Chapter 4

What three factors compose RNA and DNA strand? What is the wholesome name for these three components.
A sugar, phosphate, and base. The sugar and phosphate together form the backbone while the base carries the genetic infomation. Nucleotide.
What is a codon?
Every 3 mRNA bases form 1 amino acid in a protein sequence.
Which 2 additional steps are important for the synthesis of protiens?
Poly(A) and mRNA addition. Introns are non-coding sections of RNA that are spliced out before the RNA molecule is translated into a protein.
What makes RNA and DNA different between one another? How are the linked? Draw it.
Sugar back bone is different. DNA Sugar is deoxyribose (lost one oxygen molecule), and the RNA sugar is ribose. Linked by phosphodiester bridges.
What are the bases in RNA and DNA? Draw them.
DNA: adenosine, guanosine, cytidine, and thymine.
RNA: Adenosine, guanosine, cytidine, uracil.
What is the difference between Purines and Pyrimidines? Which bases are in each? Draw the basic formation of both. What are the conformations.
Purines have 2 rings while pyrimidine has 1. Purine includes Adenine and Guanine. Prymidine includes thymine, cytosine, and uracyl. Purine can be both syn and anti. Prymidin can only be anti.
What is the difference between a nucleotide and a nucleoside?
A nucleoside consists of a base bonded to a sugar. A nucleotide is when the nucleoside is bound to a phosphate group with an ester bond.
-A Nucleoside is a glycosylated base.
All bases exist in a ____________ forms. Draw Uracyl and Guanine.
Tautomeric forms is essentially just moving the double bonds around from the basic formation of the base to the more common form of the base. Double bond at the oxygen is the keto form, at the nitrogen it is the enol form.
Where is the phosphate group attached to the ribonucleotide and the deoxynucleotide?
It is typicaly bound to the C5' structure that is opposite the base.
What makes a DNA molecule stable? What will high pH do? Low?
Stable over wide pH. High pH will cause hydrolysis of phosphoester bond. Low pH-glycosidic bond is destabilized.
Which nucleic acids can be made from these building blocks? Which parts are important for transmitting energy?
ATP-for majority of metabolic processes (adenine, ribose, and three phosphate groups) There is GTP which has (guanine, deoxyribose, and three phosphate groups). These are involved in metabolism and protein synthesis. Only phosphate groups are involved in transmission of energy.
What is 6-mercaptopurine used for? Caffeine effective in doing?
The first is for treating leukemia by blocking cell division. Caffeine is a stimulant.
Where can DNA be found? What is the shape of the DNA in these different organisms?
DNA can be found in bacteria and viruses-circular
-It is also in Eukaryotes and Adenoviruses-linear
What did R.E Franklin discover about DNA?
He discoved through x-ray diffraction that DNA has 2 strands that form an a-helix.
What did Watson and Crick discover about DNA chain?
1:They discovered that the DNA strands were anti-parallel.
2: The backbone consisted of phosphate and sugar
3: There was a major and minor groove located at the surface that exposed the BP
4: The bases are bound by hydrogen bonds to the opposite strand. GC-3 bonds and the AT-2 bonds.
In which conformation was DNA mostly in?
DNA is in the B conformation which is right handed.
Which are the different ways DNA can be denatured? What is the melting temperature for DNA?
DNA can be denatured via addition of heat, acid, or alkali material. This will cause the disassociation of the hydrogen bonds between the hydrogen molecules. Melting Temperature is 70.1 C.
How is DNA denaturation measured?
This is measured through the ability of the DNA bases to absorb light. It is easier for the bases to absorb light when the bases are exposed in single stranded DNA. Optimal absorption is at wavelength 260.
To carry out DNA synthesis what is required?
Nucleotides are required. A primer (for initiation) DNA polymerase and a proofreading mechanism.
How are the different nucleotides added to the DNA molecule when the new strand is being synthesized?
During synthesis, the stand is added via "dNTP" so this could be dATP, dGTP, dCTP, and the side product is PPi.
What is the function of t-RNA? What is an important feature of the t-RNA?
Has an anti-codon area that recognizes the codon sequences on mRNA and caarrry AA residues that match this sequence. A pseudoknot that promotes stability.
What is required for RNA synthesis?
Nucleotriphosphates, metals, DNA template strand (3'-5') RNA polymerase.
What does RNA synthesis NOT require?
Does not require direction or proofreading.
So what is the coding region for Prokaryotes?
The coding region for prokaryotes is the TATAAT (pribnov box at -10) and the TTGACA (-35 region).
What is the coding region for Eukaryotes?
The coding region is the TATAAA (TATA box, Hogness box) at -25 and the GNCAATCT (-75 region or CAAT box)
How is the mRNA modified?
The mRNA is modified by a cap at the 5' ed and a poly (A) tail at the 3'.
What is the start codon for eukaryots and prokaryotes?
What are the stop codons?