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MCAT Biochem > Ch 6 - DNA and Biotechnology > Flashcards

Ch 6 - DNA and Biotechnology Flashcards

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1
Q

What is DNA?

A

a macromolecule that stores genetic information in all living organisms

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2
Q

What is the difference between nucleoside and nucleotide?

A
  • side: contain a 5-carbon sugar bonded to a nitrogenous base
  • tide: nucleoside + 1-3 phosphate groups added
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3
Q

What is the difference between nucleotides in DNA v RNA?

A
  • DNA: contain deoxyribose and thymine

- RNA: contain ribose and uracil

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4
Q

What model does DNA organization follow?

A

Watson and Crick

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5
Q

What is the backbone of DNA composed of?

A

alternating sugar and phosphate groups, and is always read 5; to 3’

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6
Q

How do the 2 strands of DNA relate?

A

2 strands with antiparallel polarity would into a double helix

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7
Q

What is the difference between purines nad pyrimidines?

A
  • purines (A and G) always pair with pyrimidines (CUT)
  • in DNA, A pairs with T (via 2 H bonds) and C pairs with G (via 3 H bonds)
  • RNA does not contain thymine, but contains uracil instead; thus in RNA, A pairs with U (via 2 H bonds)
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8
Q

Why are purines and pyrimidines considered biological aromatic heterocycles?

A
  • aromatic compounds are cyclic, planar, and conjugated, and contain 4n + 2 pi electrons (where n is any integer; Huckel’s rule)
  • heterocycles are ring structures that contain at least 2 difference elements in the ring
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9
Q

What are Chargaff’s rules?

A
  • states that purines and pyrimidines are equal in number in DNA molecules, and that because of base-pairing, A=T and C=g
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10
Q

What form are most DNA? When might Z DNA be seen?

A
  • most DNA is B-DNA, forming a right hand helix

- low concentrations of Z-DNA with a zigzag shape may be seen with high GC content or high salt concentration

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11
Q

What can cause denaturation of DNA

A
  • heat, alkaline pH, and chemicals like formaldehyde and urea
  • removal of these conditions may result in reannealing of the strands
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12
Q

How many chromosomes are DNA organized into in human cells?

A

46

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13
Q

What is the relationship between histone proteins, nucleosomes, and chromatin in DNA in eukaryotes?

A
  • DNA is wound around histone proteins (H2A, H2B, H3, H4) to form nucleosomes, which may be stabilized by another histone protein (H1)
  • as whole, DNA and its associated histones make up chromatic in the nucleus
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14
Q

What is the difference between heterochromatin and euchromatin?

A
  • heter: dense, transcriptionally silent DNA that appears dark under light microscopy
  • eu: less dense, transcriptionally active DNA that appears light under light microscopy
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15
Q

What are telomeres? What do they contain? What happens to them during replication?

A
  • the ends of eukaryotic chromosomes that protect from losing important genes from incomplete replication of the 5’ end of DNA strand
  • contain high GC content to prevent unraveling of the DNA
  • during replication, they are slightly shortened, although this can be (partially) reversed by the enzyme telomerase
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16
Q

Where are centromeres located and what do they do? Why do they have a high GC content?

A
  • located in the middle of chromosomes and hold sister chromatids together until they are separated during anaphase in mitosis
  • contain high GC content to maintain a strong bond between chromatids
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17
Q

What is a replisome?

A
  • replication complex

- a set of specialized proteins that assist the DNA polymerse

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18
Q

What is the first step of replicated DNA?

A

it is first unwound at an origin of replication by helicases producing 2 replication forks on either side of the origin

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19
Q

How do prokaryotes and eukaryotes differ in their origin of replication?

A
  • pro have circular chromosomes that contain only one OriC

- eu have linear chromosomes that contain many OriC

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20
Q

What to single-stranded DNA binding proteins do?

A

in both eukaryotes and prokaryotes; keep unwound strands of DNA from reannealing or being degraded once unwound by helicases

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21
Q

What do DNA topoisomerase do?

A
  • supercoiling causes torsional strain on the DNA molecule, which can be released by DNA topoisomerase, which create nicks in the DNA molecules
  • both eu/prokaryotes
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22
Q

What does DNA being semiconservative mean?

A

one old parent strand and one new daughter strand is incorporated into each of the 2 new DNA molecules

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23
Q

What is primase?

A

DNA cannot be synthesized without an adjacent nucleotide to hook onto, so a small RNA primer is put down by primase
- both pro/eukaryotes

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24
Q

What is the DNA polymerase 3? What enzyme does the same function for eukaryotes?

A
  • they synthesize a new strand of DNA; they read the template DNA 3’ to 5’ and synthesize the new strand 5’ to 3’
  • in eukaryotes, DNA polymerase alpha. gamma, or epsilon
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25
Q

What is the difference between the leading strand and lagging strand?

A
  • leading: requires only one primer and can then be synthesized continuously in its entirety
  • lagging: requires many primers and is synthesized in discrete sections called Okazaki fragments
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26
Q

What do DNA polymerase 1 do? What enzyme has the same function in eukaryotes?

A

remove RNA primers and filled gaps with DNA

- in eukaryotes, RNase H

27
Q

What do DNA ligase do?

A

fuse the DNA strands together once primer is removed and create one complete molecule

28
Q

Where do oncogenes develop from and what do they do?

A
  • develop from mutations of proto-oncogenes and promote cell cycling
  • may lead to cancer
29
Q

What is cancer?

A

defined by unchecked cell proliferation with the ability to spread by local invasion or metastasize (migrate to distant sites via the bloodstream or lymphatic system)

30
Q

What do tumor suppressor genes code for?

A

proteins that reduce cell cycling or promote DNA repair, mutations of these genes can lead to cancer

31
Q

What performs proofreading during DNA replicaiton?

A

DNA polymerase proofreads its work and excises incorrectly matched bases in the S phase
- the daughter strand is identified by its lack of methylation and corrected accordingly

32
Q

Where do mismatch excision repair occur and what genes are used?

A

during G2 phase of the cell cycle, using genes MSH2 and MLH1

33
Q

What does nucleotide excision repair do and where does it occur?

A

fixed helix-deforming lesions of DNA via a cut-and-patch process that requires an dexcisions endonuclease
- occurs in G1 and G2 phase

34
Q

What do base excision repair do and where does it occur?

A
  • fixes nondeforming lesions of the DNA helix by removing the base, leaving an apurinic/apyrimidinic (AP) site
  • an AP endonuclease then removes the damages sequence, which can be filled in with the correct bases
  • occurs in G1 and G2 phase
35
Q

What is recombinant DNA composed of?

A

nucleotides from 2 different sources

36
Q

What does DNA cloning introduce?

A

a fragment of DNA into a vector plasmid

37
Q

What does a restriction enzyme do?

A
  • used to cleave DNA before electrophoresis and Southern blotting and to introduce a gene of interest into a viral vector for gene therapy
38
Q

What do vectors contain?

A

an ORiC, the fragment of interest, and at least 1 gene for Abx resistance (to permit for selection of that colony after replication)

39
Q

What can the bacterial cell be used for once replicated?

A

to create a protein of interest or can be lysed to allow for isolation of the fragment of interest from the vector

40
Q

What are DNA libraries?

A

large collections of known DNA sequences

41
Q

What is a genomic library?

A
  • contain large fragments of DNA, including both coding and noncoding regions of the genome
  • cannot be used to make recombinant proteins or for gene therapy
42
Q

What are cDNA libraries?

A
  • contain smaller fragments of DNA and only include the exons of genes expressed by the sample tissue
  • can be used to make recombinant proteins or for gene therapy
43
Q

How are DNA molecules separated by size?

A

agarose gel electrophoresis

44
Q

What is hybridization?

A

the joining of complementary base pair sequences

45
Q

What is PCR?

A

an automated process by which millions of copies of DNA sequence can be created from a very small sample of hybridization

46
Q

What is southern blotting?

A
  • used to 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 a ss-DNA molecules o look for a sequence of interest
47
Q

What do DNA sequences use dideoxyribonucleotides for?

A
  • to terminate the DNA chain because they lack 3’-OH group

- the resulting fragments can be separated by gel electrophoresis and the sequence can be read directly from the gel

48
Q

What is gene therapy?

A

a method of curing genetic deficiencies by introducing a functional gene with a viral vector

49
Q

How are transgenic mice created?

A

by integrating a gene of interest into a germ line or embryonic stem cells of a developing mouse
- can be mated to select for the transgene

50
Q

What are chimeras?

A

organisms that contain cells from 2 different lineages

51
Q

How are knockout mice created?

A

by deleted a gene of interest

52
Q

How does the aromaticity of purines and pyrimidines underscore their genetic function?

A
  • aromaticity of nucleic acids make these compounds very stable and unreactive
  • stability is important for storing genetic information and avoiding spontaneous mutations
53
Q

What properties of telomeres and centromeres allow them to stay tightly raveled, even when the rest of DNA is uncondensed?

A

high GC content increases H bonding, making the association between DNA strands very strong at telomeres and centromeres

54
Q

Which processes occur in the 5’ to 3’ direction?

A

DNA synthesis
DNA repair
RNA transcription
RNA translation (reading codons)

55
Q

What is the difference between oncogenes and tumor suppressor genes?

A

they both cause cancer, but:

  • oncogenes promote cell cycle while mutated (stepping on gas pedal)
  • tumor suppressor genes no longer slow the cell cycle (cutting the brakes)
56
Q

How does DNA polymerase recognize which strand is the template strand once the daughter strand is synthesized?

A
  • the parent strand is more heavily methylated, whereas the daughter strand is barely methylated
  • this allows DNA polymerase to distinguish between 2 strands during proofreading
57
Q

What is the key structural difference in the types of lesions corrected by nucleotide excision repair v those corrected by base excision repair?

A
  • nucleotide excision repair corrects lesions that are large enough to distort the double helix
  • base excision repair corrects lesions that are small enough not to distort the double helix
58
Q

What is the difference between the advantages of using genomic v cDNA library?

A
  • genomic libraries include all the DNA in an organism’s genome including noncoding regions; may be useful studying DNA in introns, centromeres, or telomeres
  • cDNA libraries only include expressed genes from a given tissue, but can be used to express recombinant proteins or to perform gene therapy
59
Q

During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added?

A
  • dideoxyribonucleotides lack the 3-OH group that is required for DNA strand elongation
  • so once a dideoxyribonucleotide is added to a growing DNA molecule, no more nucleotides can be added because dideoxyribonucleotides have no 3’-OH group with which to form a bond
60
Q

In a single strand of nucleic acid, what bonds link nucleotides?

A

phosphodiester bonds bind adjacent nucleotides

61
Q

How does GC content affect melting point of DNA sequences?

A
  • the melting temperature of DNA is the temperature at which a DNA double helix separates into 2 single strands (denatures)
  • to do this, H bonds linking the base pairs must be broken
  • C-G have 3 H bonds and A-T have 2 H bonds so breaking GC would require more heat, thus higher mp
62
Q

How is cDNA formed?

A

complementary DNA formed from a processed mRNA strand by reverse transcription

63
Q

Why does prokaryotic DNA lack nucleosomes?

A

because it is circular and does not have histone proteins

64
Q

Why is uracil excluded from DNA but not RNA?

A

Cytosine degradation results in uracil

  • one common DNA mutation is the transition from cytosine to uracil in the presence of heat
  • DNA repair enzymes recognize uracil and correct this error by excising the base and inserting cytosine
  • RNA exists only transiently in the cell, such that cytosine degradation is insignificant
  • were uracil to be used in DNA under normal circumstances, it would be impossible to tell if a base should be uracil or if it is damaged cytosine

MCAT Biochem (12 decks)

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