Biol 311 Flashcards
What are the three causes of SNP
Spontaneous (rare)
Tautomerization or ionization
Induced chemical changes to the nuc
What is tautomerization?
The chemical change to a base, tracking the oil to add an alternative bade pair as hydrogen bonding is achieved
What are the 2 main forms of tautomers?
Keto and Enol
Enol forms are transitional
What is ionization
When the hydrogen/ exchange bonding of a molecule changes, porting the pairing of the wrong base pair
What are the three spontaneous mechanisms for SNP
Depurination
Deameation
Oxidative stress
Depurination
When the nitrogenous vase is removed from the nucleotide. The phosphodiser bind remains
Transcription is blocked
Deamination
The hydrolytic removal of the amine group of A C and G
Oxidative street
The presence of radical oxygen groups which bind to the nitrogen base causes the development of aromatic metabolism. Transcription is blocked
what type of bond strings AA together?
peptide bonds between the (5”)Nitrogen terminus and the (3”)Carboxyl terminus
what kind of cond is found on tRNA
anticodon, which is comp to the codon sequcen of the mRNA template
what is the ribosome comprised of and what are the different sections inside it
1/3 protein
2/3 rRNA
A P and E sites
how do the ribosome attach to mRNA
prokary: shine-dalgarno sequce
Eukary: kozak seq
synonymous mutations
a silent mutations which will cod for the same AA
nonsynonymous mutations
conservative or non-conservative
C= similar AA is encoded for (shares the same polarity)
NC= non similar AA coded for (different polarity)
what are the 4 types of mutations and when to these terms apply
silent/ synonymous
NS= conservative or nonconservative
deleterious
indels
these terms will only apply when these mutations occur in the exon.
what is referred to when a mutation occurs in the intron
an SNP
where does an intron start and end
start with GU and end with AG
what is found in the regulatory region? what does this region work to accomplish?
the enhancer and the promoter
works to establish a binding site for transcription factors and elements to initiate transcription.
what happens if the regulatory region is mutated
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
what is a sigma factor
a 5 subunit complex which positions RNA pol onto the DNA
in prokaryotes
how is transcription stopped in prokaryotes
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.
where do activators bind? where do repressors bind? where does RNA pol bind
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
role of allosteric effectors
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
what is an operon
linked genes which function under the control of a single operator
what are structural genes
genes that encode for proteins
transacting vs cisacting
affect the gene expression of distant genes
cis: are only able to affect the impact of nearby genes
what is a merozygote
a partial diploid where bacterial contains its vector and an insert of select genes (F’ plasmid)
what dies the cAMP CAp complex do and where does it attach?
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
how do glucose lvl impact cAMP
high glucose = low cAMP and low transcription
low glucose = high cAMP = high transcriptions
what is a co regulator?
proteins which can make a bridged interaction between transcription factors and RAN pol
these do not directly bind to DNA
what are the required sections for trasncription factors
DNA binding domain and activation/repression domain
what is the role of GAL 4, where does it bind
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
what is the role of GAL 3
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
what is the role of GAL 80?
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.
what is a histone octomer
a group of 8, positively charged proteins that DNA winds around to become compact.
what are the core proteins of a histone?
H2A and H2B H3 and H4
what are the 2 types of chromatin
facultative and constitutive chromatin
which type of chromatin is consistently transcriptionally active.
euchromatin, its more open and RNA pol is better able to access it
how do we alter chromatin
chromatin modification which can include histone modification(acetylation) or DNA modification.
what is the outcome of histone acetylation
the addition of an acetyl group on an AA causes increased transcritopn rates and chromatin compaction is reduced
what are the 2 effects of histone acetylation?
opening/loosening the interaction between DNA and histones
formation of an additional binding site called bromodomain
what does the addition of the bromodomain do?
acts as an additional binding site (co-activator) for transcription factors
it recruits other components
where are CpG islands found?
in the promoter
what are Unmethylated CpG islands?
clusters of unmethylated C and G which are associated with open chromatin and active transcription.
what is DNA methylation what protein does this
the addition of a methyl group; to an AA performed by HMT
what happens when methylation or histone modification occurs? when can this occur?
epigenetic inheritance, where the original DNA sequence is unaltered but impacts the phenotype of the organism
when a C comes before a G
how does epigenetics impact the germ line cells
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.
what does it mean to be maternally imprinted?
when the mother’s genes are silenced due to methylation while the father’s genes are active.
genes expressed are only from the father
what do methylated CpG islands do?
prevent the binding of the transcription factors and created a binding site fr HDAC
what are restriction sites
areas of DNA sequences that will be cleaved by specific endonucleases to create sticky ends(most of the time)
palindromic
when the restiction site sequence is read as the same on both strands (5’-3’)
what is DNA cloning
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
what are the essential factors in a vector that permit cloning
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
where will the promoter be found in a vector (an optional feature of DNA cloning)
upstream from the 5’ polylinker site
how is PCR performed
mature mRNA is converted into cDNA which then undergoes replication and the amount of the desired region/ gene grows exponentially
what happens of we want to insert a specific DNA region into a vector that lacks a cut site?
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
homeotic mutants
where one body part is mutated to resemble another
morphogen
a molecules whies effects are concentration dependant
what does the genetic toolkit do
regulate animal development by encoding for cell signalling proteins and transcription factors which have down stream effects
what are the genes that establish the posterior and anterior axis
Nanos and bicoid respectively
what are the classes reposibsile for establishing the AP body axis
maternal effect genes
gap genes
pair-rule genes
segment polarity genes
hox genes
what are maternal effect genes
genes that are required during the early development stages. these genes are nanos and bicoid which encode for transcriptions factors that impact further development
what happens with the maturnal effect genes are hmo recessive? homom dom or hetero?
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
what determins the major body axis
maternal effect genes
What are segmentation genes and what do they do?
regulate the AP axis by establishing the number and organization of body segments
what do gap genes do? what happens of they are mutated?
they divided the org into large regions
if mutated large gaps will be missing the zygote will most likey be non viable
what do pair rule genes do? mutated?
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
segment polarity genes. and when they get mutated?
impacts the organization of the segment only. mutations lead to deformations is segment polarity
segment polarity genes. and when they get mutated?
impacts the organization of the segment only. mutations lead to deformations is a segment polarity
what are hox genes
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
how do hox genes work
they regulate the expression of genes as they produce DNA binding agents that active or repress body part formation
