Cell Bio Exam 2 Questions
describe the structure of tRNA
"clover leaf" pattern=single stranded but folds back on itself to form double stranded regions
Franklin and Wilkins
(didn't get along) -wilkins stole franklins x-ray image of DNA structure and gave it to watson allowing him to discover double helix with bases facing in
whose DNA was sequenced by the two sequencing teams?
-1 team=government led prject used DNA from several people -2 team=privatley led project led by J Craig Ventor sequencing only one psersons DNA (probably his)
what percentage of the human genome is highly conserved?what are the implications of this?
-5% is highly conserved -this relfects the importance of these sequences compared to the majority of the genome as will can use them to track relatedness between organisms
what is CAP and what does it do?
-CAP is a bacterial activator protien that drives the production of enzymes that allows the bacterium to digest other sugars -in low glucose levels, there is a high concentration of cAMP which CAP binds to turning genes on to serve as another way to digest sugars
what happens to DNA during mitosis?
-DNA becomes compact (1000-fold); proteins coil and fold the DNA into higher and higher levels of organization -eukaryotic cell undergoes a carefully coordinated nuclear division that results in the formation of two genetically identical daughter cells. Mitosis itself consists of five active steps, or phases: prophase, prometaphase, metaphase, anaphase, and telophase
what is the different between proofreading abilities between DNA polymerase and primase?
-DNA polymerase: proofread as it synthesizes to minimize mistakes -Primase: doesnt proofread so primase makes a lot of mistakes
what is the difference between Li and Alu transposons?
-LI=encodes its own reverse transcriptase -Alu=doesnt encode its own transcriptase and depends on enzymes already present in the cell to help them move
what roles can RNA play that make an RNA world feasible?(5)
-RNA can store and transmit info -RNA can be structural -RNA can be catalytic -RNA can be used as a template fo it own reproduction -RNA is thought to pre date evolution
describe where RNA processing takes place and what it is.(3 steps)
-RNA processing takes place in the nucleolus -RNA processing is the steps eukaryotic RNA goes through before being exported out of the nucleous: 1)RNA capping=methyl guanine cap is added to 3' region by capping factor 2)polyadenylation=a poly AAA tail is added to the 3' region by polyadenylation factors 3)splicing=interviening introns are spliced out and exons are stiched together
what is conserved synteny and how can this be used to determine relatedness?
-conserved synteny is regions in DNA where genes are arranged in the same pattern between species -these patterns are used in comparative genomics to look at similarities between multiple genera to determine their evolutionary divergences and relatedness
what advantage does DNA have over RNA as a genetic material?(2)
-deoxyribose is more stable in the sugar phsophate backbone, so DNA can grow to greater lengths without breaking -DNA uses thyamine (not uracil) making it more stable and easier to repair
what determines the life span of mature mRNA in the cytoplasm? and what do lifespan differences do?
-differences in the nucleotide sequence of the mRNA itself -differences help the cell control how much protein will be produced
During meiosis homologous recombination also occurs, how is this different from the DNA repair mechanism/whats it called? how does this impact evolution?
-during meiosis homologous recombination occurs as chromosomal crossover which is when the chromosomes physically cross over and exchange genetic material -this is different in that it allows for genetic exchanges between maternal and paternal chromosomes which fuels evolution because it enhances the generation of genetic diversity through sexual reproduction
how does horizontal gene transfer take place? between what organisms?
-genes are exchanged between individuals of the same generation (between same or different species) -mostly occur among prokaryotes/bacteria (less common in eukarytoes)
what types of genes are predominatnly involved in human accelerated regions of the DNA? how does this account for human differences from other animals or neanderthals?
-genes predominantly involved in nueral development -it shows that we differ from them in how we think; we have accelerated nueral activity
what cells do not have a full set of homologous chromosomes?(3)
-germ cells -red blood cells -sex chromosomes
what did Selman Waksman win the nobel prize for and what did he define?
-he won the nobel prize for finding out that you can used antibiotics produced by microorganisms to deter the metabolism of another microorganism -he defined the term antibiotic
are histones modified covalently or noncovlaently? how does this affect gene expresssion?
-histones have long unstaturated fatty acid tails that stick out from nucelosome and are subject to reversable covalent chemical modifications to sontrol chromatin structure -the tails can act as molecular tags to attract other protiens for replication or transcription; these protiens can promote condensation or expansion of chromatin facilitating access to DNA which turns a gene on or off
what direction are DNA molecules replicated and why?
-in the 5'->3' direction because DNA poylmerase acts on the 3'-OH to add new nucleotides (nucleotides cant be added to the 5' end) -also, DNA polymerase can only proofread in the 3'->5' direction therefore DNA can only be synthesized in the 5'->3 direction
how can the loss or subsitution of a single base impact protien function? give an example of what it causes
-it can casue no H bonds to form between unmatched base pairs so the bases can snug up to each other changing the conformation and therefore function of a protien -it can cause mutations that have severe consequences for a cell/organisms (ex. sickle cell anemia)
what is the role of histone H1?
-it pulls adjacent nucleosomes together into a regular repeating array -it serves as a "linker" histone changes the path DNA takes as it exits the nucleosome care allowing it to form a more condensed chromatin fiber
what are the roles of the large and small subunits of the ribosome?
-large=catalyze the formation of the peptide bonds that contently link the amino acids togehter into a polypeptide chain -small=matches the tRNAs to the codons of the mRNA
what are the active site on the ribosome? and what happens at each?
-mRNA binding site=where ribsosme and mRNA stand bind -A site(Amino acid site)=where a charged tRNA is brought into carrying an amino acid -P site (Peptide chain site)= holds peptide chain in place while amino acids are added -E site(Exits site)=the site where the used up tRNA exits
what types of problems can trinucleotide repeats cause? do they doe this all the time and if not, when?
-metabolic disorders such as huntingtons disease -yes all organisms have some number of these but only once a certain threshold of them is crossed is when it casues issues
what is the major difference between prokaryotic and eukaryotic translation?
-prokaryotic= translation is coontinuous with transcription and occur at the same time in the cytoplasm -eukaryotic=transcription and translation occur at different times and is discontinusous (transcription in nucleus and translation in cytoplasm
What are housekeeping proteins? and when and what types of cells are they expressed?
-protiens that are always being expressed and therefore the gene is always on -expressed in all cells for glycolysis, DNA repair, and protein synthesis
what are the regualting DNA sequences?where are they located in prokaryotic and eukaryotic cells?
-protiens that serve as swtiches allowing cells to respond to external environment -prokaryotes=upstream close to the promoter eukaryotes=can be thousand of nucleotides away from the promoter up or downstream
what are the roles of transcription factors?(2)
-pulls apart the DNA double helix to expose template strand allowing polymerase to begin transcritpion -controls governing gene expression
what are the two types of DNA transposons?
-replicative transposon=cut and paste (LI) -non-replicative transposon= copy and paste (Alu)
What gene in particular is examined to determine relatedness? What did this show about the relatedness of humans, bacteria and archaea? Where does most of the genetic diversity in life exist?
-ribosomal RNA of the small ribosomal subunit becasue translation is fundamental to all living cells therefore this component of ribosomes is highly conserved -shows tha archaea are as different from bacteria as bacteria are from eukaryotes -most genetic diversity is between microbes
what type of repeat can be used for genomic fingerprinting? how?
-short tandem repeats (CACACA) -these repeats cause DNA polymerase to studder/slip making more or less repeats in the new synthesized DNA than there should be and we observe these differences in repeats between different people to give them a "genetic fingerprint" identifying them
Explain the difference between the coding and the template strand of DNA. Which strand is which?
-template=anitsense strand that contains the anticodons used to guide the synthesis of RNA -coding=sense strand that has the codons sequence that is read to make the RNA product
how does the chemical nature of the backbone of the DNA strand and the specific amino acids of the histone's interact?
-the 4 histones that make up the histone octamer have a high proportion of positively charged amino acids (lysine and arginine), the positive charge helps the histones bind tightly to the negatively charged sugar phosphate backbone of DNA
where is the anticodon on tRNA and where does the amino acid bind?
-the anticodon is int he middle but due to folding pattern, it is displayed outwardly to bind with the codon -the amino acid binds to the end of the tRNA opposite the anticodon on the 3' end
Describe the globin gene family and how it came about and why its important
-the globin gene family enode oxygen carrying protiens that arose from a single primordial gene through gene duplication and divergence -this is why inverts have single globin protiens while higher vertebrates have complex globin protiens -this is important because its what allows mammals to be able to give live birth
What role can mobile genetic elements play in evolution? How can they impact exon arrangements?
-they cause spontaneous mutations which accelerate the rate of evolution -they impact exon arrangement by disrupting gene activity if their in a coding region
how to chromosomes keep from getting tangled in the nucleus?
-they each occupy thier own "space" and are organized in the nucleus -the chromosomes are attached to the membrane of the nucleus to avoid breaking/tangling (like a bowl of spaghetti) (exception: genes encoding rRNA cluster in the nucleolus)
why do cells break down protiens after going to the trouble of making them? (2)
-to regulate the amount of protien in the cell -sometimes protiens are misfolded and need to be gotten rid of -when they only serve one function that has already been complete
how do retro transposons jump? (3)
-via an RNA intermediate and reverse transcriptase 1) transposable element transcribed into RNA intermediate 2)dsDNA copy is synthsized fron it by reverse trancriptase 3)the DNA copy is intserted into target location
what do humans have to do with horizontal gene transfer? (2)
-we facilitate horizontal gene transfer by taking and not finishing antibiotics resulting in an environemtn that facilitates hortizonal gene transfer -we also can creat horizontal gene transfer in a labs setting using gnetic engineering to make transgenetic organisms
what is the strongest incidence of gene silencing?
-when heterochromatin is so compact that the genes in it fail to be expressed/heterochromatin keeps genes shut down -found in the interphase X chromosomes of female mammals (X-inactivation)
what is the complexity of the smallest virus?
...not very complexni suppose...
how many primers are needed for the leading strand?
1 because it only needs initial priming because the lagging strand grows continuously
describe the 4 conditions in which the lac operon is on or off. explain why each condition occurs
1) +glucose and +lactose = OFF -glucose is present so cAMP is in low concentrations so it doesnt bind to CAP to bind and operon is off 2) +glucose and -lactose = OFF -lactose is absent so lac repressor is binds turning it off 3) -glucose and -lactose = OFF -glucose is absent so cAMP is present and binds to CAP, but is stopped by the lac repressor because lactose is absent 4) -glucose and +lactose = ON -glucose is absent so high levels of cAMP bind to CAP turning operon on and since lactose is present, the repressor isnt there to stop it and mRNA is made
what are the 6 main mechanisms for genomic evolution?
1) mutations within a gene 2) mutations in regulatory DNA 3)gene duplication and divergence 4)exon shufling 5)transposition 6)horizontal gene transfer (MMGETH= More Monkeys Get Extra Tickles Happily)
How does DNA mismatch repair work? (3)
1) the mismatch repair system makes a nick near a mismatched base pair 2) a segment of the DNA is looped and cut out by nucleases 4)DNA polymerase fills the gap with the original DNA sequence from parent strand 3)DNA ligase seals the nicks in the backbone
how do changes in RNA configuration impact gene expression? (2 ways)
1)Blocking risbosome binding sequence: RNA binding proteins can repress translation of specific mRNAs by keeping the ribosome from binding to the ribosome 2)Exposing ribosome binding sequence: increase in temp causes base pairs in mRNA to come apart exposing the ribosome binding sequence
describe the process by which microRNA's control gene expression (4)
1)RISC binds with microRNA 2)RISC used microRNA sequence to find matching mRNA fragments 2)Nuclease (RISC protien) digest mRNA then its free to do it again 3)RISC RNA can bind to multiple genes if matching sequence is there
homologous recombination takes place during meiosis but can also repair breaks during replication. how does it do this?
1)a NUCLEASE chews back the 5' end of the 2 broken strands at the break 2)with the help of enzymes, one of the 3' broken ends INVADES the unbroken homologous DNA creating a BRANCH POINT and finds a complementary base bair sequence 3)the invading strand is elongated using the complementary undamaged strand as a template 4)BRANCH POINT MIGRATION occurs during elongation and after passing the point where the brak occurs, the newly elongate strand joins back with its original partner 5)LIGATION occurs sealing any holes resulting in 2 intact DNA strands
desribe the steps of translation (7)
1)charged tRNA binds to small subunit at P site 2)initiation factors bind to the small subunit 3)ribosome moves along mRNA looking for start codon 4)once found, large subunit binds, inititaion factors fall off and translation begins 5)protiens fold as peptide chain moves out of E site 6)stop codon is reached and release factors bind to ribosome freeing the polypeptide chain 7)ribosomal subunits dissociates
What happens to the DNA during interphase? (2 steps)
1)chromosomes are extended as long, thin, tangled threads of DNA in nucleus 2)DNA replication takes place and prepares for mitosis
what are the three common types of mutations? and what causes each? describe each one and how it affects DNA/DNA replication?
1)depurination: -is caused by thermal collision with other molecules -removes a purine base (but doesnt break phosphodiester backbone) creating a missing base pair/ "missing teeth" 2)deamination: -happens sponateously -loss of an amino acid group fro a cytosine to produce a uracil which changes the DNA sequence casuing mustations 3)thyamine dimer: -caused by UV radiation -when 2 thyamines bind to each other casuing stalls in replication because it blocks DNA polymerase and makes it fall off prematurely so the rest of the strand isnt synthesiszed
what is the basic pathway for DNA repair? (3 steps)
1)excision: damgae is cut out but specialized nucleases 2)resynthesis: original DNA sequence is restored by repair DNA polymerase with fills the gap made during excision using the original strand as a template 3)ligation: DNA ligase seals the nick left in the backbone of the repaired strand using ATP/ATP hydrolysis
describe the major steps in eukaryotic trancrisption (6)
1)general transcription factors recognize and allow DNA polymerase to bind to TATA box initiating transcription 2)TFIIH phosphorylates RNA polymerase triggering a conformational change that allows transcriptional factors to fall off and capping, polyadenylation, and splicing factors to bind 3)capping factor adds 3' methyl guanine cap 4)polyadenylation factor adds 5' poly A tail 5) splicing factors take out introns and links exons 6)mature eukaryotic mRNA is selectively exported out of nucleus through nuclear pores
what are the 2 hypothesis of when introns came to be in eukaryotes and not prokarytoes?
1)introns were originally present in prokarytoes but then lost over time which explains why they can reproduce more rapidly and efficiently 2)introns are parasitic mobile genetic elements that invaded and early eukaryotic ancestor colonizing its genome and the stow away nulceotide sequence as was replicated alongside their own
what are the 4 major types of RNA and what does each do?
1)messenger RNA (mRNA)= codes for protiens 2)ribosomal RNA (rRNA)= forms the core of ribosomes 3)transfer RNA (tRNA)= transports animo acids to growing polypeptide chain 4)micro RNA (miRNA)=regulates gene expression
what are the 4 major differences between prokaryotic and eukarotic transcription?
1)prokaryotes use a single type of RNA polymerase while eukaryotes use 3 (RNAPI, RNAPII, RNAPIII) 2)prokaryotic RNA polymerase can inititate transcription on its own while eukaryotic is helped by acessory proteins 3)eukaryotic transcription initiation mechanisms are more complex because eukaryotic DNA is larger 4)Eukaryotic transcription inititiation has to deal with the packing of DNA into nucleosomes and higher chromatin structure
1)what molecules make up a ribosome and what are thier roles? 2)how many of each molecules are there?
1)ribosome is made up of two subunits that contain: -dozens of small ribosomal protiens which are used for stabilization -several ribosomal RNAs (rRNA) that are responsible for the ribosome structure and catalyze the formation of the polypeptide 2)-large subunit=49 ribosomal subunits and 3 rRNA -small subunit=33 ribosomal subunits and 1 rRNA
what are the 4 major steps in prokaryote transcription?
1)sigma factor recognizes promoter allowing RNA polymerase to bind to it 2)transcription begins, sigma factor is released, and RNA polymerase chugs down the DNA mkaing RNA 3)elongation continues until terminator is reached 4)RNA polymerase dissociates releasing the newly made RNA transcript
How does the banding pattern seen in karyotypes formed? (three steps)
1)take cell just as its getting ready to divide 2)isolate chromosomes 3)stain them using Giesma stain which produces dark bands in AT rich regions
what are the 6 steps where control of protien expression can be seen?
1)transcriptional control 2)RNA processing control 3)mRNA transport and localization control 4)mRNA degredation control 5)translational control 6)protien degredation control (TRMMTP=Tall Rapids Make Many Turtles Plummet)
What percentage of the human genome is involed in exons and regulatory sequences?
1.5% (less than 2%)
how many base pairs per turn of DNA are there?
10
how many coding region for genes are known in the DNA?
19,000 (up to 38,000)
which base location having a point mutation would result in a change in the protien sequence?
1st and 2nd are more liekly to cause a change in protien sequence
how many strands are in dna?
2 complementary chains of nueclotides
how many RNA polymerases do eukaryotic cells have?
3 (RNAPI, RNAPII, RNAPIII)
in what direction does DNA polymerase proofread?
3'->5'
what percent of human genes undergoe alternative splicing?
95%
what type of nucleotides are seen at replication origins and why?
AT rich regions because the bond between adenin and thyamine is only a double bond (not a triple like C->G) therefore 2 bonds is easier to break that 3 to begin repliaction
give an example of gene duplication and how it aided in the development of a new gene family
Bacillus subtilis=nearly half of the genes have 1 or more obvious relatives elsewhere in the genome
what are the major differences between DNA(4) and RNA (6)poylmerase?
DNA polymerase: -travels 5'->3' -makes DNA -copies pre-existing strands/templates -requires help of other protiens RNA polymerase: -travels 3'->5' -makes RNA -makes its own strand -doesnt need help from other protiens/self capable -doesnt have primers -uses general transcription factors
why is it so critical for DNA to have high fidelity?
DNA remains unchanged over many generations because harmful DNA changes are weeded out by natural selection while good ones persists; this is critical because it prevents disastrous events like cancer and stops bad diseases from developing and being passed on
what are the 3 difference between DNA and RNA?
DNA: -uses deoxyribonucleic acids (lacks oxygen) -uses thyamine base (not uracil) -double stranded RNA: -used ribonucleic acids (has oxygen/-OH group) -uses uracil instead of thyamine -usually single stranded
in what direction does transcription take place with respect to the DNA strand? respect to the chromsome?
DNA: 5'->3' chromosome: bidirectional
Watson and Crick
Determined the structure of DNA
how does directionality of DNA synthesis play into the proofreading of DNA polymerase?
If DNA were not synthesized in 5'->3' direction and proofreading occurred, then DNA polymerase would create a chemical dead end because it woul dbe profreading in the 5'->3' direction the last nucleotide would have a phosphate group which stops incoming nucleotides with phosphate groups from being able to attach to the chain, therefore DNA has to be synthesized from 5'->3' or else proofreading would not work
how does RNA interference work (4 steps) and what does it work against?
RNAI: defense mechanism to destroy foreign RNA 1)foreign dsRNA is cleaved by DICER to make siRNA fragments 2)siRNA fragments binds with RISC protiens to make RISC 3)RISC locates and destroys foreign RNAs with complementary sequence 4)RISC released to go degrade more
how can the mechanisms of RNA inerference be used to understand protien function?
RNAi can be used to study genes and proteins because it can turn off a gene in culture or in an organism and we can observe the affects of this to solidify understanding of what a specific of genes controls
What is a riboswitch?
RNAs that can regulate their own expression by containing regions that bind to signaling moecules
there are 20 amino acid and 64 possible codons, explain how this works
This is the Wobble Theory/Codon Redundancy= codons can differ in their 3rd base position and still code for the same amino acid, therefore there are more possible codons than amino acids
how can RNAi be used to treat a disease?
We can used it by turning off a gene to prevent overproduction of a substance created by a disorder or disease
what do the average transposons code for?
a specialized enzyme called transposae that mediates a transposons movement by recognizing the 'cut here' signals at the end of each transposon
How can a small number of regulators generate multiple cell types during development?
after each round of cell division a regualtory protien in added to one cell and this occurs over and over until many different daughter cells are made
which base location having a point change mutation would affect the amount of protien being produced?
all three because they can create an earlier or later stop or start codon which changes the length of the coding region and thus the protien as well
how and why do many antibiotics target protien synthesis?
antibiotics explaoit small differences between eukaryotic and prokaryotic ribosomes so that they interferen with bacterial protien synthesis killing bacteria without being toxic to humans
Is DNA parallel or antiparallel?
antiparallel
what direction are chromosomes replicated?
bidirectional
how does DNA polymerase stop itself from making as many mistakes?
by proofreading itself and going back and correcting mismatched bases
how does a ribosome know where and when to start and stop translation?
by recognizing specific start and stop codons in the mRNA sequence: -start=AUG which codes for methionine -stop=UAA, UGA, UAG
are viral genomes DNA or RNA? single stranded or double stranded?
can be DNA or RNA and can be double or single stranded (very variable!)
how does epigenetic inheritance take place on the DNA level?
changes are imposed on the chromosome that dont involve changes to the genetic code/DNA sequence
what type of cancer is affected by DNA mismatch repair?
colon cancer
Melson and Stahl
determined the nature of DNA replication was semi-conservative
do all cells respond to the same signals? and do they respond in the same way? why or why not?
different specialized cell types respond in different ways to extracellular signals which is what allows each cell to have distinctive characters that allow whole organisms to function (ex. liver cell responds differently to cortisol than a nerve cell would); if this didnt occur them organisms would not survive
Barbara McClintock
discovered mobile genetic elements by experimenting with raising and examining corn (although people didnt believe her for a long time because she was so old)
describe the concept of semi-conservative replication?
each parent stand serves as a template for the synthesis of a new daughter strand, this creates an end product of 2 complete strands that are identical to the starting strand(produces 2 copies that each combine one of the original strands with one new strand)
waht role does chromosomal structure, organization, and monidifcation play in transcriptional regualtion?
eukaryotes compact and arrange theri chrommasomes in mutiple levels (histone->nuleosome->30nm fiber->chromosmes) which not only permits a large amount of DNA to occupy a very small space, but also serves functional roles influencing gene expression
what are the 2 differences between the eukaryote and prokaryote genome?
eukaryotes: -dipliod with multiple linear chromosomes -have homologous chromosomes prokaryotes: -haploid with a single circular chromosome found in the nucleiod
How does exon duplication or shuffling impact proteins?
eukaryotic genes contain exons surrounded by introns and exon shuffling allows exons from one gene to be added to another which facilitates the evolution of new protiens
what is the difference between eukaryotic and prokaryotic transpsons?
eukaryotic=transposons use an RNA intermediate prokaryotic= do not use an RNA intermediate (DNA ONLY)
how many primers are needed for the lagging strand?
every okazaki fragment needs its own primer because the lagging strand grows discontinuously and new primers are continusuously needed to keep polymerization going
Avery, MacLeod, McCarty
experimented with mice injecting S strain and showed that DNA is the genetic carrying material
Griffith
experimented with mice injecting them with S. pnemoniae and showed that bacteria change through transformations(discovered bacterial transformation)
Hershey and Chase
experimented with viruses and e coli and proved that DNA is the genetic carrying material
Meischer
first person to identify DNA (1986) when discovered by acident when trying to isolate protiens from blood cells and expereincing DNA contaminations
what evolutionary advantage can gene duplication lead to?
gene duplication and divergence gives rise to whole new families of genes/new genes!
what types of genes are highly conserved? give example
genes in coding regions that when removed or changed could be lethal (ex. ribosomal RNAs)
which cell types can pass along a change in their DNA?
germ cells
what impact can a mutation have in a germ cell?
germline mutations affect every cell in an organism and are passed on to offspring (are hereditary)
what role did Nirenburg play in understanding translation?
he discovered that RNA fragments 3 nucleotides long (codons) could bind to a ribsosome and attaact the appropriate amino acid containing tRNA molecule
what percent of DNA is highly conserved vs slightly conserved? and what percent codes for protiens? how do these numbers related
highly conserved=4.5% slightly conserved=5% protiens=2% of the conserved (the other 3% we dont know what it does) *this tells us that only about 10% of the human genome truely matters*
what are the most abundant chromosome protiens?
histones
explain the interactions between DNA and the histones and the formation of the nucleosomes
histones are protiens that bind to DNA to make nucleosomes -nucleosomes are the basic unit of eukaryotic chromosomes and are comprimised of DNA+8 histones in a "beads on a string" configuration
how do the histones affect protien binding to the DNA?
histones can change shape and make it harder to access DNA and translate genes
how is dna held together?
hydrogen bonds between the bases
how does microRNA control of gene expression differ from RNA interference?
in both they are used to seek and destroy a particular mRNA but with microRNA it must get rid of one strand of RNA and use remaining to seek complementary RNA
how does tolemerase solve this problem when approaching a telomere? (prokaryotes vs eukaryotes)
in eukaryotes, a long repetitive nucleotide sequence is added to the end of the lagging strand template by telomerase that carried its own RNA template, once the end of the template is extended, DNA polymerase can finish synthesizing the incomplete lagging strand with conventional DNA replication to ensure no genetic material is lost (in prokaryotes its not an issue because they have ciruclar chromosomes without an end)
what is the role of alternative splicing?
it enables eukaryotes to increase the already enormous coding potential of their genomes and this may be the root of protien domains
why would a set of genes be controlled by both a repressor and an activator?
it enables the control region to integrate 2 different external signals so that the gene/operon is only expressed when both of the 2 contitions are met (in other words, it allows the set of genes to behave like a circut with switches that carry out a logic operation and can only produce a result if a specific comination is present)
what is the role of the mediator protein?
its a large complex of proteins that attracts and positions the general transcription factors and RNA polymerase at the promoter forming a TRANSCRIPTION INITIATION COMPLEX to start RNA synthesis
what class of molecule is primase?
its an enzyme that creates RNA (ribonucleic acids)
waht does it mean when a tRNA is charged?
its charged when its linked to an amino acid
why is cell memory imporatant?
its the prerequisite for the creation of organized tissues, and for the maintenance and stability of differentiated cell types
how many gene can a given protien regulate?
many genes can be regualted by a single protien
how does methylation affect protien binding to the DNA?
methylation stops polymerase from being able to recognize DNA because it closes it up
How can exon duplication occur?
misalignment/unequal crossing over leading to a modified nucleotide sequence that is spliced to produce funtional mRNA
how can we account for the number or protiens vs genes in DNA?
most of the DNA is in noncoding introns and the small amount in coding regions (exons) is what goes into making protiens
how many replication origins does a eukaryotic cell have?
multiple because they have a larger amount of DNA and if they didnt have multiple ORI's then replication would take a very very long time
is it important that primase doesnt proofread?
no becasue DNA polymerase will come and replace the RNA primer with DNA so mitakes in the RNA primer dont matter
what are the consequences of non-homologous end joining?(2)
nonmologous end joining is when the broken ends are hurriedly stuck back together before the DNA fragments drift apart and get lost, therefore this method is ricky and dirty and can lead to two things: -nucleotides being lost at site of repair while "cleaning" is done to prepare for ligaiton -any sequence changes could disrupts gene activity and the cell could suffer serious consequences
how many replication origins does a prokaryotic cell have?
one because they have less DNA/are smaller
how many protiens can play a role in regulating a given gene?
one gene can regulate a gene, or it can be many protiens (combinatorial control)
What is the error rate of DNA polymerase?
one mistake per 10^7 nucleotide pairs copied
what strand is DNA mismatch repair attracted to?
original parent strand
What primes the synthesis of DNA?
primase which adds a short stretch of RNA (RNA primer) that can be binded to begin DNA synthesis
how often will a typical prokaryote have a point mutation due to an error in the DNA polymerase compared to a eukarytoe?
prokaryote= 1 change per 10^9 copied base pairs eukaryote= 1 change per 10^10 copied base pairs
Lamarack
proposed the Theory of Inheritance of Acquired Characteristics: traits acquired in one generation are inherited to the next generation
how do exons and protien domains relate?
protien domains are each encoded by a seperate exon
how do the major and minor grooves of the chromosome affect protien binding to the DNA?
protiens maininly insert inside the major groove and make a series of noncovalent bonds with the base pairs in the groove forming a highly specifc and strong interaction, they can occur slightly in minor grooves as well but not as prevalently
define human accelerated regions of the DNA
regions of the DNA thought to reflect functions that make humans different from chimps
what are post transcriptional controls? give 2 examples
regulation of gene expression that occurs after transcription of the gene has begun; these further fine tune the expression of almost all genes ex. RNA splicing, translational control
what advantage does RNA have over DNA as a genetic material?
ribose is easier to make and its less prone to damage from UV radiation
pauling
said DNA was triple stranded with bases facing out
chargaff
said amount of adenine=guanine and thymine=cytosine (A=T and C=G)
what molecule performs RNA splicing?
small nuclear RNA (snRNA):serves as catalytic agents during splicing and are called Ribozymes
what impact can a mutation have in a somatic cell?
somatic cell mutations only affect new cells that are created from the mutated cell and are not passed on to offspring (not hereditary)
What is the role of the sigma factor?
subunit in RNA polymerase the recognizes the promoter allowing RNA polymerase to bind and begin transcription (once transcription begins, the sigma factor is released)
What makes up the backbone of DNA?
sugars and phosphates linked together by phosphodiester bonds
Where are the three main places that a point mutation can occur?
the 1st, 2nd, and 3rd base locations
how do the 30nm fibers affect protien binding to the DNA?
the 30nm fiber contains multiple histones wraped together tightly which makes it harder for polymerase to bind to DNA to translate genes
how is the 30nm fiber folded to produce the mitotic chromosome?
the answer is not yet known! but it is known that specialized non histone protiens and histone H1 fold the chromatin into a series of loops which are further condensed to make a chromosome in interphase
what problems does DNA replication has as it approached the telomere?
the leading strand can be replicated all the way to the end of the chromosome but the lagging strand cannot becuase when the final RNA primer on the lagging strand is removed, theres no enzyme to replace it with DNA (if there were no fix to this, the lagging strand would get shorter and shorter with each round of replication)
what is the life span of mature mRNA in the cytoplasm?
the life spans of mature mRNA differ depensing on the nucleotide sequence of the mRNA and the type of cell however: -bacteria/prokaryotes=shorter, about 3 minutes -eukarytoes=longer, 30min-10hours
what is the correlation between genome size and the organism complexity?
the more complex the organism, the less chromosomes it has (larger genome=less complex) *no corelation*
what role does protien quanternary structure play in transcriptional regulation?
the overall structure of the protien can inhibit the further translation of the protien if another added compound is present that indicated that there is enough of the protien
how does a positive feedback loop impact cell specialization?
the positive feedback loop ensures that daughter cells remeber what kind of cells they should be; they do this by a cell using a master transcirption regulator to transcribe its own gene activated by a transient signal and after that cell divides, its progeny cells remember this gene production even without the transient signal present
How does the mature mRNA leave the nucleus?
they are selectively exported from the nucleus for processing through the passage of nuclear pores
why are double stranded breaks so critical?
they can lead to the fragmentation of chromosomes and the subsequent loss of genes (especially in coding regions because nucleotides are lost)
why is it difficult to treat retroviruses? give example
they can persist in a latent stage as a provirus embedded in chromsomes of an infected cell and this ability to hide in host cells complicated treatment attempts (ex. HIV)
How do viruses replicate?
they hijack thier hosts biochemical machinery to reproduce themsleves using the reverse of the central dogma of biology
how likely is it that selectively nuetral mutations will be passed on and why? give an example
they may or may not be passed on because they dont really have an impact on the likelyhood of an organism reproducing (ex. colorblindness)
what is unique about retroviruses?
they use reverse transcriptase to go from RNA to DNA, essentially transcription is done backwards, this allows for integratoin of virus DNA into the host
why does A pair with T and G pair with C?
this creates complementary base pairing where a pyrimidine bind with a purine: this allows the DNA to be packed in the most energetically favorable arrangement because each base is the same width which holds the phosphate backbone equal distances apart
how is DNA's high fidelity seen across organisms, human v chimp, primates v other mammals?
this is seen by the similarity in DNA sequences in essential genes across many different organisms. (its not only seen between closely related organisms but across the entire spectrum of life)
what role does hortizontal gene transfer play in antibiotic resistance?
this leads to an increase in antibiotic resistance becuase genes that have anitbiotic resistance provide a selective advatage and are passed on/spread through populations more easily
explain the relatedness of the heterochromatin and gene slienceing?
tightly pakeed chromatin (heterochromatin) has lots of histones which inhibits access to the DNA turning the gene off causing gene silencing
what is the major role of genetic information?
to determine the characteristics of a species as a whole and of the individuals within it
what is the role of molecular chaperones in protien synthesis?
to help protiens fold correctly into the most energectically favorable stucture
what is the role of RNA processing?
to prepare mRNA for transport out of the nucleus to provide it with methylated cap and polyA tail that serves as portection during transportation so taht no important genetic info is lost during transport
donohue
told watson and crick that hey had the structure of guanine wrong and this change allowed thing to fit together discovering: anitparallel strands, A=T with two bonds and C=G with three bonds, and phosphate backbone
the number of genes in veretrabtes is very similar but the amount of DNA present can differ dramatically. explain how this occurs?
unimportant gene sequences in noncoding regions are being lost at different rates in different organisms, but the imporatant genes in coding regions remain
what is the role of chromatin remodeling complexes?
uses ATP hydrolysis to move histones along chromatin based on what needs to be turned off or on in the cell -heterochromatin=tightly packed histones=genes off -euchromatin=loosley packed histones=genes on
how common is gene duplication
very common, especially in plants
how likely is it that mutations in highly conserved genes will be passed on? why?
very likely becuase they provide a slective advantage and are more likely to be preserved and passed on between generations
what is the concept of cell memory?
when changes in gene expression which are triggered by a transient signal must be remembered by the cell; (all genes must be able to turn genes on and off in response to environmental signals)
under what conditions does CAMP increase?
when glucose is absent and lactose is present
describe how the synthesis of guanine is controlled by a riboswitch
when guanin is plentiful, it binds to mRNA making a riboswitch which causes a shift in mRNA's structure/conformation and this causes the ribosome to stop producing that specific mRNA coding for the prodcution of guanine
How does gene duplication occur?
when one of two duplicated genes is functional, the other is free to mutate into having a new function and that new gene can be passed on through generations
how is RNA polymerase tail altered in eukaryotes?
when the transcription factor TFIIH falls off, it hydrolizes ATP transfering 2 phosphates to the tail of RNA polymerase changing its configuration which causes other transcription factors to fall off (phosphylorates RNA polymerase->triggers conformational change->triggers transcritpion factors to fall off)
What is alternative splicing?
when the transcripts of many eukaryotic genes can be spliced in different ways which can each produce a distinct protien
How does the tryptophan repressor work?
when tryptophan is in high concentrations, it binds the the REPRESSOR making it active cuasing it bind to the OPERATOR where it blocks RNA polymerase from binding to the PROMOTER stoping tthe gene from being expressed(turning it off); this type of gene regualtion is ALLOSTERIC becuase it alters the activity of a protien by changing its shape
in what animal is gene sliencing seen and how?
x-inactivation seen in female calico cats; gene silencing is what cases the patchwork of fur color