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MGD > Dr Kramers Bit > Flashcards

Dr Kramers Bit Flashcards

0
Q

What is the difference between the major groove and the minor groove?

A

Major groove is wider, transcription factors are more likely to bind the major groove.

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1
Q

What is the appearance and function of euchromatin and heterochromatin?

A

Euchromatin is expressed and not condensed into solenoids, appears lighter
Heterochromatin is not expressed, not in solenoids. Appears darker.

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2
Q

What is the structure of histone?

A

Octamer of proteins consisting of a H3 H4 tetramer and 2 H2a H2b dimers

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3
Q

How does DNA form beads on a string?

A

DNA forms a nucleosome by winding twice around each histone, then joined by linker DNA.

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4
Q

How is beads on a string DNA packaged?

A

Into solenoid 30nm fibre.

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5
Q

What is the mutation in sickle cell anaemia?

A

Chromosome 11 11p15.5
A>T results in glutamate to valine.
Gene coding for beta haemoglobin.

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6
Q

What is the mutation in cystic fibrosis.

A

Chromosome 7 7q31.2
3bp CTT deletion between 5th and 6th position. Deletion of phenylalalanine, misfolded protein.
Mutation in gene coding for CFTR.

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7
Q

What is the human genome?

A

Entire DNA sequence (22 plus X and Y = 24 chromosomes)

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8
Q

How many base pairs in the genome of:
A human
A fruit fly
E. coli

A
  1. 2 x 10^9
  2. 4x10^7
  3. 6x10^6
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9
Q

What is the difference between a nucleoside and a nucleotide?

A

Nucleoside has a sugar and a base

Nucleotide has a sugar, a base and a phosphate.

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10
Q

What is the difference between ribose and deoxyribose?

A

Ribose is 5C, has inline oxygen and 4 OH groups including on methyl group.
Deoxyribose is the same but doesn’t have an OH group on carbon 2.
Ribose is in RNA, deoxyribose is in DNA.

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11
Q

Why is DNA and RNA negatively charged?

A

Phosphate group is negatively charged.

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12
Q

Where does phosphate group bind in a nucleotide?

A

5’ carbon

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13
Q

Where does the base bind in a nucleotide?

A

1’ carbon

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14
Q

How does phosphate bind the sugar?

A

Phosphate ester bond

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15
Q

Which bases are purines?

A

Adenine and guanine

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16
Q

What bases are pyrimidines?

A

Cytosine, thymine, uracil

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17
Q

What is the structure of a purine?

A

Nitrogenous, 2 rings

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18
Q

What is the structure of a pyrimidine?

A

Nitrogenous, single ring.

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19
Q

For A, give the base, and nucleoside and nucleotide for DNA and RNA

A 
Adenine
Adenosine (RNA)
Adenosine monophosphate (RNA)
Deoxyadenosine (DNA)
Deoxyadenosine monophosphate (DNA)
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20
Q

How are nucleotides joined?

A

Phosphodiester bonds

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21
Q

What groups are at the 5’ and 3’ ends of DNA?

A

5’ phosphate

3’ OH

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22
Q

How many hydrogen bonds form between C and G?

A

3

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23
Q

How many hydrogen bonds between A and Ta

A

2 hydrogen bonds

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24
Q

What is the benefit of the hydrogen bonds between bases in a base pair being almost the same length.

A

Strength

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25
Q

What is a duplex?

A

Double stranded structure of DNA - two complementary antiparallel strands.
Can form two DNA, two RNA, or one of each.

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26
Q

What is an RNA stem loop?

A

Loops formed when hydrogen bonds form between complementary antiparallel sequences in RNA

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27
Q

What is the pitch of DNA?

A

3.4nm

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28
Q

What is the diameter of a DNA Double helix?

A

2nm

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29
Q

What is the distance between adjacent DNA bases?

A

3.4nm

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30
Q

How many DNA bases per turn of the helix?

A

10

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31
Q

In what direction is DNA notated?

A

5’ to 3’

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32
Q

What are the phases of the cell cycle?

A 
Mitosis
Then either G0 (cell cycle stops, cell performs function)
Or:
G1 - cell contents replicates
Cell cycle checkpoint
S - DNA replicates
G2 - checking and repair of DNA
Cell cycle checkpoint
Mitosis
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33
Q

What catalyses DNA polymerisation in DNA replication?

A

DNA polymerase

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34
Q

How are bases added to DNA during replication?

A

Added as deoxynucleotide triphosphates,
Added to 3’ end of primer strand
Release PPi
Forms phosphodiester bond

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35
Q

What is pyrophosphate hydrolysis?

A

Hydrolyse ATP to AMPS releases pyrophosphate (PPi, P2O7 4-)

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36
Q

In what direction is DNA synthesised?

A

5’ to 3’

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37
Q

How is DNA replicated in prokaryotes?

A

Circular chromosome.
Initiation - recognise origin of replication - requires DNA polymerase. Needs a kickstart from primase - synthesis short RNA sequence (as polymerase can only extend from 3’ end)
then replicates around the circle in both directions (elongation)
Then termination - two circular chromosomes.

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38
Q

How is DNA elongated during replication?

A

The 3’ to 5’ strand is replicated by DNA polymerase in the 5’ to 3’ direction (leading strand)
The 5’ to 3’ strand is replicated in multiple Okazaki fragments in the 5’ to 3’ direction, which are fused by DNA ligase. (Lagging strand)

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39
Q

What enzyme separates the two strands of DNA?

A

DNA helices R

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40
Q

How many sites of replication are there in each chromosome?

A

Multiple - speeds it up.

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41
Q

What is the structure of a replicated chromosome?

A

Two sister chromatids (identical) joined by centromere.
P arm is shorter
Q arm is longer
Telomeres are the ends of each chromatid.

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42
Q

What are the four arrangements of chromosomes and centromeres, and are they present in humans?

A

Metacentric - central centromere
Submetacentric - shorter p arms
Acrocentric - very short p arms
Telocentric - no p arms - not seen in humans.

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43
Q

Which cells use mitosis for cell division?

A

Somatic cells

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44
Q

How many mitotic rounds occur during development?

A

50

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45
Q

What occurs in prophase?

A

Chromosomes condense

Spindle fibres appear - centrioles

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46
Q

What happens in prometaphase?

A

Chromosomes condense further
Spindle fibres attach to chromosomes via kinetochore, centrioles migrate to poles.
Nuclear membrane breaks down

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47
Q

What occurs in metaphase?

A

Chromosomes align on the metaphase plate.

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48
Q

What occurs in anaphase?

A

Centromeres divide and chromatids move to the opposite poles of the cell

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49
Q

What occurs in telophase?

A

Chromosomes de condense
Nuclear membranes reform
Spindle fibres disappear

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50
Q

What happens in cytokinesis?

A

Cytoplasm divides, two identical daughter cells form.

51
Q

What is produced via meiosis?

A

Germ line cells - oocytes and spermatozoa

52
Q

How many chromosomes are present following replication in meiosis?

A

92 (4n)

53
Q

What occurs in meiosis 1?

A

Homologous chromosomes separate - 2 identical sister chromatids of each chromosome present in daughter cells.

54
Q

What causes genetic variation?

A

Crossing over during meiosis 1 (chiasmata form, genetic material exchanged between chromatids)

55
Q

What occurs during meiosis 2?

A

Sister chromatids are separated, generate haploid cells.

56
Q

What are the consequences of meiosis?

A

Generate haploid cells (maintains diploid chromosome number in somatic cells)
Generates genetic diversity - random assortment and crossing over

57
Q

How long is spermatogenesis?

A

48 days

58
Q

Outline the process of spermatogenesis

A

Spermatogonium goes to form primary spermatocyte (diploid)
Undergoes meiosis - spermatids (haploid)
Differentiate to mature sperm.

59
Q

How long does oogenesis take?

A

12-50 years

60
Q

Outline the process of oogenesis:

A

Oogonium-> primary oocyte (diploid)
Undergoes meiosis to form an ovum which matures and 3 polar bodies which do not have sufficient cytoplasm to survive so degenerate.

61
Q

Why is crossing over necessary?

A

Homologous chromosomes don’t separate during meiosis one if crossing over hasn’t occurred.

62
Q

How often are mistakes made in meiosis?

A

30% rate of missegregation in humans

63
Q

What are the causes of missegregation?

A

Cause one third of identified miscarriages, infertility and mental retardation.

64
Q

What is the difference between genotype and phenotype?

A

Genotype is an individual’s genetic sequence.

Phenotype is how this is expressed as characteristics.

65
Q

How can the environment affect genotype and phenotype?

A

Genotype - mutagens, radiation,

Phenotype - genotype, and diet, lifestyle, chemicals etc

66
Q

What is the difference between a gene and an allele?

A

An allele is a version of a gene - there will be many different alleles for each gene in a population, some of which may be disease causing.

67
Q

What is a homozygote?

A

An individual with two identical alleles for a gene

68
Q

What is a heterozygote?

A

An individual with two different alleles of a gene

69
Q

What is a hemizygote?

A

Someone who has only one allele of a gene (on the X chromosome)

70
Q

What is the difference between a dominant and recessive allele?

A

The dominant allele determines the phenotype.

The recessive allele in a heterozygote is the non dominant allele (doesn’t determine the phenotype)

71
Q

Give an example of a trait that demonstrates codominant inheritance

A

ABO blood group

72
Q

What does the isoglutamin gene code for?

A

Glycoproteins on surface of erythrocytes - determine ABO blood group

73
Q

Give an example of a trait that demonstrates complementation

A

Albinism

74
Q

What is peculiar about complementation?

A

Two homozygous affected individuals (it’s a recessive trait) can have an unaffected offspring if it’s two different genes.

75
Q

How can more than one gene be involved in producing a phenotype?

A

For example, if multiple enzymes (each coded for by a different gene) are involved in a pathway to synthesise a product.

76
Q

What are linked genes, and what is the implication for meiosis?

A

Genes on the same chromosome - do not show independent assortment at meiosis.

77
Q

What does recombination frequency depend on?

A

Distance between genes

78
Q

What is the behaviour of genes that are far apart on a chromosome?

A

Behave almost like unlinked genes.

79
Q

What is a gene?

A

Stretch of DNA that codes for a protein, and regulates its production.
Has a chromosomal locus.
Unit of inheritance
Unit of transcription

80
Q

What are the five types of RNA?

A 
mRNA - messenger RNA a
tRNA - transfer RNA
rRNA - ribosomal RNA
miRNA - micro RNA
Non coding RNA
81
Q

In what direction does transcription occur?

A

RNA is synthesised 5’ to 3’

DNA is read 3’ to 5’

82
Q

In what direction does translation occur?

A

mRNA is read 5’ to 3’

Protein synthesised from amino terminal to carboxy terminal.

83
Q

Where is the energy needed for DNA replication found?

A

Nucleotide triphosphates are cleaved - pyrophosphate hydrolysis.

84
Q

What enzyme is used for transcription?

A

RNA polymerase

85
Q

What is a promoter sequence?

A

TATA box at -30 in eukaryotes, many upstream sequences - complex regulation
Pribnow box at -10 in prokaryotes, upstream sequences at -35 - simple regulation
Binds promoter which causes RNA polymerase to bind.

86
Q

What are the coding and template strands?

A

The coding strand holds the TATA box and as the same sequence as the mRNA that will be transcribed (except T instead of U)
The template strand has a sequence complementary to the mRNA and is the strand used to synthesise the RNA with RNA polymerase.

87
Q

What is an open reading frame?

A

The part of mRNA that has the potential to code for a protein/peptide (from start codon - methionine - to stop codon)

88
Q

How is mRNA modified post transcription?

A

Splicing
Polyadenylation at 3’ end
Capping at 5’ end

89
Q

What is the purpose of polyadenylation (tailing)?

A

Protection of mRNA from degradation by exonucleases

90
Q

What is the purpose of capping mRNA?

A

Protect mRNA from degradation.

Plays a role in translation.

91
Q

What is capping?

A

Addition of guanosine (guanosine triphosphate GTP) via a 5’ to 5’ triphosphate linkage.
The 7 Nitrogen of guanosine is methylated.

92
Q

Describe the process of polyadenylation.

A

When the sequence AAUAA is transcribed it is recognised by a specific endonuclease.
Causes transcription to cease, endonuclease cleaves the mRNA downstream of the sequence.
Roughly 200 adenosine bases are added (ATP -> PPi) using polyA polymerase.

93
Q

What are endonucleases and exonucleases?

A

Endonucleases cut within a polynucleotide - can be specific or non specific.
Exonucleases degrade polynucleotides from either 5’ or 3’ end - they are 5’ or 3’ specific.

94
Q

What are exons and introns?

A

Exons are the coding parts of mRNA, introns are removed during splicing.

95
Q

How does splicing occur?

A

Specific sequence recognised (AGGU) by spliceosome.

RNA lariat formed and removed, two ends joined.

96
Q

What is the genetic mutation in PKU and its consequences in protein expression?

A

Chromosome 12 12q22-q22.4

Single base substitution G>A results in intron skipping, unstable mRNA.

97
Q

In what proportions are mRNA, tRNA, and rRNA found in eukaryotes?

A

80% rRNA
15% tRNA
2% mRNA

98
Q

What does RNA polymerase 1 synthesise?

A

rRNA

99
Q

What does RNA polymerase 2 synthesise?

A

mRNA

100
Q

What does RNA polymerase 3 synthesise?

A

tRNA

101
Q

Why is 80% of the RNA in a cell rRNA, 15% tRNA and 2% mRNA?

A

Many types of mRNA, but only a few copies of each as they are unstable and easily degraded.
Only a few kinds of rRNA, but there are very many copies of each as they are essential for translation.
Roughly 100 kinds of tRNA, but very many copies of each.

102
Q

What is the structure of a ribosome in prokaryotes?

A

70s ribosome with 30s and 50s subunits

Consists of 3 rRNAs and 56 proteins

103
Q

What is the structure of a ribosome in eukaryotes?

A

80s ribosome consisting of 40s and 60s subunits

Consists of 4 rRNAs and 82 proteins.

104
Q

How long is a 70s ribosome?

A

20nm

105
Q

What makes up a 50s subunit?

A

5S rRNA - 120 bases
23s rRNA - 2900 bases
35 proteins

106
Q

What makes up a 30s subunit?

A

16s subunit - 1500 bases

21 proteins

107
Q

How big is an 80s ribosome?

A

32nm

108
Q

What does a 60s subunit consist of?

A

5S RNA - 120 bases
5.8S RNA- 160 bases
28S RNA - 4700 bases
49 proteins

109
Q

What does a 40s subunit consist of?

A

18s RNA - 1900 bases

33 proteins

110
Q

What direction is mRNA read in, and in what direction are polypeptides synthesised?

A

5’ to 3’, amino to carboxy terminal.

111
Q

What codon marks the initiation of translation?

A

AUG - methionine

112
Q

What are the stop codons?

A

UAA, UAG, UGA

113
Q

What is the structure of tRNA?

A

Anticodon loop - sequence complementary to codon on mRNA.
DHU loop (contains dihydrouridine)
T Psi C loop (contains pseodouridine)
Variable loop
CCA terminus at 3’ end - A forms ester bond with amino acid (OH on ribose, COOH on amino acid)

114
Q

How is tRNA activated?

A

tRNA activated to become amino acyl tRNA

Covalent ester bond between 3’ OH on 3’ adenine of tRNA and the carboxylic acid of the amino acid.

115
Q

What is I?

A

Inosine - a nucleotide, the base is hypoxantine. It’s a purine derivative.

116
Q

Which is the wobble position?

A

5’ base of anticodon, 3’ base of codon (3rd position)

117
Q

What can I pair with?

A

Uracil, cytosine and adenine

118
Q

What is the implication of wobble?

A

One tRNA species can recognise more than one codon - compensates for degeneracy in triplet code.

119
Q

What is another unusual base pairing?

A

G and U

120
Q

What enzyme catalyses the formation of amino acyl tRNA? What else is required?

A

tRNA synthetase

ATP > AMP + PPi

121
Q

How is translation initiated?

A

Ribosome dissociates into two subunits
40S subunit forms ternary complex with an initiation factor, Met tRNA and GTP.
Another initiation factor interacts with cap and guides ternary complex to bind.
The complex ‘scans’ the RNA until the anticodon on tRNA binds AUG. Requires ATP and other initiation factors.
The 60S subunit binds and GDP and initiation factors are released, met tRNA is positioned in the P site on the ribosome.

122
Q

How does elongation occur?

A

A new amino acyl tRNA binds to the A site on the ribosome (requires GTP)
The newly synthesised peptide on the amino acyl tRNA in the P site is transferred to the amino group on the new amino acyl tRNA in the A site to form a new peptide bond, catalysed by peptidyl transferase.
Translocation then occurs - the uncharged tRNA is ejected from the A site, and the tRNA carrying the polypeptide is transferred to the A site. This requires GTP.

123
Q

How is translation terminated?

A

Stop codon is reached - no corresponding tRNA.
Eukaryotic release factors 1 and 3 form a complex with ribosome.
This stimulates the hydrolysis of the ester bond between the peptide and the tRNA, protein is released.
The factors are released from the ribosome following GTP hydrolysis.

124
Q

What is a polysome?

A

Multiple ribosomes translating a piece of mRNA concurrently.

125
Q

How are transcription and translation different in bacteria?

A 
Transcription and translation are coupled
Smaller, simpler ribosomes
Different transcription factors 
Different mechanism of initiation 
Simple promoters
Different translation factors 
Single RNA polymerase 
No post transcriptional processing - splicing
Short lived mRNA.

MGD (6 decks)

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