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Biol 371 > Biol 311 > Flashcards

Biol 311 Flashcards

1
Q

What are the three causes of SNP

A

Spontaneous (rare)
Tautomerization or ionization
Induced chemical changes to the nuc

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2
Q

What is tautomerization?

A

The chemical change to a base, tracking the oil to add an alternative bade pair as hydrogen bonding is achieved

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3
Q

What are the 2 main forms of tautomers?

A

Keto and Enol
Enol forms are transitional

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4
Q

What is ionization

A

When the hydrogen/ exchange bonding of a molecule changes, porting the pairing of the wrong base pair

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5
Q

What are the three spontaneous mechanisms for SNP

A

Depurination
Deameation
Oxidative stress

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6
Q

Depurination

A

When the nitrogenous vase is removed from the nucleotide. The phosphodiser bind remains
Transcription is blocked

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7
Q

Deamination

A

The hydrolytic removal of the amine group of A C and G

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8
Q

Oxidative street

A

The presence of radical oxygen groups which bind to the nitrogen base causes the development of aromatic metabolism. Transcription is blocked

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9
Q

what type of bond strings AA together?

A

peptide bonds between the (5”)Nitrogen terminus and the (3”)Carboxyl terminus

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10
Q

what kind of cond is found on tRNA

A

anticodon, which is comp to the codon sequcen of the mRNA template

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11
Q

what is the ribosome comprised of and what are the different sections inside it

A

1/3 protein
2/3 rRNA
A P and E sites

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12
Q

how do the ribosome attach to mRNA

A

prokary: shine-dalgarno sequce
Eukary: kozak seq

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13
Q

synonymous mutations

A

a silent mutations which will cod for the same AA

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14
Q

nonsynonymous mutations

A

conservative or non-conservative
C= similar AA is encoded for (shares the same polarity)
NC= non similar AA coded for (different polarity)

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15
Q

what are the 4 types of mutations and when to these terms apply

A

silent/ synonymous
NS= conservative or nonconservative
deleterious
indels

these terms will only apply when these mutations occur in the exon.

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16
Q

what is referred to when a mutation occurs in the intron

A

an SNP

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17
Q

where does an intron start and end

A

start with GU and end with AG

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18
Q

what is found in the regulatory region? what does this region work to accomplish?

A

the enhancer and the promoter

works to establish a binding site for transcription factors and elements to initiate transcription.

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19
Q

what happens if the regulatory region is mutated

A

either binding factors for transcription are blocked and transcription is prevented

transcription is enhanced and protein lvl go up

transcription is reduced and protein lvl go down

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20
Q

what is a sigma factor

A

a 5 subunit complex which positions RNA pol onto the DNA
in prokaryotes

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21
Q

how is transcription stopped in prokaryotes

A

2 methods

1) factor in dependant; the transcription of a. C rich section followed by the A rich section. The transcribed C form a hairpin loop and the RNA pol falls off
2) Rho dependant: where the Rho protein will recognize an upcoming c-rich area and cleave the pol off.

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22
Q

where do activators bind? where do repressors bind? where does RNA pol bind

A

activators bind to the activator binding site, upstream of the protomer (brings RNA pol closer to the promoter)

repressors bind to the operator, blocking RNA pol from moving along DNA

pol binds to the promoter

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23
Q

role of allosteric effectors

A

these small molecules bind to the allosteric site and change the conformation of the protein (activator or the repressor) which will influence their ability to bind to their regions.

helps the cell respond to environmental al conditions

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24
Q

what is an operon

A

linked genes which function under the control of a single operator

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25
Q

what are structural genes

A

genes that encode for proteins

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26
Q

transacting vs cisacting

A

affect the gene expression of distant genes

cis: are only able to affect the impact of nearby genes

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27
Q

what is a merozygote

A

a partial diploid where bacterial contains its vector and an insert of select genes (F’ plasmid)

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28
Q

what dies the cAMP CAp complex do and where does it attach?

A

activates transcription, binds to the protomer

note cAMP is the allosteric effector that works to allow CAP to bind to the region on the promoter

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29
Q

how do glucose lvl impact cAMP

A

high glucose = low cAMP and low transcription
low glucose = high cAMP = high transcriptions

30
Q

what is a co regulator?

A

proteins which can make a bridged interaction between transcription factors and RAN pol
these do not directly bind to DNA

31
Q

what are the required sections for trasncription factors

A

DNA binding domain and activation/repression domain

32
Q

what is the role of GAL 4, where does it bind

A

GAL 4 is a transcription factor that operates on a positive system (involves and activator). signals for the recruitment of coregulators and RNA pol

binds to UAS (upstream activation sequences to initiate transcription)
note that it is always expressed

33
Q

what is the role of GAL 3

A

a regulatory factor that works like an allosteric molecule.

like with the lac operon, gal 3 will bind to gal and change its confirmation, allowing it to bind to GAL 80 and displace it from GAL 4, turning on transcription to metabolize galactose

note that the GAL system is not an operator

34
Q

what is the role of GAL 80?

A

GAL 80 is the repressor of GAL 4. it is always expressed and binds to the activator/inhibitor site to prevent transcription of the gal genes.

35
Q

what is a histone octomer

A

a group of 8, positively charged proteins that DNA winds around to become compact.

36
Q

what are the core proteins of a histone?

A

H2A and H2B H3 and H4

37
Q

what are the 2 types of chromatin

A

facultative and constitutive chromatin

38
Q

which type of chromatin is consistently transcriptionally active.

A

euchromatin, its more open and RNA pol is better able to access it

39
Q

how do we alter chromatin

A

chromatin modification which can include histone modification(acetylation) or DNA modification.

40
Q

what is the outcome of histone acetylation

A

the addition of an acetyl group on an AA causes increased transcritopn rates and chromatin compaction is reduced

41
Q

what are the 2 effects of histone acetylation?

A

opening/loosening the interaction between DNA and histones

formation of an additional binding site called bromodomain

42
Q

what does the addition of the bromodomain do?

A

acts as an additional binding site (co-activator) for transcription factors
it recruits other components

43
Q

where are CpG islands found?

A

in the promoter

44
Q

what are Unmethylated CpG islands?

A

clusters of unmethylated C and G which are associated with open chromatin and active transcription.

45
Q

what is DNA methylation what protein does this

A

the addition of a methyl group; to an AA performed by HMT

46
Q

what happens when methylation or histone modification occurs? when can this occur?

A

epigenetic inheritance, where the original DNA sequence is unaltered but impacts the phenotype of the organism

when a C comes before a G

47
Q

how does epigenetics impact the germ line cells

A

few genes are parent-of-origin-manner, meaning the growth and development of an embryo and are expressed as if there is only one in the cell. the genes inherited may either be active (unmethylated0 or inactive (methylated).

depending on what the embryo receives will direct its ability to develop.

48
Q

what does it mean to be maternally imprinted?

A

when the mother’s genes are silenced due to methylation while the father’s genes are active.

genes expressed are only from the father

49
Q

what do methylated CpG islands do?

A

prevent the binding of the transcription factors and created a binding site fr HDAC

50
Q

what are restriction sites

A

areas of DNA sequences that will be cleaved by specific endonucleases to create sticky ends(most of the time)

51
Q

palindromic

A

when the restiction site sequence is read as the same on both strands (5’-3’)

52
Q

what is DNA cloning

A

the combination of inserting DNA with a vector

-cDNA is extracted from an alternate cell and then inserted into a bacteria where the vector has been cut using restriction enzymes to make a new DNA

53
Q

what are the essential factors in a vector that permit cloning

A

Origin of replication
Polylinker (multiple cloning site so that restriction enzymes can cut the DNA to make that of which is coming in
Antibiotic resistance gene to only promote the replication of what is contained within the vector

54
Q

where will the promoter be found in a vector (an optional feature of DNA cloning)

A

upstream from the 5’ polylinker site

55
Q

how is PCR performed

A

mature mRNA is converted into cDNA which then undergoes replication and the amount of the desired region/ gene grows exponentially

56
Q

what happens of we want to insert a specific DNA region into a vector that lacks a cut site?

A

use PCR to amplify and isolate the region

use engineering techniques to attach the desired restriction sites onto the 5’ end as these ends will not impact the final outcome of the DNA

insert it into the vector that has been cut with the complimentary restriction enzymes

57
Q

homeotic mutants

A

where one body part is mutated to resemble another

58
Q

morphogen

A

a molecules whies effects are concentration dependant

59
Q

what does the genetic toolkit do

A

regulate animal development by encoding for cell signalling proteins and transcription factors which have down stream effects

60
Q

what are the genes that establish the posterior and anterior axis

A

Nanos and bicoid respectively

61
Q

what are the classes reposibsile for establishing the AP body axis

A

maternal effect genes
gap genes
pair-rule genes
segment polarity genes
hox genes

62
Q

what are maternal effect genes

A

genes that are required during the early development stages. these genes are nanos and bicoid which encode for transcriptions factors that impact further development

63
Q

what happens with the maturnal effect genes are hmo recessive? homom dom or hetero?

A

depend only on the mother genotype
at least 1 functional allele is needed for proper establishment of the AP axis (haplo sufficient)

if homo recess then all offspring with be mutant

64
Q

what determins the major body axis

A

maternal effect genes

65
Q

What are segmentation genes and what do they do?

A

regulate the AP axis by establishing the number and organization of body segments

66
Q

what do gap genes do? what happens of they are mutated?

A

they divided the org into large regions
if mutated large gaps will be missing the zygote will most likey be non viable

67
Q

what do pair rule genes do? mutated?

A

develop even numbered pair segments. a more narrow region than gap genes.
if one genes get muted, a specific kind of the segment pattern will be lost

68
Q

segment polarity genes. and when they get mutated?

A

impacts the organization of the segment only. mutations lead to deformations is segment polarity

69
Q

segment polarity genes. and when they get mutated?

A

impacts the organization of the segment only. mutations lead to deformations is a segment polarity

70
Q

what are hox genes

A

determines the identiy of a strucutre or segment where the order of the hox genes corresponds to the older of body regions
they are expressed in restricted regions

71
Q

how do hox genes work

A

they regulate the expression of genes as they produce DNA binding agents that active or repress body part formation

Biol 371 (4 decks)

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