epithelial cells 
Glial Fibrillary Acid Protein (GFAP): NeuroGlia
Neurofilaments: Neurons
116
Q

Plasma Membrane composition

A

Cholesterol, Phospholipids, Sphingolipids, Glycolipids, and Proteins

117
Q

When is Na/K APTase phosphorylated

A

When open to extracellular side

118
Q

Ouabain

A

Inhibits Na/K ATPase by binding to K site

119
Q

Cardiac Glycosides
Names
MoA

A

Digoxin and Digitoxin

Inhibits Na/K ATPase leading indirectly to increased Ca –> increased contractility

120
Q

Most abundant protein in the human body

121
Q

Type I collagen
Frequency
Where is it present?
Disease

A

Most common collagen (90%)
Bone, Skin, Tendon, Dentin, Fascia, Cornea, Late Wound Repair
Defective in Osteogenesis Imperfecta

122
Q

Where is type II collagen

A

Cartilage (including hyaline, Vitreous body, Nucleus pulposus

123
Q

Type III collagen
Where is it present
Disease

A

Reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue
Ehlers-Danlos (vascular type)

124
Q

Type IV collagen
Where is it present
Disease

A 
Basement membrane (basal lamina)
Alport Syndrome
125
Q

Collagen mnemonic

A 
"Be (So Totally) Cool, Read Books"
I: Bone, Skin, Tendon
II: Cartilage 
III: Reticulin 
IV: Basement Membrane
126
Q

Collagen synthesis inside the fibroblasts

A
  1. RER: translation of α chains (preprocollagen)
  2. ER: Hydroxylation of specific proline and lysine residues (requires VitC)
  3. ER: Glycosylation of pro-α-chain hydroxylysine residues
  4. Formation of procollagen via hydrogen and disulfide bonds (triple helix of 3 α chains)
  5. Exocytosis
127
Q 
Osteogenesis imperfecta 
Type of collagen
PathoPhys
Genetics 
Presentation
A 
Type I collagen defect 
Problem forming triple helix of collagen α chains 
Genetic bone disorder caused by a variety of gene defects but most common form is Autosomal Dominant 
Brittle bones (multiple fractures with minimal trauma), Blue sclerae (translucent connective tissue over choroidal veins), Hearing loss (abnormal middle ear bones), Dental imperfections (lack of dentin)
128
Q

Collagen synthesis outside of fibroblasts

A
  1. Cleavage of disulfide rich terminal regions of procollagen forming insoluble tropocollagen
  2. Reinforcement of many staggered tropocollagen molecules by covalent lysine-hydroxylysine cross linkage (by Cu2+ containing lysyl oxidase)
129
Q 
Ehlers-Danlos 
Type of collagen involved?
PathoPhys
Presentation 
# of types
Inheritance
Associations 
Don't confuse w/
A

Type III or V defect
Problems with cross linking by Cu2+ containing lysyl oxidase
Hyperextensible skin, Easy bleeding and bruising, Hypermobile joints
6 types
Can be AD or AR
Joint dislocation, berry aneurysm, organ rupture
Marfan’s

130
Q

VitC deficiency

131
Q

Alport Syndrome
Type of collagen involved
Inheritance
Presentation

A

Type IV
Variety of genetic defects but most commonly X linked recessive
Progressive hereditary nephritis, deafness, and ocular disturbances

132
Q 
Elastin 
What is it? Where is it?
What is it made of?
Scaffolding? 
Where does cross-linking take place? 
What does cross-linking accomplish?
What breaks it down?
A

Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect verbetrae –> relaxed and stretched conformations)
Rich in proline and glycine (nonhydroxylated forms)
Tropoelastin with fibrillin scaffolding
Cross-linking takes place extracellularly and gives elastin its elastic properties
Broken down by elastase (which is normally inhibited by α1 antitrypsin)

133
Q

What causes wrinkles of aging?

A

Reduced collagen and elastin production

134
Q

Southern Blot

A

DNA electrophoresed, transfered to filter, denatured, labeled with probe

135
Q

Blots mnemonic

A

SNoW DRoP
Southern - DNA
Northern - RNA
Western - Protein

136
Q

Northern Blot

137
Q

Western Blot

A

Protein used

138
Q

Southwestern Blot

A

Identifies DNA-Binding Proteins using labeled oligonucleotide probes

139
Q

Microarrays

A

Nucleic acid sequences arranged on a grid and samples hybridize to the chip
Can detect SNPs

140
Q

Enzyme-Linked Immunosorbent Assay
Indirect
Direct

A

Indirect: Test antigen to see if specific Ab is in pt’s blood. Secondary Ab coupled to a color generating enzyme is added to detect 1st Ab
Direct: Test Ab coupled to a color generating enzyme to see if a specific antigen is present in pt’s blood

141
Q

Fluorescence in situ Hybridization (FISH)

A

Fluorescent DNA or RNA probes bind to specific gene sites on chromosomes.
Used for specific localization of genes and direct visualization of anomalies at molecular level (when deletion is too small to be karyotyped)

142
Q

Karyotyping
What is it?
What tissue can it be gotten from?
Uses

A

Metaphase chromosomes are stained, ordered, and numbered according to morphology, size, arm-length ratio and banding pattern
Blood, Bone marrow, Amniotic fluid, Placental tissue
Used to diagnose chromosomal imbalances

143
Q

16S ribosome
Where is it?
Function

A

30S ribosome

Binds complimentary mRNA to initiate translation - Shine Delgarno Sequence

144
Q

Lac Operon when Glucose is added

A

Glucose –/ AC, leading to a decrease in cAMP

When glucose is not present, cAMP is high and cAMP-CAP complex promotes transcription

145
Q

Septic Shock Acidosis
What kind of acidosis
Impairment

A

Lactic Acidosis with an Anion Gap

Tissue Hypoxia –> Anaerobic Respiration and impairment of OxPhos

146
Q

How does TNF alpha affect glucose uptake

A

TNF –> Serine phosphorylation which decreases the activity of the Insulin RTK

147
Q

Floppy baby with jaundice, enlarged tongue, hypotonia, umbilical hernia, hoarse cry, constipation…
What do they have
What are they at risk for?

A

Hypothyroidism

Congenital heart defects

148
Q

How does Radiation kill tumor cells?

A

dsDNA breaks and free radicals

149
Q

Rasburicase
Mechanism
Use

A

Metabolizes Uric Acid into Allantoin which is more soluble

Tumor Lysis Syndrome

USMLE (25 decks)

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