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molecular genetics Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

why do we all have different phenotypic characteristics ?

A

due to variation which is genetic difference between individuals .

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2
Q

what are the two types of variation ?

A

. polymorphisms

. disease causing mutations

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3
Q

what are the two types of mutation ?

A

. point mutations

. frameshift mutations

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4
Q

what is point mutation?

A

single nucleotide base is changed from a sequence of DNA or RNA due to a simple mistake during DNA replication in meiosis

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5
Q

what are the consequence of point mutation?

A

often little consequence

e.g. sickle cell

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6
Q

what is frameshift mutation?

A

caused by a deletion or insertion or inversion in a DNA sequence that shifts the way the sequence is read

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7
Q

what is the consequence of frameshift mutation?

A

. more serious

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8
Q

what percentage of population have polymorphisms ?

A

> 1%

unlikely to be cause of disease as it is abundent

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9
Q

what is the consequence of polymorphisms?

A

can affect disease progression or drug response

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10
Q

what are the 4 common types of polymorphism?

A
  1. SNPs- single nucleotide polymorphism
  2. Indels - small insertion/deletions
  3. large scale copy number polymorphism - CNPs
  4. tandem repeats
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11
Q

what is the percentage of identical DNA between humans ?

A

99.9%

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12
Q

what is the most common type of polymorphism?

A

SNPs

make up 80% of the 0.1% difference between individuals

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13
Q

what type of mutation occurs in SNPs?

A

. point mutation

single nucleotide substitution of nucleotide with another

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14
Q

where does SNPs occur?

A 
1. within gene
. coding ( exons )
. non-coding ( introns)
2. between genes
. non-coding ( intragenic region )
SNPs in non coding region may alter gene splicing/transcription factor binding/regulation
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15
Q

where is it more frequent for SNPs to occur ?

A

within non-coding region due to selection pressure

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16
Q

what is property of SNPs?

A

most SNPs are neutral with no phenotype change

3-5% have a functional role and do not change phenotype

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17
Q

what are the types of SNPs?

A

. synonymous - codes for the same amino acid
. non-synonymous - alters the poly peptide chain
which has 2 possibilities
1. missense mutation - alters amino acid sequence
2. nonsense - results in premature stop codon

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18
Q

what are indels?

A

. indels are insertion or deletions of nucleotide sequences of 2-10,000 base pairs
. second most common polymorphism

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19
Q

what type of mutation occurs in indels?

A

frameshift mutation

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20
Q

what is tandem repeats ?

A

. a sequence of nucleotide can be repeated numerous times in sequence

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21
Q

what are the two types of tandem repeats ?

A
  1. VNTRs - aka mini-satellites
    10-100 base long segments repeated
  2. STRs - aka micro-satellite
    2-9 base long segments repeated
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22
Q

what are CNPs?

A

entire gene repeated or deleted

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23
Q

how is a polymorphism different from a mutation leading to a specific disease ?

A

it is due to the prevalence in population
mutation is found in <1%
if mutation leads to loss of function or expression of protein its a disease causing mutations

24
Q

where do disease mutations often occur?

A

exons

25
Q

what are disease mutation referred to as ?

A 
. point mutation
. frameshift mutation
. inversions
. copy number variations
mini and micro satellites are rare in exons
26
Q

what is non-disjunction?

A

. results in meiosis1 when one daughter cell has an extra chromosome and the other daughter cell has less
. at end meiosis2 the same daughter cell will not contain a particular chromosome , while others have an extra copy

27
Q

what are types of diseases that can occur due to non-disjunction?

A

. down’s syndrome - 3 copies of chromosome 21
. edward’s disease - 3 copies of chromosome 18
. patau’s disease - 3 copies of chromosome 13

28
Q

effect of non-disjunction in sex chromosomes?

A

. turner’s syndrome - females with only one x chromosome
. kleinfelter’s syndrome - XXY males
. metafemale syndrome - XXX

29
Q

describe chromosome shape ? ( nomenclature )

A

Each human chromosome has a short arm “p” and long arm “q” separated by a centromere.

30
Q

what can we use to look at the structure and number of chromosomes ?

A

. karyogram which is then referred to as the karyotype

31
Q

what is karyotype and why is it used?

A 
the process to look at chromosomal changes
cab be used to compare
. chromosome count
. centromere position
. banding pattern
. sex chromosomes
32
Q

describe the process of karyotype?

A 
. take cell sample
. culture in dish
. stop cell division during METAPHASE
. extract chromosome from a single nucleus
. stain with giemsa
33
Q

what are examples of molecular biology techniques used in lab to look at mutation ?

A

. DNA probe
. restriction enzymes
. gel electrophoresis

34
Q

what is DNA probe ?

A

A DNA probe is a single stranded DNA chain that contains a nucleotide sequence specific for the gene or chromosomal region of interest.
. DNA probe bind to the gene of interest
. in FISH DNA probes are directly labelled with a fluorescent tag

35
Q

what is FISH ?

A

(FISH) is a molecular technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with a high degree of sequence complementarity.

36
Q

what happens in FISH ?

A

. fluorescent DNA probes can be applied directly to chromosomes.
. so the number of chromosomes per nuclei can be counted

37
Q

what are restriction enzymes ?

A

. restriction nucleases are enzymes which cleave single stranded DNA at certain nucleotide sequence into restriction fragments
. enzymes bind to specific sequence of nucleotide
e.g. Hae 111 binds to GGCC

38
Q

what do restriction nucleases derive from ?

A

bacteria

39
Q

what is the difference between blunt ends and sticky ends ?

A

. restriction enzymes don’t always cut at the same sites
. blunt end- enzyme cuts DNA strand through the middle
. sticky end- enzymes don’t cut straight through DNA strand

40
Q

what is gel electrophoresis ?

A

process used to separate DNA and RNA fragments

41
Q

describe the process of gel electrophoresis ?

A

. both DNA and RNA are negatively charged due to phosphate group
. they are run through a density gel
. shorter fragments migrate faster ( less resistance )
. use a ladder of known fragment sizes in one lane to be able to determine your DNA or RNA sizes

42
Q

how can you visualize the DNA after gel electrophoresis ?

A

to visualize the DNA the gel is soaked in a dye ( ethidium bromide ) which binds in DNA and fluoresces under UV light

43
Q

what is PCR ( polymerase chain reaction ) used for ?

A

. it can be used to determine genetic variation between DNA samples
. DNA sequence can be copied accurately and rapidly for analysis
. PCR can amplify target sequence 100 million fold in 2-3 hrs

44
Q

what is the main ingredient used in PCR ?

A

. TaqDNA polymerase to copy DNA template using repeated cycles of replication
. it is derived from thermophilic bacterium

45
Q

explain the steps of PCR reaction ?

A
  1. heat DNA ( 94-96) degrees to separate the DNA strands
  2. slight cooling of reaction mixture ( 50-65 ) degrees to allow the hybridization/annealing of primers ( oligonucleotide)
  3. extension heat to 72 deg and TaqDNA polymerase forms a complimentary copy of the DNA strand
46
Q

what happens in the first 3 cycles of PCR ?

A

. 1st cycle - two double stranded DNA molecule
. 2nd cycle - four double stranded DNA molecule
. 3rd cycle - eight double stranded DNA molecule
and so on many cycles happen

47
Q

what are the application of PCR ?

A

. provides numerous DNA templates for mutation screening
. forensic application
. mRNA templates can be analysed
. discriminate between DNA sequence differing by a single nucleotide (SNPs)

48
Q

what is reverse transcription ?

A

RT-PCR can be used to check if mRNA is being transcribed and if protein can be translated
. reverse transcribe mRNA into cDNA using reverse transcriptase

49
Q

what is chain length termination ?

A

. addition of ddNTP
.ddNTP lacks the 3’ -OH group and cannot form a phosphodiester bond which leads to chain termination
. requires incorporation of fluorescent labelled phosphate
.PCR reaction occurs
. at the end you have different length fragments with different fluorescent tag on them
. laser+ tag identify colour tag to see which fluorescent tag goes with each nucleotide
. we know the specific sequence of nucleotide within DNA

50
Q

what are some bio methods used to understand molecular genetics ?

A

. Allele-specific PCR - detecting point mutations
. restriction fragment polymorphism analysis - detecting point mutation
. detecting variable number tandem repeats

51
Q

what is allele specific PCR ?

A

. each sample is tested with three primers in PCR reaction instead of two
. one primer is the same for both reactions the other exits in two different versions
. primer A - is for normal sequence
. primer B - is for mutant sequence

52
Q

explain the results for Allele-specific PCR ?

A

. TT = 220 bp
. CC = 205 bp
then its homozygous
. if one C and one T allele then one each 220 and 205 its homozygous

53
Q

what is restriction fragment polymorphism ?

A

. restriction enzyme cut DNA
. SNPs at the site that restriction enzyme cleaves will prevent binding and subsequent cutting
. therefore you can distinguish if a person is homozygous (1 band) , heterozygous (2 bands) or not affected by a mutation

54
Q

how to detect tandem repeats?

A

. use PCR or restriction enzyme to create DNA fragments to run on a gel electrophoresis and see how the variable number of tandem repeats- the more there is the bigger the fragment.

55
Q

are mutations always bad ?

A

NO
they are the heart of evolution and natural selection
they can lead to better prognosis in disease

Biology (30 decks)

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