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UWorld - Biochemistry > Biochem - cellular + labs > Flashcards

Biochem - cellular + labs Flashcards

1
Q

Why is the genetic code considered degenerate?

A

Because more than 1 codon can code for a particular amino acid

(61 codons, 20 amino acids)

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2
Q

What is the Wobble Hypothesis?

A

Certain tRNA molecules can recognize multiple different codons coding for the same amino acid.

This is due to the first 2 positions on the mRNA codon require traditional (Watson-Crick) base pairing, whereas the third “wobble” nucleotide undergoes non-traditional pairing.

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3
Q

Which part of DNA replication is most different between the 2 daughter strands?

A

DNA Ligase

Since DNA synthesis can only occur in the 5’ –> 3’ direction”

1 strand is synthesized continuously (leading strand)

1 strand is synthesized discontinuously (lagging strand) in a direction away from the replication fork, resulting in the formation of Okazaki fragments which get joined together by DNA ligase

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4
Q

What is the function of the following in Prokaryotic DNA replication :

a. Helicase
b. Topoisomerase II (DNA Gyrase)
c. Single-Stranded DNA-Binding Protein
d. DNA Ligase

A

a. Unwinding of double helix
b. Removal of supercoils
c. Stabilization of unwound template strands
d. Joining of Okazaki fragments on lagging strand

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5
Q

What are the functions of DNA Polymerase III? (2)

A
  1. 5’ to 3’ DNA Synthesis
  2. 3’ to 5’ exonuclease (proofreading) activity
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6
Q

What are the functions of DNA Polymerase I? (3)

A
  1. 5’ to 3’ DNA synthesis
  2. 3’ to 5’ exonuclease (proofreading) ability
  3. Removes Primer

(5’ to 3’ exonuclease activity)

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7
Q

Which amino acid is most abundant in collagen?

What is the conformation of collagen molecules?

A

Glycine

A triple helical conformation

(Glycine occupies every 3rd amino acid position)

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8
Q

Which letter corresponds to the amino acid binding site on the tRNA molecule?

A

A

The 3’ CCA Tail

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9
Q

What does a Northern Blot detect?

A

RNA

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10
Q

What does a Southern Blot detect?

A

DNA

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11
Q

What does a Western Blot detect?

Example of a probe its used to detect?

A

Protein

Antibodies

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12
Q

What does a Southwestern blot detect?

Example of a probe it can detect?

A

DNA-binding Protein

c-Jun and c-Fos

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13
Q

Reverse Transcription Polymerase Chain Reaction (RT-PCR)

  1. What is it used for?
  2. How does it work?
A

1.

Detect and quantify levels of mRNA in a sample

2.

It uses reverse transcription to create a complimentary DNA template that is then amplified using standard PCR

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14
Q

Proteins phosphorylated with mannose residues in the Golgi are destined for which cellular location?

A

Lysosome

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15
Q

Fluorence in situ Hybridization (FISH)

What is it used to identify?

A

Chromosomal translocation, duplications or deletions

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16
Q

Flow Cytometry

  1. What is it used to identidy?
  2. What pathology is it commonly used for diagnosis?
A

1.

Surface Markers (eg: CD10)

2.

Leukemias

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17
Q

What is the function of a gap junction?

What protein is responsible for forming gap junctions?

A

Intercellular communication

Connexins

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18
Q

What proteins form tight junctions?

What is the function of a tight junction?

A

Claudins & Occludin

Cell Barrier

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19
Q

What protein forms a desmosome?

What protein forms a hemidesmosome?

A

Cadherins form desmosomes

Integrins form hemidesmosomes

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20
Q

What is the function of the CAAT & TATA boxes?

A

Promote Transcription

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21
Q

Ehlers-Danlos Syndrome

  1. What is the main issue?
  2. What are the main complications
  3. What step is impaired in this disease?
A
  1. Defective collagen synthesis which can cause:

- easy bruising

- hyperextendible skin

- hypermobile joints

  1. Berry + Aortic aneurysms, organ rupture

3.

N-terminal Peptide Removal

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22
Q

What enzyme removes the RNA primer?

A

DNA Polymerase I

(only one that has 5’ to 3’ exonuclease activity)

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23
Q

I-cell disease

  1. How/Why does it occur?
  2. How does it present?
A
  1. Defect in N-acetylglucosamyl-1-phosphotransferase –>

failure of golgi to phosphorylate mannose on glycoproteins

(decreased mannose-6-phosphate) —>

proteins are secreted extracellularily rather than to lysosome

2.

High plasma levels of lysosomal enzymes, coarse facial features, gingival hyperplasia

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24
Q

Signal Recognition Particle (SRP)

  1. What is its function?
  2. What occurs if it is dysfunctional?
A

1.

Traffics protein from the ribosomes to the RER

2.

Proteins accumulate in cytosol

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25
Q

What are the functions of the following vesicular trafficking proteins:

  1. COPI
  2. COPII
  3. Clathrin
A

COPI: - Golgi –> golgi

  • cis-golgi –> ER (retrograde)

COPII: ER –> cis-golgi (anterograde)

“Two (COPII) steps forward, One (COPI) step back”

Clathrin: trans-golgi –> lysosomes

plasma membrane –> endosomes

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26
Q

Disuse of a muscle due to being in a case can result in atrophy.

How does this process occur?

A

Cytoskleton degredation via ubiquitin-proteosome pathway

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27
Q

What type of vitamin D do we get from:

a. Sunlight
b. Food/Plants

A

a. Cholecalciferol (D3)
b. Ergocalciferol (D2)

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28
Q

In a patient who has abnormal elastin due to defective cross-linking, what amino acid would be most different in comparison to a normal persons elastin?

A

Lysine

(responsible for cross-linking which gives elastin elastic propreties)

29
Q

In a patient preganant with a child with Trisomy 21 how would the following serum markers be altered:

1. Nuchal Translucency

2. B-hCG

3. PAPP-A (pregnancy associated plasma protein)

4. Inhibin A

A

1. Increased nuchal translucency

2. Increased B-hCG

3. Decreased PAPP-A

4. Increased Inhibin A

30
Q

In a patient preganant with a child with Trisomy 18 (Edwards Syndrome) how would the following serum markers be altered:

1. Nuchal Translucency

2. B-hCG

3. PAPP-A (pregnancy associated plasma protein)

4. Inhibin A

A

1. Normal nuchal translucency

2. decreased B-hCG

3. Decreased PAPP-A

4. normal/decreased Inhibin A

31
Q

In a patient preganant with a child with Trisomy 13 (Patau Syndrome) how would the following serum markers be altered:

1. Nuchal Translucency

2. B-hCG

3. PAPP-A (pregnancy associated plasma protein)

4. Inhibin A

A

1. Normal nuchal translucency

2. decreased B-hCG

3. Decreased PAPP-A

4. normal Inhibin A

32
Q

In patients with breast/ovarian cancers with the BRCA1 mutation, what DNA repair mechanism is damaged?

A

Double Stranded Recombination Repair

(A strand from the damaged dsDNA is repaired by using a complementary strand from an intact dsDNA)

33
Q

What disease occurs as a result of a defect in DNA mismatch repair?

A

Lynch Syndrome / Hereditary Nonpolyposis Colorectal Cancer

(due to microsatelite instability)

34
Q

What disease occurs as a result of having damaged nucleotide exicison repair?

A

Xeroderma Pigmentosum

(inability to repair DNA pyrimidine dimers caused by UV exposure)

Presents as: dry skin, extreme light sensitivity, increased risk for skin cancers

35
Q

Mitochondrial Myopathies

  1. How do they present?
  2. Why do they occur?
  3. How do they appear on muscle biopsy?
A

1.Myopathy (muscle damage)

Lactic acidosis

CNS issues (migraines, seizures)

2.

Failure of oxidative phosphorylation

3.

Ragged red fibers

36
Q

C-reactive protein

  1. What can it be used as a marker for?
  2. Where is it synthesized?
A
  1. Inflammation
  2. Liver

(like most proteins)

37
Q

Nitrogen Balance

  1. What is it?
  2. What raises it?
  3. What lowers it?
A

1.

It is a measure of nitrogen input - nitrogen output

2.

Raised by food such meats, eggs, legumes

3.

Lowered by urine, feces, sweat

38
Q

What are the odds that a sibling has a matching HLA type to his sibling so he can be a transplant/bone marrow donor?

A

1/4

(there is a 25% chance of 2 siblings inheriting the same haplotype)

39
Q

What inhertiance pattern is seen in Sickle Cell disease?

A

Autosomal Recessive

40
Q

Xeroderma Pigmentosum

  1. What is defective these patients ?
  2. What are effects?
A

1.

Defective Nucleotide Exicison Repair

Due to a deficiency in UV-specific Endonuclease

2.

Severe photosensitivity, hyperpigmentation is sun exposed areas, increased risk for skin cancers

41
Q

Mosaicism

  1. What is it?
  2. What is the diffence between Somatic and Gonadal/Germinline Mosaicism?
A
  1. Mosaicism is when there genetically different cells in the same individual.

2.

Somatic Mosaicism is when the mutation occurs once the person is already born and presents with symptoms. Cannot be passed down to children.

Germline Mosaicism is when the mutation occurs in the sperm/egg of an indiviudal. Mutation will pass to children

42
Q

What codon signals initiation of protein synthesis?

What codon signals termination of protein synthesis? (Stop codons)

A

Start: AUG

STOP: UGA, UAG, UAG

“U Go Away”

“U Are Away”

“U Are Gone”

43
Q

What would be the anticodon for the following mRNA sequence?

5’—- UAG —-3’

A

5’ —- CUA —- 3’

Remember the conon-anticodon binding occurs in the opposide direction

44
Q

Heterochromatin vs Euchromatin

  1. Where is it located?
  2. Is it transcriptonally active?
  3. Is it heavily methylated?
A
  1. Heterochromatin: periphery of nucleus

Euchromatin: Dispersed throughout

2.

Heterochromatin: no - doesnt make protein

Euchromatin: yes “euchromatin is expresssed”

  1. Only Heterochromatin is methylated and therefore inactive
45
Q

Enhancers and Silencers

  1. What is their function?
  2. Where are they located?
A

1.

Enhancers: increase expression of a gene on a chromosome

Silencers: Decrease expression of a gene on a chromosome

2.

They can be located upstream, downstream or within the intron

46
Q

What is the function of a promotor site?

A

It is another site where RNA pol II and other trancription factors can bind that is upstream from the TATA box

They increase gene transcriptiom

47
Q

Do tRNAs bind stop codons?

How is protein synthesis terminated?

A

No tRNAs do not bind stop codons

When the ribosome encounters a stop codon, releasing factor proteins bind to the ribosome and stimulate release of the formed polypeptide

48
Q

From childhood to puberty, what meiosis stage is the primary oocyte arrested in?

During ovulation, what meiosis stage is the secondary oocyte arrested in until fertilization?

A

Prophase of Meiosis I

Metaphase of Meiosis II

49
Q

Homeobox Genes

  1. What do they code for?
  2. What is their function?
A

1.

Transcription factors

2.

Segmental orginization of the embryo along the cranial-caudal axis

50
Q

What is the best test to see if a gene is being transcribed/expressed?

A

Northern Blot to test for the presence of its mRNA

51
Q

What is the function of Histone H1 ?

A

It helps condense DNA into its heterochromatin form

52
Q

What is Splicing?

A

It is a post-transcriptional modification process that removes introns (non-coding DNA regions) from the pre-cursor mRNA.

This leaves only the exons (DNA coding regions) in the mRNA script to be translated.

53
Q

What is alternative splicing?

Can it have negative consequences?

A

Like regular splicing, the introns will be removed.

However, different combinations of exons are selectively included and excluded from a mRNA transcript. This allows the DNA from a single gene to code for a diverse group of proteins

Yes, it can be involved in disease processes such as cancer where it can allow cells to evade host defences

54
Q

Telomerase

  1. What is its function?
  2. Which type of cell most commonly has them?
A

1.

Telomerase is a reverse transcriptase that lengthens telomeres by adding TTAGGG repeasts to its 3’ end to prevent cell death

2.

Stem cells (ex. epidermal basal cells)

55
Q

Lesch-Nyhan Syndrome

  1. What enzyme is defected?
  2. What does it result in?
  3. How does it present?
A
  1. Hypoxanthine-Guanine Phosphoribosyltransferase (HGPRT)
  2. Defective purine salvage/rescur —> increased uric acid

3. “HGPRT”

Hyperuricemia, Gout, Pissed off (agression, self-harm), Retardation, Dystonia

56
Q

HbA, HbS, HbC

  1. What amino acid differences are seen between them?
  2. What type of mutation results in HbS and HbC
  3. How would they differ on electrophoresis?
A
  1. HbA - normal

HbS - glutamate replaced with valine

HbC - glutamate replaced with lysine (lyCine)

  1. Both are Missense mutations
  2. HbA > HbS > HbC
57
Q

snRNPs

(small nuclear ribonucleoproteins)

  1. What is their function?
  2. In what disease can they be affected?
A
  1. They are an important component of the spliceosome and are required for splicing

2. Lupus** due to its **anti-smith antibodies which are directed against snRNPs

58
Q

If there is a build-up of many very long chained or branced fatty acids, which organelle is most likely not functioning?

A

Peroxisome

Function: oxidation of very long and brached chain fatty acids

59
Q

A mutation involving the enzyme Phosphoribosyl Pyrophosphate (PRPP) sythetase gene is most likely to result in what?

A

Gout

Due to increased production and degredation of purines

60
Q

Propionic Acidemia

  1. What will be elevated?
  2. What enzyme is deficient?
  3. Which amino acids can cause it?
A
  1. Propionyl Co-A
  2. Propionyl Co-A Carboxylase

3.

Valine, isoleucine, methionine, threonine

odd-chain fatty acids

61
Q

Methylmalonic Acidemia

  1. What will be elevated?
  2. What enzyme is deficient?
  3. Which amino acids can cause it?
A
  1. Methylmalonyl Co-A
  2. Methylmalonyl Co-A Carboxylase

3.

Valine, isoleucine, methionine, threonine

odd-chain fatty acids

62
Q

What is the base sequence at the 3’end of a tRNA?

A

CCA tail

63
Q

What is the most important function of the Smooth Endoplasmic Reticulum (SER)?

A

Steroidgenesis

(it is involved in the processing and synthesis of hydrophobic compounds)

64
Q

Which enzyme is responsible for causing bruises to appear greenish?

A

Heme Oxigenase

(converts heme to bilverdin)

65
Q

What substance is responsible for regulating both fatty acid synthesis and breakdown (beta-oxidation)?

A

Malonyl-CoA

(it is the rate limiting step in FA synthesis)

(it can also inhibit B-oxidation)

66
Q

Tetrahydrobiopeterin

  1. What is its abbreviation?
  2. What products require it for formation?
A
  1. BH4

2.

Tyrosine, Dopamine, Serotonin

67
Q

Protein kinase B (Akt)

  1. What signalling pathway does it activate?
  2. What does it?
A
  1. mTOR pathway

2.

It translocates to nucleus and induces genes involved in cell-survival, anti-apoptosis and angiogenesis

68
Q

What process causes vitamin C deficiency to result in scurvy?

Where does this process normally take place?

A

Vitamin C is needed for hydroxylation of proline and lysine in collagen

This takes place in Rough Endoplasmic Reticulum (RER)

69
Q

Which amino acid is most likely to become essential in a patient with homocystinuria? Why?

A

Cysteine

Since its most commonly due to Cystathione Synthase deficinecy which results in the inability to convert homocysteine to cysteine

UWorld - Biochemistry (5 decks)

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