Term
| What are the three parts of a nucleotide? |
|
Definition
Nitrogenous base
Sugar group 5-carbon
Phosphate group |
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Term
| What is the difference between deoxyribose and ribose? |
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Definition
| With deoxyribose, carbon 2 only has a hydrogen while on ribose, carbon 2 has an OH group |
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Term
| What are the purines? Pyrimidines? |
|
Definition
Purines are adenine and guanine
Pyramidines are cytosine uracil and thymine |
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Term
| How does de novo synthesis differ with Pyramidines and purines? |
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Definition
| Purines start with an activated ribose group while Pyramidines start with bicarbonate and phosphate |
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Term
| How could one define a nucleoside? |
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Definition
| 5 carbon sugar and Nitrogenous base |
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Term
| Which part of the nucleotide accounts for why there are differences in nucleic acids? |
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Definition
| Nitrogenous base because the 5 carbon sugar and phosphate group do not change |
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Term
| What type of bond links nucleotides together to form DNA? |
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Definition
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Term
| Specifically how do nucleotides link together? (what group binds to what?) |
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Definition
| 5' phosphate group on one nucleotide binds to the 3' hydroxyl group of another nucleotide |
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Term
| What gives DNA it's chain polarity? |
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Definition
| The formation of an ester bond at carbon 5 and carbon 3 |
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Term
| What direction is DNA synthesized? |
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Definition
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Term
| What links nitrogenous bases across different stands of DNA during DNA synthesis? |
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Definition
| Hydrogen bonding of the nitrogenous bases |
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Term
| How many hydrogen bonds are required to link adenine to thymine? Guanine to cytosine? |
|
Definition
2 hydrogen bonds
3 hydrogen bonds |
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Term
| Which direction Does the sugar phosphate backbone of DNA twist? |
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Definition
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Term
| Specifically, why is DNA anti parallel? |
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Definition
| Because the Phosphodiester bonds run in opposite directions |
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Term
| What is the exposed charged (charge facing outside) of the sugar phosphate backbone? |
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Definition
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Term
| How could one define DNA replication and when does it occur? |
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Definition
| Copying DNA in preparation for cell division |
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Term
| Which direction do polymerase molecules read the DNA sequence? |
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Definition
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Term
| What is the function of RNA primase? |
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Definition
| To initiate the binding of the complementary sequence to the parent sequence during DNA synthesis |
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Term
| What type of bonding is responsible for DNA elongation? |
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Definition
| Hydrogen bonding between nitrogenous bases of the different strands |
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Term
| Which enzyme synthesizes small pieces of RNA |
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Definition
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Term
| What classification of molecules does RNA primase fall under? |
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Definition
| RNA primase is a molecule in RNA polymerase |
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Term
| Which direction of DNA is continuous and also known as the leading strand? |
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Definition
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Term
| How could one define Okazaki fragments? How are they formed? |
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Definition
| Pieces of DNA on the lagging strand which are formed by Rna primase jumping ahead 1000 base pairs Creating a discontinuous strand |
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Term
| What is the general function of DNA polymerase? |
|
Definition
| To catalyze the synthesis of DNA Replication |
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Term
| Which DNA polymerase is most common in our cells? Where did it first originate? |
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Definition
| DNA polymerase 1 which originated in prokaryotes |
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Term
| What is the primary DNA polymerase seen in bacteria? |
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Definition
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Term
| How do gaps in DNA which are jumped over during DNA synthesis eventually get filled? |
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Definition
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Term
| What is the function of ligase? |
|
Definition
To catalyze the formation of Phosphodiester Between 3' and 5'
*Essentially acts as a seal |
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Term
| What are the two functions of exonuclease? |
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Definition
To remove nicks in the DNA To remove mismatched nucleotide pairs by Inserting correct sequence at the 3' end and removing everything else ahead
*ESSENTIALLY IS JUST A PROOFREADER* |
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Term
| How does exonuclease remove a mismatched nucleotide pair? |
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Definition
| By inserting correct nucleotide at the 3' end and removing the mismatch ahead (in the 3' to 5' direction) |
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Term
| What are the two single codon amino acids? |
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Definition
| Methionine and tryptophan |
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Term
| In reference to a codon, what is a wobble? |
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Definition
| Variation in the third base of an amino acid but still coding for the same thing which effects the binding during translation. |
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Term
| What can synthesize DNA via de novo Onto the terminal end of the chain? |
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Definition
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Term
| What process refers to the making of RNA chains from DNA? |
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Definition
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Term
| Specifically, when does transcription occur within a cell? |
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Definition
| When a cell is active and DNA is replicating |
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Term
| Where at in the cell is one likely to observe transcription? |
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Definition
| In the nucleus of eukaryotic cells |
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Term
| During transcription, which forms of RNA are present within the cytoplasm of the cell? |
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Definition
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Term
| What are the three major steps of transcription? (Don't define, just list) |
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Definition
| Initiation, elongation, termination |
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Term
| What is the major event that occurs during initiation? |
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Definition
| Chromatin unfolds and exposes promoter regions |
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|
Term
| What is a promoter region? |
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Definition
| A sequence of DNA which serves to attract RNA to sites to initiate transcription. |
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|
Term
True or False:
Each type of RNA has its own promoter. |
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Definition
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|
Term
| Which RNA polymerase is associated with the transcription start site? |
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Definition
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Term
| Where can the promoter region for RNA polymerase 1 be found? Specifically, what is the arrangement? |
|
Definition
On the ribosomal DNA gene.
The promoter regions can be found in between stretches of repeating nucleotide sequences. |
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Term
| Which RNA polymerase has its promoter region located within the transcribed sequence? |
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Definition
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Term
| What three major events, related to transcription, occur when RNA polymerase attaches to its promoter region? |
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Definition
1) Transcription can now occur
2) Acetylation of histones by Acetyl CoA on the N terminal regions
3) Histone becomes methylated and phosphorylated which facilitates unfolding of DNA |
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|
Term
| What occurs once a histone molecule is methylated and phophorylated? |
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Definition
| Unfolding of DNA is facilitated |
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|
Term
| Which form of RNA polymerase functions most in the creation of mRNA? |
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Definition
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|
Term
| Which form of RNA polymerase functions to produce tRNA, ssrRNA, and snRNA? |
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Definition
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Term
| Which form of RNA polymerase functions to synthesize most of the rRNA molecules? |
|
Definition
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|
Term
| What does RNA Polymerase II help produce? |
|
Definition
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|
Term
| Which form of RNA polymerase is considered "most sensitive"? |
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Definition
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|
Term
| What does RNA polymerase III help produce? |
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Definition
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|
Term
| What does RNA polymerase I help produce? |
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Definition
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|
Term
| What sequence(s) does RNA polymerase II recognize in order to begin its work? |
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Definition
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Term
| What are three functions of RNA polymerase II? (there are more than 3) |
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Definition
1) synthesize mRNA
2) Help separate DNA strands
3) Initiates transcription
4) Control the process of elongation
etc. |
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Term
| Which form of RNA polymerase forms a "claw like orientation"? |
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Definition
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Term
| Which form of RNA polymerase takes part in the synthesis of 5s rRNA? |
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Definition
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|
Term
| Where does the activity of RNA polymerase I take place? |
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Definition
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Term
| How does pre-mRNA differ from functional mRNA? |
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Definition
| pre-mRNA contains introns which must be spliced out in order to become functional mRNA |
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Term
| When does the splicing of pre-mRNA to make it functional take place? (After what process) |
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Definition
| Takes place following transcription |
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Term
| During mRNA processing, what occurs at the 5' end of the newly created mRNA? |
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Definition
| The 5' end is trimmed by ribonuclease (a.k.a. endonuclease or spliceosome). This allows the 5' terminal cap to be created. |
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Term
| What happens to internal nucleotides during mRNA processing? (post-splicing) |
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Definition
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Term
| What happens to the 3' end of a newly created mRNA during mRNA processing? |
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Definition
| The 3' end is trimmed of its terminal non-coding sequence which results in the addition of a poly-A-tail after transcription |
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Term
| During transcription, what is the significance of the CCA terminus? What form of RNA does this generally occur with? |
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Definition
| The CCA terminus is synthesized to accept amino acids and is associated with the tRNA |
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Term
| What is the ultimate fate of rRNA during transcription? |
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Definition
| It is spliced out once the process is completed |
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|
Term
| In relation to transcription, what does the term enhancer refer to? |
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Definition
| Regulatory sites which stimulate transcription regardless of distance, location, or orientation to the active site. |
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Term
| In relation to transcription, what bind to enhancers? |
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Definition
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|
Term
| What is the function of the enhancer-activator complex during transcription? |
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Definition
| Enhancers and activators on the DNA cause a loop or bending in the molecule which recruits RNA polymerase. |
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Term
| What is the ultimate goal of transcription? |
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Definition
| To process mRNA molecules in order to produce proteins |
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Term
| What is the difference between a codon and a peptide? |
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Definition
| A codon is exactly 3 nucleotides while a peptide is 2 or more CODONS |
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Term
| How could one define translation? (What is synthesized? How?) |
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Definition
| Protein synthesis via decoding mRNA sequences of nucleotides in a sequential orderly way. |
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|
Term
| What type of enzymes are involved in translational initiation? |
|
Definition
| aminoacyl-tRNA synthetases |
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Term
| How could one describe translational initiation? |
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Definition
| Ribosomal subunit binds at the 5' end and slides down to the START codon (AUG). The Large ribosomal subunit will bind and form a complex with the small ribosomal subunit which will attract tRNA carrying methionine. Once the tRNA carrying methionine binds, initiation is completed |
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Term
| When does translation end? |
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Definition
| As soon as a stop codon is reached |
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|
Term
| How many different aminoacyl-tRNA synthetases exist? |
|
Definition
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|
Term
| During tranlation, specifically, how do tRNA's with amino acids add to the mRNA chain? |
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Definition
| tRNA's with amino acids add to the mRNA chain by reading from the 5' to 3' direction |
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Term
| Which of the three translation sites does a stop codon need to be in, in order to begin termination? Once this occurs, how does the process continue? |
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Definition
| The stop codon must be in the A site in order to begin termination. Once there, a release factor of that specific tRNA synthetase binds and the protein chain is released |
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Term
| What is the function of peptidyl transferase? What is the result of this molecule's presence? |
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Definition
| During translational termination, peptidyl transferase cleaves the peptide to tRNA ester linkage which releases the peptide from the tRNA and the ribosome |
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Term
| What is the function of chaperone molecules? |
|
Definition
| Following translation, chaperone molecules assist in the folding of the newly formed protein molecule in order to make it functional. |
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Term
| What is the significance of a protein molecule having hydrophobic regions? What is the ultimate result and how does this occur? |
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Definition
| The hydrophobic regions allow the binding of signal recognition particles that help attach particles to docking proteins. This allows the proteins to be transported across membranes |
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|
Term
| What is a nonsense mutation? |
|
Definition
| A single point mutation which results in changing to a stop codon. |
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Term
| What is a missense mutation? |
|
Definition
| Single point mutation which ends up changing the amino acid |
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Term
| What is a silent mutation and what position does it occur on? What is another name for this type of mutation? |
|
Definition
A single point mutation on the third position of a codon which does NOT change the amino acid present.
Also called a sense mutation |
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|
Term
| What is a frameshift mutation? |
|
Definition
| The insertion or deletion of a single nucleotide which may result in a different protein of a nonfunctional protein |
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|
Term
| Which site does the first tRNA molecule occupy during translation? |
|
Definition
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|
Term
| Which site does the second tRNA molecule occupy during translation? |
|
Definition
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|
Term
| During translation, once the P site and the A site are occupied, what happens to the amino acid, methionine? What does this result in? |
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Definition
| The methionine molecule is transferred from the P site to the A site. And the first tRNA molecule is released. The tRNA molecule originally occupying the A site now shifts down to the P site. This happens when the RIBOSOME shifts down the mRNA molecule. Afterward the next tRNA molecule enters and the process repeats itself until a stop codon is reached |
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Term
| In which direction does the ribosome move during the elongation process of translation? |
|
Definition
| From the 5' end to the 3' end |
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|
Term
| How does adenylate compared to adenine? |
|
Definition
| Adenylate is a nucleoSIDE while adenine is a nitrogenous base |
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|
Term
| What is the starting material for purine de novo synthesis? |
|
Definition
|
|
Term
| How does purine de novo synthesis get going, assuming the starting material is present? |
|
Definition
| Glutamine donates an ammonia to the PRPP molecule which starts the process |
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|
Term
| What is the final product of purine de novo synthesis? |
|
Definition
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|
Term
| How does the product of purine de novo synthesis get converted into each of its two respective nitrogenous bases? |
|
Definition
IMP + Aspartate + Energy from GTP --> Adenine
IMP + Glutamine + Energy from ATP --> Guanine |
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|
Term
| What is the 1st product of pyrimidine de novo synthesis? |
|
Definition
|
|
Term
| Where do the phosphate molecules come from during pyrimidine de novo synthesis? |
|
Definition
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|
Term
| Describe how dihydroorotate become citadil during pyrimidine de novo synthesis? |
|
Definition
| DHO gets oxidized into orotate. Orotate gets converted into uridylate. Uridylate reacts with glycine and ammonia in order to become citadil. |
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|
Term
| What accounts for the stability of a dsDNA molecule? |
|
Definition
| The great amount of hydrogen bonding. Adenine and Thymine produce 2 hydrogen bonds while Cytosine and Guanine will produce 3 hydrogen bonds. The bonds them self are NOT strong however, the large amount of these weak bonds makes the overall molecule very stable. |
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|
Term
| What is the role of a spliceosome? |
|
Definition
| It removes the intron sequence of a transcribed pre-mRNA molecule |
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|
Term
| What is the role/function of an snRNP "snurp"? |
|
Definition
| The snRNP will combine with an unmodified pre-mRNA molecule and various other proteins in order to form a spliceosome. |
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|
Term
| What is the effect of deletions in reference to mutations? |
|
Definition
| Large deletions often result in death while small deletion will show signs of a defect. |
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|
Term
| What is an oligonucleotide? |
|
Definition
| A short nucleic acid polymer with fewer than 50 base pairs |
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|
Term
| What is the difference between nucleic acids and nucleotides? |
|
Definition
| Nucleic acids are polymers of nucleotides |
|
|
Term
| What is structurally different between DNA and RNA? |
|
Definition
DNA is double stranded while RNA is single stranded
RNA has uracil while DNA had thymine |
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