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BioChemistry for the MCAT :) > DNA and BioTechnology > Flashcards

DNA and BioTechnology Flashcards

1
Q

Nucleotide

A

Consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) and one to three phosphate groups.

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2
Q

Nucleoside

A

Consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group

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3
Q

DNA

A
  • Deoxyribose sugar
  • Double stranded
  • Uses A, T, C, G

**When replicating DNA cannot complete the synthesis of 5’ end so the chromosomes will shorten

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4
Q

RNA

A
  • Ribose sugar
  • Single Stranded
  • Uses A, U, C, G
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5
Q

DNA Backbone

A

Phosphate linked to 3’C of one sugar and 5’ phosphate group of the incoming sugar

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6
Q

Direction to Read DNA

A

5’ —> 3’
5’ will have a Free OH or Phosphate on C5
3’ will have Free OH on C3

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7
Q

Aromaticity

A

Stable ring structures that are unreactive

  • Cyclic
  • Planar
  • Conjugated
  • Follow Huckel’s Rule (4n+2 pi electrons)
  • Generally form a type of S and P hybridization orbitals causing delocalizations of the electrons adding to stability
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8
Q

Purines

A

Contain two rings

  • Adenine (A)
  • Guanine (G)
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9
Q

Pyrimidines

A

Contains 1 ring

  • Cytosine (C)
  • Thymine (T)
  • Uracil (U)
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10
Q

Watson Crick Model

A
  • Double Helix: 2 strands of DNA that run antiparallel
  • Sugar phosphate (alternating) backbone on the outside and nitrogenous bases inside
  • Complementary base pairing A-T (2 H bonds) and C-G (3 H bonds)
  • DNA is ALWAYS read 5’ –> 3’
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11
Q

Chargaffs Rule

A

Purines (A,G) = Pyrmidines (T, C) and complements match meaning %A = %T and %C = %G

***Does not hold for RNA

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12
Q

B-DNA

A

Right handed helix with major and minor grooves between interlocking strand being site of protein binding

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13
Q

Z-DNA

A

Left handed zig zag helix, high G, C content or [salt] is high

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14
Q

Denaturing

A

Separating 2 strands of DNA without altering other aspects (like its nucleotides, sugars, phosphates, etc…)

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15
Q

Reanneal

A

Denaturing conditions are slowly removed so that DNA comes together

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16
Q

Histone

A

Small basic protein that chromosomes wind around forming chromatin

  • Proteins include H2A, H2B, H3, and H4
  • H1 = not part of histone but seals DNA off
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17
Q

Nucleosome

A

DNA and the histone proteins in a compact and stable structure

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18
Q

Heterochromatin

A

Chromosome material of different density from normal in which the activity of the genes is modified or suppressed.

  • Dense and Compacted chromatin
  • Dark appearance in microscope
  • Silent Transcriptional Activity
  • DNA is highly repetitive
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19
Q

Euchromatin

A

Chromosome material that does not stain strongly except during cell division. It represents the major genes and is involved in transcription.

  • Uncondensed and Dispersed chromatin
  • Light appearance in microscope
  • Expressed Transcriptional Activity
  • Genetically Active DNA
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20
Q

Telomere

A

Repeating Unit (TTAGGG) cap at the end of each DNA strand that protects our chromosomes. High in GC content prevent unraveling

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21
Q

Telomerase

A

Enzyme that replaces the sequence lost in each replication. Highly expressed in rapidly dividing cells; Synthesizes telomeres

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22
Q

Centromeres

A

Region of DNA found in the center of chromosomes

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23
Q

Replisome

A

Specialized proteins that assist the DNA polymerases

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24
Q

Helicase

A

Unwinds DNA double helix

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25
Q

Primase

A

Synthesis of RNA primer to begin DNA replication (in the 5’ –> 3’ direction)

26
Q

DNA Polymerase Alpha and Delta

A

Eukaryotes:

Adds nucleotide to the growing daughter strand; synthesis of DNA

27
Q

DNA Polymerase III

A

Prokaryotes:

Adds nucleotide in the growing daughter strand; synthesis of DNA

28
Q

DNA Topoisomerase II (DNA Gyrase)

A

Reduces torsional strain from + Supercoils by introducing nicks in the DNA
Removes + Supercoils ahead of advancing replication forks

29
Q

RNase H

A

Eukaryotes:
Fills gaps left after RNA primer excision
5’ —> 3’ Exonuclease

30
Q

DNA Polymerase I

A

Prokaryotes:
Fills gaps left after RNA primer excision
5’ —> 3’ Exonuclease

31
Q

DNA Ligase

A

Joins DNA Okazaki fragments

32
Q

Single Stranded DNA Binding Protein

A

Prevents Reannealing of DNA double helix and degradation by nucleases during replication; stabilizes the unwound template strands

33
Q

Supercoiling

A

Wrapping of DNA on itself as the helical structure is pushed closer to the telomere

34
Q

Semiconservative Replication

A

One parental strand is retained in each of the two resulting daughter strands

35
Q

Prokaryote Replication

A

Leading Strand 5’ –> 3’
Lagging Strand 3’ –> 5’ by creating okazaki fragments
One origin of replication

36
Q

Eukaryote Replication

A

Leading Strand 5’ –> 3’
Lagging Strand 3’ –> 5’ by creating okazaki fragments
Contains multiple origins of replication - allow many parts of the DNA to be replicated simultaneously

37
Q

Cancer

A

Proliferate excessively and not subjected to cell control

38
Q

Metastasis

A

Cancer migrates to distant tissues through blood and lymphatics

39
Q

Oncogenes

A

Mutated genes that cause cancer

40
Q

Proto-Oncogenes

A

Precursor to oncogenes, before they become mutated

41
Q

Anti-Oncogenes

A

Tumor suppressor genes that inhibit the cell cycle or participate in gene repair processes

42
Q

ProofReading Repair Mechanism

A

DNA Polymerase does the proofreading during the S phase of the cell cycle - incorrect base pairs are excised and replaced with the correct one

43
Q

Mismatch Repair Mechanism

A

MSH2 / MCH1 do mismatch repair during the G2 cell cycle - detect and remove errors found in the S phase

44
Q

Nucleotide Excision Repair Mechanism

A

Excision Endonuclease does nucleotide excision during the G1 and G2 phase of the cell cycle - Removing thymine dimers (caused by UV light) that distort the helix

45
Q

Base Excision Repair Mechanism

A

Glycosylase and AP Endonuclease do Base Excision Repair during the G1 and G2 phase of the cell cycle - Remove uracil that was made by the cytosine deamination

46
Q

Recombinant DNA

A

DNA fragment is composed of nucleotides from 2 different sources. Can be multiplied by cloning or PCR to study

47
Q

Cloning

A

Introduces a fragment of DNA into a vector plasmid -

Produces large amounts of desired sequence

48
Q

Restriction Enzymes (Endonuclease)

A

Recognize sequences and cut backbone of double helix

49
Q

Sticky Ends

A

Hanging nucleotide - good for recombination of a restriction fragment with vector DNA; able to bind

50
Q

DNA Libraries

A

Large collections of known sequence

51
Q

Genomic DNA Library

A

Include coding (exon) and noncoding (intron) DNA

52
Q

cDNA (Expression) Library

A

Reverse transcribed processed mRNA only includes genes that are expressed (Exon)

53
Q

Hybridization

A

Joining complementary base pairs (DNA - DNA or DNA - RNA)

54
Q

Polymerase Chain Reaction (PCR)

A

Automated. Primers flank gene of interest, denatures and copies
DNA sequence can be created from a very small sample of hybridization

55
Q

Agarose Gel

A

Electrophoresis separates DNA by size (longer = slower)

56
Q

Dideoxyribonucleotide (ddNTP)

A

Modified base with a 3’H (lack a 3’OH) that causes sequencing of DNA to cease

57
Q

Gene Therapy

A

In diseases where gene is mutated or inactive, a normal copy of the gene is inserted into the affected tissue

58
Q

Transgenic Mice

A

Gene introduced into germ line (gametes)

59
Q

Knockout Mice

A

Created by deleting genes of interest

60
Q

Chimera

A

Contain cells from two different lineages

61
Q

Southern Blotting

A

Detect the presence and quantity of various DNA strands in a sample. After electrophoresis the sample is transferred to a membrane that can be probed with single stranded DNA molecules to look for the sequence of interest

BioChemistry for the MCAT :) (12 decks)

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