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Biochemistry > Chapter 6 DNA and Biotechnology > Flashcards

Chapter 6 DNA and Biotechnology Flashcards

1
Q

What enzyme unzips DNA in transcription?

A

Helicase

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2
Q

What enzyme prevents supercoiling?

A

Topoisomerase/Gyrase

Goes before he’s a case and prevents tangling of the DNA.

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3
Q

What enzyme adds the RNA primer in transcription?

Is it added to the leading or lagging strand?

A

Primase

Lagging, the DNA cannot be synthesized de novo it needs another molecule to hook onto.

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4
Q

What do you single-stranded binding proteins do in transcription?

A

Separates the parent strand

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5
Q

What enzyme Glooze the Okazaki fragments together?

A

DNA ligase

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6
Q

What are the different types of DNA polymerases?

A

Eukaryotic:
DNA polymerase (alpha beta and delta)
RNase H

Prokaryotic:
DNA polymerase III
DNA polymerase I

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7
Q

What DNA polymerase removes the RNA primer in eukaryotes and prokaryotes?

A

Eukaryotes: RNase H
Prokaryotes: DNA I

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8
Q

Which DNA polymerase replaces the RNA primer with DNA and transcription?

A

In eukaryotes DNA polymerase Alpha Beta Delta.

In prokaryotes DNA polymerase III.

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9
Q

What is the function of the enzyme telomerase?

A

Telomerase adds guanine and cytosine to the ends of DNA (telomeres) to prevent loss of important genetic information.

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10
Q

DNA is read in what direction? DNA is transcribed in One Direction?

A

DNA is read 3 to 5. DNA is transcribed 5 to 3.

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11
Q

What are the three types of post transcriptional modification?

A
  1. Poly A Tail (AAAAAA)
  2. 5’ Cap (A 7-methylguanosine cap is added to the 5′ end of the pre-mRNA while elongation is still in progress.)
  3. Splicing (Exons expressed. Introns Removed)
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12
Q

What are the three different mechanisms of DNA repair?

A

Base excision repair- Fixes individual nucleotides by leaving an AP site (Apurinic/Apyrimidic) which AP endonuclease removes.

Mismatch repair-Fixes mismatch base pairing during DNA replication or recombination specifically during phase G2 of the cell cycle.

Nucleotide excision repair-Fixes up to 30 nucleotides.

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13
Q

What bond links to bases in DNA?What bond links the backbone of DNA?

A

Hydrogen bonds link to bases while phosphodiester bonds link the backbone of DNA.

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14
Q

What three things make up a dNTP?

A

Deoxyribose sugar.
Nitrogenous base.
Phosphate groups (1-3)

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15
Q

What is the difference between a nucleotide and nucleoside?

A

Nucleosides lack a phosphate group.

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16
Q

How can you tell the difference between a younger strand of DNA and a newer strand of DNA?

A

The newer the strand of DNA the less methylation it has.

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17
Q

How many chromosomes do humans have?

A

46 total chromosomes.

23 from Mom 23 from Dad.

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18
Q

List the purines and pyrimidines.

A

Purines: Adenine, Guanine Pyrimidines: Cytosine, Uracil, Thymine

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19
Q

What are the rules of aromaticity?

A

Aromatic molecules must be:

  1. Cyclic
  2. Planer
  3. Conjugated (Have alternating single and double or triple bonds)
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20
Q

What is the difference between the LAC and TRP operons?

A

LAC operons are INDUCIBLE. They are only turned on when lactose is present and the enzyme lactase needs to be made for a breakdown of lactose. DEFAULT: OFF

TRP operons are REPRESSIBLE they are DEFAULT:ON and are turned off when tryptophan is present and acts as a co-repressor which binds to the operator and stops production of tryptophan synthase.

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21
Q

What signals initiation in prokaryotes and eukaryotes?

A

TATA Boxes signal initiation in eukaryotes.

Sigma factor signal initiation in prokaryotes.

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22
Q

What signals the termination and eukaryotes and prokaryotes?

A

Hairpin and Rho factor

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23
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleoside made up of a five carbon sugar (pentose)
Nitrogenous base

Nucleotide is a nucleoside with one or more phosphate groups bonded to C5 of a nucleoside

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24
Q

What type of bond links nucleotides and at what carbon do they link?

A

Phosphodiester bonds joined 3’ to 5’

Phosphate group links the 3’ carbon of one sugar to the 5’ phosphate group of the next sugar in the chain

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25
Q

What is the overall charge of DNA/RNA strands?

A

Negative

26
Q

In what direction is DNA read?

A

3’ to 5’

27
Q

In what direction is DNA built?

A

5’ to 3’

28
Q

To which carbon is the nitrogenous base linked to in a nucleoside and by what type of bond?

A

C1 linked covalently

29
Q

To which carbon in a nucleotide is the phosphate added to?

A

C5

30
Q

Which carbon determines the difference between deoxyribose and ribose?

A

C2

31
Q

How many bonds bind together Adenine and Guanine versus cytosine and thymine?

A 
GC three (stronger) 
AT two (weaker)
32
Q

What is Chargaff’s rule?

A

The total amount of A equals the total amount of T and the amount of G equals the amount of C.

Total purines will be equal to the total pyrimidines overall

33
Q

What is B-DNA?

A

Right handed helix where every turn is made up of 10 base pairs or 3.4 nm.

34
Q

What type of bond bind together the nitrogenous bases in DNA?

A

Hydrogen bonds

35
Q

How many chromosomes are found in the nucleus of a human cell?

A

46

36
Q

What are the five histone proteins found in eukaryotic cells?

A

H2A, H2B, H3, and H4

37
Q

How many base pairs are wrapped around the histone protein complex?

A

200

38
Q

What is the nucleosome?

A

Basepairs wrapped around the histone protein complex

39
Q

Which histone seals off the DNA?

A

H1

40
Q

Heterochromatin vs euchromatin

A

Heterochromatin condensed during interphase
Appears dark

Euchromatin dispersed
Appears light
Genetically active DNA

41
Q

Telomere consists of repeating sequences of which bases?

A

TTAGGG

42
Q

Centromeres are made up of high AT/GC content?

A

GC

43
Q

What molecule is released as each phosphodiester bond is made?

A

Free pyrophosphate (PPi)

44
Q

What are oncogenes and what do they develop from?

A

Mutated genes that cause cancer

They develop from proto oncogenes

45
Q

What are tumor suppressor genes (examples) and what are their functions?

A

Tp53,rb

Encode proteins that inhibit the cell cycle or participate in DNA repair processes 

46
Q

What separates the parent and daughter strand? (What characteristic)

A

Methylation. Daughter strand=lack of methylation. 

47
Q

What is responsible for proofreading incorrectly matched bases?

A

DNA polymerase

48
Q

Is there more likely to be errors in the leading or lagging strand?

A

Lagging strand, DNA ligase that binds together the Okazaki fragments does not have proofreading ability

49
Q

Mismatch Repair

A

Genes MSH2 and MLH1 detect abd remove errors in the G2 phase

Catches errors that were missed during S phase.

50
Q

Ultraviolet light and this is the formation of what ultimately leads to distortion of the double helix?

A

Leads to thiamine dimers (in adhacent thiamine residues) which distort the shape of the double helix

51
Q

What eliminates thymine dimers from DNA?

A

NER nucleotide excision repair

Thiamine dimers cause bulges in the DNA strand. Excision endonucleases cut the phosphodiester backbone and remove the defective oligonucleotide. DNA polymerase then fills the gap by synthesizing DNA in the 5’ to 3’ direction.

52
Q

What types of errors does base excision repair fix?

A

Alterations to bases ex. deamination of cytosine to your cell. Error is detected and removed by glycosylase enzyme leaving behind AP site.

AP site is recognized by a AP endonuclease that removes the damage sequence from the DNA. DNA polymerase in DNA ligase then fill the gap and seal the strand as normal.

53
Q

Recombinant DNA

A

Allows DNA fragments to be multiplied and provides a means for analyzing (heterozygous carrier screening, prenatal diagnosis of genetic diseases) altering genes and proteins

54
Q

Process of DNA cloning

A
  1. DNA of interest is cut and placed into a vector (recombinant vector/bacterial or viral plasmid) that is then 2. Transferred into a host bacterium where the bacteria are grown in colonies and isolated (plasmid contains antibiotic resistance)
  2. Restriction enzymes (recognize double stranded palindromic DNA sequences (antiparallel orientation) which cut the vector and DNA sequenence
55
Q

Difference between genomic library and cDNA library

A

Genomic libraries: contain large fragments include both coding and noncoding fragments of DNA contains ENTIRE genome of an organism (cannot be used to make recombinant proteins/gene therapy?

cDNA contain smaller fragments of DNA. Only include (coding) exons of genes (can be used to make recombinant proteins/ for gene therapy)

56
Q

What is hybridization and what is it used for?

A

The joining of complementary base pair of sequences (DNA – DNA recognition or DNA – RNA recognition)

Uses two single-stranded sequences and is a vital part of PCR reaction and southern blotting.

57
Q

Gel electrophoresis separates macromolecules based on what characteristics?

And what direction do the molecules migrate

What migrates fastest?

A

Size and charge.

Migrates to the positively charged anode

Smaller molecules migrate fastest

58
Q

Southern Blotting

A

Detects the presence and quantity of various DNA strands in a sample.

DNA is cut by restriction enzymes and then separated by gel electrophoresis.

Then transferred to a membrane that is probed with many copies of a single stranded DNA sequence. Probe binds complimentary sequence and forms double stranded DNA.

59
Q

PCR (Polymerase Chain Reaction)

A

Automated process that produces millions of copies of DNA (does not require ampifying DNA in bacteria) DNA. DNA doubles with each round.

Requires primer that is complimentary to the DNA that flanks the region of interest.

Reaction requires high temeratures too high for the dna polymerase found in humans so bacterial dna polymerase is used.

60
Q

Gene Therapy

A

Intended to cure individuals with diseases in which a given gene is mutated or inactive. A normal copy of a gene is transferred into the affected tissues essentially curing the individual.

61
Q

Transgenic mice vs Knockout mice

A

Transgene- (cloned gene) introduced into stem cells or fertilized ova.

Used to study disease process from early embryonic development through adulthood.

Knockout Mice- gene intentionally deleted

62
Q

Chimera

A

Mice/Offspring with two types of stem cells

From the transgene and from the original blastocyst

Biochemistry (10 decks)

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