Chapter 5: Molecular Biology Flashcards
Nucleic Acids
DNA is short for deoxyribonucleic acid. DNA and RNA are called nucleic acids because they are found in the nucleus and posess many acidic phosphate groups.
What modification makes the ribose special
The 2’ OH is missing
DNA Structure
I. 3.1 DNA STRUCTURE
A. General overview
- DNA – deoxyribonucleic acid
a) building block is deoxyribonucloside 5’ triphosphate (dNTP)
b) Bases:
(1) Purines
(a) Adenine
(b) Guanine
(2) Pyrimidines “cut”
(a) Cytosine
(b) Uracil
(c) Thymine
(3) A purine always pairs with a pyrimidine!
(4) A-T, A-U; C-G (Chris Gerard is strong)
c) Nucleosides are the sugar and base
d) Nucleotides are nucleosides, plus phosphate groups
(1) Polynucleotides - Nucleotides are linked by phosphodiester bonds between 3’ hydroxy group of 1 deoxyribose and the 5’ phosphage group of the next deoxyribose
B. Watson-Crick Model of DNA Structure (what about Rosalind Franklin? rude.)
- Cellular DNA is a right-handed double helix held together by hydrogen bonds between bases
- Double helix structure is antiparallel orientation
a) 5’-3’ strand lines up with 3’-5’ strand
b) A purine always binds with a pyrimidine
(1) A binds to T with 2 H bonds
(2) C binds to G with 3 H bonds (therefore slightly stronger than A—T bonds)
c) Chargoff’s rule: [A] = [T] and [G] = [C], and [A] + [G] = [T] + [C]
d) Tm = Temp at which 50% DNA is melted
(1) The more C—G bonds, the higher the Tm - Chromosome – one of several large pieces of linear ds-DNA
a) 46 chromosomes, 23 pairs in humans (>109 base pairs)
b) Single circular chromosome in bacteria (106 base pairs)
c) Circular or linear in virus - DNA gyrase – enzyme in prokaryotes that uses ATP to break and twist the circular DNA chromosome, resulting in super-coiled DNA
- Nucleosomes – DNA wrapped around histones – like beads on a string (mostly basic so they are attracted to the acidic DNA)
The building block of DNA
dNTP where N represents one of the four basic nucleosides
nucleoside
ribose with purine or pyrimidine linked to the 1’ carbon in a β-N-glycosidic linkage
In the β- N-glycosidic linkage of a nucleoside, is the aromatic bade above or is it below the plane of ribose in a Haworth projection
Above (β)
When nucleotides contain 3 phosphate residues, they may also be referred to as
deoxynucleoside triphosphates, they are abbreviated dNTP
The ribose plus phosphate portion of the nucleotide is referred to as the
backbone of DNA because it is invariable. The base is the varible portion of the builiding block. Hence there are 4 diff dNTPs and they differ only in the aromatic base.
What is the backbone in protein and the variable portion of the amino acid?
Peptide bonds with a carbon between them are the backbone and the R group attached to the alpha carbon is the variable portion
The Job of the DNA
A. Role of DNA – to transmit the genetic information passed down from parent to offspring
B. Genetic code
- Transcription – DNA to RNA
- Translation – RNA to protein
- Central Dogma – DNA → RNA → protein
a) mRNA copies DNA
b) mRNA travels to cytoplasm and hooks up with a ribosome
c) The ribosome synthesizes polypeptides with the help of tRNA - 3 base pairs = 1 codon
a) 64 codons; 61 specify AAs, the remaining 3 are stop codons (aka nonsense codons)
Stop Codons are UGA, UAA, UAG
b) Many codons that have the same first 2 base pairs code for the same AA (CUU, CUA, CUG)
A. GENETIC MUTATIONS– 3 kinds
- Point mutations – single base pair subsitutions
a) Transitions (subbing one pyrimidine for another pyrimidine)
b) Transversions (subbing a purine for a pyrimidine, or vice versa)
c) 3 subclasses:
(1) Missense: cause one AA to be replaces with another AA
(2) Nonsense: cause a stop codon to replace a regular codon
(3) Silent: change a codon into a new codon for the same AA - Insertion mutations – the addition of one or more extra nucleotides in DNA
a) Frameshift mutation! Very serious - Deletion mutations – the removal of one or more extra nucleotides in DNA
a) Frameshift mutation! Very serious
If an enzyme binds to a specific sequence of nucleotides in DNA, will the binding specifity be derived from interactions of portions of the polypeptide enzyme with the ribose and phsophate groups or with the purine and pyrimidine base?
Since the backbone is the same regardless of the nucleotide sequence, the specifity in binding must be derived from interaction with bases.
Nucleotides in the DNA chain are covalently linked by
phosphodiester bonds between the 3’ and 5’ of two diff deoxyribose
Which rxn is thermodynamically more favorable: the polymerization of nucleoside monophosphates or the polymerization of nucleoside triphosphates
During polymerization of nucleoside triphosphatesm pyrophosphate is released and hydrolyzed driving the polymerization rxn forward.
The end of the chain with a free 5’ phosphate group is written first in a polynucleotide with other nucleotides in the chain indicated in the 5’ to 3’ direction.
Make sure you understand this.
