biology exam 3 Flashcards by Mika Gorospe

what is DNA polymerase?

key molecules in DNA replication, add nucleotides one by one to grow DNA chain, incorporate nucleotides that are complementary to the template

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What is topoisomerase?

relieves the strain by breaking, swivelling, and rejoining DNA strands

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what is a helicase?

enzyme that untwists the double helix at the replication forks

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what is a primase?

synthesises short RNA primers during DNA replication

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what is a single binding protein?

bind to unpaired DNA strands to keep them from re-paring

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what is a the difference between a lagging and leading strand?

leading: DNA polymerase synthesizes along the replication fork, only requires one primer, elongates continuously by adding the new DNA from 5 prime to 3 prime end

lagging: DNA polymerase synthesizes away from replication fork, strand is primed separately through Okazaki fragments, DNA pol 1 replaces RNA nucleotides with DNA nucleotides, 3 prime end to 5 prime end

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what does DNA ligase do?

assists lagging strand by joining the sugar phosphate backbones of Okazaki fragments into a continuous DNA strand

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what are okazaki fragments?

segments within the lagging strand that synthesises discontinously,

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what is the end replication problem? what is the result of the end replication problem?

because the lagging strand cannot continue until the RNA nucleotides are replaced with DNA nucleotides, at the end of the linear chromosome, there will be a shortening of DNA after every round of replication

the ends of linear chromosomes cannot be fully replicated & the ends shorten w each round of replication

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shortening of ends of chromosomes during replication takes place because of ____ strand ONLY

lagging

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a ___ protects the ends of eukaryotic chromosomes

telomere

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what is a telomere?

protects the genes near the ends of eukaryotic chromosomes

does not contain genes & does not code for proteins, consist of multiple repetitions of one short nucleotide sequence

TTAGGG

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what is a solution to the end replication problem?

telomeres can extend the unreplicated end within the lagging strand with the use of its own RNA template

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what cells have active telomerase?

germ and cancer cells

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what is chromatin?

packages DNA into chromosomes

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what is a chromatin structure made up of? what does it form?

made up of DNA and histone proteins

forms nucleosomes which are the basic units of DNA

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what do the chromatin structures do to DNA?

condenses long thin DNA structure into short chromosomes so that it will fit within the nucleus

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___ is used to make many copies of a gene & to produce a protein product

gene cloning

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what enzyme does gene cloning rely on?

restriction enzymes

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what is a restriction enzyme?

cut DNA molecules at a limited number of a specific location called restriction sites

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what is a restriction site?

a particular short DNA sequence

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_______ cut DNA molecules at a limited number within a specific location called ______

restriction enzymes, restriction sites

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what is PCR? what is its’ function?

polymerase chain reaction, makes a bunch of copies of a certain gene

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what are the three steps of PCR?

desaturation, annealing, and extension

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how can you utilise PCR?

1. use PCR to amplify or make many copies of your specific gene 2. restriction enzymes will cut at a specific fragment, so that you can insert your amplified gene creating a recombinant plasmid 3. insert recombinant gene into foreign fragment, wait for it to divide

what is the central dogma of Biology?

dna (transcription) -> RNA (translation) -> Protein

what is transcription? what form of RNA is used?

mRNA temporality binds to complementary DNA in order to obtain genetic info to code for proteins

______ can leave the nucleus whereas _____ cannot

mRNA, DNA

_____ is single stranded whereas ____ is double stranded

mRNA, DNA

what is translation? where does this step occur?

mRNA is read and translated at the ribosomes within the cytoplasm to produce proteins

what indicates what amino acid is produced by the ribosomes?

the genetic code

how are prokaryotic and eukaryotic gene expressions different?

prokaryotic: transcription and translation occur at the same time, RNA polymerase binds to promoter region eukaryotic: transcription and translation occur separately and in different locations transcription (nucleus) translation (ribosomes) TATA box & transcription factors serves as recognition point

what is a codon

3 base sequence of nucleotides that code for a certain amino acid

what is RNA polymerase?

synthesizes RNA molecules from a template of DNA through transcription

what direction does RNA polymerase work in?

5 prime end to 3 prime end

what are the stages of transcription?

initiation elongation termination

what happens within the initiation stage of transcription?

RNA polymerase binds to promoter, DNA unwinds, polymerase initiates RNA synthesis at starting point on DNA strand

what happens within the elongation stage of transcription?

polymerase moves downstream unwinds DNA and elongates the RNA transcription, the DNA strand begins to reform a double helix

what happens within the termination stage of transcription?

RNA transcript is released and polymerase detaches from the DNA

what is RNA processing

protects the ends of RNA within Eukaryotic cells to prevent from being degraded w the addition of 3 prime poly A tail ends

3 prime poly A tail ends do what

they protect the ends of RNA to prevent them from being degraded

removing the intron region so that the exon region can bind together is an example of _____

rna splicing

what is RNA splicing

the internal parts of RNA (introns) are removed and the remaining portions (exons) reconnect and are used in translation

exons

product of RNA splicing, exons are translated into amino acid sequences

intron

waste product of RNA splicing, non coding regions that aren’t used within translation

a ____ recognises introns and slices them, the introns are not used for coding into amino acids

spliceosome

what are spliceosomes made of

proteins and small RNAs

what role does tRNA have within translation?

tRNA translates mRNA into a protein, transfers that protein to the growing polypeptide within a ribosome

how does DNA —> RNA

each tRNA enables the translation of a particular mRNA codon into a certain amino acid

how does RNA —> protein

the amino acid from tRNA is then at the other end and base pairs w complimentary codon within mRNA

a correct match of tRNA and an amino acid is assisted by __________

aminoacyl tRNA synthetase

what is a ribosome?

enzyme that catalyzes translation and synthesizes new peptide bonds in proteins

what are the different binding sites within a ribosome?

P site: carries growing polypeptide chain A site: carries the next amino acid to be added to chain E site: exit site where tRNA leaves the ribosome

what is translation initiation?

brings in mRNA, tRNA, & two ribosomal subunits together small subunits move along mRNa entail it reaches a start codon to begin translation

what is the translation elongation cycle?

codon recognition, peptide bond formation, translocation the cycle can be repeated as many times depending on what’s needed by the amino acid

what is translation termination?

ribosomes stop translation when there is a stop codon, mRNA reaches A site of the ribosome releases polypeptide & translation falls apart

what are the three types of mutations?

silent mutation missense mutation nonsense mutation

what is silent mutation

amino acid sequence has no effect

what is missense mutation

a new unexpected amino acid forms

nonsense mutation

stops translation early on due to stop codon

what is a frameshift mutation? how does this occur?

DNA code shifts resulting into many different amino acids that follow occurs randomly through insertions or deletions

what is the least severe mutation

silent mutation

what is the most severe mutation?

nonsense mutation due to the fact that translation stops all together because of the end codon

what is gene expression?

determines which genes are being turned off and on to create different cells

what’s the role of DOGMA within gene expression?

controls how much protein is used within the cells

the majority of gene expression within Eukaryotes are controlled within _____ ?

transcription initiation

an ____ is turned on within transcription initiation

activator

activator role within transcription

activates transcription by recruiting RNA polymerase to a specific gene

the role of a repressor is

turning off transcription where RNA polymerase cannot bind to a specific gene, results in no translation

the synthesis of trp operon is controlled by the ___

repressor

the following replication enzyme is responsible for catalyzing the formation of new phosphodiester bonds between nucleotides (producing a new DNA strand from nucleotides)

DNA polymerase

the following replication enzyme is used to unwind double stranded DNA into single- stranded DNA

helicase

telomerase is able to

add additional DNA repeats on to the end of linear chromosomes

a nucleosomes is the made up of

DNA and histone proteins

a plasmid is made up of

DNA

a restriction enzyme conducts this enzymatic reaction

cuts a specific DNA sequence

the following codon encodes for Glycine

GGA

evidence that the genetic code is redundant is that

four different codons (GCU, GCC, GCA, GCG) all encode for the same amino acid, alanine

the TATA box is

the site of transcription factor binding

the enzyme that catalyzes transcription (assembly of nucleotides into RNA) is:

RNA polymerase

the following step takes place last during the gene process of gene expression in eukaryotes

protein translation

the following is able to be translated into a protein amino acid sequence

mRNA exons

an aminoacyl- tRNA synthetase contains binding sites for the following two molecules

tRNA and amino acid

the enzyme that catalyzes the formation of new peptide bonds during translation is the

ribosome

the E site, P site, and A site in the ribosome are

tRNA binding sites

the following mutation will likely result in the most severe phenotype

frameshift mutation equivalent to nonsense mutation

gene expression is most frequently regulated at the stage of

transcription control

the genes in the trp operon are used to

synthesize tryptophan when tryptophan levels are low

when glucose levels are low and lactose levels are high lac operon is ____

lac operon is turned on

_____ are located a long distance from the promoter

enhancers

the following change to chromatin would increase transcription levels

treating with histone HAT

the following process can result in a change in the amino acid sequence of the protein products that are produced

alternative splicing

siRNAs and miRNAs control gene expression at the stage of

mRNA degradation

in-situ hybridisation is an experimental technique used to identify

the sequence of specific mRNAs

apoptosis is best described as

controlled and intentional cell death

if the bicoid protein was expressed on both the anterior and the posterior ends of a drosophila embryo, this would result in

an embryo with a head on both the anterior and posterior ends

iPS cell is most similar to

an embryonic stem cell

p53 is an example of (breaks)

tumor suppressor gene

cancer usually develops from

multiple mutations in both pronto oncogenes and tumor suppressor genes

______ are viruses that infect bacteria cells

bacteriaphages

DNA location

nucleus

what does RNA contain ?? ____ sr

sugar ribose

___ contains sugar deoxyribose

DNA

what contains uracil? DNA or RNA?

RNA

what contains thymine? DNA or RNA

DNA

where is the location of RNA

cytoplasm

what bonds the template and complementary DNA strands together?

hydrogen bonds

Three bases in the coding sequence of DNA are AGT. What is the tRNA anticodon that binds the mRNA codon transcribed from the DNA bases?

AGU

Three bases in the coding sequence of DNA are AGT. What is the transcribed mRNA codon?

UCA

What do 5' and 3' refer to in DNA and RNA strands?

They indicate the carbon numbers in the DNA (or RNA) sugar of the DNA (or RNA) backbone.

what type of bonds stabilize tRNA secondary structure

hydrogen bonds

what type of bonds are made between nucleotides in a new DNA stand

phosphodiester bonds

what is involved within translation?

mRNA, tRNA, and ribosomes

what is involved within transcription?

RNA polymerase, and DNA

Three bases in the coding sequence of DNA are AGT. What is the corresponding triplet in the complementary DNA strand?

TCA

all viruses contain

a protein capsid or coat

A step which occurs in the lysogenic phage replicative cycle that does not occur with the lytic replicative cycle is:

phage DNA incorporation into the bacterial chromosome

CRISPR developed for this purpose:

a means for bacterial cells to fight against viruses that they have encountered previously

Individuals who are resistant to HIV infection lack the following gene:

CCR5

The most significant virus for human health in the last thousand years is likely:

smallpox

The smallpox vaccine is:

a less deadly natural form of smallpox that infects cows

The following are strategies that have been used to make COVID-19 vaccines:

All of these strategies are being used to develop a possible COVID-19 vaccine

The Pfizer and Moderna COVID-10 vaccines are:

mRNA vaccines

The striking improvements in DNA genome sequencing cost and time has been primarily due to:

development of next-generation sequencing technology

The following species has the longest genome of the four listed:

human