Study sets, textbooks, questions
Upgrade to remove ads
Molecular Biology: Exam 3
Terms in this set (157)
T or F? Most cells in our body contain the same DNA
DNA gets converted to RNA that gets converted to proteins
messenger RNA (mRNA)
RNA that is going to be translated
Non-coding functional RNA
RNA that has a function other than translation
exception to the central dogma of biology
What do certain viruses, such as the coronavirus, use to hold their genetic information?
What do certain viruses such as the coronavirus use from their host to make proteins?
What do viruses such as retroviruses have to go through in order to replicate and make proteins?
special enzyme that will convert RNA to DNA in viruses
-polar molecule: 5' and 3' end
-bases linked by phosphodiester bond
-polymerization reaction occurs by addition to 3' end
-synthesis occurs from 5' to 3'
What are DNA and RNA similarities? (5)
-RNA has ribose, DNA has deoxyribose
-2' on RNA has hydroxyl, DNA has hydrogen
-RNA is more susceptible to hydrolysis and makes different hydrogen bonds
-RNA is less stable than DNA
-RNA contains uracil, DNA has thymine
-RNA is generated as a single-stranded molecule by RNA polymerase
What are DNA and RNA differences? (6)
thymine has a methyl group
Difference between thymine and uracil?
Because of its ability to form complementary base pairs, what can RNA form?
-conventional base pairs
-nonconventional base pairs (C-U)
What kind of pairs do RNA make?
How many hydrogen bonds are between uracil and adenine?
RNA has a hole in the middle
-Significantly deeper and narrower major groove
What is geometrically different between the RNA and DNA helix?
2' hydroxyl group
what is the primary reason RNA has a different helical shape than DNA?
turn on and off different genes
how do we get different cell types in our bodies?
enzyme that binds the DNA in a particular region
-open a short stretch of DNA
-makes a copy
-turns into an RNA molecule
Function of RNA polymerase
5' to 3'
what direction does RNA synthesis occur during transcription
Can only add onto the 3' end of the growing RNA molecle
why does synthesis occur from 5' to 3'
RNA polymerase does not have proofreading ability
what is a notable difference between DNA and RNA polymerase?
The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript.
3' to 5'
in what direction is the template strand read in for transcription?
because RNA polymerase has to make the RNA molecule from 5' to 3'
why is the template strand read from 3' to 5' during transcription?
the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine
orientation of the promoter creates a "landing pad"
How does the RNA polymerase know which direction to work in during transcription?
-promoter sequences are not found in the transcript
-bacterial promoter sequences -35 and -10 from the transcriptional start site dictate RNA polymerase binding
how are bacterial promoters different from eukaryotic cells?
-bacterial sigma factor interact with DNA to bring the RNA polymerase to the correct DNA region to initiate transcription
how is the "landing pad" identified for bacteria
protein(s) that physically interact with DNA
bacteria has ____ RNA polymerase (s) but _____ sigma factor
step where RNA has gotten to the right site of DNA by being recruited to the promoter (in bacteria)
as the polymerase breaks free from the promoter and starts synthesizing the RNA molecule
-sigma factor gets released and can initiate another round
what happens during elongation? (bacterial)
RNA polymerase does not need a primer, just a template strand
difference between RNA and DNA polymerase during elongation?
-at the end of the gene, polymerase falls off once it reaches a certain sequence
what happens during termination? (bacterial)
-formation of hairpin loop facilitates release of RNA polymerase
termination mechanism for prokaryotes?
how many types of RNA polymerase do prokaryotes have?
how many types of RNA polymerase do eukaryotes have?
RNA polymerase II
polymerase that transcribes all protein-coding genes, miRNA genes, plus genes for other noncoding RNAs
-use general transcription factors that mark the site where transcription should start
-regulatory DNA sequences far from the promoter can regulate transcription
-DNA packaging into higher order structures can alter transcription
eukaryotic differences in transcription (3)
-binding of TATA box to TATA-binding protein with TFIID, bending DNA, allowing other general transcription factors to come in and bind
-RNA polymerase II is recruited
-tfIIH phosphorylates the c-terminal tail of RNA polymerase, activating transcription
transcription initiation steps in eukaryotic cells
5' of the transcription initiation site
where are the promoters found relative to the start of transcription
-elongation and promoter escape
elongation in eukaryotic cells
-transcription doesn't make it to the end of the gene
what things could go wrong during transcription
a protein would be degraded or misfolded
what would happen if incomplete messages got to the cytosol?
1. 5' cap
2. 5' UTR (untranslated region)
3. Coding sequence (introns removed)
4. 3' UTR
5. Poly-A tail
elements of a mature eukaryotic mRNA (5)
1. 5' UTR
2. Coding sequence (introns removed)
3. 3' UTR
elements of a mature prokaryotic cell (3)
-the addition of an atypical guanine that gets added onto the 5' end of the mRNA
5' to 5' triphosphate bridge
how is an atypical guanine attached to the 5' end of mRNA
adds guanosine to the 5' end of mRNA
-act immediately by associating with RNA polymerase
-serve as binding site for proteins (ribosome) that are going to help facilitate its nuclear exit
-protects mRNA from being broken down
function of capping enzyme
string of adenine nucleotides
what occurs at the end of a mRNA transcript
polyadenylation factors (proteins that associate with RNA)
how are adenine nucleotides added to the end of the transcript?
-facilitates nuclear exit
-protects rna from being broken down
function of poly-a tail
presence of poly-A tail and 5' cap
what identifies a complete transcript
-phosphorylation of the c-terminal tail domain of RNA polymerase acts as a landing pad for capping, splicing, and polyadenylation factors
how are the polyA tail and 5' cap added to mRNA?
as the RNA polymerase moves along the DNA , generating the mRNA
when are the polyA tail and 5' cap added to mRNA?
eukaryotes have intervening sequences called introns
major difference between bacterial and eukaryotic transcripts
intervening sequences that do not become part of the final coding sequence and get removed
process by which introns get removed
-if regions are not coding, mutations will not have an effect
-allow for alternative splicing, creating additional proteins
-important for evolution by insertion of exons to create novel proteins
why is there extra DNA (introns)?
-sequences in the RNA direct the machinery
how does a cell determine what's an intron and what's an exon?
2' hydroxyl on adenine reacts with nucleotides at the exon-intron border 5' of the gene
-covalently attaches, creating a branch point
-free hydroxyl group interacts with nucleotide on intron-exon sequenece on 3' end of gene, creating a lariat
-lariat gets broken down by cell, nucleotides are recylced
2 steps of splicing
complex that performs the splicing reaction
-contains protein and RNA
spliceosome function and composition
using complementary base pairing
how to find the landing pad during splicing?
small nuclear RNAs
-RNA in spliceosome
directs the location of binding and performs chemistry
function of the RNA in spliceosome
the snRNA protein complex
-when a cell mix and matches exons
-to change protein binding properties
-to alter cellular localization, enzymatic activity, protein stability, and post-translational modifications
why would alternative splicing retain or bypass functional units? (2)
only ____ mRNAs can be exported from the nucleus
where does translation occur
do cells express different genes at the same rate?
prokaryotic mRNAs are not very long-lived
difference between life span of prokaryotic and eukaryotic mRNAs?
-at the promoter
-exit from the nucleus: capping, polyA tail, splicing
-stability of the mRNA
-increase/decrease protein degradation
what places can the cell regulate to control mRNA and protein concentrations?
-remove 5' cap and poly-A tail
-these mRNAs are recognized by proteins (exonuclease) and will digest the mRNAs
how can the cell control the disrupt of a mRNA
Francis Crick and Sydney Brenner
who determined that the genetic code is a triplet code? (3 nucleotides code for an amino acid)
Nirenberg and Matthaei
who determined what codons code for what amino acids?
-used synthetic RNAs and radiolabeled amino acids in a cell free system to demonstrate what UUU, AAA, and CCC coded for
what did Nirenberg and Matthaei do to determine what codons code for what amino acids?
-create synthetic RNAs by trapping the triplets with ribosomes and tRNA to decipher the rest of the genetic code
What did Leder, Khorana and others do to determine what codons code for certain amino acids?
how many potential reading frames are there when determining codons?
act as a translator when converting nucleotide information into amino acid/proteins
-anticodon on tRNA uses complementary base pairing to form cloverleaf structure
transfer RNAs (tRNAs) with an amino acid covalently attached at 3' end function
An enzyme that joins each amino acid to the appropriate tRNA.
-uses energy of ATP to conjugate aa to tRNA
-leaves a high energy bond that is used to drive polypeptide chain formation in the ribosome
what does aminoacyl-tRNA synthetase do?
3' to 5'
in what direction does the anticodon on tRNA interact with the mRNA?
multiple codons encode the same amino acid
-a single tRNA can often recognize more than one codon because of expanded-base pairing
-in most cases, there is more than one tRNA for an amino acid
reasons the genetic code is degenerate
Flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon.
single change in a nucleotide base
leads to a stop codon in place of an amino acid
a change in amino acid, but with similar chemical properties
missense mutation (conservative)
a change in an amino acid, but with very different chemical properties
missense mutation (nonconservative)
insertion and deletion
these types of mutations cause frame shifts (2)
-mixture of protein and RNA (mainly RNA)
-large subunit and small subunit
what's the "mRNA decoder"
-70S (50S and small 30S)
-60% rRNA, 40% protein
-simultaneous transcription and translation
-free in cytosol
-binds shine-dalgarno sequence
-uses formyl-methionine (initiator tRNA)
-mRNAs are polycistronic
structure and function of bacterial ribosome (7)
-80S (large 60S and small 40S)
-40% rRNA, 60% protein
-free in cytosol or bound to rough ER for secreted protein
-uses 5' cap followed by first AUG
-mRNAs are monocistronic
structure of eukaryotic ribosome (5)
-ribosomal RNA gives the complex its structure
-RNA catalyzes the peptide bond reaction
-catalytic site is in the RNA of the large subunit
similarities between bacterial and eukaryotic ribosomes
a type of RNA that can act as an enzyme
-formation of peptide bonds (covalently link amino acids)
what happens in the large ribosomal unit?
-matches tRNA to mRNA (complementary base pairing)
what happens in the small ribosomal unit?
-large ribosomal unit
-small ribosomal unit
-components of ribosome (6)
-new tRNA enters an empty A site and base pairs
step 1 of protein production
formation of peptide bond
-done by ribosomal RNA
-covalently bonds amino acid from tRNA to amino acid on incoming tRNA
-prevents chain from falling out of ribosome
step 2 of protein production
the amino terminal
what is the first part of the protein that's going to come out of the ribosome?
-peptide bond formation with carboxyl group of preexisting amino acid to newly incoming amino group
why does the amino terminal come out first during protein production?
large subunit shifts exactly three nucleotides relative to small subunit
-shifting to next codon in mRNA
-ejects tRNA and leaves a free A site
step 3 of protein production
brings ribosome back to original position three nucleotides down to begin the cycle again
step 4 of protein production
protein that acts as a quality control mechanism to ensure that the right tRNA gets put into the ribosome
-does so by using the energy of GTP hydrolysis
elongation factor Tu (EF-Tu)
Enzymes that catalyse the hydrolysis of GTP.
--helps promote the shift in the small subunit down the mRNA
-beings with AUG
-initiator tRNA with methionine binds in p-site of small subunit with translation initiation factors
how does protein translation start in eukaryotes?
-begins with Shine-Dalgarno sequence (special sequence in the mRNA)
how does protein translation start in bacteria?
-bacterial mRNAs are polycistronic (read as one long mRNA but code for multiple different proteins)
-need to have ribosome binding sites
why do bacterial cells use Shine-Dalgarno sequence to start translation? (2 reasons)
mutations that alter a stop codon
-binding of a release factor to the ribosomal site
-catalysis using a water reaction that will release the polypeptide chain from the p-site tRNA
-ribosome dissociates and subunits can bind a new mRNA
what happens once the RNA reaches a stop codon?
string of ribosomes simultaneously translating regions of the same mRNA strand during protein synthesis
by measuring the number of ribosomes on an mRNA
how do scientists get a sense of the efficiency of translation?
degrades unneeded, damaged, or faulty proteins by cutting them into small peptides
-use ATP to unfold protein
-hydrolyzes the peptide bond to break protein into small peptides
how do proteasomes work? (2 step)
enzyme that digests protein
-protease in the middle
-protein domains that cover up protease
-barrel shape structure
structure of proteasome
A protein that attaches itself to faulty or misfolded proteins and thus targets them for destruction by proteasomes
1. chaperones to help fold
2. bind co-factors or other proteins
4. proper cellular localization
possible post-translational modifications for protein function (4)
-early RNAs provided genetic, structural, and catalytic functions
-expected properties: storing information and self-replicating, catalyzing reactions
RNA world hypothesis
-ribose is readily formed from formaldehyde (one of the likely chemical components of early Earth)
-deoxyribose is harder to make and requires protein catalysis
evidence of RNA world hypothesis (2)
-chemically more stable
-can make longer chains
-double stranded allows for higher fidelity in repair
-use of thymine contributes to ability to repair since deamination of cytosine makes uracil (easier to recognize a mistake)
why would DNA take over as information storage instead of RNA? (4)
-certain pieces of DNA were lost from cells so they only retained the DNA that made the cell type
-parts of the DNA might be permanently turned off so that only the right genes were expressed
historical hypotheses on how cell types became differentiated (2)
putting the nucleus (genetic information) from a differentiated frog cell into an egg cell with the nucleus removed could become a whole organism
-so no DNA was lost
What did Sir John Gurdon demonstrate?
-through contacts in the major and minor groove
-amino acid side chains make hydrogen (ionic and hydrophobic) bonds with nucleotide base pairs
-each base pair has unique patterns of hydrogen bond donors so the protein transcription and regulatory factors can recognize a specific sequence in the DNA
how do proteins interact with DNA? (3)
two of the same proteins
two different proteins coming together
the initial step of transcription
if you were going to regulate gene expression, what would you try to regulate?
in response to the environment
when would you like to express multiple genes (to make proteins) at the same time?
cluster of genes that are co-regulated
regulatory DNA sequence in the promoter region (distinct from -35 and -10 sequences)
bacterial genes tend to be organized into ______
prevent RNA polymerase from initiating transcription
these promote RNA polymerase transcription initiation
when tryptophan concentration in E. coli cells is too low, is the operon on or off?
when tryptophan concentration in E. coli cells is too high, is the operon on or off?
enzymes that exist in active and inactive forms
it increases the distance between them
what does tryptophan do to the alpha helices on the repressor when bound?
-creates a perfect shape that fits right into the grooves of DNA where it can bind and block the ability of the RNA polymerase to activate transcription
what happens when the helices on tryptophan are bound to the repressor?
what is the preferred carbon source for E. coli?
by breaking down a molecule of lactose
how can glucose be made?
an enzyme that breaks down lactose
enzyme that allows lactose to get into the cell
-creates a single RNA overall
parts of the lac operon (3)
structural gene on lac operon whose function is unclear
-turn on expression to create glucose rapidly
-turn on cAMP, promoting CAP activator binding to the DNA, recruiting in RNA polymerase, creating high level of expression
what does the lac operon do when there's a lot of lactose and no glucose?
inducer in LAC operon
-binds to lactose repressor, changing the shape, not attaching to DNA so RNA polymerase can transcribe lac operon
Describes the way in which groups of transcription regulators work together to regulate the expression of a single gene.
1. PCR amplifies a particular sequence of DNA or cut a piece out with restriction enzymes
-contains proper restriction enzyme sites at 5' and 3' end
first step of expression in E.coli in the lab
-digest the expression vector with the same restriction enzymes that matches with PCR product
second step of expression in E.coli in the lab
ligate the insert with the vector
third step of expression in E.coli in the lab
transform into competent cells (lab e.coil strains that have been cultured in a way where they can take up new pieces of special DNA)
fourth step of expression in e.coli in the lab
-plate onto petri plates with agar and antibiotic to kill any cell that did not take up plasmid
fifth step of expression in e.coli in the lab
Other sets by this creator
german 101 vocab
breaking into wall street flashcards
Recommended textbook solutions
Campbell Biology, AP Edition
Cain, Jackson, Minorsky, Reece, Urry, Wasserman
Fundamentals of Biochemistry: Life at the Molecular Level
Charlotte W. Pratt, Donald Voet, Judith G. Voet
Miller and Levine Biology
Joseph S. Levine, Kenneth R. Miller
Fundamentals of Biochemistry
Charlotte W. Pratt, Donald Voet, Judith G. Voet