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Genetics > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

Describe the structure of DNA

A

Double helix

Composed of two strands

  • Sugar-phosphate backbone on the outside
  • Nucleotide bases on the inside

Nucleotide bases formed complementary pairs (Chargaff’s rule)

the complementary strand is antiparallel to the main strand

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2
Q

Pyrimidine

A

Cytosine, Thymine, Uracil (RNA), have 1 ring structures

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3
Q

Nucleotide

A

DNA building blocks composed of five carbon deoxyribose sugar, a nitrogenous base, and one or more phosphate groups.

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4
Q

What is each strand of dna composed of?

A

Nucleotides

Sugar-phosphate backbone

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5
Q

Purine

A

Adenine, Guanine, have 2 ring structures

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6
Q

What is semiconservative replication?

A

In 1958, Meselson and Stah

Replication generates two identical duplexes (double -stranded helices) of DNA

The two complementary strands of the original DNA separate from one another and become templates for the synthesis of new complementary strands

Each new DNA duplex now has one parental strand and one daughter strand

-*Parent strand serves as template strand for new strand

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7
Q

Nucleosides

A

5-carbon sugar + nitrogenous base (hydrophobic)

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8
Q

Describe the Sugar-phosphate backbone

A

Deoxyribose sugars alternate with phosphate groups due to phosphodiester bonding (covalent bond)

Sugar phosphate backbone is hydrophilic

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9
Q

Are the nitrogenous bases hydrophilic or hydrophobic explain?

A

Bases are hydrophobic and turn towards the interior of the double helix- Bases are inside because they are hydrophobic

Sugar phosphate backbone is hydrophilic

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10
Q

phosphodiester bond

A

a type of covalent bond formed between 2 nucleotides in a nucleic acid strain
formed between the 5’ phosphate group of one nucleotide and the 3’ OH of the adjacent molecule

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11
Q

parental strand

A

the DNA strand acting as a template to direct the synthesis of a new “daughter” strand

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12
Q

describe strand polarity

A

5’ end = phosphate group 3’ end = hydroxyl group

Phosphate group and hydroxyl group allow the formation of the phosphoditer bond and formation of sugar phosphate backbone

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13
Q

What type of bond forms between the complementary base pairs?How many?

A

hydrogen bonds joining the 2 strands into a helix
Complementary nucleotides form hydrogen bonds by the attraction of + and – charges

2 hydrogen bonds between A-T
3 hydrogen bonds between G-C

  • Takes more energy to break g- c bonds because they have more bonds
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14
Q

antiparallel

A

opposite 5’ and 3’ orientations of 2 complementary nucleic acid strands- one is 5’ to 3’ and the complementary strand is 3’ to 5’

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15
Q

daughter strand

A

a newly synthesized strand of DNA that is complementary to a template strand

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16
Q

Describe the configuration of the nucleotide bases

A

The nitrogenous base is attached to the deoxyribose sugar to the 1’ carbon by a covalent bond

The hydroxyl group is attached to the 3’ carbon

Forms the phosphodiester bond with the phosphate group

The phosphate group is attached to the 5’ carbon

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17
Q

dNMPs

A

Monophosphate forms of deoxynucleotides

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18
Q

dNTPs

A

Triphosphate configurations- forms of deoxynucleotides

Used as energy because they have more phosphates so more energy to release

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19
Q

what is the difference between RNA and DNA?

A

2 hydroxyl groups instead of one in RNA
uradine instead of thymines
ribose is used instead of deoxyribose

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20
Q

enzyme

A

specialized protein that has a special function in metabolic pathway

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21
Q

Describe the function of DNA polymerase?

A

(make polymers) catalyses the formation of the phosphodiester bonds between the 3’ hydroxyl group of one nucleotide and the 5’ triphosphate group on the other
- catalyses complementary base pairing during strand elongation

-Two of the phosphate groups are removed, leaving the nitrogenous bases in their monophosphate form in the sugar-phosphate backbone

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22
Q

What does it mean that two strands are complementary and antiparallell?

A

Two strands are complementary to each other (ie A pairs with T, G pairs with C)

  • A purine always pairs with a pyrimidine via hydrogen bonds
  • If it didn’t, there would be bulges and kinks in the helix

The two strands are antiparallel (because of complementary base pairing)

One strand is 5’- ATCG-3’, the other strand is 3’-TAGC-5’

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23
Q

The proportion of base pairs equals:

A

A=T, C=G

A+T) + (G+C) = 1.0 (or 100%

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24
Q

what is the bp turn for the helix?

A

Helix has a right-hand twist of ~10 bp(base pairs)/turn

Twist creates a major and minor groove for protein interactions

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25
Q

What would happen if complementary strands were parallel?

A

if the complementray stands would align in the same direction (both 5’ to 3’) the charges of the complementary nucleotides would repel and no hydrogen bonds would form the antiparallel orientation brings the partial charges into alignment to form hydrogen bonds

26
Q

Outline the general steps of DNA replication in all lifes organisms

A

DNA replication is universal throughout Life’s organisms
 Differences in the mechanisms have evolved over time, but the process is universally the same

  1. Each strand of the parental DNA molecule remains intact during replication
  2. Each parental strand of DNA serves as a template directing the synthesis of a complementary, antiparallel daughter strand
  3. Completion of replication results in the formation of 2 identical daughter duplexes, each composed of 1 parental strand and 1 daughter strand
27
Q

What does the phrase DNA replication is bidirectional mean?

A

DNA replication is bidirectional, forming a “replication bubble”

  • Prokaryotes have a single origin of replication- bc their dna is a circle (bacteria_
  • Eukaryotes have multiple origins of replication- ours is longer more complex so that’s why we have multiple so everything can be replicated in a timely manner
  • As DNA unwinds it will synthesize both strands at once BUT one strand is 3’-5’ and one is 5’-3’ so it creates a biredirectional approach that happens simultaneously
28
Q

List the enzymes needed for DNA replication?

A 
Helicase 
DNA topoisomerase
Single-stranded binding proteins (SSB)
Primase
DNA polymerase III 
DNA polymerase I 
DNA ligase
29
Q

Describe the function of Helicase

A

unwinds the double helix

breaks the hydrogen bonds, allowing for the double-stranded DNA to unwind (like a zipper unzips)

unwinding of the strands occur ahead of the advancing replication fork

30
Q

Describe the function of DNA topoisomerase

A

Relaxes supercoiling

(When you try to unwind something that’s already tightly wound it winds up more tightly somewhere else so this helps relax it and prevents it from breaking)

binds to the DNA and relaxes supercoiling

Prevents the DNA from twisting back upon itself

Also has ligase function that if DNA breaks it can glue it back up and be ready for more replication

31
Q

Primer

A

created by primase

is 12-24 bp in length (acts as a starting place telling the DNA polymerase to come and attach nucleotides)

Made of RNA, complementary to the template DNA strand

a short single stranded segment that begins the daughter strand and provides a 3’ OH end to which a new DNA nucleotide can be added by DNA polymerase

32
Q

Describe the function of Primase

A

synthesizes RNA primers

binds to the site of initiation and creates a primer (starting point of DNA Replication)

33
Q

Describe the function of the Single-stranded binding proteins (SSB)

A

Prevents re-annealing of separated strands

Act like a little plug to prevent strands from coming back together because the base pairs will want to complementary base

bind to the unwound strands, preventing them from reforming the DNA duplex

34
Q

Which direction is DNA synthesized in?

A

Template strand reads 3’->5’ direction

The new strand elongates in 5’->3’ direction

35
Q

Describe the function of DNA polymerase I

A

removes and replaces RNA primer with DNA

removes the RNA nucleotides one-by-one and replaces them with DNA nucleotides that are complementary to the parental strand

Begins with the 5’ nucleotide of the RNA primer and progresses in the 3’ direction

Uses a 5’->3’ exonuclease(cut out RNA) activity to remove the RNA nucleotides

Uses a 5’–> 3’ polymerase(add make more DNA) activity to add DNA nucleotides

Continuously pushes the gap in the 3’ direction until there is only a single nucleotide bp gap

36
Q

Describe the function of DNA polymerase III

A

synthesizes DNA

is an enzyme that adds nucleotides complementary to the template strand. But needs RNA! (brings the DNTPS takes off 2 of the phosphates and attach into sugar phosphate backbone)

Template strand reads 3’->5’ direction

The new strand elongates in 5’->3’ direction

Adds nucleotides to the 3’ end (hydroxyl) of the previous nucleotide

The primers provide the initial 3’ OH group for DNA polymerase to add the first nucleotide

Nucleotides are complementary to the parental strand

37
Q

Describe the function of DNA ligase

A

joins DNA segments together (ie “glues”)

When we remove primer it’ll glue the 3’ hydroxyl end of where the primer was with the nucleotide to the 5’ phosphate group and close up gaps

comes in and fills the gap by creating the final phosphodiester bond between the two nucleotides that joins the Okazaki fragments

38
Q

replisome

A

complex that contains the proteins and enzymes required for replication

One at each replication fork

One carries out DNA synthesis in the 5’ ->3’ direction continuously following the leading strand

The other carries out DNA synthesis discontinuously in the 5’ ->3’ direction, but in the opposite direction of the replication fork on the lagging strand

39
Q

polymerase

A

an enzyme that makes polymers bigger molecules

40
Q

replication bubble

A

a region of active dna replication containing replication forks on each end an origin of replication in the middle and leading and lagging strands in each half of the bubble

41
Q

leading strand

A

In DNA replication, the continuously synthesized strand

42
Q

lagging strand

A

In DNA replication, the discon- tinuously synthesized strand whose Okazaki fragments are ligated to complete new strand synthesis.

43
Q

Okazaki fragments

A

DNA fragments ~ 100 -200 bp long (in Eukaryotes, shorter in prokaryotes), that are later joined together by DNA ligase as DNA polymerase I removes the primers and replaces with nucleotides

44
Q

bidirectional

A

the method of dnA replication that synthesizes new DNA in both directions from a replication origin

45
Q

Describe how DNA proofreading occurs?

A

DNA polymerase I has the ability to “stop” and reverse replication to remove an incorrect nucleotide
- Will replace it with the correct one

The protein structure of the polymerases resemble a “hand and thumb”

Nucleotide errors result in improper hydrogen bonding in the base pairs, resulting the daughter strand being displaced

  • Blocks the addition of more nucleotides and rotates the strand into the 3’ -to -5’ exonuclease site in the polymerase
46
Q

How does Replication differ in us?

A

Unlike prokaryotes, our DNA is linear within the nucleus

Replication of circular DNA creates 2 complete copies of the parental DNA

Linear DNA cannot fully replicate and replication falls short

Due to RNA primers near the end of the lagging strand

This shortens the chromosome after each successive replication

Problem is solved in telomeres

47
Q

What is bidirectional expansion caused by in bacteria?

A

Bidirectional expansion is caused by the expanding replication bubble and DNA synthesis at the replication fork

48
Q

exonuclease

A

cut out RNA

49
Q

polymerase

A

add make more DNA

50
Q

What must be removed before replication is complete?

A

RNA primers must be removed before replication is complete

Otherwise you have RNA interspersed within your DNA!

When DNA polymerase III reaches a primer, it leaves a single stranded gap that must be filled between the nucleotide and the primer

51
Q

Are DNA polymerase I and DNA ligase active on both the leading and lagging strands?

A

YES

Just more prominent on the lagging strand because it has more primers to remove

52
Q

How often do replication errors occur?

A

Replication errors occur ~1 every billion (10 9 ) nucleotides

53
Q

What is torsional pressure and how is it fixed?

A

During replication, the unwinding and creation of the replication fork causes torsional pressure within the parental strands

Results in supercoiling, twisting more than just the double helix naturally would

Ex. Holding a rubber band stationary on one end, and twisting the other

  1. topisomerase cuts one or both DNA strands
  2. DNA strands rotate to remove the super coils
  3. Topoisomerase rejoins the DNA strands
54
Q

telomeres

A

Non-protein coding (junk DNA, repeating chunkc aaaaaa)

Made up of 1000s of 6-12bp repeats, totally 2 to 20kb long at birth

Each successive replication shortens the telomeres in somatic cells

Contains a knotted fold in the DNA called the T-loop,

55
Q

T-loop,

A

protects the telomere from enzymatic degradation by joining with a protein complex called shelterin

Early breakdown= early aging and genetic diseases

56
Q

telomerases

A

in Germ-line cells

(enzyme containing RNA) that adds repetitive DNA sequences to the ends of telomeres

57
Q

Hayflick limit

A

number of replication cycles in the cell’s life span (~50-70 cycles)

58
Q

i

A

Unlike prokaryotes, our DNA is linear within the nucleus

Replication of circular DNA creates 2 complete copies of the parental DNA

Linear DNA cannot fully replicate and replication falls short

Due to RNA primers near the end of the lagging strand

This shortens the chromosome after each successive replication

59
Q

i

A

Lagging strands are shortened after each replication event when the RNA primer is removed and not replaced with DNA nucleotides
Leading strands are synthesised to the ends of linear chromosomes

60
Q

what can telomere shortening cause?

A

Causes genomic instability, resulting in increased mutations
 Can lead to various cancers
 Dyskeratosis congenita -> bone marrow failure
 Idiopathic pulmonary fibrosis -> progressive lung disease
 Many more…

Shortening can also be caused by
 Smoking
 Stress
 Poor overall health (obesity, inflammation)  Chemical exposures, ROS,

61
Q

replication fork

A

site where the double stranded DNA is unwound to create 2 single stranded DNA templates

Genetics (12 decks)

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