Chapter 6: DNA and Biotechnology Flashcards Preview

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Flashcards in Chapter 6: DNA and Biotechnology Deck (62):
1

nucleoside components

nucleoside components (2)

 

  1. five-membered sugar ring (pentose) 
    • 4 carbons + 1 oxygen
    • The C-5' is hanging off of the ring
  2. nitrogenous base
    • adenine, thymine, guanine, cytosine
    • Attached to the C-1' of the pentose ring

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2

southern blotting

 

steps?

Southern Blotting

  • Technique used to detect the presence of a specific DNA sequence in a sample using a probe sequence.

Steps

  1. DNA is cut by restriction enzymes then separated by gel electrophoresis.
  2. The DNA fragments are separated in the gel.
  3. A radioactive-labeled DNA sequence is added, which is complementary to the DNA fragment we desire to identify.
  4. The radioactive-labeled DNA sequence anneals to the DNA fragment of interest
  5. Use an x-ray to find the radioactive-labeled DNA sequence and DNA fragment of interest

 

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3

recombinant DNA

artificially made DNA strand that was made by combining multiple gene sequences

4

Base excision repair

repair when a base is damaged by external factors.

 

1) Glycosylase removes the damaged base by cleaving its glycosidic bond, resulting in an Apurinic/Apyrimidic (AP) Site

2) Endonuclease removes the AP Site

3) DNA polymerase adds new DNA

4) DNA ligase connects the fragments via a phosphodiester bond 

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5

components of nucleotides

made up of:

  1. five-membered sugar ring (pentose)
    • 4 carbons + 1 oxygen
    • The C-5' carbon is hanging off of the ring
  2. nitrogenous base
    • Adenine, Thymine, Guanine, Cytosine
    • Attached to the C-1'
  3. phosphate group
    • Attached to the C-5' 

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6

Is the breaking of the bond to the phosphate group on ATP endothermic or exothermic? Why?

EXCEPTION: ATP

  • Breaking the phosphate group bond is exothermic.
  • Usually breaking bonds are endothermic to put energy into it and break it.
  • However, since breaking the bond releases more energy than is put into it, breaking it is exothermic

7

DNA libraries

 

 

DNA libraries = large collections of known dNA sequences

 

 

8

what direction does DNA polymerase synthesize DNA?

What direction does it proofread and repair DNA?

Synthesizes: 5' to 3'

 

Proofreads and Repairs: 3' to 5' as an endonuclease or exonuclease

9

Structure of adenine

adenine is a purine

 

squiggly line represents where adenine connects to the sugar

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10

Differences between DNA and RNA

(4)

DNA vs RNA

  1. Strand
    • DNA is double stranded;
    • RNA is single stranded
  2. Pentose carbon 2
    • DNA has a deoxygenated carbon #2 on the pentose sugar
    • RNA has an oxygenated carbon #2 on the pentose sugar
  3. Thymine and Uracil
    • DNA uses thymine
    • RNA uses uracil instead
  4. Movement
    • DNA cannot pass nuclear pores and is confined to the nucleus
    • RNA can pass nuclear pores and leave the nucleus; to make proteins via transcription and translation

11

How many bonds does Adenine and Thymine form?

What about Guanine and Cytosine?

A = T

2 hydrogen bonds

 

 

G ≡ C

3 hydrogen bonds

12

knockout mice

mice with genes purposely removed in order to study the result

13

structure of guanine

guanine is a purine

squiggly line represents where guanine connects to the sugar

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14

Nucleic Acid Hybridization

Nucleic Acid Hybridization

Technique used to determine how similar two strands of nucleic acids are to each other.

Technique to see if two strands anneal to each other.

  1. You take a single strand of DNA.
  2. You add another single strand of DNA or a strand of RNA.
  3. If the two strands anneal to each other, that means they are complimentary in those regions and similar.

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15

are the strands of DNA parallel or antiparallel to each other?

The strands of DNA are antiparallel to each other

parallel but in opposite directions

 

  • one strand runs 5' to 3' down the page
  • other strand runs 3' to 5' down the page
    • (or 5' to 3' up the page)

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16

nucleic acids

what are the made up of?

 

 

nucleic acids: DNA and RNA

are made up of polymers of nucleotides

Structure:

  • nucleotides are joined together into long strands
  • Linked by phosphodiester bonds between the phosphate group of one nucleotide and the third carbon of the pentose sugar of another nucleotide
    • Phosphate-sugar backbone
  • *Notice the phosphodiester bonds in the picture

 

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17

what are the DNA bases and what are their ribonucleoside names?

 

How is the ribose modified in DNA?

Adenine ⇒ 2’ deoxyadenosine

Guanine ⇒ 2’ deoxyguanosine

Cytosine ⇒ 2’ deoxycytidine

Thymine ⇒ 2’ deoxythymidine

 

In DNA, the ribose has no hydroxyl group at the 2' carbon

18

helicase

enzyme involved in DNA replication that separates the double-stranded DNA into separate single strands

 

it unwinds and unzips DNA into separate strands

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19

DNA polymerase I

 

Ribonuclease H and DNA polymerase δ

DNA polymerase I

  • Prokaryotic DNA replication enzyme
  • Removes and replaces RNA primers with DNA

 

Ribonuclease H and DNA polymerase δ​

  • Eukaryotic DNA replication enzymes
  • Ribonuclease H = Removes RNA primers 
  • DNA polymerase δ = Adds DNA to the area

20

Semiconservative replication

DNA replication is always semiconservative.

Because one parent strand remains in each of the two resulting identical double-stranded DNAs

21

Heterochromatin vs Euchromatin

They are 2 types of chromatin.

 

Heterochromatin - chromatin that is densely packed, transcriptionally inactive, and dark under an electron microscope

  • Remember: Heterosexuals have tight buttholes because they don't have to do anal.

 

Euchromatin - chromatin that is loosely packed, transcriptionally active, and light under an electron microscope

  • Remember: Eugenia has a loose butthole and always reads (transcriptionally active), and she is light skin

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22

DNA gyrase (toposisomerase II)

DNA replication enzyme that prevents supercoiling right before the replication fork

23

what direction is DNA and RNA read in?

5' to 3'

24

How do G≡C base pairs affect melting point?

the more G≡C base pairs, the higher the melting point.

 

This is because G≡C base pairs are very stable and have strong bonds, requiring more energy to break

25

Draw a short segment of DNA

2 base pairs long

 

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26

Primase 

 

How does it work differently for the lagging and leading strand

Primase

enzyme involved in DNA replication that places RNA primers on the parent strands so that the daughter strands can be synthesized.

 

  • Many RNA primers are added to the lagging strand, resulting in Okazaki fragments
  • 1 RNA primer is added to the leading strand

 

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27

What is Dideoxyribonucleotide and why is it useful for determining DNA sequences?

Dideoxyribonucleotide is a deoxyribonucleotide but without a hydroxyl -OH group at the 2' and 3' carbons.

 

This prevents a phosphodiester bond from forming at the 3' carbon and 5' phosphate group in the backbone.

 

Scientists can add this to the end of a sequence so that the sequence does not get any longer and they can read it.

28

complementary DNA (cDNA)

 

how is it made?

cDNA

  • Single-stranded gene of DNA that scientists use for creating clones, mapping chromosomes, sequencing genes, making proteins, for gene therapy, etc.
  • It only contains exons (the expressed regions of DNA)
  • Scientists use techniques to reverse transcribe mRNA to form cDNA

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29

Histones

 

Nucleosomes

histones - Proteins that fold DNA into chromatin and chromosomes

 

nucleosomes - DNA wrapped around a histone protein core

30

structure of uracil

uracil is a pyrimidine

 

squiggly line represents where uracil binds to the sugar in RNA

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31

Metastasis

the migration of cancer cells to other tissues

32

DNA is polymerized in what direction?

 

What direction are the phosphodiester bonds connected in?

Polymerized from 5' to 3'

 

phosphodiester bonds are connected in the 3' to 5' direction

33

Nucleotide exicision repair

when UV light damages nucleotides in DNA, causing a bulge in the strand.

Usually forming a Thymine Dimer - connection between nearby Thymines.

 

1) Endonuclease removes the damaged nucleotides.

2) DNA polymerase adds in new nucleotides

3) DNA ligase connects the fragments together forming a phosphodiester bond

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34

what is the overall charge of DNA and RNA?

Why?

Both DNA and RNA have an overall negative charge

 

Because their phosphate groups carry a negative charge

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35

structure of cytosine

cytosine is a pyrimidine

squiggly line represents where the cytosine binds to the sugar

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36

purine derived bases

how many rings

pure as gold

has 2 rings

purine: adenine + guanine

 

Remember: there are two gold rings involved in marriage: wife's ring and husband's ring

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37

DNA is made up of what 3 components?

base + D-β-ribose + phosphate group

 

38

What happens when DNA is denatured?

The hydrogen bonds between base pairs are disrupted

This separates the strands.

 

The phospho-sugar backbone and attached bases do not break.

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39

what are the requirements to be aromatic?

 

are purines and pyrimidines aromatic?

  • cyclic
  • planar
  • alternating single and multiple bonds/lone pairs)
  • stable
  • unreactive
    • because they have delocalized pi-electrons that can spread around the entire compound and make it unreactive/stable
  • 4n + 2 pi electrons

 

Yes, purines and pyrimidines are aromatic

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40

If a sample of DNA has 20% G, what is the % of T?

Chargaff's Rules

 

20% G = 20% C

30% A = 30% T

41

origin of replication

 

How many do eukaryotes have during DNA replication? Prokaryotes?

the first region of the DNA that is replicated.

It is a region with a lot of A=T base pairs, since they only have 2 H-bonds and are easier to separate for replication

 

  • Eukaryotes have multiple origins of replication during DNA replication
  • Prokaryotes have only one origin of replication during DNA replication

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42

Centromeres

 

When does it dissapear during Mitosis?

 

What kind of chromatin is it made up of?

region of DNA found in the center of chromosomes that holds the sister chromatids together.

 

It is a G≡C dense region, due to the 3 strong hydrogen bonds

 

The sister chromatids separate during the anaphase of mitosis

 

It is made up of heterochromatin which is densely packed and transcriptionally inactive, so it does not undergo transcription

43

polymerase chain reaction

 

what does it require?

 

Does Human DNA polymerase work for it?

PCR

  • Technique used to take very little of a DNA sequence and to make many copies of it quickly. 
  • requires: RNA primers, nucleotides, heat resistant Taq DNA polymerases, and heating/cooling cycles
    • Human DNA polymerase does not work for this because it is not heat resistant

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44

single-stranded DNA binding proteins

proteins involved in DNA replication that keep each single strand separated from each other

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45

vector

prokaryotic circular DNA plasmid that can insert its DNA into the host genome

46

Which nucleotides are coenzymes in krebs cycle?

NADH and FADH2

are nucleotides that are coenzymes in krebs cycle

They are involved in oxidation and reduction

 

47

DNA polymerase III

 

DNA polymerase α and δ

DNA polymerase III

  • prokaryotic DNA replication enzyme
  • It adds DNA from 5' to 3'

 

 

DNA polymerase α and δ

  • eukaryotic DNA replication enzymes
    • DNA polymerase α begins DNA synthesis 5' to 3'
    • DNA polymerase δ continues DNA synthesis 5' to 3'
  • DNA polymerase δ can also replace RNA primers with DNA

 

48

How does DNA polymerase differentiate between the parent and daughter strand?

DNA polymerase can differentiate the two strands based on how methylated they are.

 

The parent strand is more methylated.

 

49

structure of thymine

thymine is a pyrmidine

squiggly line represents where thymine bonds to the sugar

 

 

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50

prokaryotic DNA vs Eukaryotic DNA

Each involves a different DNA polymerase for replication

 

Prokaryotic DNA: closed circular plasmid with a single origin of replication. They lack histone proteins so they do not form nucleosomes. Also lack telomeres.

 

Eukaryotic DNA: open linear DNA with multiple origins of replication. Contain histone proteins, forming nucleosomes. Also contain telomeres

51

pyrimidine derived bases

how many rings

CUT the Pie

1 ring

Pyrimidine: cytosine + uracil + thymine

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52

Telomeres

What kind of chromatin are telomeres made out of?

Have a lot of what type of base pairs?

What happens to them after replication?

do eukaryotes and prokaryotes have them?

 

Telomerase

 

 

Telomeres

  • TTAGGG nucleotide sequences at the ends of each strand of DNA that protect the genetic information in our chromosomes
  • Telomeres are made out of heterochromatin which are packed tightly and transcriptionally inactive.
  • Have high G≡C content; strong connections
  • After each round of replication, telomeres get shorter
  • Eventually, telomeres become too short, causing our cells to age and stop functioning properly.
    • Eventually, cell division stops
  • Only eukaryotes have telomeres
    • Prokaryotes don't because their DNA is circular

 

Telomerase - an enzyme that adds telomeres to the end of chromosomes

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53

DNA polymerase I

 

DNA polymerase III

 

What direction do they read? What direction do they add DNA?

Both are involved in prokaryotic DNA replication:

Read from template strand 3' to 5' and add DNA from 5' to 3'

Proofread backwards from 3' to 5'

 

DNA polymerase I - enzyme that replaces RNA primers, adds DNA in between okazaki fragments, and proofreads as an exonuclease/endonuclease

 

DNA polymerase III - enzyme that adds DNA and proofreads as an exonuclease/endonuclease

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54

In DNA:

are the bases on the inside or outside of the helix

what about the backbone?

bases are on the inside of the helix connecting by hydrogen bonding

 

The phosphate and ribose backbone are on the outside of the helix

55

chargaffs rules

states that for a double-stranded DNA,

%A = %T

and

%G = %C

and

%pyrimidine = %purine.

 

Only works for DNA, not RNA

56

gel electrophoresis

technique used to separate molecules based on their size and charge.

 

Charge molecules go to a specific side of the gel.

The bigger size the molecule, the slower it moves

57

DNA ligase

 

What is a problem with DNA ligase?

enzyme involved in DNA replication that connects okazaki fragments of the lagging strand together via phosphodiester bonds

 

DNA ligase does not proofread, so the lagging strand is more likely to have mutations

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58

which nucleotide is used for energy?

ATP

Adenosine Triphosphate is a nucleotide for energy

It is oxidized

59

oncogenes

a gene that has the potential to cause cancer if mutated

60

restriction enzymes

enzymes that cut DNA into fragments at specific sites

61

leading strand

 

lagging strand

Leading Strand - strand at the replication fork that is replicated in continuously towards the replication fork.

 

Lagging Strand - strand at the replication fork that is replicated in discontinously away from the replication fork. 

The lagging strand DNA is formed in okazaki fragments

62

what are the deoxyribonucleotide names?

2' deoxyadenosine 5' phosphate

2' deoxyguanosine 5' phosphate

2'deoxycytidine 5' phosphate

2' deoxythymidine 5' phosphate