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Step 1 review cards > Biochemistry: Molecular > Flashcards

Biochemistry: Molecular Flashcards

1
Q

Chromatin structure

A

Heterochromatin DNA that is looped around a histone octamer to form a nucleosome “beads on a string” formation

Phosphate groups on the DNA = (-) charge

Lysine and arginine AAs on histone = (+) charge

note this structure is for all chromatin DNA that is NOT mitochondrial DNA. Mitochondrial DNA is circular and does not warp around histones

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2
Q

Heterochromatin

A

Condensed from of chromatin that is functional inactive (cant be transcribed)

Is darker on EM since it is denser

High levels of methylation ; low levels of acetylation

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3
Q

Barr bodies

A

Inactive X chromosomes that may appear on the nucleus of heterochromatin DNA

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4
Q

Euchromatin

A

Less condensed version fo chromatin DNA. Able to be transcribed

Is lighter on EM

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5
Q

DNA methylation

A

Act of adding a methyl group to DNA segment ends.

Does not change the DNA sequence at all, but makes the whole sequence “silenced” or not able to be transcribed.

  • commonly seen as a natural part of the following:
  • aging
  • exposure to carcinogens
  • genomic imprinting
  • inactivation fo X chromosomes*
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6
Q

Histone methylation

A

Adds a methyl group to histones, provide an almost complete (90%) “silence” of the wrapped heterochromatin.
- some of the heterochromatin can still unpackage and become euchromatin and be transcribed, but its very little

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7
Q

Histone acetylation

A

Addition of Acetyl groups tot he histone, causing all heterochromatin to unpackage and become euchromatin
- increases transcription

removes the histones (+) charge via adding the acetyl groups to lysine and arginine AAs

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8
Q

Histone deaceytlation

A

Removal of acetyl groups, causes packaging of euchromatin into heterochromatin around the histones

makes lysine and arginine AAs (+) again

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9
Q

Nucleoside vs nucleotide

A

NucleoSide = base + deoxyribose (Sugar ONLY)

NucleoTide = base + Deoxyribose + phosphaTe group w/ 3’5 bonds

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10
Q

Purines vs Pyrimidines

A

Purines = 2 rings

  • A/G
  • “Pure as gold” (AG)

Pyrimidines = 1 ring

  • C/T/U
  • “CUT the PY”
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11
Q

Deamination reactions of the purines and pyrimidines

A

Cytosine -> uracil

Uracil -> thymine

Adenine -> hypoxanthine

Guanine - > xanthine

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12
Q

Amino acids needed for purine synthesis

A

Glycine

Aspartate

Glutamine

“Cats purrine until the GAG”

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13
Q

H bonds and respect to melting point temps

A

C-G bonds = 3 H

A- T bonds = 2 H

More H bonds = high melting point

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14
Q

What drugs affect pyrimidine synthesis only?

A

Leflunomide: inhibits dihydroorotate dehydrognease
- aspartate + phosphate -> orotic acid

5-Fluorouracil (5-FU) & capecitabine: inhibts thymidylate synthase
- dUMP -> dTMP

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15
Q

What drugs affect purine synthesis only?

A

6-mercaptopurine (6-MP) & azathioprine: inhibit the whole thing

Mycophenolate & ribavirin: inhibit Inosine monophosphate dehydrogenase
- IMP -> GMP

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16
Q

What Drugs that affect both purine and pyrimidine synthesis?

A

Hydroxyurea: inhibits ribonucleotide reductase

Methotrexate (MTX), and trimethoprim (TMP): inhibit dihydrofolate reductase in humans and material respectively
- MTX = autoimmune and cancer ; TMP= antibiotic

17
Q

Leach-Nyhan syndrome

A

X-linked recessive Genetic disorder where there is absent HGPRT enzymes

  • cant convert hypoxanthine -> IMP and guanine -> GMP
  • results in over production of uric acid
Symptoms 
H: hyperuricemia 
G: Gout 
P: Pissed off (increased aggression and thoughts of self mutilation)
R: Retardation 
T: DysTonia

Treatment:

  • Allopurinol (1st line)
  • feuxostat (2nd line)
  • both are Xanthine oxidase inhibtors*
18
Q

4 Genetic code features

A

1) Unambiguous

2) degenerate/redundant
- “wobble” codons exist meaning that codons that have the same first 2 letters, but different 3rd letter can encode for the same AA
- exception is met (AUG) and Tryptophan (UGG). These can only be made from these specific 3 letters

3) no overlapping
- codons are read from a fixed point and continuous sequence

4) universal
- is conserved throughout evolution
- exception is mitochondrial DNA

19
Q

Telomerase effect on DNA replication

A

Found in eukaryotes only

Adds a DNA “cap” ( TTAGGG) to the 3’ end of chromosomes to prevent degradation with each duplication

  • this is a common dysregulated cells in cancer*
20
Q

Mutations ranked in order of damage

A

1) frame shift
- deletion or insertion fo a nulceotide(s) not divisible by 3
- causes a “shift” in the entire sequence

2) nonsense mutation

3) missense mutation
- changing one purine or pyrimidine to change 1 codon to signal for 1 different AA only

4) silent mutation

21
Q

Lac operon

A

Classic example of a prokaryote operon response to environmental change

In the presence of high glucose and no lactose = NO transcription

  • repressor protein is bound
  • adenylate Cyclase is antagonized 100%

In the presence of low glucose and no lactose = mild transcription

  • adenylate Cyclase is no longer antagonized - > increases cAMP -> binds CAP protein to operon and transcribes little amounts of DNA
  • repressor protein is still bound though

In the presence of low glucose and lactose = high transcription

  • adenylate Cyclase is no longer antagonized - > increases cAMP -> binds CAP protein to operon and transcribes lots of DNA
  • repressor protein is no longer bound (lactose represses the repressor)
22
Q

Types of RNA polymerases in eukaryotes

A

RNA 1 poly:

  • makes rRNA (“rampant RNA” most common type)
  • only present in nucleolus

RNA 2 poly:

  • makes mRNA, MiRNA, and snRNA
  • present everywhere
  • a-amanitin inhibts RNA 2 poly

RNA 3 poly:

  • makes tRNA
  • present everywhere
23
Q

RNA polymerases in prokaryotes

A

RNA 1 poly in prokaryotes makes all RNA types

  • Rifampin is the antibiotic that blocks RNA poly in prokaryotes*
24
Q

Exons vs introns

A

Exons:

  • contain actual protein coding information
  • are substituted in and out for specific proteins “alternative splicing”

Introns:

  • contain gene expression information
  • are always removed in forming mRNA
25
Q

TRNA structure and function

A

T-arm = tethers the tRNA molecule to a ribosome
- required for binding

D-arm = allows for Detection of tRNA by a specific AA and vise versa

  • allows for the proper AA to bind
  • “charges” the tRNA

Function = carry amino acids to ribosomes

a mischarged tRNA reads the codon from mRNA properly, but binds the wrong AA to the codon

26
Q

What are possible covalent modifications to a novel protein?

A

Phosphorylation

Glycosylation

Hydroxylation

Methylation

Acetylation

Ubiquitination

27
Q

Ribosomal subunits for eukaryotes and prokaryotes

A

Eukaryotes

  • 40s+ 60s = 80s
  • all are EVEN

Prokaryotes

  • 30s + 50s = 70s
  • all are ODD
28
Q

Elongation phase of protein synthesis

A

“APE”

A site = incoming amino Aminoacyl-tRNA binds to A site

P site = rRNA catalyzes peptide bond between already present AA and new AA to form a poly peptide. The polypeptide is moved to the tRNA in the P site

E site = peptidyl t-RNA (tRNA without an AA) is moved from P -> E site and exits the ribosome

29
Q

Cell types based on cell cycles

A

Permanent cells:

  • cells that remain in G0 phase (arrest phase) permanently
  • least affected by chemo
  • neurons. Skeet always and cardiac muscle cells, RBCs

Stable (quiescent) cells:

  • cells that are in G0 phase but can enter G1 phase of mitosis if stimulated
  • hepatocytes, lymphocytes, PCT, periosteal cells

Labile cells:

  • cells that never go into G0 (arrest) phase
  • most affected by chemo
  • bone marrow, gut epithelium, skin, hair follicles

Step 1 review cards (24 decks)

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