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Y1 Fundamentals of Life Science > L1 - Structure of DNA > Flashcards

L1 - Structure of DNA Flashcards

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Biology 101 flashcards
1
Q

Briefly describe what DNA is?

A
  • DNA is a nucleic acid
  • A macromolecule
  • Made up of 2 polynucleotide chains
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2
Q

What sub-units are polynucleotides made up of?

A

Nucleotides

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3
Q

What components make up a DNA nucleotide?

A
  • 5’ carbon sugar called 2-deoxyribose - a stable sugar
  • Nitrogenous base
  • Phosphate group attached to the 5’ end of 2-deoxyribose
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4
Q

Name the 4 different nitrogenous bases and their complementary base pairs

A

A for adenine
T for thymine
G for guanine
C for cytosine
A with T
G with C
* must always write full names not shorthand

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5
Q

Name the bond which attaches the nitrogenous base to 2-deoxyribose in DNA?
What is the purpose of this bond?

A

N-glycosidic bond
Gives stability to 2-deoxyribose and the nitrogenous base

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6
Q

What term is used to describe the combination of 2-deoxyribose and a nitrogenous base?

A

Nucleoside

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7
Q

When does a nucleoside become a nucleotide?

A

When a phosphate is bound to the 5’ carbon on 2-deoxyribose by a phosphodiester bond

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8
Q

Describe the terms 5’ prime end and 3’ prime end in relation to DNA

A
  • Successive nucleotides bond together by phosphodiester bonds to form a DNA strand
  • The phosphate is at the 5’ end
  • The free hydroxyl group is at the 3’ end
  • 2-deoxyribose determines the orientation
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9
Q

What term is used to describe the relation between 2 DNA strands?

A
  • DNA strands run anti-parallel to each other
  • DNA strands are complementary to each other
  • The second strand runs in the 5’ to 3’ direction but with a different orientation
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10
Q

What type of bonding is between nitrogenous bases? Why is this beneficial?

A

Hydrogen bonding
Allows stability of the 2 polynucleotide chains running ani-parallel

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11
Q

How many hydrogen bonds are between each complementary base pair?

A

Guanine and cytosine have 3 bonds
Adenine and thymine have 2 bonds

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12
Q

Which bases are purines and pyrimidines?

A

A and G = purine (2 carbon ring)
T and C = pyrimidine (1 carbon ring)

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13
Q

What is the key advantage of having the purine and pyrimidine structure?

A
  • Even though they are different bases, they take up the same spacial area in the nucleus
  • Compact to allow more DNA in the nucleus
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14
Q

What is a benefit towards DNA structure, as a result of hydrogen bonding?

A
  • Allows a twist (helix) to the anti-parallel structure
  • Forms the DNA double helix
  • Allows the information needed in the nucleus to be compacted, to allow the DNA to be unwound to carry out eukaryotic functions
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15
Q

Why is a double helix able to form?

A
  • The phosphate groups are on the outside with the nitrogenous bases in the centre
  • Provides stability and flexibility
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16
Q

What two areas form on a DNA double helix?
What are their functions?

A
  • Major and minor grooves
  • Allows eukaryotic processes to be carried out
  • Some sequences of DNA can only be exposed though these grooves
  • Aids transcription factors or replication machinery to bind
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17
Q

What reaction is involved in nucleotides bonding to subsequent nucleotides?

A
  • Condensation reaction
  • Removal of water molecule
  • Forms a 3’ 5’ phosphodiester bond

*need all of this info to gain full marks

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18
Q

Define DNA replication

A

When a cell divides, both daughter cells must receive a complete set of genes, so the DNA molecules (chromosomes) must replicate accurately before division

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19
Q

Where is DNA found in prokaryotes?

A

The entire genome is on one circular chromosome

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20
Q

Describe the process of asexual reproduction in a prokaryote

A

1) Entire genome is on one circular chromosome
2) The chromosome replicates once to produce two chromosomes that are identical (except for rare mutations)
3) Two identical daughter chromosomes move towards opposite end of the cell, towards the poles
4) Process of partitioning - cell divides the daughter chromosomes into singular daughter cells when partitioned

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21
Q

When does DNA replicate in eukaryotic cells?

A

DNA replicates in the S phase of the cell cycle

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22
Q

When are genes expressed in the cell cycle?

A
  • Occurs in G1 and G2 and occasionally in the S phase (these are only genes not highly expressed)
  • Silent or temp. silent genes ate replicated late in the cycle as they may be needed later on
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23
Q

What are the general features of eukaryotic DNA replication?

A
  • DNA replication is semi-conservative
  • Bi-directional process
  • Proceeds from a specific point called the origin
  • Proceeds in the 5’-3’ direction
  • Occurs with a high degree of fidelity
  • Multi-enzymatic process
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24
Q

What does semi-conservative mean in DNA replication?

A

From the parent double strand, one of each of those double strands is used to form the new daughter strand, by acting as a template and complementary base pairing

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25
Q

What is the role of enzyme helicase in replication?

A
  • Unwinds the double helix of DNA ready for replication
  • By disrupting the H bonds between complementary base pairs creating a replication fork of two strands running in antiparallel directions.
  • This occurs at specific regions (origins of replication),
26
Q

What are SSBP? What are their functions?

A
  • Single-stranded binding protein
  • Keep the replication fork open, bind and stabilise the single strand of DNA to keep it unwound
  • 2 of these are present
27
Q

What is the purpose of an RNA primer?

A

Allows DNA polymerase to attach to the primer and begin the process of replication

28
Q

What enzyme is needed to synthesise an RNA primer?

A

Primase

29
Q

Describe the role of primase and a primer

A
  • Adds ribonucleoside triphosphates to synthesise a primer (primase)
  • Binds to the initiation point of the 3’ - 5’ parent chain (primase)
  • Runs in the 5’-3’ direction (primase)
  • DNA polymerase will attach to the primer
30
Q

What is the role of DNA polymerase? What direction does it move along the DNA strand?

A
  • Attaches to the primer and adds nitrogenous bases to the base on the template strand, so the base pairs are complementary
  • 5’ to 3’ direction
31
Q

How many bases per second does DNA polymerase add?

A

1000/sec

32
Q

How many nitrogenous bases are required by DNA polymerase?

A

All 4 dNTPs (deoxyribonucleotides)

33
Q

What two factors are key for DNA polymerase to act?

A

Template strand and a primer

34
Q

What key function can DNA polymerase carry out?

A
  • Proof reading
  • Able to ‘check over’ previous bases which have undergone complementary base pairing
  • Ensures fidelity in the replication process
35
Q

What is the function of exonucleases?

A

Remove nucleotides from the end of a DNA strand
Work in a 5’ to 3’ or 3’ to 5’ direction

36
Q

What is the function of ligase?

A

Joins the ends of single DNA strands by forming new phosphodiester bonds

37
Q

What is the function of alpha polymerase?

A

Synthesises the RNA primer, initiation of DNA synthesis and the lagging strand

38
Q

What is the function of beta polymerase?

A

Repair DNA

39
Q

What is the function of gamma polymerase?

A

Replicate mitochondrial DNA

40
Q

What is the function of delta polymerase?

A

Synthesise the leading strand, filling DNA gaps after removal of primer

41
Q

What is the function of epsilon polymerase?

A

Repair of DNA

42
Q

Which forms of DNA polymerase are also able to act as exonucleases? In which direction?

A

Gamma, delta, and epsilon
All in the 3’ to 5’ direction

43
Q

What are the 3 stages of DNA replication?

A

Initiation
Elongation
Termination

44
Q

Briefly describe the process of DNA replication

A

1) Helicase unwinds and unzips the DNA double helix by breaking H bonds between complementary bases
2) Single-stranded binding proteins will bind to each of the parent strands - keep the replication fork open
3) Primase acts to allow a primer to attach to each strand of DNA, in a 5’ to 3’ direction, using the 3’ to 5’ parental strand as a template
4) Elongation - the DNA polymerase attaches to the RNA primer and will lay down complementary bases according to the parent template strand in a 5’ to 3’ direction
5) This occurs on both strands
6) The exonuclease will come in and remove the RNA primer, recognising that the RNA primer has ribose and uracil, and so is not part of DNA
7) DNA polymerase proof reads and fills any gaps on the replicated strands
8) Ligase uses condensation reactions to reform the sugar-phosphate backbone between nucleotides through 3’5’ phosphodiester bonds

45
Q

What is the leading strand?

A

The continuous strand. DNA polymerase can always add complementary bases, and continue replication, as it is in the 5’ to 3’ direction

46
Q

What is the lagging strand?

A

Not continuous. Has to wait for the helicase to break the H bonds between bases, and for the RNA primer to be activated on the strand, to allow DNA polymerase to carry out replication

47
Q

What are the small replicated DNA fragments on the lagging strand known as?

A

Okazaki fragments

48
Q

How is DNA replicated on the lagging strand?

A
  • A primer is added using primase, with DNA polymerase able to add free nucleotides which are complementary.
  • Process has to happen in a 5’ -3’ direction
  • Use of multiple primers and okazaki fragments
  • Same process after with exonucleases and ligase
49
Q

How many origins of replication are there in prokaryotes? Why?

A

One
Due to the small size

50
Q

How many origins of replication are there in a eukaryote? Why?

A

Multiple
Large genome so needs to be a faster process

51
Q

Draw a diagram of how origin points result in a continuum two daughter strands
Why does this happen?

A

Due to the process of replication being bi-directional

52
Q

How long does replication take in eukaryotes?

A

8 hrs

53
Q

How long is a full cell cycle for a specialised, differentiated cell?

A

16-18 hrs

54
Q

What are found at the ends of the new daughter cells, and why?

A
  • Telomeres
  • There isn’t a proceeding 3’ -OH when the RNA primer is removed at the 5’ end. There is a gap which has to be filled, because this causes a loss of genetic information in that region
55
Q

What are telomeres rich in?

A

They are G:C rich and attached to the end of the genome

56
Q

Why are telomeres so important?

A

Highly conserved
Serves an important function in protecting the sequence of DNA

57
Q

Are telomeres involved in coding?

A

They are a non-protein coding region
Simply a series of bases for protecting the genome and ending the termination sequence

58
Q

What is the function of gyrase?

A

A topoisomerase which relaxes supercoil produced when the molecule is twisted during replication. Also facilitates unwinding at the beginning of replication

59
Q

What is the function of telomerase?

A
  • Makes and replicated the telomeres
  • Uses a short RNA template to add short DNA repeats to the short end of linear chromosomes when the last primer is removed using RNA template
60
Q

What happens to telomeres as you age?

A
  • Become shorter after every replication by 10-15 bases
  • Increases the risk of age related diseases because the genome is not as well protected
61
Q

What is the human telomere sequence?

A

TTAGGG/ AATCCC repeats

62
Q

Where can the enzymes involved in replication also be used?

A
  • PCR
  • Making recombinant DNA
  • Detecting mutations at the molecular level

Y1 Fundamentals of Life Science (17 decks)

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