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yr 1 uni work > 113 > Flashcards

113 Flashcards

1
Q

mendels law of segregation

A
  • the 2 forms of a gene (alleles) present in each parent segregate independently
    -formulated this law by studying the results of monohybrid crosses (a cross between 2 true-breeding individuals differing in only 1 character)
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2
Q

gregor mendel overview

A
  • The father of genetics
  • Worked with peas
  • Discovered dominant and recessive traits
  • Discovered the concept of gene (‘heritable factor- gene wasn’t discovered yet)
  • Discovered the formulation of the basic laws of inheritance
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3
Q

what are variations in inherited characteristics due to

A

existence of alternative version of heritable factor called alleles

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4
Q

mendels law of independent assortment

A
  • Each pair of alleles assorts independently of each pair of alleles during gamete formation
  • Relates to the situation where the inheritance of 2 or more different pairs of alleles is being studied
  • He made law by looking at the inheritance of 2 characters at the same time
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5
Q

dihybrid crosses

A

in F2 2 new phenotypes are called recombinants, ratio of 9:3:3:1, if no independent assortment there would not be 2 new phenotypes

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6
Q

what link did sutton make

A

link between behaviour of chromosomes during meiosis and Mendel’s laws

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7
Q

what did sutton observe

A
  • Chromosomes occur in pairs in somatic cells
  • Chromosome pairs segregate equally into gametes- as each allele is on a different member of a chromosome pair and moves to opposite poles in anaphase 1
  • Different pairs assort independently- explained by random way that chromosomes line up in metaphase
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8
Q

what does chromosome theory of inheritance state

A

-Mendels heritable factors are located at the loci on chromosomes
- its the chromosomes that undergo segregation and independent assortment

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9
Q

where does mitosis occur

A

somatic cells

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10
Q

where does meiosis occur

A

germ line

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11
Q

what does meiosis produce

A

4 haploid gametes

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12
Q

what does mitosis produce

A

2 identical diploid cells

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13
Q

whats synapsis in meiosis

A

lining of homologous chromosomes

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14
Q

mitosis role

A

growth and tissue repair

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15
Q

meiosis role

A

to produce gametes and introduce genetic variability

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16
Q

whats a chromatid

A

1 of teh 2 identical strands of replicated chromosomes

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17
Q

sister chromatids

A

2 identical chromatids held together by common centromere after replication

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18
Q

4 processes that leads to genetic variability

A

-mutation
- Independent assortment of chromosomes in meiosis 1 – no. of possible combinations of chromosome types in 2^23
- Crossing over between homologous chromosomes during meiosis 1
- Random fertilization of ova by sperm – random choice of which sperm fuses with egg

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19
Q

no. of possible chromosome combinations in the offspring

A

2^46

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20
Q

when does crossing over occur

A

during pachytene phase of prophase 1

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21
Q

crossing over

A

-The process of genetic recombination that gives rise to new combinations of linked genes
-Begins with synapsis- pairing of homologous chromosomes
-The synaptonemal complex is a protein zipper that holds homologous chromosomes together in the tetrad
-results in recombinant chromosomes with new combinations of linked genes – new combinations of alleles

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22
Q

recombination frequency

A

the % of the progeny that inherit a combination of alleles that differs from either parent
RF= no. of recombinants/ total no. of progeny
X100

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23
Q

how else is RF estimated

A

studying testcross
e.g. crossing a double heterozygote with a double recessive. For genes on different chromosomes the recombination frequency will be 50% (due to independent assortment)

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24
Q

highest Rf value you can possibly get

A

50%

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25
Q

gene nomenclature

A

mutants were given a name that reflects their phenotype usually abbreviated e.g. black(b) and vestigial (vg). normal allele (wild type) is written with a + sign

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26
Q

RF to centimorgan

A

1% recombination = 1cM

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27
Q

why don’t cM map distances add up

A

multiple crossovers could occur leading to an underestimate of the distance between 2 loci

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28
Q

coupling vs repulsion heterozygotes

A

– 2 possible arrangements of alleles in a double heterozygotes. Shouldn’t make a difference to the recombinant %. Which offspring a recombinant and parental would be different though. The largest phenotypic classes in the progeny will be the largest classes

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29
Q

sex linkage

A

First observed in drosophila (flies)
Males only need 1 copy of allele whereas females need 2
Males always get their X chromosome from their mother

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30
Q

incomplete dominance

A

Where dominant allele does not completely mask the effect of the recessive allele at the same locus. E.g. in humans is Familial Hypercholesterolaemia (blending of traits)

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31
Q

co-dominance

A

Where each allele affects the phenotype in separate, distinguishable ways (no blending)

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32
Q

pleiotropy

A

Where a single gene has multiple effects on the phenotype

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33
Q

polygenic inheritance

A

Where a single trait is determined by multiple genes – a characteristic of this is that the trait shows continuous variation in the population e.g. height

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34
Q

epistasis

A

When one gene masks or modifies the expression of another gene. Affects dihybrid cross ratio now being 9:3:3:1

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35
Q

deviations from Medelian ratios

A

sex linkage
incomplete dominance
co-dominance
pleiotropy
polygenic inheritance
epistasis

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36
Q

cytogenetics

A

the study of the structure and function of chromosomes – used for the screening and diagnosis of inherited chromosomal disorders

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37
Q

karyotype

A

preparation of chromosomes arranged in size order – used to detect change in chromosome number and structure

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38
Q

whats giemsa staining for

A

makes chromosomes easier to look at

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39
Q

metacentric

A

centromere in centre

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40
Q

sub-metacentric

A

centromere off-centre

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41
Q

acrocentric

A

centromere very close to end

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42
Q

polyploidy

A

whole extra sets of chromosomes
- Diploid 2n
- Triploid = 3n
- Tetraploid= 4n
Rare in animals, common in plants

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43
Q

aneuploidy

A

some additional or missing chromosomes
-Occurs in 50% of human conceptions
-Most lead to embryonic death or spontaneous abortion
-Only autosomal aneuploidy that isn’t fatal is down syndrome
-More common on the sex chromosomes e.g. XO, XXY, XXXY

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44
Q

monosomy

A

2n-1 (chromosome missing)

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45
Q

trisomy

A

2n+1 (additional chromosome)

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46
Q

cause of aneuploidy

A

non-disjunction
can happen in meiosis 1 or 2
in meiosis 2, 1 of the end cells is normal

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47
Q

why does chance of having child with down syndrome increase with age

A

eggs are held at metaphase so as you get older more of chance of something going wrong
by age 40, 1:100 chance

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48
Q

characteristics of down syndrome

A

short stature
sterile
characteristic facial features
intellectual disability
heart defects
susceptibility to leukaemia and Alzheimers

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49
Q

screening for chromosome abnormalities

A

amniocentesis and karyotyping
blood tests to detect specifc proteins
ultrasound scans- measure size of nuchal pas at nape of neck associated with downs syndrome

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50
Q

turners syndrome

A

only viable human monosomy
1 in 2500 female births
no Y chromosome
sterile as sex organs don’t mature
oestrogen replacement therapy leads to the development of secondary sex characteristics

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51
Q

Klinefelter’s syndrome

A

most common genetic abnormalities
1:500-1000 male births
multiple X chromosomes

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52
Q

Klinefelter’s syndrome characteristics

A

phenotypically male with female characteristics
tall
sterile
may have interlectual disability
treated with hormone therapy (testosterone)

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53
Q

cri du-chat syndrome

A

5p minus syndrome
1 in 50 000 births
- cat like cry
-defects in glottis and larynx
- wide face and saddle nose
-physical and intellectual disability
- range in severity dependent on how much deletion occured

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54
Q

prader-willi syndrome

A

deletion in long arm of chr15 (15q1.12)
1 in 15 000 births
-Poor suckling reflex in infants
-Uncontrollable eating later in life
-Obesity/Diabetes
-Poor sexual development in males
-Only occurs when affected chromosome in inherited from he father

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55
Q

why does Prader Willi syndrome come from the father

A

due to genomic imprinting- process that affects certain genes whereby either maternal or paternal copy of gene is silenced

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56
Q

angelman syndrome

A

when same segment is missing as prader-willi but from the maternally derived chromosome
-Happy demeanour
-Inappropriate outburst of laughter
-intellectual disability
-Severe speech problems
-Stiff limb movements
-Seizures

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57
Q

familial downs syndrome

A

t(14;21)
translocation
accounts for 5% of downs cases
One of the chr21s is attached to one of the chr 14s

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58
Q

chronic myelocytic leukaemia

A

22-9 translocation
spontaneous- not heritable
1: 50-100 000
very high WBC count
95% of people with CML have the Philadelphia chromosome
Translocation creates the BCR-ABL fusion gene- an oncogene that stimulates over-production of white blood cells
CML is most common in middle aged/elderly
Accounts for 15-20% of all cases of leukaemia

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59
Q

what did friedrich miescher discover and how

A

nucleic acid- used pus from used bandages in Crimean war to get WBCs, then purified nuclei and extracted these nuclei.
found precipitate rich in phosphate and nitrogen ‘nuclein’
N-rich fraction= protein
acidic p-rich fraction= nucleic acid

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60
Q

frederick griffiths transformation experiments

A
  • Used 2 strains of streptococcus pneumoniae – one R that is benign and another S that is virulent
  • R is benign as it is lacking a protective capsule, it is recognised and destroyed by hosts immune system
  • S strain is virulent ad the polysaccharide capsule prevents detection by hosts immune system
    the genetic material was capable of reprogramming R-form cells into S-form disease causing cells.
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61
Q

Oswald Avery

A

built on Griffith experiments by trying to identify the ‘transforming principle’
- until this it was thought it was proteins
positive reaction to dische test for deoxyribose of DNA

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62
Q

hershey-chase experiment

A

electron microscope study shows the virus itself doesn’t enter cell so they tested to see if it was protein or DNA being inserted into cell

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63
Q

bacteriophages

A

type of virus composed of DN A and protein that infect bacterial cells

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64
Q

Chargaff’s ‘rule’

A

-interested in the 4 bases
-examined ratios of DNA in various organisms
-discovered ratio of 4 bases is not 1:1:1:1
- ratio is species specific
-base rule composition always obeys a strict rule, A=T and G=C

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65
Q

Rosalind franklin

A

photograph 51- x-ray diffraction photo of DNA taken in 1952 by raymond gosling
helped solve the structure of DNA

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66
Q

purines

A

adenine and guanine

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67
Q

pyrimidines

A

cytosine and thymine

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68
Q

conclusion from x-rat diffraction (photo 51)

A

DNA is double helix
is 2nm
length between each turn is 3.4nm
distance between repeating units is 0.34nm
10 nucleotide pairs per turn

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69
Q

Meselson-Stahl experiment

A

bacteria cultured in medium with 15N
tranferred to medium 14N
DNA sample centrifuged after first replication

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70
Q

what does DNA polymerase require

A

single stranded template DNA
all 4 nucleotide triphosphates (dNTPs)
free 3’ hydroxyl (primer)

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71
Q

what does DNA polymerase do

A

synthesises DNA in 5’ to 3’ direction
inserts complementary nucleotides
uses energy from breaking phosphate bonds
Proofreading ability- can remove incorrectly inserted nucleotides

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72
Q

synthesis of leading strand

A

1- helicase unwinds and separates 2 strands
2-single-stranded binding proteins prevent DNA strands from re-annealing

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73
Q

helicase

A

unwinds the helix

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74
Q

single stranded binding proteins

A

hold helix open
involved in DNA replication

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75
Q

primase

A

synthesis the RNA primers needed for initiation of DNA synthesis

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76
Q

DNA polymerase III

A

in prokaryotes (similar does same job in eukaryotes)
extend the DNA (or RNA) strand from 3’ end, copying the template

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77
Q

DNA polymerase I

A

removes the RNA primer and fills in gaps between Okazaki fragments

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78
Q

DNA ligase

A

seals the gaps between Okazaki fragments

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79
Q

Archibold Garrod

A

diseases where the patient is unable to carry out a particular biochemical reacton ( inborn errors of metabolism
studied alkaptonuria
first to connect inherited human disorders with Mendels law of inheritance

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80
Q

alkaptonuria observations

A

Urine of alkaptonuria patient contains large amounts of homogentisic acid (originally called alkapton)
Alkaptonuria is inherited – autosomal recessive

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81
Q

alkaptonuria hypothesis

A

Alkaptonuria patients lack the enzyme (homogentisic acid oxidase) for breaking down homogentisic acid
Lack of enzyme due to defect in a gene

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82
Q

beadle and tatums 1 gene 1 enzyme experiments

A

Were interested in how genetic changes may effect metabolism
Had been using drosophila as model organism but due to their complexity it was difficult to prove a single gene was responsible for a particular chemical reaction
Neurospora (bread mould) a more simple organism lead them to win Nobel prize in physiology or medicine 1958

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83
Q

neurospora

A

bread mould
have a haploid stage in life cycle
so genetic changes are easy to study as recessive traits will apear in offspring

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84
Q

auxotroph’s

A

mutant strains that cannot synthesis a particular molecule required for growth
so will only grow if they are supplied with that molecule

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85
Q

screening for auxotroph’s

A
  • Culture individual spores on complete medium
  • Transfer to minimal medium to identify possible auxotroph’s
  • Test candidates for growth on MM supplemented with different classes of nutrients (vitamins or amino acids or nucleotides)
  • Test candidates for growth on MM supplemented with individual amino acids (or vitamins or nucleotides)
  • Identify the amino acid that allows your mutant to grow
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86
Q

class 1 of arginine auxotroph’s

A

mutants grow on:
MM +ornithine
MM + citrulline
MM + arginine

87
Q

class 2 of arginine auxotroph

A

mutation on gene B
mutants grow on
MM + citrulline
MM + arginine

88
Q

class 3 arganine auxotroph

A

mutation on gene C
mutants grow on
MM + arginine (only)

89
Q

what did beadle and tatum propose

A

enzyme in a pathways was controlled by 1 gene, role of a gene is to encode an enzyme and that for each enzyme there is a gene, this later devolped into one gene, one polypeptide

90
Q

pulse-chase experiment

A
  • Provided evidence for messenger RNA
  • Did by 15, label with radioactive uracil
  • Saw the uracil move into the cytoplasm
91
Q

transcription steps

A

initiation
elongation
termination

92
Q

transcription- initiation -

A

unlike DNA polymerase RNA polymerase does not require a primer
Catalysed by RNA polymerase

93
Q

transcription- elongation

A
  • RNA polymerase moves along the DNA template, unwinding the double helix and catalysing the addition of ribonucleotides to the 3’ end of the growing RNA molecule
94
Q

UAA, UAG and UGA are what

A

stop codons to signal end of translation

95
Q

AUG role

A

start codon and also codes for methionine

96
Q

genetic code is almost universal

A

the same codons are used for the same basic amino acids from the simplest bacteria to complex organisms, indicating that it must have been established very early during evolution

97
Q

specifying amino acids

A
  • mRNA cannot act as a physical template for amino acids
  • adapters required to link mRNA and amino acids
  • adapters are transfer RNAs (tRNA)
98
Q

tRNA structure

A

-approx. 80 nucleotides long
-single stranded but base pairs within the chain
-clover lead structure further fold to make L shaped molecule
-anticodon at 1 end
-amino acid attachment site is the 3’ hydroxyl group at the end of the RNA chain
-each tRNA is specific for a single amino acid determined by its anticodon
-tRNAs are the adapters
-specific attachment carried out by amino-acyl tRNA synthetases (activating enzymes)

99
Q

attachment process for attaching an amino acid to its RNA

A

1- ATP hydrolysed and amino acid joined to AMP
2- Correct tRNA binds and amino acid transferred from AMP to the tRNA

100
Q

wobble base pairing

A

Often when different bases code for the same amino acid it is the 3rd base that differs (not always)

101
Q

the ribosome

A

-Composed of ribosomal RNA and proteins
-2 subunits – large and small
-Binds mRNA and amino acyl-tRNAs
-Catalyses stepwise formation of peptide bonds (amino acids added from N to C terminus)
-Moves in 5’-3’ direction along mRNA
-By recognising the correct start codon, ribosomes ensures correct reading frame is used

102
Q

protein synthesis - initation steps

A

1-Small ribosomal subunits binds mRNA near its 5 end (recognised AUG start codon)
2-Initiator tRNA binds to AUG start codon
3-Large subunits binds so that the initiator tRNA fits into the p-site on large subunits
4-Require energy from GTP hydrolysis and proteins called initiation factors (help stabilise initiator tRNA and to assemble ribosomes

103
Q

protein synthesis- elongation steps

A

1-Incoming aminoacyl tRNA base pairs with codon in the a site – requires GTP hydrolysis
2-Peptide bond forms between amino group of new amino acid and the COOH group of the amino acid in the p-site – catalysed by peptidyl transferase
3-Growing polypeptide chain now in the a site
4-Translocation- tRNA moves in the p-site is ejected and the ribosome moves along the mRNA chain- requires GTP hydrolysis
5-Growing chain now in the p site and the a site is free to accept the next incoming aminoacyl tRNA

104
Q

protein synthesis - peptide bond formation

A

-Bond catalysed by peptidyl transferase
-Peptide bond is between the C and N of different amino acids

105
Q

protein synthesis- termination steps

A

1- Stop codon in A-site
2- There are no tRNAs for stop codons
3- Release factor enters a site instead of amino acyl tRNA
4- Water added to end of polypeptide chain
5- Completed polypeptide released from tRNA in p site
6- Ribosome dissociated, 2 X GTP hydrolysed

106
Q

polyribosomes in eukaryotes

A

Nuclear membrane- mRNA transported to cytoplasm before translation occurs

Several different organelles- proteins must be trafficked to correct site

107
Q

polyribosomes in prokaryotes

A

No nuclear membrane- transcription and translation coupled
No organelles- proteins diffuse through cytoplasm

108
Q

mutations

A

permanent change in the DNA of a cell, such as a change in gene position/number (chromosomal mutation) or change in nucleotide sequence (point mutation). Mutations are rare and occur randomly also important for genetic variation

109
Q

mutations in somatic tissues

A
  • cells not passed on to offspring
    -passed on to all cells descended from the original mutant
    -85% of cancers are caused by these mutations
110
Q

mutations in germ line tissure

A
  • cells are passed on to offspring
  • cause of inherited genetic diseases
  • raw material from natural selection produces evolutionary change
111
Q

causes of mutation

A
  • spontaneous - DNA replication
  • induced (mutagens)
    chemical- base analogues, modifying intercalating agents
    physical- ionising radiation, Uv
112
Q

spontaneous mutations

A

occur due to inherited instabilities in DNA

113
Q

base tautomerism

A

-Nucleotides can change to other conformations e.g. isomers and tautomers (at low rate)
-During DNA replication an incorrect base is inserted to form mismatched pair

114
Q

chemicals that resemble DNA bases - mutations

A

1.Chemicals that resemble DNA bases but pair incorrectly when incorporated in DNA (base analogues)
5 bromouracil is incorporated into DNA as though it were thymine, once incorporated it rearranges into a form resembling cytosine, upon DNA replication, can result in a point mutation converting AT bp to a GC bp

115
Q

chemicals that remove amio group - mutations

A

chemicals that remove the amino group from adenine or cytosine e.g. nitrous acid/nitrate
Deamination of C to U
Replication of DNA containing deaminated C results in A being inserted
Daughter strand base pairing changed from CG to TA
Occurs spontaneously at low rates
Uracil not usually found in DNA
Uracil DNA glycosylase has a specific role in removing U from DNA to prevent mutations

116
Q

chemicals that add hydrocarbon groups- mutations

A

chemicals that add hydrocarbon groups to nucleotide bases
alkylating – many of these chemicals are mutagens, addition of ethyl group at the O6 position alters base pairing, resulting in a point mutation converting GC bp to AT bp
EMS- ethyl methane sulfonate

117
Q

intercalating agents- mutations

A

Insert between bases and distort DNA helix
Interfere with replication
Tend to cause frameshift mutations
e.g. ethidium bromide

118
Q

mutations- ionising radiation

A

physical agent
Can directly ionise DNA or ionise water to produce free radicals
Cell cycle arrest and DNA repair (error prone) = apoptosis
Can damage bases and cause double-strand breaks

119
Q

mutations- UV

A

physical agents
pyrimidine dimers
UV irradiation is absorbed by pyrimidine bases C and T
Covalent bonds can form between adjacent C and T nucleotides- pyrimidine dimers
Blocks DNA synthesis leaving a gap opposite the site of damage

120
Q

xeroderma pigmentosum

A

hereditary condition
deficient in NER (nucleotide excision repair
characterised by development of skin cancer at early age in parts exposed to sun

121
Q

single gene disorders

A

caused by point mutations in single genes
individually very rare but collectively affect 1-5% of population
high morbidity and mortality in children

122
Q

autosomes

A

all chromosomes apart from X and Y

123
Q

cystic fibrosis overveiw

A

A disorder originating in secretory epithelial tissue
Most common life-shortening genetic disorder affected north European Caucasian population
Carrier frequency 1 in about 25
CF births 1 in about 2500
If untreated they die before their 5th birthday- not life can be extended into adulthood

124
Q

symptoms of CF

A

accumulation of mucus in the lungs, pancreas, digestive tract, and other organs
multiple effects including chronic bronchitis and recurrent bacterial infections

125
Q

CFTR

A

Cystic fibrosis transmembrane conductance regulator

126
Q

what does CF gene (CFTR) code for

A

for chloride channel
regulates the flow of cl- accross the membrane

127
Q

most common mutation causing CF

A

ΔF508- defect in c- transport causes extracellular mucus to become thicker and stickier
-Deletion of 3 base pairs (bp) results in loss of phe (F) residue at position 508
-Protein does not fold normally and is more quickly degraded
-There are >800 different CFTR mutations that cause CF

128
Q

treatment for CF

A

life is prolonged by antibiotics and daily massages to clear mucus away from airways

129
Q

medicines for CF

A
  • Drugs to improve function of mutated protein – gating mutations can be treated with gate opening drugs, other mutations treated with combination therapies that bring more of the chloride channels to surface and help those channels to operate more effectively
  • Gene therapy- provide patients with a copy of the correct chloride channel
    Clinical trials for integrating and non-integrating gene therapies are underway
130
Q

sickle cell anaemia

A

autosomal recessive
affects 1 in 625 Afro-Caribbean/American births

131
Q

sickle cell anaemia symptoms

A

anaemia, joint pain, swollen spleen, frequent severe infections

132
Q

sickle cell anaemia treatments/cure

A

regular blood transfusions
bone marrow transplant

133
Q

what cause sickle cell anaemia

A

mutation in the gene for b-chains of haemoglobin; leads to incorrect folding of the protein
The defective haemoglobin forms long chains of rigid polymers (after O2 released) which deform the RBC

134
Q

benefits of being sickle cell carrier

A

resistant to malaria, so where high rates of malaria there’s also high rates of sickle cell

135
Q

autosomal dominant pedigree

A

males and females affected
affected individual have an infected parent
50% chance of the affected parent having an affected child

136
Q

Huntington disease

A

late-onset degeneration of the brain
occurrence 1 in 24 000

137
Q

Huntington disease symptoms

A

jerky movements, personality changes, deterioration of walking, speaking, swallowing, death will result from complications such as chocking, infection or heart failure

138
Q

molecular causes of Huntington’s disease

A

defect on chr 4
HD gene contains CAG repeats (glutamine)
11-34 repeats is normal
36-125= HD

139
Q

familial hypercholesterolaemia symptoms

A

high levels of cholesterol in bloodfrom an early age
cholesterol deposits build up in joints
cardiovascular disease

140
Q

FH treatment

A

cholesterol-lowering drugs e.g. statins
low cholesterol diet

141
Q

causes of FH

A

due to low density lipoprotein (LDL) receptor
the LDL binds and carries cholesterol in the blood stream

142
Q

FH frequency and homo/het

A

incomplete dominance
homozygous- have 6 fold increase in blood cholesterol
heterozygous- have 2 fold increase in blood cholesterol-heart attacks by age 35
hh= 1 in a million
Hh- 1 in 500 birth

143
Q

what is dominant phenotype cause by in FH

A

haploinsufficiency

144
Q

pedigree for sex linked recessive traits

A
  • Female are carriers and mostly males are affected
  • Carrier female will transmit 50% of sons affected and 50% female are carriers
  • Affected male cannot transmit to sons by will transmit to 100% of daughters
145
Q

haemophilia

A

sex linked recessive disease
blood clotting disorder

146
Q

haemophilia symptoms

A

uncontrollable bleeding, tendency to extensive brusing, bleeding joints

147
Q

haemophilia A

A

mutation in the gene for factor VIII on X chromosome, 1 in 5000 males

148
Q

haemophilia B

A
  • Christmas disease
    mutation in gene factor IX on X chromosome
    1 in 30 000 males
149
Q

duchenne muscular dystrophy

A

muscle wasting disease
1 in 3500 males
sex-linked recessive
currently incurable- new gene therapies under research

150
Q

how is duchenne muscular dystrophy caused

A

affected gene codes for a muscle protein called dystrophin, the dystrophin gene is largest known human gene making it prone to rearrangements
dystrophin is part of a protein complex that connects cytoskeleton of a muscle fibre to the surrounding extracellular matrix through the cell membrane
muscles in DMD die, death occurs by age 20 from respiratory or cardiac failure

151
Q

bioinformatics definition

A

using computer technology to collect, store, analyse and disseminate biological data and information
(simply- computer-aided biology)

152
Q

why do we need bioinformatics

A

We need bioinformatics as the growth databases of genetic information and sequencing cost of per human genome is reducing- becoming possible to analyse genome to diagnose disease

153
Q

example uses of bioinformatics

A
  • Genome sequence and annotation
  • Protein structure and molecular binding
  • DNA identification
  • Omics studies
154
Q

common problems for bioinformatic begginners

A
  • Large number of tools available – when to use and what
  • Most tools and databases are not very user friendly
  • The outputs can look intimidating
  • Many different file formats
155
Q

DNA barcoding

A

allows species identification through short section of DNA
- Cost effective
- genes regions that are similar within the same species and distinct across different species
- Commonly used genes
Animals: MT-CO1, 16S rRNA
Fungi: ITS (internal transcribed spacer)
Bacteria: 16S rRNA or 18S rRNA
The different bases forms a unique ‘barcode’ for each species in the selected gene region

156
Q

FASTA

A

a smple format for nucleotide/amino acid sequence and little else

157
Q

sequencer

A

device that can automate the process of determining the DNA bases

158
Q

read (bioinformatics)

A

nucleotide sequence generated by a sequencer

159
Q

search (database)

A

Typically you would say you “search” a database or perform a “search”, to describe the process of looking for specific information in a database

160
Q

query (database)

A

The formal and structured request for data in databases. Often used interchangeably with search. In BLAST, it refers to your input sequence

161
Q

subject (BLAST database)

A

The sequences that your query sequence is compared to.

162
Q

what can DNA barcoding be used for

A

building phylogenetic trees
often recorded in Newick format

163
Q

Newick format

A

designed for computer and hard to read for humans

164
Q

phylogenetics

A

the study of the evolutionary history and relationships

165
Q

clade

A

a group of organisms that includes a single ancestor and all of its descendent.

166
Q

branch

A

: Shows the path of transmission of genetic information from one generation to the next; the longer the lines, the more genetic change (or divergence) has occurred. The branch length are usually the number of genetic changes per site (i.e. if 1 base difference for a 100-base sequence, the length will be 0.01) .

167
Q

sequence alignment

A

A way of arrange amino acids or nucleotides sequences to identify regions of similarity (put the sequences next to each other in a way that they line up well)

168
Q

primary key (database)

A

A unique ID for identifying an entry in a table in a database. Minor technical difference to Accession number.

169
Q

fields

A

a set of attributes

170
Q

retrieve (database)

A

identifying and extracting data from a database

171
Q

accession number (database)

A

Unique IDs used in databases, a bit like how your bank account number is unique

172
Q

genecards

A

a human gene databae with extensive info on each gene - it collects information from different databases and provides links to the sources

173
Q

advantages of bacteria for genetics

A
  • Easily cultured
  • Short generation time: 20 -30 mins
  • Haploid- only 1 copy of gene- can see phenotype much easier as if diploid you would need 2 copies if It was recessive
174
Q

bacteriophages

A

infect bacteria- structurally and functionally diverse

175
Q

lytic (or virulent) bacteriophage life cycle

A

multiply and then lyse bacterial cell which releaes bacteriophage particles

176
Q

temperate bacteriophage life cycle

A

(or lysogenic bacteriophage) can integrate into bacterial chromosome and then remain dormant, replicating with the bacterial DNA

177
Q

recombination definitions

A

the coming of DNA from 2 individualls into a single genome

178
Q

Gene transfer and recombination occurs through 3 processes

A

transformation- uptake of naked DNA
transduction- transfer of bacterial genes from 1 bacteria to another bacteri

179
Q

2 types of transduction

A

generalised- occurs with virulent phage t4
specialised- occurs with temperate phage- lambda

180
Q

conjugation

A

The ability to form sex pili and to transfer DNA by conjugation is determined by a plasmid called F (for fertility) factor
F factor replicates in synchrony with bacterial chromosome, in a way that one end of the DNA molecule passes through the cytoplasmic bridge into the recipient cell (called an exconjugant) where it circularises
The donor keep a copy of the F factor

181
Q

regulation of gene expression in bacteria

A
  • Often controlled at the level of initiation of transcription
  • Transcription begins when RNA polymerase binds to a promoter
182
Q

control of tryptophan biosynthesis

A

regulated synthesis of repressible enzymes

183
Q

negative regulation

A

binding of repressor/tryptophan to operator blocks transcription

184
Q

control of lactose metabolism

A

regulated synthesis of inducible enzymes

185
Q

negative expression in bacteria

A

binding of a protein to an operator prevents transcription
Trp operon, expression is off when tryptophan binds to repressor which then binds to the operator
Lac operon, expression is off in the absence of lactose when the repressor binds to the operator

186
Q

positive regulation in bacteria

A

binding of molecule to the operator turns on gene expression
cAMP receptor protein

187
Q

cAMP receptor protein (cRP)

A

lactose is present
glucose is scarce (cAMP high)
abundent lac mRNA synthesis

188
Q

prokaryotes

A
  • Unicellular
  • No membrane-bound organelles
  • Between 500 and 4000 genes
  • Small genomes
  • Circular DNA
189
Q

eukaryotes

A
  • Unicellular or multicellular
  • All organelles are membrane-bound
  • Between 6000 and 30 0000
  • Large genomes
  • Linear DNA organised into chromatin
190
Q

why are eukaryotic genomes so large

A
  • lots of genes
    lots of non-coding DNA
191
Q

non coding DNA consists of

A
  1. Gene regulatory sequences (e.g. promoters)
  2. Introns (non-coding sequences within genes)
  3. Sequences of no known function (including repetitive DNA sequences)
192
Q

exon

A

represented in final mRNA

193
Q

intron

A

intervening sequence in the transcribed region that is not represented in the final mRNA

194
Q

repetitive sequences

A

interspersed repetitive DNA

tandemly repetitive (satellite) DNA

195
Q

interspersed DNA

A
  • Repeated units scattered throughout genome
  • Single unit 100-10 000bp
  • Copies not necessarily identical but closely related
  • Makes up 25-40% of most mammalian genomes
  • E.g. alu elements make up 5% of the mammalian genome
196
Q

tandemly repetitive (satellite) DNA

A
  • Can be broadly classified according to the length of a single repetitive region:
    Regular satellite DNA- 100 000-10 million bp per site
    Minisatellite DNA- 100-100 000 bp per site
    Microsatellite DNA- 10-100 bp per site
  • Much satellite DNA is located at telomers and centromeres – suggesting structural role
  • Some genetic disorders are caused by long repeats of a sequence within a gene e.g. hunting tons disease
197
Q

heterochromatin

A

highly condensed during interphase, not actively transcribed

198
Q

euchromatin

A

less condensed during the interphase, able to be transcribed

199
Q

chromatin structure

A
  • Chromosomes are composed of chromatin (protein + DNA)
  • Chromatin is an intricate form of packaging for DNA (10 000- fold compaction)
  • DNA in a cell must be packed in an organized manner to be accessible for transcription and replication
  • This involves association with specific proteins (Histones) and the formation of chromatin
  • Eukaryotic chromatin is much more complex than prokaryotic chromatin
200
Q

histones

A

proteins with positively charged amino acids that binds to the negatively charged DNA

201
Q

what form is most chromosomes in during interphase

A

euchromatin

202
Q

what happens to chromatin during meiosis and mitosis

A

chromatin folds further- condenses- highly condensed chromatin also occurs during interphase in some regions of the chromosomes – heterochromatin

203
Q

DNA methylation

A

(associated with gene silencing)
Attachment of methyl groups (-CH3) to DNA bases
Triggers formation of a compact chromatin structure
Associated with inactive DNA
Accounts for genomic imprinting in mammals

204
Q

histone acetylation

A

(associated with gene activation)
Attachment of acetyl group (-COCH3) to histones
Acetylated histones grip DNA less tightly
Acetylation/deacetylation is involved in switching genes of and on

205
Q

closed chromatin

A

DNA methylated
histones now acetylated

206
Q

open chromatin

A

DNA unmethylated
histones acetylated

207
Q

RNA polymerase 1 in eukaryotes

A

ribosomal RNA

208
Q

RNA polymerase 2 in eukaryotes

A

mRNA

209
Q

RNA polymerase 3 in eukaryotes

A

small RNAs e.g. tRNA

210
Q

how does transcription begin

A

when RNA polymerase binds to promotor

211
Q

what do DNA sequences adjacent to gene (promotor) do

A
  • Determine where the transcription of the gene is initiated
  • Determine the rate of transcription
212
Q

the TATA box

A
  • A key part of the promoter
  • Provides the site of initial binding of the transcription initiation machinery
  • Located 10-35 bp upstream of the transcription start site
213
Q

preinitiation complex before transcription processes

A
  1. Binding of TFIID: includes the TATA-binding protein (TBP) + TATA-associated proteins (TAFs)
  2. Sequential addition of other ‘general transcription factors’- first TFIIA and TFIIB
  3. Then binding of TFIIF + RNA polymerase OO
  4. Followed by the TFIIE + TFIIH- to form the preinitiation complex

yr 1 uni work (13 decks)

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