DNA structure & replication

Question 1

central dogma

Answer 1

DNA → RNA → protein

(replication) transcription → translation

Question 2

Frederick Griffith

Answer 2

Proved there is hereditary element

• pre-biotic era
• used mice to study S. pneumoniae
• shiny/smooth strain = deadly
• rough strain = killable

Question 3

Griffith experiment

Answer 3

1. rough strain → mouse lives
2. smooth strain → mouse dies
3. heat-killed smooth strain → mouse lives
4. rough strain + heat-killed smooth strain → mouse dies

Heat-killed smooth strain mixed with rough strain caused rough strain to mutate into smooth strain

Question 4

Avery, Macleod & McCarty

Answer 4

showed DNA is hereditary factor mentioned in Griffith experiment

• developed transformation procedure using extract from heat killed smooth strain

Question 5

Avery, MacLeod & McCarty experiment

Answer 5

proved DNA is hereditary element in Griffith experiment

• treated heat-killed smooth bacteria with 3 enzymes: protease, DNase & RNase
• result: DNase → mouse lives
• DNA destroyed by DNase

Question 6

protease

Answer 6

enzyme that catalyzes proteins

Question 7

DNase

Answer 7

enzyme that catalyzed DNA

Question 8

RNase

Answer 8

catalytic enzyme for RNA

Question 9

Hershey-Chase experiment

Answer 9

1. T2 bacteriophage
   
   • infection begins by phage attaching to bacteria cell surface
   • new phase made inside bacterial cell
   • T2 have DNA + protein (no RNA)
2. DNA labeled with ³²P
3. proteins labed with ³⁵P
4. all blended
   
   • removes ghosts
5. should find ³²P labels in bacterial cells if DNA = hereditary material

Question 10

what is DNA made up of?

Answer 10

phosphates

Question 11

what is RNA made up of?

Answer 11

sulfur

Question 12

DNA structure

Answer 12

1. nucleotide
2. sugar
3. nitrogenous bases

Question 13

nucleotide components

Answer 13

1. sugar
2. nitrogenous base
3. phosphate

Question 14

sugar components

Answer 14

1’ - base

2’ - OH or H

3’ - OH

4’ - 5’

5’ - phosphate

Question 15

name types of nitrogenous bases

Answer 15

1. pyrimidine - single ring
   
   • thymine
   • cytosine
   • uracil (RNA)
     
     • “Cut the Py”
2. purine - double ring
   
   • adenine
   • guanine
     
     • “Pure things Are Good”

Question 16

Rosalind Franklin

Answer 16

used x-ray diffraction to examine crystal strucure of DNA

• her research used by Watson & Crick to determine DNA structure
  
  • uncredited
• key findings
  
  • duplex
  • constant diameter
  • phosphates on outside
  • 10 bases per turn

Question 17

Edwin Chargaff

Answer 17

found %T = %A and %G = %C

• Watson & Crick used his research to figure out DNA structure

Question 18

DNA characteristics

Answer 18

1. antiparallel strands
   
   • 5’ to 3’ end
2. A-T and G-C
3. phosphodiester & hydrogen bonds

Question 19

why are G-C bonds stronger than A-T bonds?

Answer 19

G-C bonds have 3 H-bonds while A-T bonds have 2 H-bond

Question 20

phosophodiester bonds

Answer 20

covalent bonds btwn 2 nucleotides in nucleic acid strain

• btwn 5-phosphate & 3-OH of adjacent nucleotide

Question 21

pyrimidine

Answer 21

single ring

• thymine
• cytosine
• uracil (RNA)

Cut the Pi – pie = 1 circle

Question 22

purine

Answer 22

double ring

• adenine
• guanine

Pure things Are Good

Question 23

bacteriophage

Answer 23

(phage) virus whose host is a bacterium

Question 24

phage

Answer 24

bacteria virus

Question 25

Watson & Crick

Answer 25

proposed double helix (DNA) in 1953 * know 1 strand, can make otro strand

Question 26

Mesellson & Stahl

Answer 26

proved DNA replication is semiconservative * used ¹⁴N/¹⁵N

Question 27

DNA replication process

Answer 27

1. separate strands & keep apart * break bonds * start @ origin of replication * keep undwiding DNA ahead of replication complex 2. initiate DNA synthesis * DNA polymerase needs primer w/ 3'-OH & ssDNA for template 3. generate accurate DNA copy per strand * strands = antiparallel * synthesis = bidirectional

Question 28

charactericstics of origin

Answer 28

1. A-T rich * less H-bonds → easier to pull apart 2. recruits helicases to open up DNA & begin replication

Question 29

helicase

Answer 29

proteins that use ATP to break H-bonds btwn DNA strands

Question 30

single-stranded binding proteins (SSBs)

Answer 30

bind to stranded (single) regions of DNA to keep them

Question 31

how to solve supercoiling when separating strands (DNA replication)

Answer 31

1. topoisomerase 2. DNA gyrase

Question 32

toposoimerase

Answer 32

enzyme that cuts loop to prevent supercoiling

Question 33

DNA gyrase

Answer 33

bacterial topoisomerase

Question 34

which direction is DNA synthesized?

Answer 34

5' to 3'

Question 35

which direction is DNA template read?

Answer 35

3' to 5'

Question 36

DNA polymerase

Answer 36

responsible for DNA synthesis of new strands during replication & repair

Question 37

DNA primase

Answer 37

makes a short RNA primer

Question 38

DNA polymerase III

Answer 38

major DNA replication enzyme in prokaryotes

Question 39

leading strand

Answer 39

continuously synthesized strand in DNA replication * continues to replication bubble (5')

Question 40

lagging strand

Answer 40

strand discontinuously synthesized * Okazaki fragments * starts @ 3' end

Question 41

Okazaki fragment

Answer 41

short fragment of newly synthesized DNA * part of lagging strand * ligated to otro Okazaki fragments to complete lagging strand synthesis

Question 42

what is chemically happening in DNA synthesis?

Answer 42

new nucleotides are added to each strand

Question 43

deoxynucloetide triphosphates (dNTPs)

Answer 43

triphosphoate forms of deoxynucleotides

Question 44

what happens if DNA polymerase II makes a mistake?

Answer 44

1. pause 2. notice error 3. takes out error 4. redo (proofreading)

Question 45

DNA polymerase I

Answer 45

major DNA replication enzyme that replaces primers w/ DNA

Question 46

DNA ligase

Answer 46

seals nicks in DNA

Question 47

histone

Answer 47

proteins that coat DNA

Question 48

telomere function

Answer 48

* protect important genes * does not code for anything * has repetitive DNA @ end of chromosome * lose some during division * telomeres disappear after multiple divisions \*cancer cells = telomeres that didn't disappear

Question 49

telomerase

Answer 49

ribonucleoprotein complex * RNA component * guides proper attachment * template for reverse transcription * protein component * reverse transcriptase * synthesizes DNA based on RNA template * reverse transcription * lenthems telomeres

Question 50

what are the most frequent mutations in cancers?

Answer 50

reactivation of telomerase

Question 51

molecular techniques

Question 52

spectrophotometry

Answer 52

quantify nucleic acids & proteins * DNA concentration & purity * purine/pyrimidine rings absorb UV light * 260mm commonly used to detect DNA * 280mm used to detect proteins * measure absorbance ratio

Question 53

restriction enzymes

Answer 53

cut DNA @ specific sites * Palindromic sequences - reads on both strands of DNA when read in 5' to 3' direction * some yield sticky or blunt overhangs

Question 54

vectors

Answer 54

plasmids from bacteria * carrier of DNA molecules * transfer & replicate DNA