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Genes and Environment > W6 > Flashcards

W6 Flashcards

1
Q

what is genetics

A

the study of variation between and among living things, and how this variation is inherited

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2
Q

contrast genotypes and phenotypes

A

genotypes describe the genetic constitution of an organism, whereas, phenotype describes the morphological, biochemical and behavioural properties of an organism resulting from a specific genotype and its interaction with the environment

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3
Q

describe the genome

A

it is the total amount of genetic material in a chromosome set ie. in humans, it is one set of chromosomes

  • the genetic material is DNA
  • sequencing a genome is working out the base sequence of the dna
  • it does not tell us the function of the sequence
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4
Q

describe the human genome

A
  • 1mm between each ucleotide
  • stretches 3200km
  • would take 9.5 years to read through 600bases per minute
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5
Q

describe the 1000 genomes project and its application

A
  • aims to provide a deep characterisation of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype
    eg. E Asian, S asian, African and European ancestry

GWAS: genome wide association studies

  • rapid scanning markers across complete sets of DNA or genomes of many people to find genetic variations associated with a particular disease
  • particularly useful in finding genetic variations that contribute to common, complex diseases such as athsmad, cancer, diabetes, heart disease and mental illness
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6
Q

what do geneticists do

A

establish the ways variation between species and within individuals is inherited

  • identify how genes are expressed
  • examine the inheritance at the population level
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7
Q

what can cause variation

A
  1. environmental factors:
    - eg. FASD; fetal alcohol spectrum disorder
    +2%-5% of births in the US
    +growth retardation, characteristic facial features
    +CNS anomalies including intellectual impairment
    cause: chronic heavy alcohol use or frequent heavy intermittent alcohol, but not all
    +genetic factors? metabolism
  2. genetic factors:
    - huntingtons disease
    - normal people have two copies of the HD gene on chromosome 4; in this gene there is a repeated seuqnde of bases CAG, max. 35
    - if there are more than 42 repeats, then get HD
    +mentally stimulating mice by enriching environ. can help to delay onset and progression of motor symptoms
  3. a combination of genetic and environmental factors, the most common:
    - epigenetic
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8
Q

describe epigenetics

A
  • changes in geen expression that do not involve changes in DNA
  • they may be passed from cell to cell, parent to offspring
    eg. methylation is an epigenetic event whereby promotors control gene expression (methylation refers to the addition of CH3 groups to bases in DNA which can prevent gene expression

note: child abuse leaves epigenetic markers on a Childs genes
- different patterns of DNA methylation and gene expression compared to those who were not

eg. stress during pregnancy
- more behavioural problems than those whose mothers had calmer pregnancies
- higher rates of methylation in the promotor of the gene for the glucocorticoid receptor

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9
Q

describe human polymorphisms

A
  1. variation with no differences to viability eg. hair colour, length
  2. variations with differences to health eg. CF gene, albinism, Ehlers-danlos
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10
Q

describe the different types of variation that can occur

A
  • mutation can occur in any organism
  • variation at different stages of development
  • variation can be increased/decreased by human intervention
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11
Q

describe the hypotheses

A
  • until 1900s, it was not know what was passed on in the germ cells, previously however, the knowledge that offspring resembled parents and that selective breeding occurred was known
  • humorous or vital heat from parts of the body collected in the semen and shaped the form of the offspring
  • homunculus, that the sperm had a little person that then grew
  • epigenesis, substance in the gametes
  • Darwin- gennules
  • mendel: hereditary factors in the germ cells
  • johannsen- gene
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12
Q

describe briefly, Mendel’s ideas and experiment

A
  • he picked seven traits on seperate chromosomes with no unusual dominance
  • since the flowers self pollinated, he cut off the stem and therefore, self pollination. did not occur

he opened flowers and collected pollen, which was then spread into anthers

in his notes, there were visible ratios seen

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13
Q

describe curing cancer

A
  • cancer is associated with changes in DNA

- over time, there is a decreasing mortality rate and a increasing survival rate

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14
Q

what is a gene

A

the fundamental physical and functional unit if heredity, which carries information from one generation to the next is the gene
- a gene is a segment of DNA (deoxyribose nuclei acid)

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15
Q

what is DNA?

A
  • DNA is a double stranded molecule
  • it is a polynucleotide
  • it is made up of many (poly) nucleotides linked together
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16
Q

describe the structure of a nucleotide

A
  • a nucleotide consists of 3 parts:
  • a deoxyribose sugar, phosphodiester bonds link successive sugars
  • each carbon is numbered
  • a nitrogenous base: A-purine, G-purine, C-pyrimidine, T-pyrimidine
  • nucleotide pairing is complementary ie. G-C and A-T
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17
Q

where are genes found

A
  • mostly located in chromosomes

- position of a gene on a chromosome is called a locus

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18
Q

where are chromosomes found

A

in prokaryotes in the cytosol

- in eukaryotes in the nucleus

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19
Q

what is a chromosome

A
  • consists of DNA and protein
  • DNA+ protein= chromatin
  • the chromosomes are only visible dusting cell division

chromosomes may consist of one of one or more molecules of DNA depending on the stage in the cell cycle
eg. one stick is one molecule of DNA, two sticks=sister chromatids=2 molecules of DNA

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20
Q

describe the nucleosome

A
  • histone H1 clamps DNA to the core

- DNA double helix could around a core of eight histone molecules

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21
Q

describe one way of regulating gene expression

A
  • histone modification
  • genes are switched on and off so they are no active all in all cells at all times

euchromatin:

  • genes are switched on whereby there is a active chromatin
  • unmethylated cytosines
  • acetylated histones

heterochromatin

  • genes switched off whereby chromatin is silent
  • methylated cytosines
  • deacetylated histones
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22
Q

describe dna replication in reference to the molecules of DNA at each stage

A
  1. occurs during the S stage of the cell cycle
    - 2 molecules at beginning of mitosis
    - 1 molecule of DNA at beginning of G1
    - 1 molecule of DNA at beginning of S
    - 2 molecules of DNA at beginning of G2
  2. semi conservative
  3. antiparralell

note: there are two checkpoints for DNA replication, one is at the beginning of M, the other is at the end of G1

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23
Q

describe DNA replication in a prokaryote

A
  • circular chromosome
  • only one replication origin
  • two replication forks
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24
Q

describe replication origins in reference to organism type

A
  • eukaryotes have multiple replication origins, eg. in mammals, there are 25000
  • in yeast there is a specific sequence of DNA at the replication origin called the ARS with 120 bases, 11 of which are the same for each ARS
  • mammals it seems to be chromatin structure rather than a DNA sequence at a replication origin. A complex of proteins forms ORC (origin replication complex)
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25
Q

describe the sliding clamp in DNA replication

A

the clamp is a complex of proteins in the shape of a donut which keeps the DNA polymerase in place and increases efficiency of replication

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26
Q

contrast the differences between eukaryotic and prokaryotic DNA replication

A
  1. Okazaki fragments:
    - prokaryotes: approx 1000 bases
    - eukaryotes: approx 100-200 fragments
  2. speed:
    - humans are at 3000 bases per minute
    - bacteria: 30, 000 bases per minute
  3. enzymes:
    whilst prokaryotes have DNA polymerase 3, eukaryotes have a wide variety for different parts, eg. one for lagging strand, one for leading strand
  4. nucleosomes in eukaryotes:
    - are disassembled and assembled at the replication fork
27
Q

outline prokaryotic DNA replication

A
  1. helices seperate strands of DNA
  2. replication occurs from 5’ to 3’ on leading strand with single stranded binding proteins keeping the strands apart and DNA topoisomerase receiving supercoiling
  3. DNA polymerase 3 forms new strands from 5’ to 3’ on the complementary template
  4. beta clamp keeps DNA pol 3 in place
  5. 1 RNA primer is used in leading strand whereas multiple are used on the lagging strand to start replication
  6. short sequences formed on the lagging strand are called Okazaki fragments
  7. primers are removed and gaps are filled with complementary bases. Okazaki fragments are joined
28
Q

what is needed for chromosomes to replicate

A
  1. telomeres: provide structural stability, replication and positioning
  2. centromeres: essential for segregation at cell division
  3. origins of replication: DNA replication start point
29
Q

describe telomeres

A
  • repeated sequences that are unique in species eg. for humans TTAGGG is repeated about 2500 times, Arabidopsis is TTTAGGG
  • protects ends of chromosomes by looping or recruiting protective proteins
  • there are problems with the lagging strand whereby unreplicated DNA is degraded so telomeres shorten with age
  • resulting in a loss of 50-200 bases each round of replication
  • since genes on ends of chromosomes are lost, cell dies
30
Q

describe the relationship between telomerase and aging

A
  • telomerase is absent from many cell types
  • present in germ cells, stem cells and cancer cells
  • since unreplciated DNA is degraded, therefore telomeres shorten with age
  • loose about 50-200 bases each round of replication
  • genes on ends of chromosomes are lost, so the cell dies

Premature Aging:
- Werner syndrome due to shorter telomeres or a mutation in the WRN gene which produces a protein that has a role in preserving the ends of chromosomes

31
Q

describe the issue of telomere replication

A
  • telomere réplication refers to replication at the ends of chromosomes
  • it is fine for the leading strand since there is continuous replication right to the 5 prime end
  • the lagging strand had a problem since there is not enough DNA template for the primer
  • this means there is overhang that is not replicated
  • there will be missing Okazaki fragments
  • molecule becomes shorter
32
Q

describe the process of telomerase replication

A

WHEN TELOMERASE IS AVAILIABLE

  • enzyme telomerase extends the lagging strand. primer attaches and DNA polymerase completes the replication
  • telomerase has a complementary RNA part which is the template for the extension
  • doesn’t requite a template to extend the lagging strand
33
Q

outline the methods of DNA repair in detail and how errors can occur

A
  • errors are made during DNA replication and exposure to certain environmental factors

repair:

  1. DNA proofreading: errors during replication can be repaired on the spot. the DNA polymerase can go backwards 3’to 5’ and cut out a nucleotide and replace the base
  2. Mismatch repair: when a nucleotide was mispaired and this was also missed during proofreading then the mismatch repair proteins excise the mismatched nucleotide and some adjacent nucleotides. DNA polymerase 1 adds the correct nucleotides. DNA ligase rapairs the remaining nick
  3. excision repair: when a nucleotide is damaged, the excision repair proteins excise the damaged nucleotide and some adjacent nucleotides. DNA polymerase 1 adds the correct nucleotide 5’ to 3’ replication of the short strand. DNA ligase repairs remaining nick
34
Q

describe PCR in terms of what it is and what it does

A
  • mimics DNA replication
  • need to know something about sequence to design the primers
  • can amplify regions up to approx. 2kb
  • so sensitive, you can use primers with the whole human genome and amplify a specific sequence
  • makes millions of copies of a DNA sequence

what does it use?

  • DNA
  • 4 deoxyribonucleotide triphosphate enzymes
  • enzyme
  • primers
35
Q

outline the PCR process

A
  1. DNA made single stranded by heating to 95 degrees
  2. primers complementary to ends of the region of interest are annealed: 60-65 degrees
  3. primers are 15-20 bases
  4. TAQ polymerase: DNA polymerase, adds new bases complementary to template DNA
  5. a sequence of DNA can be amplified millions of times after several cycle of PCR
36
Q

how does one calculate the chance of the same sequence in another region of the genome

A
  • we are told the sequence of interest is of 20 bases

since there are four bases, it is (¼)^20

37
Q

describe TAQ polymerase

A
  • contains DNA polymerase 3
  • bacteria Thermus aquatics lives in hot springs
  • adds new bases complementary to the template DNA
38
Q

what was the conclusion from Garrod’s work

A
  • a gene encodes for an enzyme
39
Q

how can Alkaptonuria occur

A

normally, tyrosine is converted to Homogentistic acid and then maleyacetoacetic acid, which then becomes co2 and H20. however, a metabolic block can occur whereby homogentistic acid is oxidised and results in Alkaptonuria

40
Q

how can Phenylketonuria occur

A

usually, phenylalanine becomes phenylpyruvic acid, however, an error in metabolism can occur whereby a fault Phenylalanine hydroxylase enzymeresults in PKU

41
Q

what are Guthrie cards and what issues surround them

A
  • blood sample cards from a heel prick on babies for treatable conditions such as PKU
  • these are kept for 50 years, issues of data misuse, data safety
42
Q

describe PKU in terms of the effect on diet and current trends

A

avoid: milk, eggs, cheese, nuts, soybeans, chicken, steak, other beef products, fish, chocolate, peas
limit: pasta, rice, bread, biscuits, certain fruits and vegetables

females with PKA go back on the diet when pregnant
- current trend in PKU is that all people stay on diet

43
Q

describe how cretinism can occur

A

dwarfism

from the diet, there is tyrosine, however, due to metabolic blocks, thyroxine is not produced

44
Q

describe how albinism can occur

A

tyrosine comes from diet, however, due to a metabolic block, tyrosine cannot be converted to melanin

45
Q

describe the Beadle and Tatum 1930s experiment

A
  • used Neurospora crassa that grows on minimal medium
  • the spores were irradiated and produced mutants which would only grow if supplements were made to minimal medium
  • a complete media means all grew
  • minimal media means some don’t grow
  • then one compound was added at a time
  • this was used to investigate which supplements supported growth
  • it was found that Neurospora crass grows with Arginine
  • it would sometimes grow if other compounds closely related to arginine were added to the medium

prototroph: grows on minimal media
auxotroph: requires a supplement in the medium

46
Q

list the three compounds from Beadle and Tatum’s experiment that were like Arginine

A
  1. ornithine
  2. citrulline
  3. arginine

this followed a metabolic pathway, so even if there was a metabolic block somewhere, as long as the next molecule, ie. one of the above were added and assuming the enzymes were functioning, then the biochemcial pathway would still go on

47
Q

describe the changes to the definition of what does a gene do change over time

A
  1. a gene can code for an enzyme (hypothesis one)
    however, other inherited traits related to other proteins eg. collagen and fibrin
  2. a gene codes for proteins (second hypothesis)
    but, some proteins are made up of more than one unit for which there is a seperate gene
  3. so a gene codes for a polypeptide eg. an alpha or beta globin in haemaglobin (third polypeptide). note: there is a seperate gene for alpha globing on chromosome 16, an a seperate gene for beta globin on chromosome 11

a gene also codes for RNA, eg. tRNAm rRNA, miRNA, snRNA

48
Q

what is a metabolic block

A

in a biochemical pathway, specific enzymes are required for one substrate to become another. a metabolic block can inhibit or deform enzyme function

49
Q

what are the two types pf chromosome numbers and what is important about them for species

A

haploid: - two of each type of chromosome
- the two similar chromosomes are described as homologous

diploid: one copy of each chromosome

chromosome numbers are constant for a species

50
Q

what are the lowest and highest diploid numbers in reference to examples and what do chromosome numbers indicate

A

lowest diploid number at 2 is in the ascaris roundworm
highest number for a mammal is the dog
- chromosome number does not indicate complexity or evolutionary relationships of the organsim

51
Q

what is the definition of karyotype, karyoyfram, autosome and sex chromosome

A

karyotype: sorted chromosomes
karyogram: a drawing of chromosomes with banding shown
autosome: a chromosome not involved in determining the sex of the organism
sex chromosome: a chromosomes involved in determining the sex of the organism

52
Q

what is karyotyping and on what basis does it occur

A

chromosomes of a species can be sorted on the basis of :

  1. size
  2. centromere position, metacentric, submetacentric, afrocentric, telocentric
  3. satellites (extra dots on top of the chromosomes)
  4. banding patterns: nucleolar organiser regions where by rRNA genes become rRNA. giemsa stain for G banding
53
Q

what are the ways in which chromosome numbers can change

A

aneuploidy: where you add or subtract 1 or 2 chromosomes
polyploidy: more than 2 sets of chromosomes
euploidy: +/- complete haploid sets of chromosomes eg. triploid bananas (3N), tetraploid grapes (4N)
where N is one set of chromosome

54
Q

what is an example of aneuploidy on autosomes

A

Trisomy 21:

  • 47, XX/XY, +21
  • chromosome 21 has the AFP gene that produces amyloid proteins. there is now a third copy of the gene leading to extra amyloid proteins~~~biochem pathway
  • incidence increases with maternal age, rising exponentially around 35-39(in the past it was 29.3 years in mothers)
  • TRANSLOCATION: leading to structural changes in chromosomes. whereby you can loose some of the NOR region on the acrocentrics because there are 10 ofnthem with same sequence, 13, 14, 15, 21, 22
    note: deletion is possible

note: other autosome aneuploidy conditions:
- trisomy 18: 47, XX, +18
- trisomy 13: 47, XX, +13

55
Q

what is an example of a euploidy on sex chromosomes

A

Kinefelter syndrome:

  • XXY
  • 1/500 newborns
  • can have variability in features depending on interaction with other chromosomes
  • small testes
  • reduced testosterone
  • delayed or incomplete puberty
  • breast enlargement
  • reduced facial and body hair
  • infertility
56
Q

describe the relationship between maternal age and chromosomal conditions

A

older eggs are significantly more likely to have abnormally functioning spindles - which causes an increased rate of chromosomal problems in the mature eggs
- in chromosomal normal eggs, the chromosomes will line up straight on the spindle, however, in chromosomally abnormal eggs, chromosomes line up erratically - a mishap during chromosome seperation is much more likely

57
Q

outline aneuploidy at specific stages of meiosis

A

anaphase 1 of meiosis: non-disjunction

  • the parent cell chromosomes will not seperate into 2 daughter cells, all chromosomes will go into one cell and the other cell empty
  • the two daughter cells will seperate, 2 daughter cells will have 2N, whereas the other TWO daughter cell will be empty

anaphase 2 of meiosis: non-disjunction

  • the parent cell separates into two daughter cells as per normal with each daughter cell 2N
  • aneuploidy occurs when one of these daughter cells do not seperate into two other daughter cells with N, instead, one daughter cell has 2N and the other cell is empty
  • the other daughter cell from the parent cell will seperate as normal

note: from parent to daughter cell, the daughter cell chromosomes are still stuck together

58
Q

outline aneuploidy in mitosis after fertilisation

A

non-disjunction occurs at anaphase of the cell

  • cells that do not have at least 2 chromosomes die
  • normal cells would have one red and now white, not stuck together
  • some cells could have two red lined together and a white alone: THIS IS CALLED A MOSAIC ie.+21 and normal

can also occur in blastocyst

59
Q

how can translation result in balanced and unbalanced chromosomal numbers in trisomy 21

A
  • since there are 10 acrocetrics with the same NOR regions, 13, 14, 15, 21, 22
  • translocation can result in either no phenotype of a phenotype depending on whether the 21 is balanced or not
  • if translocation carrier 21:21 balanced, no phenotype
  • trisomy 21: 46, XX, t(14, 21) ie. translated 21 on a chromosome 14, 2 chromosome 21 as well
  • trisomy 21: 46, XY, t(21, 21), translocation of 21 is on chromosome 21 ie. there are two chromosomes 21 on the one position
60
Q

where are chromosomes found and when are they visible

A

.

61
Q

what is the position of a gene on a chromosome called

A

.

62
Q

what the types of testing for chromosomal disorders in pregnancy

A
  1. preimplantation diagnosis (PGD), with iVF. this occurs before embryo in utero
  2. ultrasound, looking for neural fold in 12-20 wks
  3. Triple test of maternal blood
  4. Cf DNA in maternal blood

invasive testing:

  1. chorionic villus sampling
  2. amniocentesis
63
Q

what is tested for in triple test of maternal blood

A
  1. AFP: alpha-fetoprotein is a protein that is produced by the foetus, high indicator of spina bifida
  2. hCG: human chorionic gonadotropin is hormone produced with the placenta
  3. Oestriol is an estrogen produced by both the foetus nd the placenta
    depending on the stage of pregnancy, can be higher or lower in trisomy 21
64
Q

what is involved in Cf DNA in maternal blood

A

Cf- cell free

  • non invasive
  • looking for foetal DNA in mother blood
  • can determine trisomy or not
  • 10wks

Genes and Environment (12 decks)

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