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93 Cards in this Set
- Front
- Back
What is a Genome? |
All the DNA present in a cell
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Genotype |
genes that are not visibly expressed or observed |
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Phenotype |
genes that are observable |
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What does the Central Dogma consist of? |
1. DNA Replication 2. Transcription 3. Translation |
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What is Transcription? |
the production of mRNA from genes of DNA. A template DNA strand is used to produce a complimentary RNA strand |
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What is Translation? |
the production of proteins from mRNA |
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Differences in DNA and RNA strand numbers? |
DNA: double stranded RNA: single stranded |
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Type of sugars in DNA |
deoxyribose |
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Type of sugar in RNA |
ribose |
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Nucleotides present in DNA |
A, T, C, and G |
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Nucleotides present in RNA |
A, U, C, and G |
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Number of bonds between nucleotides C and G |
3 Hydrogen bonds |
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Number of bonds between nucleotides A and T or A and U |
2 hydrogen bonds |
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What are histones? |
proteins that DNA wraps itself around |
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What are Nucleosomes? |
protein + DNA combination |
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What is chromatin? |
compact structure made of many nucleosomes bound together |
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What does semi-conservative mean in DNA replication? |
the template strand is used + newly synthesized complimentary strand = new DNA double helix |
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What is the role of Dna A? |
binds to the origin of replication to begin DNA replication. breaks the hydrogen bonds between the nitrogen bases to separate the 2 strands. Local region becomes single stranded. This breaking requires ATP. |
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What is the role of Dna B Helicase? |
It unwinds the 2 strands from each other and "opens" up the double helix. |
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What is the role of Dna Gyrase? |
Creates little notches in the sugar-phosphate backbone to relieve stress due to supercoiling. Prevents the backbone from breaking during replication. It is a form of topoisomerase found in E.coli |
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What does SSB stand for in SSB proteins? |
Single strand binding proteins |
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What is the role of SSB proteins? |
prevent the separated DNA strands from joining back together |
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What is the role of DNA Primase? |
produces the RNA primer. Short RNA strands made of 10 nucleotides that are complimentary to the template DNA strand |
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What is the role of DNA Ligase? |
Joins the DNA fragments together using phosphodiester bonds between 3' hydroxyl of the growing strand and the 5' phosphate of an Okazaki fragment |
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True or False: Most prokaryotes have a bidirectional replication from a single origin of replication. |
TRUE
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True of False: Archaea just have one origin of replication |
FALSE. Some archaea have more than 1 origin of replication |
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What are replicaton forks? |
replication forks are a complex of the entire DNA replication process |
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what is a replicon? |
a segment of DNA that contains a single origin of replication. Eukaryotes have multiple origins of replication therefore have multiple replicons whereas prokaryotes have a single origin of replication so the entire DNA strand is considered a replicon. |
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What direction does DNA synthesis occur in? |
5' to 3' direction |
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What directs the direction of replication? |
template strand |
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What does DNA polymerase III contain? |
10 proteins & 2 core enzymes |
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What do core enzymes do? |
1. proof read 2. bind both strands of DNA at the same time |
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What is a replisome? |
A protein complex including DNA polymerase III |
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What is the role of Topoisomerase? |
relives tension caused by rapid unwinding. |
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What is a primosome and what is it involved in? |
It is a combination of primase + other proteins and is involved in primer preparation |
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Explain the term Leading Strand |
- Leading strand (5'-3') direction is synthesized starting from the 3' end. DNA polymerase follows the helicase as it unwinds the helix and adds complimentary nucleotides. Polymerase needs a single RNA primer to help it begin DNA synthesis. |
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What direction is the lagging strand synthesized in? |
still 5' to 3', but it is synthesized in fragments since the parental strand is 5' to 3' |
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Describe synthesis of DNA in the lagging strand |
There are new RNA primer is needed for every Okazaki fragment. New DNA polymerases are also needed. DNA fragments are joined by ligase to form a complete strand. RNA primers and primosomes are then removed. |
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Describe the proofreading that is carried out by DNA polymerae III |
using exonuclease the mismatched bases are removed off where it is easiest to remove them, the 3' end |
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Codons |
sequence of 3 nitrogen bases and code for a single amino acid. Found in mRNA
Ex: AUG: start codon and codes for Methionine
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Name the codon that intiates the completion of DNA replication. |
Stop codon. This signals a trailer sequence that contains a terminator sequence used to stop transcription. Termination needs the aid of rho factors sometimes. |
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What happens before the start codon? |
coding region begins with the DNA sequence 3' TAC 5' which produces AUG |
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Name the 3 types of RNA and their functions |
1. mRNA: messanger RNA: carries the gene for protein synthesis 2. tRNA: transfer RNA: carries amino acids to different sites during protein sythesis 3. rRNa: ribosomal rNA: make up ribosomes |
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What is Polycistronic mRNA? |
mRNA found in prokaryote cells. They are mRNA that can code for several different polypeptide chains. |
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what is a sigma factor? |
helps the core enzyme of RNA polymerase to recognize the start of genes
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holoenzyme |
core enzyme + sigma factor. only the holoenzyme can begin transcription
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Name all the steps in Transcription |
1. Initiation 2. Elongation 3. Termination
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Describe Initiation |
RNA polymerase binds to a sequence on the DNA called the TATA box or the Pribnow box. |
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Describe Elongation |
A bubble is created through the separation of the two strands. The RNA polymerase follows the bubble until transcription is complete. |
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Describe Termination |
RNA polymerase dissociates. Termination factors (specific sequence of codons) use the aid of rho factors to signal this |
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What are the differences in transcription of eukaryotes? |
1. have 3 RNA polymerases 2. promoters have combinations of many elements 3. RNA polymerase II is a large aggregrate containing 10 + subunits |
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RNA polymerase II function? |
catalyzes production of hereogeneous nuclear RNA (hnRNA) also known as pre-mRNA which undergoes post-transcriptional modification to generate mRNA |
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What modifications are made during transcription? |
Pre-mRNA is altered to mature mRNA when it has it's 3' poly A tail attached to it, its 5' cap of 7 methylguanosine, and the introns removed by splicing |
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What do the cap and tail do? |
protect the mRNA from degradation and signal it is ready for transport to the cytoplasm. The cap also helps ribosomes recognize it in the cytoplasm |
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What do spliceosomes do? |
a large complex where splicing of the pre-mRNA occurs |
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Alternative splicing |
sometimes pre-mRNA is spliced so different patterns of exons remain |
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What is different about transcription in archaea? |
introns are left in the mature mRNA |
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Code degeneracy |
up to 6 different codons can code for the same a.a. |
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sense codons |
61 codons can code for a.a |
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stop (nonsense) codons |
do not code for codons, just signal the start, stop and termination of transcription |
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Name the direction of synthesis of translation |
N terminal (amino) --> C-terminal (carbonxyl) |
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What is the site of translation? |
ribosome |
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What is a polyribosome? |
a combination of mRNA and ribosomes. Used in translation |
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What is tRNA's role in translation? |
tRNA attaches to the a.a and helps build the protein
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Aminoacyl-tRNA synthetases |
a type of catalyst that helps change precursor a.a.'s to amino acyl tRNA |
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What is the minimum number of aminoacyl tRNA synthetase enzymes needed to attach a.a's to all the various tRNA molecules? Why? |
20. The aa-tRNA deliver a specific a.a to the ribosome to add to the polypeptidechain that is being produced. But a specific tRNA can only pick up its related a.a. |
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What is amino-acyl tRNA? |
It is a specific type of tRNA that grabs its related a.a and brings it to the ribosome to match up with it's related codon during the formation of the polypeptide chain. |
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What is missing in context to the amino-acyl tRNA? a.a. + tRNA + _____ ----> aminoacyl- tRNA + AMP + PPi |
ATP |
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What 2 molecules are needed to assist ribosomes with protein synthesis? |
Initiator factors and initiator tRNA |
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Describe Initiation of Translation |
1. fMet tRNA binds to the 30S ribosomal subunit 2. the 30S ribosomal unit contains a 16s ribosome that is complimentary to the Shine Delgarno sequence on the mRNA. So when the mRNA comes in it binds to the ribosome in the correct location through hydrogen bonding 3. The 50S ribosomal subunit finally comes in and attaches to the 30S ribosomal subunit |
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What is the Elongation cycle in Translation? |
the addition of amino acids to a growing polypeptide chain |
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Name the 3 phases of Elongation |
aminoacyl tRNA binding, transpeptidation reaction, translocation. It also involves several elongation factors |
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Describe ELongation in Translation. |
1. a.a. corresponding to the proper mRNA codon is added to the end of the polypeptide chain called the C-terminal end 2. tRNA binding sites are the A, P, E site 3. ribosome moves from codon to codon along the mRNA. |
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A site |
in the A site the codon on the mRNA is matched with its anticodon which has an a.a. on it. This complex is brought in by an aminoacyl tRNA corresponding to the codon in the A site. Then moves to the P site
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P site |
the attached a.a. is added to a growing polypeptide chain and is detached from the anticodon |
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E site |
the anticodon moves from the P site to the E site and leaves |
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Peptidyl transferase |
catalyzes the bonding between adjacent a.a. called a transpeptidation reaction to form the a.a. chain |
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Where does Termination of Protein synthesis take place? |
UAA, UAG, or UGA codons |
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What are release factors? |
the help to recognize the stop codons |
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There are ___ RF(s) in prokaryotes and ____ RF(s) in euaryotes |
3 and 1 |
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What do molecular chaperones do in protein folding? |
help to fold polypeptides, help to transport proteins across the membranes and protect the cells from thermal damage |
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Domains |
structurally independent regions of polypeptide that are separate by less structured regions |
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Protein splicing |
removes inteins of the polypeptide before folding and keeps the exteins |
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housekeeping genes |
consecutive genes that are constantly being expressed. Necessary for life |
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inducible genes |
genes that code for inducible enzymes and are only expressed when needed such as Beta galactosidase. Only if the levels of something are too high or too low is there repression of the gene (turned off) or induction (turned on) |
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What is the cause of induction and repression? |
the rate of transcription |
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Beta galactosidase |
an inducible enzyme that helps to break apart lactose (made of a molecule of galactose and and a molecule of glucose) through hydrolysis. By breaking apart these two molecules lactose is used to provide energy to the cell, when glucose levels are low |
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What does an inducer do? |
a molecule that binds to the repressor protein. This doesn't allow for the co-repressor to bind to the repressor which means the repressor can't bind to the operator site on the DNA. This means RNA polymerase can come in and bind. It essentially promotes transcription. |
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Repressor proteins |
a molecule that binds to DNA with the help of a molecule called the co-repressor (active). It takes up the binding site to where RNA polymerase usually binds and therefore blocks transcription from occurring. |
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Activator proteins |
promote transcription by promoting the binding of RNA polymerase |
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With the help of an inducer the activator protein can bind to the DNA. This promotes the binding of RNA polymerase even more to the DNA molecule |
if there is an inhibitor and it binds to the activator protein, the activator protein cannot bind to the DNA molecule. No transcription happens. |
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What is an operon? |
sequence of genes that code for a protein. Contains a promoter region, a operator region, and a structural gene |
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What is the role of DNA polymerase I? |
It removes the RNA primer and fills the gap in with a DNA primer |