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Exam 3-my Q's Flashcards

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Biology 101 flashcards
1
Q

What is a mutation?

A

a heritable change in a DNA sequence

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2
Q

what are the classifications of genes by what chromosome the gene is location on?

A

autosomal, x linked, somatic, germ line (germinal)

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3
Q

are somatic mutations inherited?

A

no, they are not passed down

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4
Q

are germ line mutations inherited?

A

yes, if the mutation affects germ cells of progeny

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5
Q

What are the classifications of mutations by type of molecular change

A

nucleotide substitution

insertions and deletions

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6
Q

What are the types of nucleotide substitutions, define them

A

transition: pyrimidine replaced with other pyrimidine, or purine with purine
transversion: pyrimidine replaced with purine or vice versa

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7
Q

how are transversions and transitions further classified? define

A

silent- changes codon into another that codes for the same AA
missense- results in AA change
nonsense- changes a codon into a stop codon

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8
Q

what are the 2 types of missense mutations

A

conservative- chemically similar AA

non conservative- chemically different AA

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9
Q

What kind of mutation causes sickle cell anemia

A

non conservative missense mutation, nucleotide substitution

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10
Q

what is a frameshift

A

if there is an insertion or deletion of any # of nucleotide pairs that is not a multiple of 3, the reading frame changes

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11
Q

What is a frameshift likely to cause?

A

usually truncated non functional proteins

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12
Q

what is a nonsense mutation likely to cause

A

truncated pp, might still be functional

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13
Q

What are the mutation classifications by function/ phenotype (9)

A

neutral- no effect
null- complete function loss
leaky- reduced function
loss of function-decreases or eliminates function
gain of function-
lethal-
nutritional- affects biochem pathway
conditional- only appears under certain factors (ex temp)
suppressor mutation- 2nd mutation that reverses the original

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14
Q

are loss of function mutations often recessive or dominant?

A

recessive

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15
Q

are gain of function mutations often dominant or recessive?

A

dominant

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16
Q

How does UV light affect DNA?

A

it causes pyrimidine dimers that are bulky, DNA polymerase cant replicate it and skips it. can lead to a mutation

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17
Q

How do DNA polymerases deal with UV damage in DNA

A

some can replicate over the dimer by replacing the pyrimidine dimers with A’s by default.

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18
Q

Describe the process of mismatch repair

A

happens after DNA replication if anything is missed.
incorrect base is cut
the parent strand is identified my methylation
a part is excised and replaced
DNA ligase joins gaps

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19
Q

What is the mutation rate after mismatch repair

A

1x10^9 nucleotides

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20
Q

explain how DNA is repaired by photoreactivation repair

A

UV damage is reversed, PRE photolyase cleaves the bond between T’s only in the presence of light.

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21
Q

What kind of organisms can perform photoreactivation repair

A

bacteria and yeast, not higher eukaryotes

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22
Q

Explain base excision repair

A

damaged non bulky chemically modified or inappropriate bases can be removed this way

  • An incorrect base is excised and an AP site is left in its place (empty spot)
  • AP endonuclease cleaves the AP site and the nucleotide is removed
  • a nucleotide is added with the other strand as a template
  • DNA ligase covalently joins the nucleotides.
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23
Q

explain nucleotide excision repair

A

can be used to remove bulky pyrimidine dimers and stretches out damaged DNA.

  • the damaged strand is cut upstream and downstream of the damaged site.
  • new DNA is synthesized using undamaged strand as template
  • DNA ligase fills gaps
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24
Q

If the base pair AT experiences a transition mutation, what would the result be?

A

AT is replaced with GC

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25
Q

What can mistakes in DNA replication lead to? how does it happen?

A

insertions or deletions.

one strand can slip, creates a looped out nucleotide.

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26
Q

What strand slippage leads to insertions? deletions?

A

insertion- if new strand slips
deletion- if template strand slips
during replication

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27
Q

What are spontaneous lesions?

A

naturally occurring DNA damage

caused by depurination, could lead to random ntd replacement.

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28
Q

What does the deamination of a cytosine lead to?

A

uracil

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29
Q

what are mutagens what can they do

A

they cause DNA damage and can act by replacing, altering or damaging a base
they are an agent (chemical or radiation) that causes an increase in the rate of mutation

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30
Q

What are the 4 types of mutagens

A

base analogs, alkalating and intercalating agents, UV light and ionizing radiation

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31
Q

explain what alkylating agents and intercalating agents do

A

alkylating- transfer alkyl groups to DNA converting nitrogenous bases to unwanted chemicals
intercalating- create a wedge between base pairs

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32
Q

explain what ionizing radiation does

A

x rays result in oxidative DNA damage that can lead to mutations

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33
Q

what do restriction endonuclease enzymes do and how are they used

A

cleave phosphodiester bonds between nucleotides within a nucleic acid, they are used in recombinant DNA technology

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34
Q

where are restriction endonucleases seen naturally and what is their function

A

in bacteria, function is to protect bacteria from infection of bacteriophages

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35
Q

how do restriction endonucleases know what to do?

A

they recognize and bind to restriction sites in DNA and cleave at a specific location in that site.

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36
Q

explain what a staggered cut is

A

REs make staggered cuts when DNA fragments have hanging ends that are sticky

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37
Q

explain what a blunt end is

A

REs cut right in the middle of the restriction site where DNA strands do not have sticky ends

38
Q

what are DNA cloning vectors

A

DNA molecules that accept DNA fragments and replicate them in a host cell

39
Q

What are the requirements for a cloning vector

A
  • several common restriction sites
  • must be able to be introduced into a host cell
  • must have the ability to replicate independently or have a oric
  • must have a selectable marker (like an antibiotic resistant gene)
  • may have specific sequences that allow for sequencing inserted DNA
  • may have a gene that identifies host cells that carry recombinant plasmids
40
Q

List the steps to cloning a DNA fragment

A
  1. plasmid is removed from bacterial cells and cut with an RE vector, the DNA of interest is isolated and cut with the same RE in order to create compatible sticky ends
  2. DNA fragments are added together along with DNA ligase to form a recombinant DNA
  3. Ligation mixture is introduced into host cells by transformation
  4. transformants (bacterial cells that took up the plasmid) are identified by growing on selective medium
41
Q

Explain blue to white screening

A

allows for the identification and selection of recombinant plasmids.
when lac z and beta galactosidase cleave to x gal a blue color is created

41
Q

Explain blue to white screening

A

allows for the identification and selection of recombinant plasmids.
when lac z and beta galactosidase cleave to x gal a blue color is created

42
Q

what is needed for a blue to white screening to work

A

intact lac z gene and at least 1 restriction site

43
Q

what are the possible outcomes of the blue to white screening test

A
  1. if insert is not ligated into lac z gene, the multiple cloning site will H bond back together resulting in blue colonies
  2. if insert is ligated into the lac z gene, the reading frame of the plasmid is interrupted producing a different protein other than beta galactosidase, results in white colonies
44
Q

What are the possible methods of testing if your plasmid took the clone gene

A

PCR
sequence the plasmid
white to blue screening

45
Q

What are DNA libraries and how are they constructed

A

constructed from many overlapping fragments of the genome.
the genomic DNA (gDNA) is extracted from cells and cut randomly with REs to break into fragments
the overlapping fragments are inserted individually into cloning vectors
it is a collection of recombinant DNA containing bacteria representing the entire genome

46
Q

Explain how reverse transcriptase is used to produce cDNA libraries

A

mRNA is extracted from cells and oligo(dT) primer is added
reverse transcriptase synthesizes complementary DNA (cDNA) strand, resulting in ds RNA/DNA hybrid
RNA in the hybrid is partially digested with RNAase
DNA polymerase I synthesizes a 2nd DNA stand
DNA ligase joins the gaps

47
Q

what is PCR

A

polymerase chain reaction- a method for amplifying or copying target DNA sequences

48
Q

what is needed for PCR

A 
DNA target
polymerase (taq)
ligase
exo/endonucleases
primer-ssDNAs one for each strand, must be complementary to the opposite ends of the target sequence
nucleotides- dNTPs
mg-cofactor usually in buffer
49
Q

List the steps of PCR

A

a single run is of 25-30 cycles, each cycle has 3 steps: denaturation, annealing and extension
1st cycle: DNA denatured at 95C
temp lowered to 55-65- allowing primers to anneal to complementary DNA sequences on template strands. temp raised 72C to allow taq pol to extend primers, synthesizes complements to template
end of 3rd cycle:
2 copies of target sequence created, 6 are longer, longer products will get diluted out.

50
Q

why can taq polymerase withstand the heat in PCR

A

it is from archea bacteria that live in hot springs, it is very heat resistant

51
Q

what is electrophoresis

A

a separation method that separates biological molecules by their sizes by migrating them through a stationary medium under the influence of an electric field

52
Q

what is the role of the medium agarose in electrophoresis

A

it is a polymer that provides resistance to mol movement

53
Q

List the steps of electrophoresis

A

DNA sample is loaded into the well
electrical current is applied
DNA migrates towards + anode
visualize with gel red to see how far DNA travelled

54
Q

List the steps of nucleic acid hybridization

A
  • NA in a sample separated by electrophoresis
  • NA is denatured to prepare for hybridization as gel is running
  • NAs transferred from gel to NA binding membrane
  • membrane probed with an ssDNA dinucleotide
  • the bound probe is detached
55
Q

What charge to nucleic acids have

A

negative charge

56
Q

what information can we learn from NA hybridization

A

if the NA is present (band or no band)
how large is the NA (how far did the band travel)
about how much of the NA is present (how thick is the band)

57
Q

what is the difference between DNA sequencing by chain termination and PCR

A

only one of the 2 strands is sequenced in chain termination, only one primer is needed

58
Q

what is the effect a dideoxynucleotide has on transcription?

A

it stops it because it has an H where the OH should be, DNA polymerase cant go past it

59
Q

explain the steps of gene sequencing by chain termination

A

1- dNTPs and a small amount of ddNTP, primer, DNA polymerase and the DNA template strand are all placed together. each ddNTP has a different fluorescent color
2- synthesis starts mostly with normal dNTP but when ddNTP is inserted, the replication terminates
3-fragments are separated by capillary gel electrophoresis
4-fluorescence if the ddNTP terminating each strand is detected and a sequence is generated

60
Q

Explain how third generation sequencing works

A

DNA pol located in a nanopore anchored to a solid substrate binds a ssDNA mol to be sequenced
DNA pol adds a tag to synthesize DNA
tag is cleared off each base and is added to the DNA strand

61
Q

What is a knockout organism

A

an organism where a single gene has been “deleted” only possible with non essential genes

62
Q

how are knockout organisms created

A

a targeting vector containing a mutated version of the gene of interest is transformed into embryonic stem cells growing in a culture.
homologous recombination in the embryonic cell replaces the gene of interest with the mutant
recombinant ES cells are then selected and microinjected into an embryo in the blastocyst stage.
embryos are implanted into surrogate
surrogate gives birth to chimeric offspring (some KO stem cells some normal)
chimeric animal is bred to generate homozygous KO animal

63
Q

what does CRISPR-Cas stand for

A

clustered regularly interspersed short panel repeat sequences- cas is a protein

64
Q

what is a CRISPR locus

A

consists of clustered repeats with non repetitive spacer sequences

65
Q

where do spacer sequences come from in CRISPR

A

derived from portions of an invading genome from a prior invasion

66
Q

Explain how CRISPR can edit a genome sequence

A

cas 9 is introduced into target cell along with ss guide RNA complementary to the genomic sequence.
cas 9 generates double stranded DNA break, the break is repaired and an insertion or deletion is generated.

67
Q

what is genetic engineering

A

alteration of a cell/ organism genome

68
Q

what is a genetically modified organism

A

carries a gene transferred from another species and is expressed to produce a protein product.

69
Q

what is biotechnology

A

a use of biological organisms (or their cells/ molecules) to create a product or process that is useful to humans

70
Q

explain how biotechnology can be used in agriculture

A

transgenic crops are created to resist herbicides and pests or can be nutritionally enhanced

71
Q

explain how genetically modified animals are used in biotechnology

A

to study gene function, serve as animal models in human disease. can also be genetically altered to resist disease when the animal is used in food production

72
Q

how are pharmaceutical products a part of biotechnology

A

therapeutic proteins are used to treat diseases like insulin

73
Q

What is RFLP

A

restriction fragment length polymorphism are variations in the length of DNA fragments produced by restriction endonucleases

74
Q

what is population genetics

A

it analyzes the amount and distribution of genetic variation amoung individuals in populations

75
Q

what is a population

A

a group of individuals of the same species that live in a defined area and can breed

76
Q

what factors can cause variation in population genetics

A

single nucleotide polymorphisms

microsatellites

77
Q

what are SNPs

A

single nucleotide polymorphisms, differences in nucleotide pairs present at a single site in the genomes of 2 or more naturally occurring individuals

78
Q

how common are SNPs in humans

A

1 in 500 to 1000 bps

79
Q

what are microsatellites

A

repeats of a short sequence motif (2-6 bps long) sequence is repeated a certain number of times

80
Q

how common are microsatellites in the human genome

A

very, there are more than 1 million

81
Q

where is it possible to find microsatellites

A

anywhere in the genome, could be introns, exons, caps or tails

82
Q

how can satellites be analyzed

A

through PCR to determine the number of repeas present, the higher up the bigger the molecule the more repeats

83
Q

how is variation measured

A

genotype frequency allele frequency using the hardy wienburg law

84
Q

what are the conditions for the hardy weinberg law to apply, what is the term for this

A

large random mating populations in the absence of evolutionary forces, hardy wienberg equilibrium

85
Q

what factors influence changes in allele frequencies

A 
non-random mating (inbreeding)
natural selection 
mutation
migration 
genetic drift
genetic bottleneck effect
86
Q

what is genetic drift

A

a small number of individuals originate from a new population of species

87
Q

what is the genetic bottleneck effect

A

a large number of population undergoes drastic temporary reduction in numbers

88
Q

what is gene therapy

A

the use of genes as therapeutic agents to cure disease or alleviate symptoms

89
Q

what was the 1st genetic disease treated with gene therapy

A

SCID severe combined immunodeficiency disease, no functional T cells generated in body
setback was cancer in many patients

Genetics (8 decks)

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