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CELS 191 > human genome module > Flashcards

human genome module Flashcards

1
Q

what does SNP stand for an what is it

A

a single nucleotide polymorphism, are single nucleotide sites in the DNA that commonly vary within populations

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2
Q

why did they sequence the human genome

A

identify all human genes, and their roles.
analyze genetic variation between humans.
sequence the genomes of several model organisms used in genetics.
develop new sequencing techniques and
computational analyses.
to share genome information with scientists and the general public as fast as possible.

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3
Q

how many base pairs and genes does the human genome have

A

6 billion base pairs and around 20,000 genes

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4
Q

what were some of the key findings of the human genome

A

There are fewer genes than expected
Less than 2% of our genome codes for proteins
The genome is dynamic
We still don’t know what many of our
protein-coding genes do
Most human genes are related to those of
other animals
All humans are 99.9% similar at sequence
level

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5
Q

how much of genome actually codes for proteins

A

less than 2 percent

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6
Q

how common are SNPs, in numbers

A

one in every 300 bases

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7
Q

where do our SNPs come from

A

they come mostly from our parents but as we develop we form some unique to us

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8
Q

what are the three types of SNP

A

linked, non coding and coding

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9
Q

why are most SNPs harmless

A

they are harmless as they fall outside of the coding regions of DNS

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10
Q

whats a linked SNP.

A

an SNP located close to a gene but not in coding or regulatory sequences, are inherited but have no effect on the protein.

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11
Q

whats causitive SNP

A

and SNP that is located in the gene sequence, either coding or non coding

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12
Q

whats a non coding SNP

A

one that is in the regulation sequence, changes where, when and how much protein produced. Likely to not do much but based on the nature of the variation may alter the regulation of the protein production.

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13
Q

whats a coding SNP

A

these are in the exon, these may change the amino acid sequence. Could potentially be problematic and code for early termination. But likely wont cause a large scale change due to redundancy of the genetic code.

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14
Q

whats an STR

A

a short tandem repeat

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15
Q

whats an inDel

A

small insertion or deletion mutations

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16
Q

whats the second most common varient type

A

SNP is first, inDel is 2nd

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17
Q

what can inDels cause

A

can cause reading frame shift if the amount of bases deleted is not a multiple of 3. and the mutation is in the exon region

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18
Q

what does STR stand for

A

short tandem repeats

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19
Q

what is an STR

A

STRs are repeats of 2-5
nucleotides, found in specific
regions of genome

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20
Q

how do STRs provide a genetic fingerprint

A

each person inherits two alleles from their biological parents. these alleles can have different lengths of STR at the same site. the mother may have 8 CAG repeats and father only 3, so the person is 3,8 at STR 1.

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21
Q

why does STR work for fingerprints

A

because the likely hood of two different people having the same STR lengths at 20 different sites is slim to none.

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22
Q

whats CNV stand for

A

copy number varients

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23
Q

what is a CNV

A

this is a large section of DNA, over 500 base pairs that are present in different amounts with reference to the human genome.

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24
Q

how do we do comparative genomics and explain the process

A

we do it in a process called aligning, this is when we line up two sequences of DNA and mark each point where the sequences are the same.

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25
Q

what does conserved mean

A

it means things that are the same in the genomes of two separate species.

26
Q

things that differ in two different species genomes could be what

A

could potentially be encoding for the organisms specific biology.

27
Q

what can we learn about an organsism by comparing its genome

A

What sort of genes they have
§ How differences between species arise
§ Relationships between species

28
Q

DNA from dead things can remain in the environment, why might it be hard to compare this DNA with human genome

A

DNA degrades and is masked by more modern DNA
DNA bases are also modified as they degrade,
sometimes changing the sequence.

29
Q

how much DNA do we share with the neanderthal

A

for non africans we share 2-4 %

30
Q

why don’t most africans share DNA with neanderthal

A

because the homo sapiens that evolved in africa never migrated out of africa to go interbreed with the neanderthal

31
Q

whats the amount of DNA shared between Melanesian and denisovans

A

4-6%

32
Q

mutations that can be inherited are called

A

germline mutations

33
Q

what causes a somatic mutation

A

damage to DNA by UV, radiation or chemicals or incorrect copying of DNA

34
Q

how many mutations in our genome do we develop ourselves as a fetus

A

60

35
Q

what affects the outcome of a mutation on the phenotype

A

the location of it in the human genome, environmental factors( diet and toxin exposure), other genes (background genes)

36
Q

whats a loss of function mutation

A

A mutation that might break a gene to cause it to not work as well as normal, or not work at all.

37
Q

why are loss of functions generally recessive

A

because there are two copies of each gene. if one is defective, its defects can be covered by the normal gene on the other chromosome.

38
Q

whats a gain of function mutation

A

when a mutation causes a gene to work too well, or to do something unexpected.

39
Q

why are gain of functions generally dominant

A

Gain of function mutations are often dominant, because having an allele that works too well or does something novel, will not be replaced by the normal copy of the gene.

40
Q

whats polygenic disorder

A

involve several genes acting together or
environmental factors interacting with genes.

41
Q

whats monogenic disorder

A

a disease caused by one set of alleles

42
Q

why do most genetic disorders not follow a straightforward inheritance pattern

A

Polygenic disorders involve several genes acting together or environmental factors interacting with genes.

43
Q

for most diseases, having a disease related variation means what

A

not necessarily anything, having a disease related variation does not mean youll get the disease

44
Q

why does getting a disease variation not mean youll get the disease

A

because most diseases are combinations of genotype and environment

45
Q

most genes are what not what

A

probabilistic not determinalistic

46
Q

how do we get information about a gene from its phenotype

A

by studying organisms that are naturally mutant for a gene, or creating our own mutations. using this we can figure out how mutations lead to phenotype change and learn what that gene is supposed to do.

47
Q

what is genetic screening and how can we do it

A

genetic screening is when we increase the rate of mutation, then select a phenotype of interest, then sequence the genome to identify the mutation. the mutation rate can be increased through increased interbreeding or inducing mutations with mutagens.

48
Q

what is transgenesis

A

Take a gene you are interested in, copy it and insert it into another organism

49
Q

whats a targeted mutation

A

Deliberately break a particular gene to see what happens

50
Q

what study does genetic screening, transgenesis and targeted mutation create

A

these makeup functional molecular genetics.

51
Q

whats a model organism

A

Model organisms are ones that can be easily raised in a controlled environment and are easy to manipulate genetically. these organisms also sharing large amounts of genes with humans

52
Q

why does transgenesis work

A

because the DNA code is universal, so

53
Q

what is a transgene

A

a gene that we have taken from one organism and put into the next

54
Q

transgenesis method? 5 steps

A

1: isolate gene interested in
2: insert into male pronucleus or fertilised egg
3: reimplant egg into parent organism
4: if successful, all resulting cells should contain that gene
5: screen offspring for transgene

55
Q

whats one way of carrying out a target mutation

A

CRISPR-Cas9

56
Q

method of CRISPR

A

make a guide RNA that binds to gene of interest, combine RNA and Cas9 protein, insert this complex, the complex enters the nucleus binding to the DNA at the point complementary to the RNA, the CRISPR makes a cut at the target site, the DNA will then try to repair itself

57
Q

in CRISPR what are the two ways the DNA can repair itself,

A

with or without a template of that DNA

58
Q

what happens when DNA repairs without template after CRISPR

A

DNA repair enzymes try to patch up the cut.
v This often results in errors as there is no template to read from.
v Small InDels are created at the target site,
the gene is potentially disrupted, or mutated (a).

59
Q

what happens when there is a template for DNA to repair itself after CRISPR

A

if there is a template the correct gene will be reinserted by the DNA enzymes

60
Q

what are 3 ways we can fix germline mutation

A

3 parent babies, Pre-implantation genetic diagnosis, and CRISPR gene-edited babies

61
Q

whats 3 parent babies

A

where the faulty
gene is on the mitochondrial DNA,
nuclear transfer to a donor egg can be
used.

62
Q

whats preimplantation genetic diagnosis

A

in families with an identified risk, IVF
can be used to make embryos from the
parents’ eggs and sperm. These
embryos can be tested before
implantation, and only healthy embryos
implanted.

CELS 191 (30 decks)

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