Term
| How did scientists find out that DNA was the genetic material and not proteins? |
|
Definition
| experimentally through the Griffith Avery experiment and Hershey Chase Experiment |
|
|
Term
| What did the Griffith Avery experiment entail and what did it show? |
|
Definition
it used streptococcus bacteria and injected mice with two strands and a mix of those strands. Could isolate the heat killed S, so knew it was somehow passed down (through genes).
Part II: put mixed strain cells in all kinds of macromolecules, only DNA passed S strain on
CONCLUSION: DNA is genetic information |
|
|
Term
| What did the Griffith Avery experiment entail and what did it show? |
|
Definition
| labeled two bacteriophages (protein and DNA) with isotopes of P and S (P on DNA) and agitated to remove protein coats. S were only found out of cell and P only in cell and then went on to produce new viruses. Convinced community that DNA was genetic information |
|
|
Term
| what contains the carrying capacity of DNA? |
|
Definition
|
|
Term
| what allowed scientists to hypothesize that DNA replication is semi-conservative? |
|
Definition
| the double strandedness of DNA |
|
|
Term
| in what direction does DNA synthesis occur? |
|
Definition
| from the 5' to the 3' end |
|
|
Term
| Can DNA grow from the 5' end? |
|
Definition
|
|
Term
| What happens during the S phase of the cell cycle in terms of DNA? |
|
Definition
| it replicates in both directions from replication forks that open up the 2 strands of DNA to create bubbles |
|
|
Term
| what does semi-conservative replication mean? |
|
Definition
| that one of the parent strands is conserved in each of the two new daughter strands |
|
|
Term
| Mendelson and Stahl proved what about DNA? How did they prove it? |
|
Definition
that DNA is semi-conservative.
Replicated DNA in a heavy isotope of nitrogen and then a light one, so parent strand is heavy, daughter is light, and then suspended in cesium chloride which creates its own density gradient. DNA were often in the middle, i.e. semi conservative b/c one new strand and one parent strand. |
|
|
Term
| What is the replication origin? What is it rich in? |
|
Definition
the replication orgini is a specific DNA sequence that is recognized by proteins involved in initiating DNA replication
-it is rich in AT bonds since those are easier to open than C-G bonds |
|
|
Term
| what are the proteins that jump on the replication origin called? |
|
Definition
|
|
Term
| what happens at the replication forks? |
|
Definition
| new strands of DNA are synthesized |
|
|
Term
| what is the name of the enzyme that latches on to a dNTP to synthesize DNA at the replication fork? |
|
Definition
|
|
Term
| What are the four things DNA Polymerase III needs? |
|
Definition
1. unpaired base in DNA template strand
2. free 3' end on growing strand, i.e. a primer
3. a dCTP?
4. Mg++ ions |
|
|
Term
| What happens in replication of DNA? |
|
Definition
| RNA binds to separated DNA strands and then DNA Polymerase III latches on and begins replicating the DNA. Has an editing function to make sure that it has put on the right base. If not cuts it out. |
|
|
Term
| is the DNA polymerase low or high fidelity? |
|
Definition
|
|
Term
| Do the synthesis function and editing function of DNA polymerase take place in the same part of the enzyme? |
|
Definition
| No, they have their own functional domains in the protein |
|
|
Term
| continuous synthesis correlates with the lagging or the leading strand? |
|
Definition
|
|
Term
| How is the lagging DNA strand synthesized? |
|
Definition
| the RNA primer put in by DNA primase, builds a new starter piece, then the DNA polymerase fills in the gap between the RNA primer and the previous one, then falls off. DNA polymerase I cuts out the RNA and replaces it with DNA, then DNA ligase seals the gap to get a continuous piece of DNA |
|
|
Term
| How long is the RNA primer? |
|
Definition
| about 3-5 nucleotides long |
|
|
Term
| how long are average DNA strands? |
|
Definition
| about 1000-3000 nucleotides long |
|
|
Term
| What do we call the fragments of RNA that are changed into DNA by DNA Polymerase I? |
|
Definition
|
|
Term
| if the replication origin is the middle of an opened bubble which way do replication forks move? |
|
Definition
| in both directions away from the replication origin |
|
|
Term
| Do the Okazaki fragments have to be linked before a new one can be formed? |
|
Definition
| NO, they are ligated bit by bit. the most recently synthesized DNA on both strands are the strands closest to the replication forks |
|
|
Term
| what does DNA helicase do? |
|
Definition
| it unwinds the DNA as parental strands separate |
|
|
Term
| what does DNA primase do? |
|
Definition
| it synthesizes RNA primers |
|
|
Term
| what two enzymes form the primosome? |
|
Definition
| the DNA helicase and DNA primase |
|
|
Term
| what is the DNA binding protein? |
|
Definition
| it is the protein that binds to DNA whenever it opens up into a single strand to stabilize the strand |
|
|
Term
| What is the function of DNA gyrase? |
|
Definition
|
|
Term
| what enzyme is responsible for DNA repair? |
|
Definition
|
|
Term
| What is telomere end replicaton? |
|
Definition
| it is the process by which the new strand of DNA gets a telomere added |
|
|
Term
| why does telomere end replication happen? |
|
Definition
because the newly syntehsized strand is not long enough to put in a new RNA primer to reach the end of the telomere on the parent strand.
-if this didn't happen the strand would be prone to degradation or attacks from enzymes. |
|
|
Term
| what happens in telomere end replication? |
|
Definition
| -there is a separate telomerase enzyme with it's own RNA molecule to synthesize short DNA sections! (2009 NOBEL) |
|
|
Term
| do the telomeres of the parents and daughter strands have to be the same length? |
|
Definition
| No, just have to be in the same range, i.e. you don't want a coding region to be cut off or in the telomere |
|
|
Term
| as we age do our telomeres get shorter or longer? |
|
Definition
|
|
Term
| what is the central dogma? |
|
Definition
|
|
Term
| What is reverse transcriptase? |
|
Definition
| It is an enzyme that copies single stranded RNA into double stranded DNA and integrates the DNA into the host cell (this is how viruses work) |
|
|
Term
| what determines the amino acid sequence in proteins? |
|
Definition
|
|
Term
| what is the function of mRNA? |
|
Definition
messenger RNA
codes for a protein |
|
|
Term
| what is the function of rRNA? |
|
Definition
ribosomal RNA
codes for different ribosomes
Eukaryotes: 18S and 28S
Prokaryotes: 16S and 23S |
|
|
Term
| what is the function of tRNA? |
|
Definition
transfer RNA
-carries amino acids to the ribosome |
|
|
Term
| what is the function of snRNA? |
|
Definition
small regulatory RNA
has lots of jobs/functions |
|
|
Term
| do RNA form intra chain secondary structure? |
|
Definition
yes if there are complementary base pairs
i.e. a region TAG loops and pairs with CTA |
|
|
Term
|
Definition
| the process of copying RNA from DNA |
|
|
Term
| RNA has a complimentary sequence to the DNA _______ strand |
|
Definition
|
|
Term
| RNA has the same sequence as the DNA _______ strand |
|
Definition
|
|
Term
| what base does RNA have in place of a base in DNA? |
|
Definition
| uracil instead of thymine |
|
|
Term
| What are the main ways RNA transcriptase differs from DNA transcriptase? |
|
Definition
RNA:
-needs a template but not a primer
-CAN do denovo synthesis
-does not need a helicase (uses NTPs)
-has no editing function |
|
|
Term
| What are the main components of the RNA transcriptase? |
|
Definition
| the enzyme, the DNA unwound by enzyme jaws, RNA flipped out by enzyme flap, NTPs (substrate) that matches up with DNA template |
|
|
Term
| what end does RNA grow from? |
|
Definition
|
|
Term
| what kind of RNA transcriptase transcribes rRNA in eukaryotes? |
|
Definition
|
|
Term
| what kind of RNA transcriptase transcribes mRNA in eukaryotes? |
|
Definition
|
|
Term
| what kind of RNA transcriptase transcribes tRNA and snRNA in eukaryotes? |
|
Definition
|
|
Term
| what parts of the cell have their own RNA transcriptase enzymes? |
|
Definition
| chloroplasts and mitochondria |
|
|
Term
| what kind of RNA transcriptase transcribes tRNA and snRNA in prokaryotes? |
|
Definition
| there is only one RNA polymerase for prokaryotes |
|
|
Term
| How does transcription work? |
|
Definition
| RNA polymerase begins at the promotor region, sigma factor binds, transcription starts, RNA polymerase reaches terminator/stop site and falls off, RNA released |
|
|
Term
| what is the promoter region? |
|
Definition
| a sequence of DNA that tells the RNA where to go to start transcription |
|
|
Term
| what is the sigma factor? |
|
Definition
| a subunit of the polymerase that recognizes the promoter region (only in bacteria) |
|
|
Term
| what is the numbering of the first part of the coding sequence in RNA? |
|
Definition
|
|
Term
| what are the two regions that must be present in the prokaryotic promoter? |
|
Definition
| the -35 consensus sequence and the -10 consensus sequence or TATA sequence |
|
|
Term
| How do we know that the consensus sequences are important? |
|
Definition
| because if they are mutated in the lab then transcription is lost |
|
|
Term
| what dictates the direction of transcription? |
|
Definition
|
|
Term
| What are the two different ways that transcription can be terminated in prokaryotes? |
|
Definition
| Rho or Hairpin/Rho-independent |
|
|
Term
| What happens in Rho termination? |
|
Definition
| a secondary sequence of RNA is recognized by the rho protein. Protins jumps on RNA and pulls out transcript which stops the whole mechanism. this works on Rho-dependent genes--so they code for this? |
|
|
Term
| What happens in Rho-independent/hairpin termination? |
|
Definition
| -there are 2 long complementary RNA sequences that fold up to make a hairpin structure which signals for transcription to stop |
|
|
Term
| What is asymmetric transcription? |
|
Definition
| Each gene is only transcribed in one direction, (and only from one side of the DNA?) |
|
|
Term
| what does polycistronic mean? |
|
Definition
| when prokaryotic transcripts have coding information for more than one gene in a single transcript |
|
|
Term
| What are the main differences between prokaryotic and eukaryotic transcritps? |
|
Definition
| eukaryotic transcripts only code for one gene, euk have 5' cap 7-methylguanosine and AAAAA polyadenylation at 3' end |
|
|
Term
| what is the name of the group attached to the phosphates at the 5' end of eukaryotic RNA? |
|
Definition
|
|
Term
| what does the polyadenylation on the 3' end of the eukaryotic RNA prevent? |
|
Definition
|
|
Term
| Do prokaryotes or eukaryotes have non interrupted coding regions in RNA? |
|
Definition
|
|
Term
| what interrupts the coding regions in eukaryotic DNA? |
|
Definition
|
|
Term
| what is another name for the coding region? |
|
Definition
|
|
Term
| what is another name for the non-coding region? |
|
Definition
|
|
Term
| when are the introns in eukaryotic DNA cut out? |
|
Definition
|
|
Term
| the exons are very [large or small?] compared to the entire gene? |
|
Definition
|
|
Term
|
Definition
| mRNA that has the introns cut out and the coding regions spliced together |
|
|
Term
| where is the mature mRNA located? |
|
Definition
|
|
Term
| what structure splices mRNA? |
|
Definition
|
|
Term
| how do the snRNAs splice mRNA? |
|
Definition
snRNAs form base pairs with the 5' end of the intro and a region near the 3' end, the one near the 3' end is called the spliceosome.
-the intron loops out, the 5' end is cut and attached near the 3' end an then the 3' end is cut, the cut out intron forms a loop called a lariat |
|
|
Term
|
Definition
| an snRNA and associated proteins that cut out the introns from mRNA |
|
|
Term
| what is the result of splicing? |
|
Definition
|
|
Term
| where does splicing occur? |
|
Definition
|
|
Term
| what is the excised intron from RNA called? |
|
Definition
|
|
Term
| what is alternative splicing? does it occur in eukaryotes or prokaryotes? |
|
Definition
when multiple proteins are generated from RNA transcripts from a single gene.
This happens in both eukaryotes and prokaryotes and in 60% of all mRNA |
|
|
Term
| what is the advantage of alternative splicing? |
|
Definition
| it allows for proteins to be made with slightly different functions, i.e. to give parts of one kind of tissue two different jobs |
|
|
Term
| does splicing happen mostly in eukaryotic or prokarotic cells? |
|
Definition
| mostly in eukaryotic since that is where introns and exons are |
|
|
Term
| does alternative splicing happen mostly in eukaryotic or prokarotic cells? |
|
Definition
|
|
Term
| what are some of the main differences in transcription between prokaryotes and eukaryotes? |
|
Definition
prokaryotes have circular DNA
Eukaryotes:
-have a nucleus, where this takes place
-have linear DNA
-have 5' capping and 3' polyadenylation
-have intron splicing |
|
|
Term
|
Definition
| the process by which protein is synthesized from RNA |
|
|
Term
| what is the structure of tRNA? |
|
Definition
-looks like a cloverleaf
-made up of an amino acid, d loop, t loop and the anti codon for 3 bases |
|
|
Term
|
Definition
| the t RNA synthetase take energy from ATP and attach an amino acid through a high energy bond. |
|
|
Term
| what is the enzyme that loads the amino acid onto tRNA? |
|
Definition
|
|
Term
| what is a eukaryotic ribosome made up of? |
|
Definition
large subunit:
~49 proteins
3 RNA
28 S
small subunit
~33 proteins
1 RNA
18 S |
|
|
Term
| what part of the ribosome is thought to possess the peptidyl transferase activity? |
|
Definition
| the 28S and 18 S ribosomal RNA parts |
|
|
Term
| what is the peptidyl transferase activity? |
|
Definition
| it is the main enzymatic function of the ribosome that forms the links between amino acids during protein synthesis |
|
|
Term
|
Definition
| a series of 3 bases that codes for a specific amino acid |
|
|
Term
|
Definition
| a series of 3 bases that codes for a specific amino acid |
|
|
Term
| how many codons are there? |
|
Definition
|
|
Term
| what is the start codon? what amino acid does it code for? |
|
Definition
|
|
Term
| what is special about the stop codons? |
|
Definition
| there is no tRNA that matches up with these/no tRNA that has this anti codon (because the whole point is to stop making the protein) |
|
|
Term
| what does it mean that codons are degenerate? |
|
Definition
| that there are multiply ways to code for a specific amino acid. i.e. there are multiple codons for cysteine |
|
|
Term
| the genetic code (codons) is almost universal, what are the exceptions? |
|
Definition
| mitochondria and chloroplasts |
|
|
Term
|
Definition
| a 3 base sequence of amino acids |
|
|
Term
| where MUST reading frames start from? |
|
Definition
| from the first AUG sequence |
|
|
Term
| what is the region between the 5' end and the first AUG sequence called? |
|
Definition
| the UTR, untranslated region |
|
|
Term
| what are the 3 sites in the fully assembled ribosom? |
|
Definition
E site (exit)
P site (peptide)
A site (for amino acid) |
|
|
Term
| where is the mRNA binding site located in the ribosome? |
|
Definition
| in the small ribosomal sub unit |
|
|
Term
| what is a fully assembled ribosome composed of? |
|
Definition
| a large subunit, a small subunit and has the 3 binding sites and the site for mRNA to bind |
|
|
Term
| what are the three phases of translation? |
|
Definition
1. Initiation
2. Elongation
3. Termination |
|
|
Term
| what happens in intiiation? |
|
Definition
the formation of the initiation complex:
-need initiator tRNA which binds to mRNA and moves along looking for the first AUG sequence
part B:
the large ribosomal subunit binds, amino acetyl tRNA binds and the frist peptide bond is formed from the peptidly transferase activiity and the large subunit breaks the bond between the tRNA and methionine. |
|
|
Term
| where does the energy for the peptide bond between amino acids come from? |
|
Definition
| From charging the tRNA with the energy from breaking the ATP bond |
|
|
Term
| what happens in elongation? |
|
Definition
| a new tRNA binds to the ribosome, the previous tRNA that has already created the peptide bond falls off,the large subunit moves over to open up a space for a new tRNA, the recently binded one creates a peptide bond. |
|
|
Term
| what is attached to the start of the amino acid chain? |
|
Definition
|
|
Term
| What happens in termination in translation? |
|
Definition
| the ribosome reaches the stop sequence and a release factor binds instead of a tRNA. The amino acid chain ends and falls off and a carboxy group is attached to the end. the ribosomal subunits separate. |
|
|
Term
| what happens to ribosomal recognition in polycistronic mRNA? |
|
Definition
| ribosome binds and releases before each protein coding region |
|
|
Term
|
Definition
| when multiple ribosomes are simultaneously translating one mRNA (staggered start) |
|
|
Term
| what are the different levels of gene expression? |
|
Definition
major site: transcription
nucleus: replication and transcription
cytoplasm? mature mRNA to protein synthesis |
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|
