Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Microbiology 301 > Exam 2 > Flashcards

Exam 2 Flashcards

lecture 8-14

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

what are merozygotes?

A

bacteria that are partially diploid when conjugation introduces different parts of the lac operon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are the three types of genetic transfer?

A

conjugation: transfer of DNA from one bacterium to another following direct cell-to cell contact through sex pilus, relaxosome initiates this transfer
transduction: transfer DNA between bacteria cells via a bacteriophage, lytic vs lysogenic
transformation: process by which a bacterium will take up extracellular DNA released by dead bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what is a palindromic sequence?

A

a sequence that when read in one direction is identical to its complementary sequence read in the same direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

how does reverse transcriptase PCR (RT-PCR) work?

A

reverse transcriptase copies the mRNA strand of interest into cDNA, the single-stranded cDNA is then used as template DNA for traditional PCR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

how does PCR work?

A

denaturation: DNA strands are denatured into single strands
annealing: strands are annealed and primers bind to either side of the template DNA strand
extension: DNA polymerase then copies the target sequence between the primers by adding dNTPS to the ends to build

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

how does the CRISPR-Cas system work?

A

acquisition: DNA entering cell is identified, processed and inserted into CRISPR array as a new spacer
expression: transcribed into a long CRISPR precursor RNA, cleaved by Cas proteins and processed into crRNAs which are complementary to the target sequence, crRNA combined with Cas protein to form an effector complex
interference: effector complex binds homologous foreign DNA by base pairing, Cas protein cuts the foreign DNA at the effector complex binding site (PAM)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

how does transformation work?

A

large fragment of DNA binds to the surface of a competent cell, extracellular nuclease cut the DNA into fragments, one segment is degraded and a single strand is transported into cell and aligns with homologous region on the bacterial chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

how does cloning a DNA fragment into a vector work?

A

first purify desired DNA and vector (plasmid), digest both with a restriction endonuclease to cleave out the target sequence, then mix the chromosomal DNA fragments with the digested vector and add DNA ligase to join them together, introduce the recombinant vector with chromosomal DNA into host
bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

how can you determine that your gene is transformed through cloning?

A

empty vector, transformation with gene, transformation with other part of genome, use either antibiotic resistance or amino acid synth to select

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

how does the Sanger method of DNA sequencing work?

A

uses DNA polymerase to copy a strand of DNA (between the two primers), but DNA synthesis is terminated at specific nucleotides by adding dideoxyribonucleotides (ddNTPs) (lack a 3’ hydroxyl group which allows new nucleotides to bond) to the reaction, the fluorescent protein on the ddNTP marks the base where the sequence stoped, this is repeated at every length

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what are some new sequencing techniques?

A

ion torrent/protein: when a new base is added a pyrophosphate (PPi) is given off as well as an H+, creates a more acidic solution which we can measure
Single Molecular Real Time (SMRT) Sequencing: fluorochromes are attached to a phosphate that is cleaved off the dNTPs and ends up in the pyrophosphate product rather than being added to the DNA strand, flash of light of a wavelength specific to each fluorochrome is emitted as each base is added
illumina sequencing: each base is fluorescently labeled, then recorded, and then another is labeled and repeat

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

how does restriction enzyme digestion work?

A

specific DNA sequences are cut using restriction endonuclease or other enzymes that recognize and bind specific DNA sequences and cleave at specific nucleotides, used to prepare DNA for cloning

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

how do southern blots work and what do they detect?

A

detect specific DNA sequences by using an electric current to move cut DNA sequences (by DNA endonucleause) through gel, smaller fragments will move faster through the membrane, these segments are then transferred onto a filter and exposed to a radio-labeled DNA probe that will bind to the gene of interest

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how do northern blots work and what do they detect?

A

detect specific RNA sequences by using a denaturing gel to break down the RNA and then use electrophoresis to separate them by size, a labeled DNA probe complementary to the RNA sequence of interest is then used to visualize it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

how do western blots work and what do they detect?

A

detect specific proteins by using gel electrophoresis to separate different proteins by molecular weight

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

how do you determine the sequence of primers that could be used to amplify a DNA sequence by PCR?

A

(DNA sequence runs 5’ to 3’)
first primer is the same as the first part of the sequence (5’ to 3’)
second primer is the complementary strand running the opposite way as the template strand (primer runs 5’ to 3’ starting at the 3’ end of the template strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

why were fluorescent proteins a revolutionary innovation as molecular tools?

A

they can be imaged in live tissues, they can be used to study the localization of other proteins in vivo, and they can be targeted to localize individual organelles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is polycistronic RNA?

A

an mRNA that encodes multiple protein prodcuts but its expression is still controlled by a single promotor and a single terminator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is an alternative name for F’ factors?

A

plasmids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what are the parts of the lac operon?

A

promoter: binds to RNA polymerase
CAP site: positive regulation site for catabolite activator protein (CAP), cis factor, CAP itself upregulates transcription
operator: negative regulation when bound by repressor protein, operator binding site is cis factor
protein-coding genes: lacZ, lacY, and lacA
terminator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what are the structural genes of the lac operon and what do they do?

A

lac Z: encodes B-galactosidase, cleaves lactose and lactose analogues, converts lactose into allolactose (small effector molecule)
lac Y: encodes lactose permease, membrane protein required for transport of lactose and analogues into the cell
lac A: encodes transacetylase, covalently modifies lactose and analogues, its functional necessity remains unclear

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what do inducers do?

A

bind to repressors, preventing them from binding to DNA or bind to activators and cause them to bind to DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what do repressors and activators do?

A

repressors inhibit transcription by binding to operator and blocking RNA polymerase from binding, negative control
activators increase transcription by binding near the promotor and facilitating RNA polymerase and general transcription factor interactions, positive control

24
Q

what do co-repressors and inhibitors do?

A

co-repressors bind to repressors and cause them to bind to DNA
inhibitors bind to activators and prevent them from binding to DNA

25
Q

what is attenuation?

A

when transcription starts but is stopped shortly after once the ribosome reaches the attenuator which prevents the ribosome from continuing transcription, since transcription and translation occur at the same time attenuation is used to keep too much tryptophan from being made

26
Q

what is the function of the CAP site, promotor, and operator on the lac operon?

A

CAP site: acts as positive regulation-site for catabolite activator protein (CAP) (when cAMP-CAP complex binds to the CAP site transcription rate increases)
promotor: binds RNA pol holoenzyme to start transcription
operator: acts as negative regulation when bound by repressor protein (the lacI gene product) (transcription rate decreases when repressor is bound to operator)

27
Q

what is the primary level at which genes are regulated in prokaryotes?

A

transcriptional

28
Q

what does the general transcription factor TFIID do?

A

binds to the TATA box and recruits RNA polymerase II to the core promotor to start transcription

29
Q

what does the mediator complex do?

A

mediates RNA polymerase II
and the regulatory transcription factors

30
Q

what do general transcription factors do in eukaryotes?

A

from the pre-initiation complex, provide a scaffold for RNA polymerase II to bind to, and bind to the TATA box

31
Q

euchromatin vs heterochromatin?

A

euchromatin is less condensed and contains active genes, heterochromatin is highly condensed and does not contain active genes

32
Q

what do CpG islands do?

A

recruit CpG binding proteins and can be either methylated or unmethylated (methylation results in activator proteins not binding to the methylated cytosine, inhibiting transcription)

33
Q

what are the steps of RNA interference?

A

processing of RNA transcript by Drosha and DGCR8, transport to cytoplasm, processing by Dicer, binding to RISC, binding to target mRNA

34
Q

what did Mello and Fire observe?

A

the lowest amount of mex-3 probe staining was in those injected with double-stranded RNA, suggesting that double-stranded RNA is more potent at silencing mRNA than is antisense RNA

35
Q

what are ribozymes?

A

RNA molecules with catalytic activity

36
Q

what does the TERC ncRNA do?

A

facilitates the binding of telomerase to the telomere and acts as a template for DNA replication

37
Q

what are the two ways in which chromatin modification by HOTAIR inhibits transcription?

A

through direct inhibition of RNA polymerase binding and through attraction of other chromatin-modifying enzymes

38
Q

what are piRNA sequences complimentary to?

A

mRNA from a transposable element

39
Q

what is the CRISPR-Cas system similar to?

A

the immune system

40
Q

transition vs transversion mutations

A

purine (A or G)
pyrimidine (C or T)
transition: pyrimidine to another pyrimidine or purine to another purine
transversion: pyrimidine to purine or vice versa

41
Q

neutral vs induced vs somatic vs spontaneous vs conditional vs germ-line mutations

A

neutral: don’t alter function
induced: caused by environmental agents
somatic: non-heritable mutations in cells other than gametes
spontaneous: occur naturally as a result of natural processes
conditional: affects phenotype only under specific conditions (temperature sensitive)
germ-line: heritable mutation in cells that give rise to gametes

42
Q

silent vs point vs mis-sense vs frameshift vs non-sense mutations

A

silent: alter codon but not amino acid encoded
point: single base pair change
mis-sense: change the amino acid sequence of proteins but never truncate them
frameshift: addition or deletion of nucleotides in multiples of one or two
non-sense: changes codon to a stop codon

43
Q

depurination vs deamination vs tautomeric shift

A

depurination: linkage between purines and deoxyribose break
deamination: cytosine and 5-methylcytosine deaminate to create uracil or thymine
tautomeric shift: a temporary change in the structure of a nitrogenous base

44
Q

what is the Ames test used to determine?

A

the mutagenicity of chemical compounds (how likely the compound is to induce a genetic mutation)

45
Q

proofreading vs photoreactivation repair vs nucleotide excision repair

A

proofreading: DNA polymerase detects base mismatches and fixes them
photoreactivation repair: photolyase splits thymine dimers restoring the DNA to original condition
nucleotide excision repair: removes and replaces pyrimidine dimers that were induced by UV light

46
Q

what are the most frequent types of mutations caused by the replication machinery?

A

small insertions/deletions of repeat sequences resulting from slippage (trinucleotide repeats)

47
Q

in drospophilia segmentation genes function in what order?

A

gap, pair rule, segment polarity

48
Q

what do homeotic selector genes do?

A

specify the development of specific body parts

49
Q

gap vs pair-rule vs segment polarity vs maternal effect genes in drosophilia

A

maternal effect: define the anterior and posterior ends
gap: responsible for dividing the embryo into the head, thorax, and abdominal regions of the adult
pair rule: divide segments into regions and defines segment borders
segment polarity: divide segments more and split into anterior and posterior halves

50
Q

what do HOX genes do in drosophilia?

A

once the segment positional information is established, homeotic genes (HOX) are expressed indicating what the segment will differentiate into, homeotic genes are activated as targets of the segmentation genes and determine the adult structures formed by each segment

51
Q

what are the epigenetic factors that help regulate gene expression?

A

DNA methylation, histone modifications, non-coding RNA expression, and chromatin structure

52
Q

what is transgenerational epigenetic inheritance?

A

inheritance of epigenetic changes across generations to descendant who had no direct exposure to an environmental agent

53
Q

what does natural selection act on?

A

phenotypic differences that come from genetic mutations or from epigenetic changes

54
Q

a male rat (therefore not pregnant) was exposed to an environmental toxin such as methyl mercury, in what generation of his descendants would one look for evidence of transgenerational epigenetic inheritance?

A

grand-offspring (F2 generation)

55
Q

what are the types of DNA repair on a single strand?

A

repair is activated when one strand is cleaved and uses the opposite strand for repair
base excision repair: N-glycosylases recognize abnormal base and cleave AP endonuclease cuts on 5’ side
nucleotide excision repair: UvrA, B, C, and D recognize and remove a short segment of damaged DNA, DNA polymerase and ligase finish the repair job

56
Q

what type of DNA repair fixes double stranded breaks?

A

repair is activated when both strands are cleaved, homologous recombination repair fixes double-strand breaks by using sister chromatid as the template to allow DNA polymerase to copy the undamaged sequence into the damage strand

57
Q

broadly outline the steps that you would expect a MicroRNA to go through from transcription to a functional complex

A

transcription of the RNA, folds into a hairpin, binds to exporter protein and is moved to the cytosol, cut by DICR to 20-25bp, and binds to RISC in a single strand complex

Microbiology 301 (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions