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MLB 111 > Unit 4 - Nucleic Acid and Information Flow > Flashcards

Unit 4 - Nucleic Acid and Information Flow Flashcards

1
Q

Name and describe DNA

A

Deoxyribonucleic acid - molecule by which hereditary info is transmitted from generation to generation.

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2
Q

What is DNA made up of

A

A double helix consisting of subunits called nucleotides, which is composed of; 5-carbon sugar, a base, and one or more phosphate groups

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3
Q

How is the carbon group illustrated

A

Indicated by a pentagon, in which 4/5 vertices represent the position of a carbon atom. They are numbered clockwise with primes (1’, 2’, etc)

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4
Q

describe the sugar found in DNA

A

It is deoxyribose (meaning minus oxygen) because the chemical group projecting downwards from the 2’ carbon is a H atom rather than an OH hydroxyl group

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5
Q

Describe the phosphate group attached to the 5’ carbon

A

It will have negative charges on two of its O atoms. Cellular pH 7 = ionization of the OH group (loss of proton, negative charge) therefore DNA is a mild acid

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6
Q

What bases are usually found in a nucleotide of DNA

A

Adenine, Guanine, Thymine, Cytosine

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7
Q

Distinguish between purines and pyrimidines

A

Purines (double ring) - A & G

Pyrimidines (single ring) - T & C

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8
Q

Difference between nucleoside and nucleotide

A

Nucleoside - the combo of sugar and base
Nucleotide - the combo of a nucleoside with one or more phosphate groups

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9
Q

What is important about nucleoside triphosphates

A

They are the molecules that are used to form DNA and RNA, and they’re carriers of chemical energy in the form of ATP and GTP

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10
Q

What bond connects nucleotides and what are they called

A

Covalent bond, called phosphodiester bond

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11
Q

Why are phosphodiester bonds good

A

They are relatively stable bonds that can withstand stresses such as heat and substantial changes in pH that would break weaker bonds.

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12
Q

What do the phosphodiester linkages give the DNA

A

polarity

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13
Q

How do we use the different ends of the molecule to write a sequence

A

where the nucleotide has a free phosphate (eg. 5’) will be known as the 5’ end and where the nucleotide has a free hydroxyl (eg. 3’) is known as the 3’ end.

sequence will be written as 5’-AGCT-3’ or 3’-TCGA-5’

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14
Q

What 3 pieces of information allowed researchers to build a molecular model of DNA

A
  1. results from X-ray crystallography of DNA (Rosalind Franklin & Maurice Wilkins)
  2. published results showing DNA extracted from various organisms cells showed: no. of base A=T and no. of base G=C (Erwin Chargaff)
  3. determined that if bases were to pair they’d pair: A-T and G-C (Jerry Donohue & John Griffith)
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15
Q

What was the final DNA structure that watson and crick came up with

A

Double helical structure, with the backbones on the outside, the bases pointing inwards, and A paired with T & G paired with C

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16
Q

How big is a DNA helix

A

In one complete turn of the helix, there are 10 base pairs, and the diameter of the molecule is 2nm

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17
Q

What are the major groove and minor groove in DNA

A

uneven pair of grooves formed by the outside contours of the twisted strands

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18
Q

Why are major and minor grooves important

A

Proteins that interact with DNA often recognise a particular sequence of bases by making contact with the bases by the major or minor groove

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19
Q

What is the main characteristic of the individual DNA strands

A

They are antiparallel - they run in opposite directions

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20
Q

What different models of the DNA structure are there

A

Watson-Crick Structure - each atom is represented as a color coded sphere

Ribbon Model - sugar phosphate backbones wind around the outside of the bases paired between the strands

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21
Q

what would happen if two purines/pyrimidines were paired

A

2 purines - the backbones would bulge
2 pyrimidines - the backbone would narrow

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22
Q

What causes the complementary bonding of bases

A

The H bonds that form between A & T (2 H bonds) and between G & C (3 H bonds)

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23
Q

How is stability maintained in the DNA molecule if H bonds are weak

A

Because they are added together, millions of the weak bonds along the molecule make the structure more stable.

The interactions between bases in the same strand also increase stability, due to base stacking. (the nonpolar, flat bases group together away from H2O molecules, hence the stacking as tightly as ppossible on top of each other)

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24
Q

What is the process of DNA creating exact copies of itself called

A

Replication

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25
Q

Give a brief description of replication

A

The 2 strands of the parental double helix unwind and separate into single strands, each of these strands serves as a template for the synthesis of a complementary daughter strand.
The synthesis of a new strand is then carried out by DNA polymerase.
At the end there are 2 molecules, each containing one parental and one daughter strand

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26
Q

What makes errors in replication rare

A

DNA polymerase’s proofreading function

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27
Q

What is a mutation

A

a change in the genetic information in DNA

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28
Q

what is the central dogma of molecular biology

A

DNA transcribed to RNA translated to proteins

29
Q

What is the first step in decoding DNA

A

Transcription - genetic info in a molecule of DNA is used as a template to generate an RNA molecule.

30
Q

What is the second step in decoding DNA

A

Translation - a molecule of RNA is used as a code for the sequence of amino acids in a protein

31
Q

What is an example of an exception to the usual central dogma

A

Genetic info is transferred from RNA to DNA in the replication of HIV

32
Q

What is gene expression

A

The production of a functional gene product, such as a protein

33
Q

What is the difference in DNA replication of prokaryotes and eukaryotes

A

prokaryotes:
- transcription & translation occur in the cytoplasm

eukaryotes:
- transcription occurs in the nucleus & translation occurs in the cytoplasm

34
Q

What is the advantage of the way that eukaryotes replicate DNA

A

The separation between transcription and translation allows for additional levels of gene regulation that aren’t possible in prokaryotic cells

35
Q

Differences in RNA vs DNA

A

RNA:
- ribose sugar
- 2 OH groups
- uracil (U)
- uracil has a hydrogen attached to it
- 5’ is a triphosphate

DNA:
- deoxyribose sugar
- 1 OH group
- thymine (T)
- thymine has a methyl group attached to it
- 5’ is a monophosphate

36
Q

What are the physical differences in RNA and DNA

A
  • RNA molecules are much shorter than DNA molecules
  • RNA is single stranded, as opposed to DNA double stranded
37
Q

What characteristics do folded RNA structures have

A

Can have a 3D complexity similar to that of proteins, and can serve as catalysts in biochemical reactions

38
Q

What is the RNA world hypothesis

A

the hypothesis that the earliest organisms relied on RNA for both catalysis and information storage

39
Q

if RNA played a key role in the origin of life, why do cells now use DNA for information storage and proteins for other cellular processes

A

Because DNA is much more stable than RNA, and proteins are much more versatile, it is assumed that life evolved away from RNA-based, to DNA, RNA, and proteins with specialised functions

40
Q

What is an RNA transcript

A

The RNA sequence synthesized from a DNA template

41
Q

How is the RNA transcript produced

A

Produced by polymerization of ribonucleoside triphosphates

42
Q

What is RNA polymerase

A

The enzyme that binds to DNA and carries out the polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript

43
Q

How does RNA polymerase act

A

By adding successive nucleotides to the 3’ end of the growing transcript

44
Q

What is the nontemplate strand

A

The strand of DNA that isn’t used as a template for RNA synthesis during transcription.

45
Q

What else is the nontemplate strand known as and why

A

Coding, sense, and plus strand because it matches the RNA sequence

46
Q

What are the 3 stages of transcription

A
  1. Initiation - RNA polymerase & other proteins are attracted to double-stranded DNA. The DNA strands are separated, and transcription begins
  2. Elongation - successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand
  3. Termination - RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released
47
Q

What direction is the RNA synthesized in

A

They grow in a 5’-3’ direction, nucleic acids are synthesized by addition to the 3’ end (3’ direction)

48
Q

What does it mean that the DNA template and RNA strand are transcribed are antiparallel

A

The DNA template runs in the opposite direction from the RNA. The RNA transcript is synthesized 5’-3’, and the DNA template is read in a 3’-5’ direction

49
Q

What are promoters

A

A regulatory region where RNA polymerase and associated proteins bind to the DNA duplex in the process of transcription

50
Q

What is the TATA box

A

a DNA sequence present in many promoters in eukaryotes and archaea that serves as a protein-binding site for a key general transcription factor

51
Q

What is the terminator

A

a DNA sequence at which transcription stops and the transcript is released

52
Q

What dictates which strand of DNA is transcribed

A

depends on the orientation of the promoter - when promoters are in opposite orientation transcription occurs in opposite directions because transcription can only proceed by successive addition of nucleotides to the 3’ end

53
Q

What does transcription regulation depend on

A

Whether the RNA polymerase & associated proteins are able to bind with the promoter

54
Q

What is a sigma factor

A

a protein that associates with RNA polymerase that facilitates its binding to specific promoters

55
Q

How do sigma factors work

A

Once transcription is initiated, the sigma factor dissociates and the RNA polymerase continues transcription on its own

56
Q

Where do sigma factors mediate promoter recognition

A

in bacteria

57
Q

What proteins bind to the promoter in eukaryotes

A

At least 6 proteins known as general transcription factors

58
Q

What is needed in addition to the assembly of the general transcription factors

A

Transcriptional activator proteins - each of which binds to a specific DNA sequence (known as an enhancer)

59
Q

What do transcriptional activator proteins do

A

help control when and in which cells transcription of a gene will occur.

60
Q

what do transcriptional activator proteins bind to

A

enhancer DNA sequences and with the proteins that allow transcription to begin

61
Q

What do TAP do once they’re bound to enhancer DNA sequences

A

They attract a mediator complex of proteins

62
Q

What is a mediator complex and what does it do

A

A complex of proteins that interacts with the Pol II complex and allows transcription to begin - the mediator complex recruits the RNA polymerase to the promoter

63
Q

What RNA polymerase complex is responsible for transcription in eukaryotes

A

Pol II

64
Q

What needs to be so that transcription can be initiated

A

The mediator complex and Pol II complex need to be in place

65
Q

How large is the transcription bubble in bacteria

A

Transcription bubble - 14 base pairs

region of paired RNA DNA in the bubble - 8 base pairs

66
Q

What provides the energy that drives the reaction to create new phosphodiester bonds attaching the incoming nucleotide to the 3’ end

A

The oxygen attacks the bond, seizes an electron and the phosphate bond breaks, releasing energy

67
Q

What does the polymerization reaction release

A

a phosphate-phosphate group - has a high energy phosphate bond which is split by another enzyme

68
Q
A

MLB 111 (4 decks)

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