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BDS1 BAMS: Molecules and Cells > Molecular Biology 1-3 > Flashcards

Molecular Biology 1-3 Flashcards

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1
Q

What are nucleotides?

A

Monomeric units (building blocks) of DNA and RNA

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2
Q

What are nucleotides comprised of?

A

A base, a sugar and a phosphate group

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3
Q

What are the 2 types of nucleic acid?

A

Deoxybribonucleic acid (DNA) and ribonucleic acid (RNA)

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4
Q

What are the functions of DNA and RNA?

A
  • Direct synthesis of proteins

- Transmit genetic information

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5
Q

What are bases?

A

Nitrogenous, aromatic, heterocyclic rings

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6
Q

What are the 2 groups of bases?

A

Purines and pyrimidines

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7
Q

Which bases are purines?

A

Adenine, guanine

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8
Q

Which bases are pyrimidines?

A

Cytosine, thymine, uracil

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9
Q

Which bases does DNA have?

A

Adenine, thymine, guanine, cytosine

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10
Q

Which bases does RNA have?

A

Adenine, uracil, guanine, cytosine

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11
Q

How many rings do purines have?

A

2

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12
Q

How many rings do pyrimidines have?

A

1

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13
Q

What type of sugar is in RNA?

A

Ribose

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14
Q

What type of sugar is in DNA?

A

Deoxyribose (missing oxygen on C2)

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15
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleosides don’t have a phosphate group - only base and sugar

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16
Q

Describe the structure of a nucleoside

A
  • Composed of a base and sugar (ribose or deoxyribose)

- Linked by N-glycosidic bond between 1’-C of sugar and N-9 of purine ring or N-1 of pyrimidine ring

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17
Q

What are the bases in DNA?

A

Deoxyribonucleotides

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18
Q

What are the bases in RNA?

A

Ribonucleotides

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19
Q

Where is ATP produced?

A

In the mitochondria

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20
Q

What is ATP?

A

Adenosine 5’ triphosphate

Main biological energy store

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21
Q

What is cAMP?

A

Cyclic AMP
Adenosine -3’5’- monophosphate
A second messenger in the action of many hormones

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22
Q

What is the sugar in ATP?

A

Ribose

ATP is a ribonucleotide

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23
Q

What is the sugar in cAMP?

A

Ribose

cAMP is a ribonucleotide

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24
Q

How is cAMP synthesised?

A

ATP is catalysed by adenyl cyclase, converted to cAMP and PPi and H+ ions (in the presence of Mg2+)

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25
Q

How is cAMP broken down?

A

cAMP and H2O catalysed to AMP and H+ by a phosphodiesterase (in presence of Mg2+ ions)

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26
Q

Describe how cAMP functions as a second messenger

A
  1. Hormone binds to receptor in plasma membrane
  2. Adenyl cyclase is stimulated
  3. Increased adenyl cyclase activity leads to increased production of cAMP inside the cell
  4. cAMP acts inside the cell to alter rate of one or more processes
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27
Q

What is the synthesis of cAMP catalysed by?

A

Adenyl cyclase

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28
Q

What is the breakdown of cAMP into AMP and H+ catalysed by?

A

A phosphodiesterase

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29
Q

Where is DNA found in the cell?

A

Mainly in the nucleus

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30
Q

Describe the structure of the DNA backbone

A
  • DNA backbone consists of deoxyriboses linked by phosphodiester bridges
  • Sugar of one nucleotide joined at C-3’ (OH) to phosphate group attached to C-5’ of sugar of the next nucleotide (3’-5’ phosphodiester bond)
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31
Q

Describe the structure of DNA

A
  • DNA is double stranded
  • Structure held together by hydrogen bonding between base pairs
  • 2 chains wound around each other to form a regular double helix
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32
Q

Which base does adenine pair with, and how many hydrogen bonds are formed?

A

Adenine with Thymine (or uracil in RNA)

A 2 T (forms 2 hydrogen bonds)

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33
Q

Which base does guanine pair with and how many hydrogen bonds are formed?

A

Cytosine with Guanine

C 3 G (forms 3 hydrogen bonds)

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34
Q

Where is RNA found in the cell?

A

Found primarily in the cytoplasm

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35
Q

Name 3 ways in which RNA differs from DNA

A
  1. Uracil replaces thymine (pairs with adenine)
  2. Ribose sugar replaces deoxyribose
  3. Single stranded (no base pairing)
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36
Q

Explain what a ‘hairpin loop’ is in RNA, and how is this formed?

A

Local double stand formation can occur within RNA - RNA folds back on itself forming a hairpin loop. Local base pairing occurs.

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37
Q

When is the only time that RNA can have a small section of a double stranded loop?

A

When RNA folds back on itself forming a hairpin loop

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38
Q

What are the 3 types of RNA?

A
  1. mRNA (messenger RNA)
  2. tRNA (transfer RNA)
  3. rRNA (ribosomal RNA)
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39
Q

What type of RNA makes up the majority of RNA in the cell?

A

rRNA - makes up 80% of RNA in the cell

40
Q

What is the sedimentation coefficient (S)?

A

A measure of the relative sizes of RNA

41
Q

What percentage of RNA is tRNA?

A

15%

42
Q

What percentage of RNA is mRNA?

A

5%

43
Q

Where is genetic information contained?

A

The base sequence in DNA contains genetic information (genetic code) in all cells

44
Q

How is the genetic code transmitted?

A

The genetic code is transferred via genes

45
Q

What are genes?

A

Specific stretches of DNA which code for a protein (average size = 1000-2000 bp)

46
Q

What is the amino acid sequence determined by?

A

The nucleotide sequence of its corresponding gene

47
Q

What is the whole genetic information within a single cell nucleus called?

A

Genome

48
Q

What is the genome of a cell?

A

All the genetic information within a single cell nucleus

49
Q

How many base pairs are in a human genome?

A

2,900,000 kilobases

50
Q

Describe the stages of protein synthesis

A
  1. In the nucleus, DNA unfolds (H bonds split) to expose base pairs on template stand
  2. Transcription: RNA polymerase copies sequence of bases in template strand of DNA to produce mRNA
  3. mRNA is translated by tRNA, using ribosome as a functional support (in cytoplasm)
51
Q

What does tRNA do?

A
  • Carries each amino acid to ribosome (one specific tRNA for each amino acid)
  • Contains anticodon (3 bases) complementary to codon (3 bases) on mRNA
  • Amino acid is transferred to growing polypeptide chain
  • Sequence of mRNA codons determines the sequence of amino acids in protein
52
Q

Describe the structure of a ribosome

A

Small and large subunits, contain proteins and rRNA

53
Q

What happens to thymine when DNA is transcribe to mRNA?

A

Thymine replaced with uracil

54
Q

How many amino acids are there?

A

20

55
Q

How many tRNAs are encoded by triplet code?

A

4^3

64

56
Q

The genetic code is degenerate. What does this mean?

A

A single amino acid may be coded for by more than one codon (each codon codes for a specific amino acid though)

57
Q

How does a cell know when to start protein synthesis and when to terminate protein synthesis?

A

Start codon: AUG (codes for methionine)
The first amino acid in every protein is always Met
Stop codons: UAA, UAG, UGA

58
Q

Which codon is the start codon?

A

AUG - codes for methionine

59
Q

Which codons are stop codons?

A

UAA, UAG, UGA

60
Q

What is a mutation?

A

Permanent alteration in a DNA (gene) sequence

61
Q

What are the causes of a mutation?

A
  • Errors in DNA synthesis that can occur spontaneously at low frequency
  • Chemical mutagens
  • Ionising radiation
62
Q

What effects might substituting one base for another have?

A
  • Conservative mutation: amino acid is replaced by one with similar properties
  • Non-conservative mutation: amino acid is replaced by one with different properties
  • No mutation: in many cases, a change in the third position of the codon does not change an amino acid
63
Q

What is a conservative mutation?

A

Amino acid is replaced by one with similar properties

64
Q

What is a non-conservative mutation?

A

Amino acid is replaced by one with different properties

65
Q

What is the open reading frame (ORF)?

A

Part of the reading frame that has the ability to be translated

66
Q

What happens during translation?

A

During translation, the cellular machinery reads each codon -> end up with a fully functional protein

67
Q

What effect does insertion or deletion of a base have?

A
  • Causes a frame-shift/open reading frame is shifted
  • Whole sequence is changed - different type of protein will be translated
  • If any of these changes introduces or removes a stop codon: premature or delayed termination
68
Q

What type of mutation causes sickle cell anaemia?

A

Single base substitution: non-conservative mutation
GAG to GTG in the beta-chain of haemoglobin
Replaces glutamic acid with valine

69
Q

What is a silent mutation?

A

A base mutation which does not alter the amino acid - in many cases, a change in the third position of the codon does not change the amino acid (genetic code is degenerate, amino acids are coded for by more than one codon)

70
Q

What is gene cloning?

A

A process which allows the production of large numbers of copies of a particular piece of DNA

71
Q

How are genes usually cloned?

A
  • By isolating genes of interest using restriction enzymes, followed by gel electrophoresis and inserting them into plasmid
  • Plasmid is then introduced into a bacterium and the bacterium grows producing large numbers of cells and hence many copies of the gene
  • Gene can then be reisolated using the same restriction enzyme
72
Q

What do restriction enzymes do?

A
  • Cut double stranded DNA at specific DNA sequences

- Sequences are typically 4-6 base pairs in length and “palindromic” i.e. they read the same in both directions

73
Q

Define “palindromic”

A

Reading the same backwards as forwards

74
Q

Most restriction enzymes make a “staggered cut”. What does this allow?

A

Produces sequences with “sticky ends”

Allows DNA fragments to re-associate by base pairing

75
Q

What does DNA ligase do?

A

An enzyme that joins two strands of DNA together

76
Q

What is gel electrophoresis?

A

A technique used to separate DNA fragments based on their size

77
Q

Describe the stages in gel electrophoresis

A
  1. Samples are applied to a gel immersed in buffer and a current is applied
  2. Negatively-charged DNA migrates from the negative electrode (top of gel) to the positive electrode (bottom of gel)
  3. Larger DNA fragments migrate more slowly than smaller fragments
78
Q

Describe the procedure of gene cloning

A
  1. A restriction enzyme is chosen that cuts on either side of the gene of interest
  2. The gene is separated from other DNA fragments by gel electrophoresis
  3. A suitable plasmid is linearised (cut at one point) using the same restriction enzyme
  4. The cut plasmid and gene are mixed and the sticky ends of the plasmid and the gene are allowed to “anneal” (associate by base pairing)
  5. The annealed ends are covalently joined using DNA ligase
  6. The plasmid is reintroduced into bacterium
  7. Bacteria are grown into a colony - antibiotic resistance genes in plasmid used to select colonies containing plasmids
  8. Cloned cells are lysed and plasmids isolated by centrifugation
  9. Plasmids cut with restriction enzyme releasing cloned gene
79
Q

Why are plasmids containing gene of interest genetically engineered to contain antibiotic resistance genes?

A

To allow us to select only the bacteria that have taken up the plasmid of interest

80
Q

What is the purpose of DNA sequencing?

A

Used to determine the base sequence of DNA

81
Q

What are the 2 main types of DNA sequencing?

A

Sanger sequencing

Next Generation sequencing

82
Q

What is Sanger sequencing?

A
  • A DNA sequencing method
  • Used for small scale projects
  • Synthesis of new strands complementary to a template strand in vitro
83
Q

What is Sanger sequencing also known as?

A

The dideoxynucleotide chain termination method

84
Q

What are the reaction components required for Sanger sequencing?

A
  1. Single stranded DNA template
  2. Primer
  3. dNTPs
  4. ddNTPs
  5. DNA polymerase
  6. Label
85
Q

What is the single stranded DNA template in Sanger sequencing use for?

A

Its sequence is to be determined, used for the synthesis of a complementary strand

86
Q

What is a “primer” in Sanger sequencing?

A

A short stretch of DNA (olignonucleotide ~20 bases long), serves as a primer for synthesis of the complementary DNA strand by elongation

87
Q

What are dNTPs?

A

Deoxynucleotides: dATP, dCTP, dGTP, dTTP

Building blocks of DNA

88
Q

What are ddNTPs?

A

Dideoxynucleotides: ddATP, ddCTP, ddGTP, ddGTP

Modified nucleotides that terminate DNA strand elongation

89
Q

Which reaction component is required in Sanger sequencing to terminate the DNA strand?

A

Dideoxynucleotides: modified nucleotides

90
Q

What does DNA polymerase do?

A

Catalyses DNA strand synthesis

91
Q

Why is a label important in Sanger sequencing?

A

Required to visualise the products

92
Q

What type of labels are used in Sanger sequencing to enable visualisation of the products?

A 
Fluorescent labels (IRD800)
Radioactive (35S)
93
Q

How do ddNTPs terminate DNA strand elongation?

A
  • 3’-OH group of dNTPs replaced by an -H in corresponding ddNTPs
  • Because they lack the 3’-OH required to form a phosphodiester bond with the next nucleotide, this results in chain termination
94
Q

Why are ddNTPs added at a much lower concentration than dNTPs (ratio of 1:10 to 1:300)?

A

To allow strand elongation sufficient for sequence analysis

95
Q

Outline the steps in DNA sequencing

A
  1. DNA to be sequenced is mixed with primer
  2. Primer binds to 3’ end of DNA 3
  3. DNA-primer mixture divided into 4 separate reaction tubes containing:
    - all 4 dNTPS
    - one of the 4 ddNTPs
    - DNA polymerase
  4. Chain synthesis then proceeds in each of the 4 reaction tubes
  5. Gel electrophoresis for separation of reaction products
  6. DNA bands detected by autoradiography or by laser in an automated sequencer
  7. DNA sequence deduced from the pattern of bands in the 4 lanes
96
Q

What is Next Generation Sequencing?

A
  • High throughput sequencing
  • No need for cloning, highly scalable
  • Can sequence millions of genes and entire genomes at once
  • Cheap and rapid
  • Requires substantial bioinformatics analysis

BDS1 BAMS: Molecules and Cells (13 decks)

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