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Human Biosciences > Genetics > Flashcards

Genetics Flashcards

1
Q

5 features of genetic information that have to be true for it to be able to work?

A

Stable for storage over time

Be able to faithfully replicated (semi conservative replication)

Be able to control expression of traits ( encode the sequence of proteins)

Be able to change in a controlled way

But also available for direct cellular processes

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2
Q

DNA has the structure of? Therefore leading to the creation of?

A

Double helix

Minor grooves and major grooves

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3
Q

What is a nucleotide?

A

Polymer made up of the repeating units of a sugar a base and a phosphate

Phosphate binds to sugar, which binds to base

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4
Q

Sugar + base =?

A

Nucleoside

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5
Q

Deoxyribose + adenine =?

A

Deoxyadenosine

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6
Q

Deoxyribose + guanine?

A

guanosine

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7
Q

Deoxyribose + cytosine?

A

cytidine

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8
Q

Deoxyribose + thymine?

A

thymidine

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9
Q

How do you know which end is the 5’ end and which is the 3’ end?

A

The 5’ end which have carbon 5 (the chimney) bonded to a phosphate group

The end will have an OH group on carbon 3

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10
Q

What is the directionality of a DNA strand?

A

5’ to 3’

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11
Q

DNA strands are anti parallel in a double stranded structure, what does this mean?

A

They are going in opposite directions (still going 5’ to 3’)

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12
Q

What holds DNA strands together?

A

Hydrogen bonds between complementary base pairs

Adenine to thymine

Cytosine to guanine

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13
Q

What’s a 2 carbon ring base called and what are the examples?

A

Purine

Adenine and Guanine

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14
Q

What’s a single carbon ring called, and what are the examples?

A

Pyrimidine

Cytosine and thymine

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15
Q

A purine will always bind to a?

A

Pyrimidine

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16
Q

How many hydrogen bonds between Adenine and thymine?

A

2

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17
Q

How many hydrogen bonds between Guanine and cytosine?

A

3

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18
Q

Why is the minor and major groove created?

A

Base pairs are planar

Stack?

Hydrophobic interactions

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19
Q

What type of double helix is DNA?

A

Right handed, (put left thumb up, direction of fingers shows the right hand direction)

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20
Q

Genetic information is carried in?

A

The sequence of bases in DNA = digital code

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21
Q

How does the structure of DNA provide a mechanism for heredity?

A

You can control the expression of traits (encode the sequence of proteins)

Be able to change in a controlled way

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22
Q

What is the genome?

A

All the DNA in the nucleus of a cell (ie. the complete set of genes of an organsism)

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23
Q

What’s special about mitochondria and chloroplasts in terms of DNA?

A

They have their own small circular genomes

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24
Q

Nuclear genetic material is distributed among discrete units called?

A

Chromosomes

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25
Q

How are nucleosomes formed?

A

DNA wraps twice around 8 core histone proteins to form nucleosomes

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26
Q

How are chromatin fibres formed?

A

Histon H1 brings the nucleosomes together

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27
Q

How is chromatin fibre folded into loops (part of the chromosome)?

A

Chromatin fibres are further condensed by scaffold proteins

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28
Q

What is the net result of creating chromatin fibre which then forms the chromosome?

A

Each DNA molecule has been packaged into a mitotic chromosome that is 10,000 fold shorter than it’s fully extended length

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29
Q

2 types of chromatin?

A

euchromatin

heterochromatin

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30
Q

Features of euchromatin?

A

Less compact DNA form

Contains genes that are frequently expressed

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31
Q

Features of heterochromatin?

A

More compact

Contains DNA that is not transcribed

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32
Q

What are nucleoli?

A

Regions where chromosomes carrying rRNA cluster, rRNAs are synthesised and ribsomes are assembled

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33
Q

Chromosomes organise themselves into discrete patches called?

A

Chromosome territories

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34
Q

Where are active genes normally located?

A

In the euchromatic region of the chromosome, and near the chromosomes territory boundary

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35
Q

What does transcription do very basically?

A

Prodcues an RNA molecule that is complementary to one strand of DNA

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36
Q

DIfferences in RNA compared to DNA?

A

RNA has the sugar ribose instead of deoxyribose

Has the base uracil instead of thymine

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37
Q

What do differences in RNA mean?

A

RNA is More chemically reactive than DNA as RIbose has 2’ OH group (so less stable so only used for short term storage of information, whereas DNA is long term)

RNA is more prone to mutate than DNA, as cytosine deamination to uracil can’t be detected and repaired in RNA

RNA is single stranded and not double, meaning there is no backup of genetic information (but it can still base pair with itself)

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38
Q

What enzyme helps synthesise RNA and describe its structure?

A

RNA polymerase, Has area where the short region of DNA has been separated, and a ribonucleoside triphosphate uptake channel allows the ribonucleosides to come in

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39
Q

What direction is RNA synthesised?

A

5’ to 3’ direction (so DNA will be read 3’ to 5’)

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40
Q

How is energy provided for the formation of a phosphodiester bond when synthesising RNA?

A

Breakage of phosphoanhydride bond of NTP (the phosphate chain in the nucleoside triphosphate, 2 are lost and the other binds to the sugar backbone with the base attached)

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41
Q

What does mRNA do?

A

Messenger RNA

Code for proteins

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42
Q

What does rRNA do?

A

Ribosomal RNA

Forms the basic structure of the ribosome and catalyze protein synthesis

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43
Q

What do tRNA’s do?

A

Transfer RNA, central to protein synthesis as are adaptors between mRNA and amino acids

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44
Q

What is the transcriptome?

A

Set of all RNA molecules

Varies on the cell (different genomes)

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45
Q

What is the central dogma?

A

Information flow from DNA to RNA via transcription then from RNA to Protein via translation

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46
Q

How is mRNA processed before it leaves the nucleus?

A

The 5’ end of the mRNA gets “capped” with an atypical nucleotide

The 3’ end of the mRNA gets a tail of poly-A nucleotides

Introns (non coding sequences) have to be removed from the mRNA

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47
Q

One way in which a bacterial gene is different to a eukaryotic gene?

A

In a bacterial gene all the gene is a protein coding region (exon)

In a eukaryotic gene there are protein coding regions (exons), but also non-coding regions (introns)

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48
Q

Describe briefly the splicing process that occurs in pre mRNA to remove introns?

A

3’ clevage and addition of a poly(A) tail

Intron excision occurs by snRNA’s that bind to proteins to form snRNP’s, which form the core of the splicesosome

The splicesosome causes the intron to bend and one side which break and bind to itself forming a intron lariat

Exon ligation then occurs to create the mRNA reading for translation

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49
Q

What can alternative splicing lead to?

A

More than one gene being expressed from one gene

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50
Q

Describe mRNA’s keaving the nucleus?

A

RNA binding proteins mark a mature mRNA for export from the nucleus

Leaves through nuclear pore

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51
Q

What determines how much protein is translated by a gene relating to the mRNA?

A

The stability of the mRNA, as it’s being degraded by the cell

So more stable it is the more times it can be translated

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52
Q

How many types of amino acids?

A

20

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53
Q

How do we know that genetic code isn’t read overlapping?

A

Single base mutations only affect one amino acid

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54
Q

What is proflavin?

A

Planar molecule that intercalates between base pairs in DNA

Causes frameshift mutations (insertion of an extra base, or deletion of a base)

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55
Q

What is the genetic code of mRNA read in?

A

Sets of 3 nucleotides called codons

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56
Q

Some amino acids have more than one tRNA, meaning they are?

A

degenerate

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57
Q

The genetic code is universal, meaning?

A

It’s found in all organisms, however there are variations in mitochondria

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58
Q

Very bsaically what do mRNA, tRNA and rRNA do in translation?

A

mRNA carries the genetic information

tRNA deciphers the codons of the mRNA

rRNA makes up the ribosome

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59
Q

Structure of tRNA?

A

Anticodon loop which binds to mRNA, (bases will be opposites)

Acceptor stem which binds to correct amino acid, via a high energy ester bond. This is initiated by specific enzymes

60
Q

Structure of rRNA?

A

Made up of a large subunit and a small subunit

4 RNA molecules and lots of protein molecules

Has 3 binding sites
A-site = aminoacyl-tRNA site
P-site = peptidyl-tRNA site
E-Site = exit site

61
Q

What are the 3 steps in translation called?

A

Initiation
Elongation
Termination

62
Q

What are the steps of initiation?

A

Translation initiates at the start codon (AUG)

The start codon is bound by the initiator tRNA (will always be UAC, which is methinonine

Binding of the initiator tRNA to the small subunit allows the large subunit to bind and the ribosome to assemble

P-site is filled with initiator tRNA but the A-site is empty

The tRNA with an anticodon that corresponds to the codon in the A-site binds

The amino acid on the tRNA in the P-site is transferred onto the amino acid on the tRNA in the A-site

63
Q

Steps of elongation?

A

The now empty tRNA moves to the exit site and is released, so now there is a peptidyl tRNA in the A site

The ribosome slides down the mRNA so that the tRNA with the growing peptide is in the P-site, leaving the A site free to bind to another tRNA

The growing peptide chain is transferred to the aminoacyl tRNA, converting it to a peptidyl tRNA

This cycle continues

64
Q

Describe the termination step?

A

When the stop codon is reached, translation will stop

There are no tRNAs with anticodons that bind to Stop codons. Instead stop codons are bound by termination factors

Translation ends with the mRNA and ribosomal subunits diassembling and the release of the newly synthesised protein

65
Q

What direction is polypeptide synthesis?

A

N to C (amino-terminal to carboxy terminal)

66
Q

Why is the ribosome a ribozyme?

A

It catalyses the formation of a peptide bond

67
Q

What are telomores?

A

Highly repetitive DNA that allows the ends of chromosomes to be replicated, also protects the ends of chromosome being mistaken as broken

68
Q

What are centromers?

A

Repetitive DNA which forms the spindle attachment site in mitosis

69
Q

WHat is the origin of replication?

A

Special sequence where duplication of the DNA begins, each chromosome will have many origins

70
Q

What occurs in the S phase?

A

DNA replication

71
Q

What occurs in the M phase?

A

Mitosis

72
Q

WHat do you need for DNA synthesis?

A

Enzyme DNA polymerase

DNTP’s

Single stranded template DNA

Primer 3’-OH (allows replication to start)

Results in DNA synthesis 5’ to 3’ direction

73
Q

What’s more accurrate DNA polymerase or RNA polmerase?

A

DNA polymerase

74
Q

2 terms of DNA polymerase uses to be accurate?

A

Accurate polymerization 5’ to 3’

Accurate exonucleolytic proofreading 3’ to 5’

75
Q

What direction is DNA replication?

A

Bidriectional- moves away from the origins of replication

76
Q

Do genome sizes vary?

A

Yes largely

77
Q

Features of a bacterial genome?

A

Small compact and usually circular

78
Q

Features of genetic material?

A

Single circular double stranded DNA molecule which is a chromosome or nucleoid

No histone proteins

Associated with Mg2+ and polyamines

May also contains smallers circular DNA’s called plasmids

79
Q

What happens at the replication fork?

A

Both strands are copied
In a 5’ to 3’ direction

(one continuous (leading strand) and one discontinues (lagging strand))

80
Q

As DNA replication can only go 5’ to 3’ direction how is it replicated in the other direction (in the lagging strand)?

A

Discontinous

Primase synthesises short RNA Primers copied from DNA

DNA polymerase elongates RNA primers with new DNA to from okazaki fragments

Nucleases remove RNA at 5’ end of neighbouring fragment and DNA polymerase fills the gap

DNA ligase connects adjacent Okazaki fragments

81
Q

What do helicase enzymes do?

A

Unwinds double stranded DNA, using ATP

82
Q

What do single-stranded binding proteins do?

A

Prevent base pairing until DNA polymerase arrives

83
Q

What is primase?

A

A specialised RNA polymerase

84
Q

Why is DNA replication fast?

A

DNA polymerase is binded to a sliding clamp which encircles the double stranded DNA

Sliding clamp is loaded around DNA by a clamp loader

85
Q

What is the replisome?

A

large protein complex that carries out DNA replication

86
Q

In eukaryotes, what do histone chaperones do?

A

Load histones on to newly synthesised DNA

87
Q

What do topoisomerases do?

A

Helicase unwinding of DNA causes supercoiling (“twists”) ahead of the replication fork, which need to be unwound

So they unwind these twists

88
Q

What does mismatch repair protein MutS do?

A

Detects incorrect base pairing in newly synthesised DNA

89
Q

What is associated with mutations in mismatch repair proteins?

A

Predisposition to cancers

90
Q

Overall what contributes to very low error rate in DNA synthesis?

A

5’ - 3’ polymerization errors = 1 in 10^5

3’ - 5’ exonucleolytic proofreading 1 in 10^2

Strand-directed mismatch repair 1 in 10^2

Combined 1 in 10^9

91
Q

What do you require for PCR?

A 
Taq DNA polymerase
dNTPs
Template DNA
Primer
Buffer (Mg2+)
92
Q

Steps of PCR?

A

High temperature 95 degrees -Denaturation

Double DNA strand melts open as hydrogen bonds break

Low temperature 45 degrees - annealing

Primase binds to DNA polymerase attaches and starts copying DNA

Intermediate temperature - Extension

Optimum temperature for polymerase and extension of fragment

93
Q

What part of DNA is amplified during PCR?

A

Only DNA between primers

94
Q

What are primers?

A

Short roughly 20 bp long single stranded DNA, marker for DNA polymerase to bind on to

Chemically synthesised

95
Q

In gel electrophoresis of DNA moving to the positive electrode, what factors affect it’s movement?

A

Shape and size

Smaller fragments move faster

96
Q

What are the limitations of PCR?

A

Sequence inforamtion is required to design 2 primers

Limit on length of amplified fragment

Very sensitive to reaction conditions

Tiny amounts of contaminating DNA will also be amplified

97
Q

What’s a gene libary?

A

Collection of recombinant clones

Can screen for clones containing gene of interest

98
Q

Describe transgenics?

A

Genes between species

Genetic code is universal, so expression is possible

99
Q

In eukaryotes what are the 3 enzymes that transcribe different sets of genes?

A

RNA polymerase I
RNA polymerase II
RNA polymerase III

100
Q

What is required for RNA polymerase to bind to the RNA strand?

A

A transciption factor binded to the control region

101
Q

What are Cis-acting regulatory regions?

A

DNA sequences recognised by proteins

102
Q

What are the 2 types of Cis-acting regulatory genes and features of them?

A

The promoter:
Very close to the protein coding region, and includes the initiation begins and a “TATA” box ( sequence that allows transcription factors to bind and therefore RNA polymerase II)
Basal factors including RNA pol II bind here

The enhancer (Upstream activating sequences)
Regulatory sites that can be distant from the promoter
Activators and repressors bind here

103
Q

What are trans-acting proteins?

A

Transcription factors, bind to the promoter and enhancer to control transcription of the gene

104
Q

Describe the process of RNA polymerase binding to the RNA strand?

A

TBP binds to the TATA box

TBP recruits TFIID complex and TFIIB to the promoter

RNA pol II and further transcription factors bind to the promoter to give the basal transcription complex

105
Q

Describe the gal4 system in yeast?

A

Gal4 is bound to enhancer region, but Gal80 is also bound to it, meaning there is no transcription of Gal1

However if galactose is present it binds to Gal80, removing it from Gal4 so RNA pol II can bind and Gal1 can be transcribed

106
Q

How can chromatins stop transcription?

A

By condensing

107
Q

Describe the 4 ways in which DNA can be made accessible to transcription factors (uncondensed)?

A

Chromatin remodelling complex binds:
1. Remodelling the nucleosomes

  1. Histone chaperone removes histones
  2. Histone chaperone replaces histones with other histones

Histone modifying enzyme binds:

  1. Specific pattern of histone modification
108
Q

Where can core Histones be genetically modified by covalent addition of functional groups?

A

On their N-terminal tails

109
Q

Differences in bacterial gene expression compared to eukaryotes?

A

No nuclear membrane
One cytoplasmic compartment
No histones
Coupled transcription and translation

110
Q

Features of an operon in bacteria?

A

Has one promoter
All genes in an operon are transcribed together
The mRNA is translated to give separate proteins

111
Q

Describe the lac operon in bacteria?

A

Has a promoter region, lacZ, lacY and lacA which make mRNA which then makes B-galactosidase, B-galactoside permease, B-galactoside transacetylase

Which results in lactose metabolism

When no lactose present, there is no transcription as lac repressor is bound

When lactose is present, it binds to lac repressor removing it so proteins are created

112
Q

What are polycistronic transcripts?

A

Transcripts that able to produce multiple proteins from one mRNA transcript

113
Q

How can single pre-mRNAs produce mutiple products?

A

Alternative splicing

114
Q

How is alternativ splicing regulated?

A

By activators and repressors

115
Q

What about mRNA’s determines how much protein is translated in the cell?

A

The stability of the mRNA

116
Q

What does injecting double strands of RNA do?

A

Reduces the expression of specific genes, by reducing the levels of mRNA

It does the by the clevage of target RNA

Translational repression and eventual destruction of target RNA

Formation of heterochromatin on DNA from which target RNA is being transcribed

117
Q

How are eukaryotic genomes arranged as?

A

Linear chromosomes

118
Q

What are transposons (jumping genes)?

A

Can replicate and insert into other parts of the genome

Some transpose via mRNA

119
Q

Transposons 2 categories?

A 
DNA transposons (cut and paste)
Retrotransposons (Copy and paste, using RNA polymerase, and reverse transcriptase)
120
Q

What are LINEs?

A

Long interspersed nuclear elements

121
Q

What are SINEs?

A

Short interspersed nuclear elements

122
Q

Most mobile elements in bacteria are?

A

DNA transposons

123
Q

Most mobile elements in eukaryotes are?

A

Retrotransposons

124
Q

Process of Retrotransposons transpose?

A

Transcription of retrotransposon to form mRNA

Which is translated to form a reverse transcriptase

Then there is reverse transcription of RNA to DNA via the reverse transcriptase

Synthesis of second double DNA strand

Insertion of retrotransposon make into genome

125
Q

Features of Eukaryotic genomes in relation to their variability?

A

Highly variable in size

Much of the variability is attributable to repeated sequences and other non coding DNA

Transposons can insert copies elsewhere in the genome

Retrotransposons transpose via RNA

126
Q

Features of Sanger sequencing, Next generation sequencing (NGS), and single molecule sequencing

A

Sanger sequencing - Accurate but low throughput

NGS - Extremely high throughput, but difficult to assemble repeated sequences

Single molecule sequencing - Error rate, high cost, long sequences can be done

(nanopore can be used in field)

127
Q

What are polymorphisms?

A

2 or more alleles of a gene, common in a population

caused by different base order

128
Q

Why does most genetic variation genetic variation have no phenotypic effect?

A

Very small amount of genome codes for proteins

129
Q

What do wild type genes produce?

A

Functional proteins

130
Q

What do mutant genes produce and what does this infer?

A

Often non functional proteins, therefore in diploids most mutations are recessive

Also means mutations are lethal in haploid or hynozygous diploid

Some mis-sense mutations are lethal

131
Q

Example of a conditional lethal mutation?

A

Temperature sensitive

As protein only functional at certain temperatures

132
Q

Features of mitosis?

A

Somatic cells
Produces genetically identical daughter cells
2n = 2n + 2n

Happens to all the chromosomes not just one

133
Q

Features of meiosis?

A

Haploid gamete production
2n = n x 4
Genetically different daughter cells

Happens to call chromosomes not just one

134
Q

Where does homologous recombination occur?

A

Prophase of meiosis 1
Homologous chromosomes pair
Crossing over occurs

135
Q

What are animals sterile sometimes?

A

Don’t have homologous chromosomes

136
Q

What occurs in recombination?

A

Start with 2 double strands of DNA which are homologous (1 from mother, 1 from farther)

Double stranded break occurs

MRX performs 5’ to 3’ resection (removes some of strand)

Dmcl and Rad51 strand invasion causes 2 holiday junctions

Which can then be cleaved to produce non cross over products or cross over products

137
Q

What can homologous recombination cause In meiosis?

A

Generates cross overs- creates holliday junctions which are then broken in a certain way to create crossing over potentially

138
Q

Effects of base substitutions in coding regions?

A

Sileent - Base changed will still code for the same amino acid

Neutral - amino acid that is now coded for is very similar to the original - protein not affected

Mis-sense - new amino acid coded for does affect the overall protein created

Nonsense - if the base change causes a stop codon to form - protein will be incomplete

139
Q

What’s a frameshift mutation?

A

When you insert or delete a base and codons are read completely differently

140
Q

What are rare alleles termed as and what are normal alleles termed as?

A

Mutations

Wild type

141
Q

2 common single gene mutations?

A

Sickle cell amenia

Cystic fibrosis

142
Q

4 mechanisms cells have to prevent mutation?

A

Proofreading DNA polymerase

Postreplication mismatch repair

DNA repair by homologous recombination

Cell cycle checkpoints

143
Q

2 environmental factors that can cause mutations?

A

Radiation

Chemical mutagens

144
Q

2 types of mutations and which is more common?

A

Transition - Purine is replaced by a purine, or pyrimidine is replaced by a pyrimidine

Transversion - Purine is replaced by pyrimidine or visa versa

Transistions are more common as transversions are normally detected as there is a larer change in shape

145
Q

3 examples of chemical mutagens?

A

Intercalating agents: (planar molecules)
Insert between base pairs resulting in frameshift mutations

Base analogues
Incorporated into DNA in place of normal base ( as chemically similar), mis-pair as they hydogen bond to different things so synthesised strand will be different, resulting in a base substitution

Base modifying agents
Covalently alter a base causing it to mispair
Resulting in a base substitution

146
Q

Features of when homologous recombination repairing double strand breaks?

A

Break is accurately repaired
Universal process
Non-reciprocal
Local loss of heterozygosity (A to a)

147
Q

Features of homologous recombination generating cross overs?

A

In eukaryotes occurs in meiosis
Breakage and joining of DNA
Reciprocal
Genetic rearrangement

Holliday junctions are generated (from D loops)

Cut horizontally = chromosomes without crossover

Cut vertically = chromosomes with crossover

Human Biosciences (69 decks)

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