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66 Cards in this Set

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In DNA replication, what are the fragments on the lagging strand called?
Okazaki fragments
What's the function of DNA primase?
Sythesize RNA primer on a DNA strand.
What are the functions of DNA polymerases?
1. Sythesize New DNA
2. "Proof Read" DNA
What does DNA ligase do during DNA replication?
Joins adjacent nucleotides.
What's the function of helicases?
Unwind the double helix.
How many ori sites do small circular DNA's of bacteria have?
One.
How many ori sites do chromosomes of Eukaryotic cells have?
multiple.
What does the parent strand at the 3' end of the template determine?
The leading strand in continuous replication.
What does the parent strand at the 5' end of the template determine?
The lagging strand.
What happens when DNA polymerases attatch to the lagging strand?
DNA polymerase makes new DNA,
removes RNA primer, and then DNA ligase joins adjacent fragments.
What forms the backbone of a DNA strand?
What are they structured?
Phosphates bound to deoxyribose sugars.
The 3' carbon of one sugar is linked through a phosphodiester to the 5' carbon of the next sugar
What is the specific type of double helix that is formed by DNA?
Right handed double helix.
What types of bonds hold the AT and GC base pairs together?
hydrogen bonds
What is the position of two DNA strands with respect to each other?
Antiparallel.
What is the major stabalizing force for the double helix?
Hydrophobic forces.
Explain the two experiments showing that our genetic material is DNA.
Avery, MacLeod, and McCarty, 1944 Experiment
• purified S strain extracts to characterize the transforming principle
• if DNA in the extract is destroyed, the transforming principle is lost
• pure DNA isolated from the S strain extract transforms R strain

Hershey and Chase, 1952 Experiment
• virus marked with radioactive isotopes. Protein labeled with 35S and DNA with 32P
• T2 bacteriophage (virus) mixed with bacteria and then thrown into a blender to shear virus from the cell
• bacteria are then separated from virus by centrifugation
• only radioactive DNA enters the bacteria
• conclusion: DNA is the genetic material
The process by which DNA copies:
Replication.
The process by which DNA makes RNA:
Transcription.
With separate chromosomes, eukaryotic cells replicate the ends of these chromosomes using...?
Telomerase
- an RNA/ protein complex that makes repeated copies of a DNA sequence at chromosomal ends using an RNA template
Do bacteria with circular DNA have a problem with replicating the ends?
No.
Why are proofreading mechanisms needed, and what are possible consequences of a failure to repair DNA?
Proof reading mechanisms are needed to correct mistakes made by DNA polymerase.
A possible consequence of a failure to repair DNA would lead to mutations and cause loss of genes specifying enzymes in biosynthetic pathways
What are the two "proof reading" mechanisms of DNA and how do they work?
•mismatch repair
- scans DNA after replication and corrects base-pairing mismatches
•excision repair
- mechanism to remove abnormal bases
What is the relationship between genes and enzymes in a Biochemical pathway?
Each gene specifies are particular enzyme.
What is the central dogma of DNA?
What observations conflict with this?
• DNA codes for the production of DNA (replication) and of RNA (transcription).
• RNA codes for the production of protein (translation).
• genetic information is stored in a linear message on nucleic acids.

Conflicting observations:
• some viruses use RNA instead of DNA as genetic material
• retroviruses convert RNA back to DNA (reverse transcriptase)
What is required for RNA transcription?
DNA-dependent RNA polymerase plus the four nucleotides (ATP, GTP. CTP and UTP).
How does transcription work?
• RNA polymerase and other proteins bind at the promotor.
• template strand is read 3' to 5' and the mRNA is synthesized 5' to 3'.
• termination sites free the RNA transcript from the template.
List the classes and explain the functions of RNA that are transcribed from DNA.
• mRNA- messenger RNA. The template for protein synthesis.
• tRNA- transfer RNA. The "adapter" molecule that converts nucleic acid sequence to protein sequence.
• rRNA- ribosomal RNA. The structural and sometimes catalytic molecule of the ribosome.
Define RNAi (interference), and explain how RNAi is useful for studies of gene function.
• double stranded RNA
• normal regulator of gene expression
• used to block specific gene expression
• potential for disease treatment
What is the direction of DNA synthesis, and what is made to start it?
Synthesis 5' to 3' and
starts with an RNA primer.
During DNA replication, in what direction is the strand read?
Read from 3' to 5'.
What is the difference between DNA polymerase III and DNY polymerase I?
DNA polymerase III synthesizes DNA in between fagments of RNA primer.
DNA polymerase I replaces the RNA primer fragments with DNA.
How can you tell what end of a DNA strand is the 3' or 5' end?
The 3' end is characterized by an OH molecule, while the 5' end is has an OPO3- molecule.
What are the steps in which DNA is synthesized on the lagging strand?
1. Primase creates fragments of RNA primer.
2. DNA polymerase III synthesizes DNA between the RNA primer.
3. DNA polymerase I replaces RNA primer with DNA.
4. DNA ligase joins adjacent fragments.
How do genes determine phenotype?
The synthesis of proteins.
SG:
What is the evidence the genes determine phenotype by coding for proteins?
The Beadle and Tatum experiment (mutants in bread mold, 1940s).
The experiment shows that when genes are mutated, they are unable to produce protiens that are essential for their survival.
Otherwise said, mutations cause loss of genes specifying enzymes in biosynthetic pathways.
What is kind of RNA strand is created by transcription from DNA?
mRNA; and the transcripted piece is called an RNA transcript.
In what direction is RNA transcribed, and what are the two involved sites called?
RNA is transcribed from 5' to 3'.
Transcription starts at the initiation site with a promoter, and it ends at the termination site.
What does RNA transcription require?
DNA-dependant RNA polymerase and the four nucleotides (ATP, GTP, CTP, and UTP--the nucleoside triphosphates)
SG:
Describe the process of transcription, and define coding strand and non-coding strand.
Transcription begins when RNA polymerase binds to a promoter site on the DNA. As the DNA unwinds, an RNA transcript is synthesized from 5' to 3' from a template strand. Transcription ends at the termination site.
What is a codon?
A codon is a sequence of three nucleotides that codes for the production of a specific amino acid.
Using the genetic code, write the corresponding anticodon sequence when given the codon (and vice versa).
U-A
C-G
What was the Nirenberg and Matthaei experiment?
Developed a method for in vitro protein synthesis requiring added mRNA.
SG:
What is the importance of AAtRNA synthetases to the process of protein synthesis?
AAtRNA synthetases "charge" or join tRNA with the appropriate amino acid.
Where is the genetic information in mRNA?
The codons.
How many tRNA's are there for each amino acid?
One.
What does it meant for tRNA to be "charged"? How does this happen, and where does the energy come from?
When tRNA is "charged," it has been joined by an amino acid. This is done by the aminoacyl-tRNA (AAtRNA) synthetases and the energy comes from ATP hydrolysis.
What does mRNA bind to in translation?
A ribosome.
A ribosome is made of two subunits, a small one and a large one. On the large subunit, there are four binding sites; what are they, and what at each?
T.A.P.E.

T (transfer) site- tRNA first binds, carrier by T or transfer factor
A (amino acid) site- tRNA binds to the anticodon
P (polypeptide) site- tRNA adds an amino acid to the growing chain
E (exit) site- empty tRNA exits the ribosome
SG:
What is peptidyl transferase?
RNA of the large rRNA subunit (RNA enzyme or ribozyme).
SG:
Briefly describe the events occuring during protein synthesis.
Initiation:
* mRNA forms a complex with the ribosome and charged tRNA.
* translation begins at the initiation codon (AUG)
* Hydrolysis of GTP signals completion.

Elongation:
* the growing polypeptide chain is attached to an amino acid in the P site.
* the next codon to be read is present beneath the A site.
* a peptide bond is formed between the new amino acid and the growing chain, transfering the chain to the tRNA in the A site
* EF-G (eEF2 GTP) binds and moves the ribosome moves down one codon moving the peptide-tRNA to the P site and the cycle repeats.

Termination:
* translation of a particular protein ends when the ribosome encounters one of three termination codons (UAG, UAA or UGA)
* release of polypeptide and ribosomes catalyzed by release factors (RF1 and RF3 GTP).
What is the initiation codon in translation?
AUG (the amino acid for this is sequence is methionine)
What are the three termination codons for translation?
UAG, UAA and UGA
In what direction does the ribosome travel the mRNA during translation?
5' to 3'
Name the complex created when more than one ribosome is involved in translation from a given mRNA molecule.
polysome
What is the significance of mRNA forming a circle?
Ribosomes are more readily recycled and used again.
What does the endoplasmic reticulum (ER) produce?
cell membranes, membrane proteins, and proteins destined to be secreted.
Where are proteins sythesized in the cell, and how are they able to leave the cell?
Proteins are synthesized in the cytosol of a cell. Those proteins that are destined for secretion have a "signal sequence" that attaches to "docking sites" on the surface of the ER. The protein then enters the RER, which gives it access to a system including transport vesicles and Golgi apparatus for modification and localization to sites within or secretion outside of the cell.
What are some insights gained from knowing that proteins destined for cell secretion have a "signal sequence"?
Other proteins made in the cytosol may have signals determining cell destination
How are proteins activated after translation?
phosphorylation, proteolysis, or glycosylation.
What are three ways that single base change can alter protein products?
1. misssense: results in one amino acid change
2. nonsense: results in stop codon
3. frame-shift: change "reading-frame" of genetic message
Where does DNA replication start on a chromosome?
At an origin or replication (ori).
In transcription, what is the difference between a coding strand and a non-coding strand?
A coding strand is used as the template during transcription. A non-coding strand is complimentary to the coding, or template, strand. Therefore, it can be assumed that the sequence of the mRNA is identical to the non-coding strand, except for the exchange of TTP for UTP.
As far as the ability to signal for specific anino acids during translation, what is the difference between an initiator codon and a termination codon?
An initiator codon signals for an amino acid, where as a termination codon only signals for a release factor.
How many amino acids does a normal codon translate for?
One.
What represents a mutation that would cause the greatest disruption of the protein produced?
One in which the protein is cut short by a termination codon.
What components are the minimal requirement for the biosynthesis of proteins?
mRNA, tRNA, and ribosomes