DNA replication and transcription Flashcards
What is northern blotting used to detect for?
RNA
What is western blotting used to detect for?
proteins
What is ELISA used to detect?
proteins
What is southern blotting used to detect?
DNA
Name 2 main roles of transcription factors in eukaryotic organisms
recruiting RNA polymerase
regulating transcription rate
AUG is the start codon found on _____
RNA
Note AUG is not the start codon found on DNA (DNA does not contain uracil); AUG is the start codon on RNA sequences that signifies the start sequence for translation, not transcription
What is a ligand?
- a molecule that binds reversibly to a protein, delivering a signal in the process. In ligand and protein binding, there are no chemical bonds being broken or formed.
- ligands can be thought of as signaling molecules, and can travel through the bloodstream, watery fluids within the organism, or within a cell itself.
- Proteins receiving ligands can be receptors, channels, or the the start of a complex series of intertwined proteins. The protein will undergo a conformational change when bound to a ligand.
Describe the environments of the solvent surrounding DNA, the DNA backbone itself, and the nitrogenous base pairs in terms of hydrophilicity and hydrophobicity?
solvent surrounding DNA = hydrophilic
DNA backbone = hydrophiliic d/t the hydroxyl groups and the phosphate, which allow the DNA to interact with water
DNA nitrogenous base pairs = hydrophobic d/t the nitrogenous bases with many carbon atoms and few polar groups
What is chromosomal amiplification?
when a segment of a chromosome is duplicated
What is translocation?
when recombination occurs between nonhomologous chromosomes, creating gene fusion: where a new gene product is made from parts of two genes that were not previously connected.
What is balanced vs unbalanced translocation?
balanced: where no genetic information is lost
unbalanced: where genetic information is lost or gained
Distinguish between an oncogene and a tumor suppressor gene
oncogene: a gene that can cause cancer when it is mutated or expressed at high levels
tumor suppressors: opposite function in that their deletion or decreased levels of expression can cause cancer
Distinguish between excision repair and post replication repair
excision repair: DNA repair mechanism that occurs before DNA replication
Post-replication repair: DNA repair that occurs during or shortly after DNA replication
The 3’ end of the mRNA (after the stop codon) isn’t translated into protein, but often contains regulatory regions that influence _________ gene expression
post-transcriptional
function of small nuclear RNA (snRNA)
- associate with other proteins to form snRNPs (small nuclear ribonucleic particles) complexes in the spliceosome, and thus are used for splicing the introns out of hRNA (heterogenous nuclear RNA)
- regulation of transcription factors
- maintaining telomeres
the sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called the __1__, and the point where RNA polymerization actually starts is called the ___2___
1) promoter
2) start site
The strand that is actually transcribed (in transcription) is called the _____ strand. Give 3 other names for this strand.
template strand
other names: non-coding, transcribed, or antisense strand
The strand that has the same sequence as the transcript RNA strand (except that it has T instead of U) is called the ____ or ____ strand
coding, or sense strand
In prokaryotes, the AUG start codon will only initiate translation when it is preceeded by a ______ sequence
Shine-Dalgarno
What nitrogenous base(s) makes up the 5’ cap on mRNA
guanine
What nitrogenous(s) bases makes up the ploy A tail on mRNA
adenine
what is a spliceosome?
a complex that performs hnRNA splicing
What is a somatic cell?
any cell in the body other than reproductive/germ cells
what is feedback inhibition?
refers to molecules regulating a process within the cell based on concentration of that molecule. A high concentration of that molecule can enhance one pathway while a low concentration of that molecule can inhibit that pathway, or vice versa i.e. presence of lactose and how it affects the lac operon
positive gene regulation
- a signaling molecule generates a complex that interacts with DNA to increase transcription rates
i. e. the activator increases the affinity that RNA polymerase has for the promoter, thus increase transcription rates
negative gene regulation
refers to signaling molecules that interact with repressor proteins that decrease/inhibit gene expression
True or False: in order to express a gene, the gene must be unwound from its histones
true
(histones must be deacetylated to unwind the DNA so that it can be transcribed)
how does methylation promote gene silencing?
a methyl group binds to cytosine via methyl transferase enzyme
methylation can affect transcription by either physically preventing the binding of transcriptional proteins to the gene, or by attracting additional proteins to that area of the DNA that will cause the DNA to become more condensely wrapped around histones, thus inactivating the transcription of those genes because those genes cannot be accessed by transcriptional proteins
what is gene expression?
refers to the ability of taking information on DNA to produce a product (proteins, rRNA, tRNA, etc.)
Distinguish between the function of a repressor protein and activator proteins
repressor proteins inhibit transcription
activator proteins enhance transcription
Where is snRNA found?
in the nucleus
-note that snRNA performs splicing of the hnRNA to make mRNA, and splicing occurs in the nucleus
Are gene products always proteins?
No. tRNA, rRNA, and snRNA genes are not polypeptides; they’re made of RNA
Function of DNA gyrase?
enzyme used to supercoil and condense the prokaryotic genome; uses ATP to cut the DNA and twist the 2 sides of the circle around each other
Eukaryotic DNA is wrapped around an octamer of ______ to make beads of nucleosomes
histones
the string between the histone beads in eukaryotic DNA is bound by a single _____ histone
linker
When stained, darker regions of DNA are called ______, whereas lighter regions of DNA are called _____
heterochromatin, euchromatin
centromeres are made of heterochromatin and ____ DNA sequences
repetitive
Where are the centromeres located in the following types of chromatin?
1) metacentric
2) submetacentric and acrocentric
3) telocentric
1) middle so that each chromatin arms are the same size
2) between middle and end so that each chromatin has both p (short) and q (long arms)
3) end so that each chromatin only has 1 long arm (hence no short arms)
Why aren’t telomeres found in prokaryotic DNA?
because prok. DNA is circular
What’s the common repeating unit of telomeres in many vertebrates, inc. humans and mice?
5’-TTAGGG-3’
What are intergenic regions of DNA?
noncoding DNA
-note that this DNA may direct the assembly of specific chromatin structures and contribute to the regulation of nearby genes, but they themselves have no known function
What is a gene?
a DNA sequence that codes a gene product
-aka coding DNA
What are single nucleotide polymorphisms (SNPs)?
refers to single nucleotide changes across members of the same species, which ultimately results in various mutations and gene differences
- most are found in noncoding regions
- SNPs found in coding regions can lead to specific traits and phenotypes i.e. something might taste bitter to one person but not to another
What is a tandem repeat?
- short of long repeats of DNA sequences
- they may be stable or unstable. unstable is associated with disease.
- heterochromatin, centromeres, and telomeres are rich in tandem repeats
The Central Dogma of biology refers to the process of DNA being transcribed into RNA, which is then translated into protein. In other words, this is the process by which _____ is used to create actual _____
information, products
What are the stop codons in transcription?
UAA, UGA, UAG
Mneumonic:
-U Are Annoying
-U Go Away
-U Are Gone
What is the codon for tryptophan?
UGG
-note that this is the only codon that codes for tryptophan
Do the stop codons code for any AA? If so, what are they?
No. they don’t code for any AA
What phase during interphase does DNA replication occur?
S phase
Is DNA semiconservative, conservative, or dispersive?
semiconservative (each daughter has one strand of DNA from the parent, and one new strand of DNA)
- conservative would mean that one daughter cell has both parental strands of DNA, and the other daughter would have both new strands of DNA
- dispersive would mean that each DNA strand would have a mixture of both parental and newly synthesized DNA, and so each daughter would have 2 of these mixed DNA strands
Functions of helicase
an enzyme that unwinds the double helix and seperates the 2 strands of DNA
Where does helicase being unwinding DNA?
at the ORI (origin of replication)
How many ORI do prok. and euk. have?
prok have 1 d/t their DNA being circular
euk. have many
What protein finds the ORI sequence in prok. and euk.?
DnaA in prok
3 other proteins in euk.
Why are 2 out of the 3 euk. proteins that are responsible for finding the ORI sequence only synthesized during the M and G1 phase of the cell cycle?
Once synthesized, the proteins are rapidly destroyed once the S phase begins to ensure that DNA replication doesn’t initiate during other phases
What are topoisomerases?
enzymes that cut one or both strands up and downstream from helicases to relieve the excess tension creates by the helicases; hence they prevent up and downstream from supercoiling
What are SSBPs (single-stranded binding proteins)?
protects ssDNA that has been unwrapped and separated by helicase and also helps to keep the strands separated
separated DNA strands are aka a(n) _____ complex
open
1) The primosome synthesizes the ________ in DNA replication.
2) The central component of the primosome is an _____ polymnerase called _____
1) RNA primer
2) RNA, primase
primase is an ____ polymerase that synthesizes the ____
RNA, RNA primer
DNA polymerase synthesizes the new DNA strand in the _____ direction, and reads the parents strand in the ____ direction
synthesizes in the 5’ to 3’
reads the parent in the 3’ to 5’
DNA polymerase is part of a large complex of proteins called the _____
replisome
The leading strands in DNA replication elongate ____ without requiring additional _____ to be laid down
continuously, RNA primers
Lagging strands require occasional ____ to be laid in order to continue DNA replication of that strand
RNA primers
Does the leading or lagging strand contain Okazaki fragments?
lagging
replication of the _____ strands leads into the replication fork, while replication of the ____ strands is discontinuous and results in Okazaki fragments
leading strands, lagging strands
Disinguish between DNA Pol I & III in prok.
DNA Pol I: starts adding nucleotides at the RNA primers (5’-3’ polymerase activity); has poor processivity; has 3’-5’ exonuclease activity (proofreading); is able to remove the RNA primer via 5’-3’ exonuclease activity; plays a role in excision repair
DNA Pol III: 5’-3’ polymerase that starts ~400bp downstream from where DNA Pol I started (hence takes over DNA Pol I polymerase activity); high processivity; 3’-5’ exonuclease activity; no known function in repair pathways
Name the basic functions of DNA Pol II, IV, and V in prok.
DNA Pol II: a backup for DNA Pol III; also participates in DNA repair pathways
DNA Pol IV & V: play important roles of the prok. checkpoint pathway
What is 3’-5’ exonuclease activity?
refers to the ability to remove a nucleotide it just added if it was incorrect
_____ is a ribonucleic protein complex containing an RNA primer and a reverse transcriptase enzyme (makes DNA from RNA)
telomerase
In humans, the RNA template in telomerase is ______
3’-CCCAAUCCC-5’
-note that this is reverse for DNA telomeres 5’-TTAGGG-3’
In most organisms, telomerase is only expressed in the ___ line, _____ stem cells, some ____ and ____ cells.
germ line, embryonic stem cells, WBCs and cancer cells
What type of RNA is coding RNA and what type of RNA is non-coding RNA?
coding RNA = mRNA
noncoding RNA = tRNA, rRNA, snRNA, miRNA (microRNA), siRNA (small interfering RNA), piRNAs (PIWI-interacting RNAs), and long ncRNA
In mRNA, the 5’ region is not translated into protein, and is aka _____
5’UTR (untranslated region)
What is the open reading frame (ORF) of mRNA?
the portion of the mRNA that gets translated into protein; starts at the start codon and ends at the stop codon
the 3’ end of mRNA often contains regulatory regions that influence ____-transcriptional gene expression
post-transcriptional
What is hnRNA and is it found in prok, euk, or both?
hnRNA = heterogenous RNA and is immature or precursor mRNA that must undergo processing to become (mature) mRNA
Only euk have hnRNA
Transfer RNA (tRNA) carries AA from the ___ to the ___ to be added to the growing protein
cytoplasm to the ribosome
What are ribozymes?
the catalytic RNA component of the ribosome
What are small nuclear RNA (snRNA)
RNA that associate with other proteins to form snRNP (small nuclear ribonucleic particles) complexes in the spliceosome
What are the primary functions of microRNA (miRNA) and small interfering (siRNA)?
they can either increase or decrease translation rates
What’s the primary purpose of PIWI-interacting RNAs (piRNAs)?
prevent transposons from mobilizing
What’s the primary purpose of long ncRNA?
regulate initiation complex assembly on promoters and help regulate splicing and translation
Why is no RNA primer needed in transcription?
because transcription already uses RNA
Does RNA polymerase have exonuclease activity?
No
Because RNA polymerase has no exonuclease activity, does his mean that transcription has a high or low fidelity rate?
has a low fidelity rate compared to replication
Why do RNA viruses have increased rates of mutation?
because RNA polymerase has no exonuclease activity, which means it’s replication has low fidelity and is prone to more mutations
In transcription, distinguish between the promoter and the start site?
promoter: the sequence of nucleotides on DNA that activates RNA pol. to begin transcription
start site: the point where RNA pol. actually starts transcription
Where does DNA replication and RNA transcription begin?
DNA replication begins at the ORI site(s)
RNA transcription begins at the start site (after the promoter has been activated to activate RNA pol.)
What is the strand called that is being transcribed? What is the complementary strand called that is not being transcribed?
transcribed strand = non-coding strand or anti-sense strand
complementary strand to transcribed strand = coding or sense strand (has the same sequence as the transcript except has T in place of U)
Transcription starts and proceeds downstram towards the ___ end of the coding strand transcript
3’
In prok. transcription: all RNA are made by the same RNA polymerase (aka the core enzyme), which is made up of 5 subunits. What are these subunits?
2 alpha, 1 beta, 1 beta prime, and one omega subunit
What is the sigma factor?
the sigma factor is required to initiate transcription by helping RNA Pol. find and bind to the promoter; it’s another subunit that binds to the core enzyme/RNA polymerase to form the holoenzyme.
Stage 1 of Prok. Transcription: Initation: RNA Polymerase scans for and binds to the promoter, forming a closed complex. What are 2 primary promoters in prok?
“Pribnow box” at -10 and the “-35 sequence”
Stage 1 in prok. transcription: initiation: after RNA Pol binds to the promoter and forms a closed complex, what happens next?
The RNA pol. then unwinds the DNA double helix to create an open complex for transcription. Once the open complex and several phosphodiester bonds have been formed, the sigma factor leaves the RNA pol. complex
Stage 2 in prok. translation: elongation: One ____polymerase complex synthesizes the entire molecule
RNA polymerase
Stage 3 of Prok. transcription: termination: when the termination signal is detected, in some cases w/ the help of a protein called ___, the polymerase fallso ff the DNA, releases the RNA, and the ______ closes
rho, transcription bubble closes
Where does transcription occur in prok and eukaryotes
Occurs in cytoplasm in prok and in nucleus in euk.
In splicing, the spliceosome, or snRNPs, recognize the H bond to conserved nucleotides in the intron. What are these nucleotides (2 sequences). The snRNPs also recognize a(n) ____ 15-45 bases upstram of the 3’ splice site. This aligns the hnRNA so splicing can take place
GU at the 5’ end and an AG at the 3’ end
adenine 15-45 bases upstream
What is alternative splicing?
refers to the various/multiple patters that can be made form one hnRNA gene sequence; hence, the one DNA gene sequence that gets transcribed into an hnRNA doesn’t always have to become the same exact mRNA, and therefore, multiple types of proteins can be made from the same gene sequence d/t alternative splicing patterns
The 5’ cap is a methylated ____
guanine
The 3’ poly A tail is a string of several hundred _____ nucleotides
adenine
both the cap and tail on mRNA prevent _____ of mRNA by exonucleases that are free in the cell
digestion
How many RNA Pol. do prok and euk have?
prok only have 1. euk have many, but the primary ones are RNA Pol. I, II, & III
In Eukaryotes:
1) RNA pol. I transcribes most _____
2) RNA pol II transcribes most ______
and 3) RNA pol III transcribes most ______
1) rRNA
2) hnRNA (and so mRNA)
3) tRNA
True or false: transcription stops at the stop codon
False
True or False: both replicatoin and transcription occur with the same fidelity
false: transcription process has lower fidelity (hence higher mistakes are made in transcription; this is d/t no RNA Pol exonuclease activity)
Which of the following functions is NOT typically attributed to small nuclear RNA (snRNA)?
A) processing of pre-mRNA
B) regulation of transcription factors
C) coordinating AA addition in translation
D) maintaing telomeres
C) coordinating AA addition in translation
*note that snRNA is located inside the nucles, and translation does not occur inside the nucleus, but rather the cytoplasm. Also, it is the job of the tRNA to coordinate AA addition in translation.
How could changing the half life of mRNA lead to phenotypic changes?
A) A shorter mRNA half-life would lead to a truncated protein
B) A longer mRNA half-life would increase the amount of time the mRNA stays bound to the template strand of DNA, and reduce the amount of protein translated.
C) Differences in mRNA folding could alter the rates of translation
D) More or less of the protein encoded by that mRNA would be translated.
D) More or less of the protein encoded by that mRNA would be translated.
*note the mRNA half-life has nothing to do with the length of the protein; protein size is dictated by the length of the reading frame on the mRNA molecule and the number of codons in the translated region. Choice C is a correct statement but doesn’t address the question of half-life
