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BIOCHEM Mod 2 > DNA/RNA > Flashcards

DNA/RNA Flashcards

1
Q

What is contained in the nucleus?

A

Proteins, nucleotides, carbohydrates, and lipids

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2
Q

What is posttranslational modification?

A

once protein synthesis is complete, they need to be modified to change function whether they are going to be intracellular or extracellular proteins

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3
Q

What is the precurser to protein synthesis?

A

mRNA

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4
Q

What is the function of nuclear pores?

A

nucleus membrane channels that actively transport RNA, ribosomes, proteins, carbohydrates and lipids (smaller molecules simply diffuse)

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5
Q

What is the role of importins or exportins?

A

They are carrier proteins (nucleoporins); proteins with nuclear export sequence (NES) are actively transported out of the nucleus via these carrier proteins

RNA uses a NES-containing RNA-binding protein that also uses exportin

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6
Q

What is the most important structure inside the nucleous and how many are they? What is their role?

A

Chromatin; 46 chromosomes

unwinding exposes genes for DNA replication, DNA to RNA transcription and mRNA translation

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7
Q

What are the six classes of Histones?

A

H1, H2A, H2B, H3, H4, H5

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8
Q

What is the primary role of Histones?

A

post-translationally modified which either expose or conceal DNA sequences for gene transcription or repair of DNA damage

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9
Q

What are Histones made of?

A

Protein (positive/negative/uncharged/AA/primary structure/alpha helices(secondary structure)

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10
Q

What is the role of nuclear matrix/scaffold?

A

protect and maintain the structure and integrity of the DNA molecule

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11
Q

What are laminopathies?

A

groups of disorders associated with the mutations that affect the proteins of the nuclear membrane or lamina (dystrophies and dysplasias)

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12
Q

What must take place before DNA replication?

A

pre-replication complex which is composed of 4 proteins

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13
Q

What are the four steps for pre-replication complex?

A
  1. origin recognition complex binds to the origin of replication

2 & 3. Two regulatory proteins (CDC6 and CDT1) ensure the cell is prepared for DNA replication

  1. minichromosome maintenance complex contains the proteins essential for the establishment of the REPLICATION FORK
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14
Q

What is the replication fork?

A

point where the two DNA strands separate into leading strand and lagging strand and DNA copying occurs

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15
Q

What enzyme is responsible for the first step in DNA replication after the pre-replication complex?

A

DNA Helicase unwinds the DNA double helix

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16
Q

What happens on the leading strand?

A

DNA polymerase replicates the DNA strand from the 5’ to 3’ direction towards the replication fork; process is continuous

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17
Q

What happens on the lagging strand?

A

DNA polymerase adds short chains of nucleic acids, called Okazaki fragments in the 5’ to 3’ direction away from the replication fork

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18
Q

What is the role of the enzyme DNA ligase?

A

Joins the Okazaki fragments on the lagging strand

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19
Q

What is the role of DNA topoisomerase?

A

cuts the phosphate backbone, “untangles” the DNA strands, and then repairs the cut leaving the DNA unaltered

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20
Q

What is Transcription?

A

synthesis of mRNA from DNA; RNA polymerase transcribes DNA strand (only one strand - known as template trand) from 3’ to 5’ direction

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21
Q

What is the main difference between replication and transcription?

A

in transcription, multiple RNA polymerase can transcribe on a single DNA gene sequence. CANNOT have this during DNA replication

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22
Q

How does reverse transcriptase inhibitors (retrovirals) effect HIV?

A

inhibit the enzyme for reverse transcriptase (viral enzyme that copies its RNA to DNA, aka Retrovirus)

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23
Q

What is the genetic code?

A

3 bases = 1 codon and 1 codon = 1 AA. **AA can be represented by more than 1 codon

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24
Q

What is the complex that must be formed in order to have protein synthesis?

A

Ribosome made up of 60S subunit and 40S subunit

25
Q

What does protein synthesis require?

A

mRNA, tRNA, ribosome and accessory proteins called initiation factor and elongation factor

26
Q

What is the purpose of tRNA?

A

has to line up with and bind to the initiating codon (mRNA); composed up the anticodon and carries AA

27
Q

What is the role of 60S subunit in Ribosome?

A

stabilize ribosome, peptide bond formation and movement of the ribosome along the mRNA strand

28
Q

What is the role of 40s Subunit in Ribosome?

A

helps in establishing the proper AUG codon start site on the mRNA

29
Q

What is the P-site?

A

peptide chain that grows on the 60S subunit when the tRNA is at this site on the 40S subunit

30
Q

What is the A-site?

A

new AAs bind here

31
Q

What are macrolides and how do they effect protein synthesis?

A

Antibiotics that inhibit protein synthesis in bacteria by taking advantage of the 50S subunit (blocking movement of ribosome along the mRNA) and does not effect the 60S subunit in humans

32
Q

What is the function of the post-translational chaperones?

A

preventing misfolding and aggregation

33
Q

Mad Cow Disease/Bovine Spongiform Encephalopathy (human equivalent Creutzfeldt-Jakob disease)

A

infectious, misfolding proteins known as prions; misfolding proteins aggregate into amyloid plaques creating holes in normal brain tissue

S&S: dementia, hallucinations, seizures, memory and speech problems, nervous tissue damage

TxT: chaperone proteins

34
Q

What is post-translational trafficking?

A

directs a protein to its correct (final) destination after synthesis; if misfolding happens, it is sent to a retention center to get fixed

35
Q

What is the final step in protein synthesis and why does it happen?

A

Post-translational modification (phosphorylation, lipidation, disulfide bond, acetylation, glycosylation, or ubiquitination)

It happens based on the body’s needs

36
Q

Why is control of gene expression important?

A

Regulated by DNA promoter regions and allows for selective initiation and cessation of metabolic pathway; without it would be total chaos in the body

37
Q

What is Gene Expression?

A

Binding of different transcription factors and/or enhancers to promoter sequences are essential for positive or negative control of transcription

38
Q

What is the similarity between the 4 methods to control gene expression?

A

bind to enhancer promoter region of DNA

39
Q

What are the 4 methods to control gene expression?

A

helix-turn-helix
Leucine zipper
helix-loop-helix
Zinc finger

40
Q

What enzymes control gene expression by reversible acetylation of histone and what do they do?

A

histone acetyl transferases (HATs): adds acetyl group

histone deacetylases: remove acetyl group which blocks access of RNA polymerase to DNA

41
Q

What is neutral mutation?

A

change of codon making a change in the AA however the new AA has the same chemical properties (hydrophilic, hydrophobic, charge, etc.)

42
Q

What is Silent Mutation?

A

Change of codon results in the same AA

43
Q

What is missense mutation?

A

change in codon resulting change in AA with different chemical properties

44
Q

What is nonsense mutation?

A

change of codon resulting premature stop codon in the middle of the sequence. Stop codon is not at the end

45
Q

What are Frameshift -1 and Frameshift +1

A

can add or delete at the same time; removal or add codon letter resulting in an entire shift of AA sequence

46
Q

What is transition mutations?

A

single purine nucleotide is changed for a different purine or a pyrimidine to pyrimidine
( A G or T C)

47
Q

What is transverse mutation?

A

Pyrimidine to purine or purine to pyrimidine
T –> A or G C –> G or A
A—>T or C G—>C or T

48
Q

What and how do mutations occur in DNA?

A

chemical, radiation and viral can cause single or double strand breaks or DNA cross-linking with itself or proteins

49
Q

What are the enzymes and steps involved with DNA repair?

A

Single-nucleotide mutations, endonucleases enzymes sense and remove (excision) the incorrect base and the correct nucleotide is replaced by a polymerase and ligase

Cell cycle checkpoints also verify accuracy of DNA replication prior to division

50
Q

characterstics, S&S, TXT of Xeroderma Pigmentosa

A

autosomal recessive mutations in the enzymes required for the repair of thymidine dimers

Thymidine dimers are a common cross link that occurs between adjacent thymidine dimers to form a cyclobutane ring (hydrocarbon ring) when exposed to UV; this ring compromises the shape and function of DNA

S&S: basal cell carcinoma, squamous cell carcinoma and malignant carcinoma

TxT: reduce sun exposure and supportive care (die by age 20)

51
Q

What is the cell cycle?

A

cell pathway which defines times of cell division, replication, cell growth and functional activities

52
Q

Where do the two checkpoints occur in the cell cycle to check for DNA damage and what is involved?

A

G1-S checkpoint and G2-M checkpoint; p53 protein will detect damage of DNA and if there is damage, it will activate the inhibitor p21 which blocks the cyclin D-CDK4 complex and subsequently the G1 to S transition or G2 to Mitosis transition

53
Q

Activity during interphase G1 of cell cycle?

A

prep for DNA synthesis, cell growth and protein production, cyclin E activates CDK2 allowing progression into S-phase

54
Q

Activity during interphase S of cell cycle?

A

DNA replication; RNA transcription low except for that involved in histone production

55
Q

Activity during interphase G2 of cell cycle?

A

synthesis of micrtobules for mitotic spindle and chromosome packing; process controlled by dephosphorylation of tyrosine in the maturation/mitosis-promoting factor complex; CDK2 leads to mitosis (point of no return; if cell is unprepared, Cdc25 inactivated

56
Q

What are the phases in mitosis and what enzyme and phase is responsible for separating the sister chromosome?

A

Prophase, metaphase, anaphase and telophase

separase is the protein and it happens during anaphase

57
Q

Activity during interphase G0?

A

no cell replication/division; cell cycle progression inhibited by protein cyclin-dependent kinase inhibitor 2A (blocks CDK4 with cyclin D interaction); G0 cells lose cell cycle proteins including cyclins and CDKs.

58
Q

How are microtubules related to cancer treatment? (non-hodgkin’s lymphoma, wilm’s tumor and acute lymphoblastic leukemia)

A

Vincristine can block growth of microtubule polymerization during G2 and M phase, stopping mitosis at metaphase

59
Q

How does TAXOL effect cancer treatment? (breast, lung, ovaries, head and neck cancers and Kaposi’s sarcoma)

A

stabilizes microtubules preventing sister chromatid separation in M phase

BIOCHEM Mod 2 (8 decks)

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