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Techniques of Molecular Medicine > DNA and RNA structure and function > Flashcards

DNA and RNA structure and function Flashcards

1
Q

What is the shape of the code in DNA?

A

Linear

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2
Q

What is the acid that makes up DNA called?

A

Deoxyribonucleic acid

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3
Q

What charge is DNA?

A

Negatively charged

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4
Q

Why is DNA negatively charged?

A

Due to the lone pairs on the phosphate ions

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5
Q

What type of reaction occurs between the bases that make up DNA?

A

Condensation reactions

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6
Q

What are the two types of bases found in DNA?

A

Purines

Pyrimidines

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7
Q

Which bases are purines?

A

Adenine and Guanine

Pure As Gold

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8
Q

Which bases are pyrimidines?

A

Cytosine and Thymine

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9
Q

What differentiates the purines and pyrimidines?

A

The number of rings that make up their structure

Purines have double rings and Pyrimidines have single rings

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10
Q

Hydrogen bonds between complementary bases are equally strong

TRUE or FALSE

A

FALSE

Thymine and adenine form two bonds, their bond strength is weaker than cytosine and guanine which form three bonds.

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11
Q

Describe the structure of DNA

A

Double helix

Antiparallel strands make up the DNA ladder that folds to make the double helix

DNA double helix is not symmetrical

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12
Q

What makes the double helix of DNA not symmetrical?

A

The differences in the grooves of the double helical structure

There is a major and minor groove

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13
Q

Describe the pearl necklace structure that forms as DNA is compressed

A

DNA wraps around histones

These then clump together to make the characteristic shape

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14
Q

How long is the DNA in a human cell?

A

2 metres

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15
Q

How many base pairs are found in the human genome?

A

3,3 billion base pairs

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16
Q

How long is the DNA in our bodies?

A

20 million km

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17
Q

What are the two main functions of DNA?

A

Replication

Transcription and translation

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18
Q

What is the aim of replication?

A

Pass the information from the parent cell to daughter cells

Not exact

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19
Q

What is the role of transcription and translation?

A

Code for all the proteins in a cell

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20
Q

What type of replication is involved in DNA replication?

A

Semi-conservative replication

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21
Q

What makes DNA replication semi-conservative?

A

Each strand of DNA acts as a template for the synthesis of a new complementary strand

The new DNA double helix will contain a copy of the old and new strand

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22
Q

Describe the process of semi-conservative replication

A

Helicase opens up the DNA at the replication fork

Single-strand binding proteins coat the DNA around the replication fork to prevent the rewinding of DNA

Topoisomerase works at the region ahead of the replication fork to prevent supercoiling

Primase synthesizes RNA primers complementary to the DNA strand

DNA polymerase III extends the primers, adding on to the 3’ end to make the bulk of the new DNA

RNA primers are removed and replaced with DNA by DNA polymerase I

Gaps between DNA fragments are sealed by DNA ligase

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23
Q

What is the role of DNA polymerase III?

A

Extension of the new complementary strand

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24
Q

What is the role of DNA polymerase I?

A

Removes RNA primers and replaces them with DNA

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25
Q

What is the role of topoisomerase?

A

Works ahead of the replication fork to prevent supercoiling

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26
Q

What is the role of single-strand binding proteins?

A

Coat around the replication fork to prevent the template strands from winding back together

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27
Q

To which end does the DNA polymerase add complementary bases to?

A

3’ end

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28
Q

What is another important job of DNA polymerase I?

A

Proofread the new strand

Remove the vast majority of nucleotides they wrongly added to the chain

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29
Q

What is required to make the phosphodiester bonds between bases?

A

ATP

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30
Q

Where does the ATP come from?

A

Phosphate groups of the nucleosides

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31
Q

Where does replication start?

A

Origins of replication

32
Q

What are origins of replication?

A

Specific locations on the DNA that are identified by specific proteins

33
Q

How do origins of replication start replication?

A

Specialized proteins recognize the origin, bind to the site and open up DNA

34
Q

What happens when the DNA starts to become replicated?

A

Forms a replication bubble

Caused by the replication forks moving in different directions

35
Q

Do the replication forks move towards the same or different directions?

A

DIfferent directions

36
Q

One polymerase III enzyme controls replication of the DNA replication fork

TRUE or FALSE

A

False

Two polymerase III molecules act on the replication fork

37
Q

What are the two strands that make up the replication fork named?

A

Lagging strand

Leading strand

38
Q

In what direction is the leading strand replicated?

A

In the 3’ to 5’ direction

The new strand is in the 5’ to 3’ direction

39
Q

In what direction is the laggging strand replicated?

A

In the 5’ to 3’ direction

The new strand is in the 3’ the 5’ direction

40
Q

DNA polymerase III can replicate DNA in both directions

TRUE or FALSE

A

FALSE

DNA polymerase can only make DNA in the 5’ to 3’ direction

41
Q

What is the difference in the replication between the lagging and the leading strands?

A

The leading strand is oriented in such a way that the DNA polymerase can act on the strand immediately to form a continuous strand of DNA

Since the lagging strand rins from the 5’ to 3’ direction, the new strand is made in fragments

The DNA polymerase comes off and reattaches to the newly exposed strand exposed by helicase

42
Q

What are the names for the fragments formed by replication of the lagging strand?

A

Okazaki fragments

43
Q

What is the role of the sliding clamp in DNA replication?

A

Holds the DNA pol III in place so they don’t float off during replication

44
Q

What stain can be used to localize genes on chromosomes?

A

Giemsa stain

45
Q

What affects the degree of staining of a gene?

A

Gene density

Transcription activity

46
Q

What regions stain more darkly with G staining?

A

AT-rich regions

Gene poor compare to GC-rich regions

47
Q

What is the use of gene staining?

A

Identify chromosomal abnormalities

48
Q

What percentage of DNA is coding DNA?

A

2%

Represents 25000 genes

49
Q

What other DNA is found in the genome?

A

Introns

UTR

Near gene

Dark matter

50
Q

What is transcription?

A

Process by which we form an mRNA sequence that is later translated to form a protein

51
Q

What is TATA?

A

Promoter that tells the cell when gene needs to transcribed

Contains a transcription factor binding site where regulatory elements are recognised by specialised proteins

52
Q

What are the 3 phases of transcription?

A

Initiation

Elongation

Termination

53
Q

Describe the initiation phase of transcription

A

TBP binds to the TATA box

Bound TBP triggers the transcription factors TFIIA and TFIIB to bind

These transcription factors stimulates the assembling of the general transcription factors and RNA Pol II to the promoter

TFIIh pry apart the double helix at the transcription start site and activates RNA Pol II

Transcription factors binding to the transcription binding site causes DNA binding proteins to activate, causing DNA to bend

54
Q

How does TFIIh cause the double strands to pry apart?

A

Uses energy from ATP hydrolysis

55
Q

Where are the double strands pried apart?

A

At the transcription start site

56
Q

How does TFIIh activate RNA Pol II?

A

By changing its conformation

Release the RNA Pol II from general factors

57
Q

How is bending of the DNA strand beneficial to the transcription process?

A

Activators are allowed to come into with the mediator proteins that stimulate RNA polymerase II

58
Q

Describe the formation of the hybrid RNA-DNA region

A

DNA enters from the front of the polymerase and is unzipped to avail the template strand for RNA synthesis

59
Q

The DNA strands and nascent RNA strand exit the cell through the same channel following elongation

TRUE or FALSE

A

FALSE

They exit through different channels

60
Q

How does the cell make sure the DNA and RNA strands leave the cell through different channels?

A

RNA is guided by proteins that leads it to the correct end of the transcription bubble

DNA prying causes the DNA to want to go back to its natural conformation, so the strands reunite at the trailing end of the transcription bubble

61
Q

What is another role, apart from synthesising nascent RNA, of RNA Pol II?

A

Proofreads the RNA molecule whilst synthesizing it

62
Q

How does the RNA Pol II know it has reached the end of the gene it is transcribing?

A

CPSF and CSTF recognize and bind the poly-A signal in the transcribed RNA

These transcription factors tell RNA Pol II it has reached the end of the gene

63
Q

What other effects do CPSF and CSTF have on the transcription of nascent RNA?

A

Recruit other proteins to carry out RNA cleavage and polyadenylation

Tells other enzymes to start post transcriptional modification

64
Q

How does the RNA pol II stop transcription of a gene?

A

Eventually detaches through a not entirely known mechanism

65
Q

What is the aim of post-transcriptional modification?

A

Stabilise the mRNA molecule

66
Q

Why does the mRNA require stabilisation?

A

It is easily degraded by cellular proteins since it is a single strand

67
Q

Examples of post-transcriptional modifications done to RNA

A

7-methylaguanosine group is added to the 5’ end of pre-mRNA to protect it from degradation by ribonucleases

3’ end of the molecule is cleaved and 250 adenine residues are added to form the poly-A tail

Introns are removed and exons are re-connected through intra-exon bonds to form mature mRNA

68
Q

To which end of the mRNA is the 7-methylguanosine cap added?

69
Q

To which end of the mRNA is the poly-A tail added?

70
Q

What do we call the removal of introns from mRNA?

71
Q

What is alternative splicing?

A

Refers different ways to remove introns and bind exons together

72
Q

Methods of alternative splicing

A

Constitutive splicing

Exon skipping

Intron retention

Mutually exclusive exons

Alternative 5’ splice site

Alternative 3’ splice site

73
Q

What is the benefit of alternative splicing?

A

Root cause of the complexity between humans

74
Q

What are the differences between RNA and DNA?

A

RNA is single stranded, DNA is double stranded

Complementary base to Adenine is Uracil in RNA and Thymine in DNA

The sugar backbone is ribose in RNA and deoxyribose in DNA

75
Q

What do we mean when we say the genetic code is redundant?

A

A protein can be coded for by more than one codon

Techniques of Molecular Medicine (12 decks)

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