Genetic Information Transfer Flashcards
Genetic info is stored in a class of molecules called _____.
nucleic acids
The central dogma of genetic information transfer…
- DNA polymerase replicates DNA.
- RNA polymerase transcribes DNA > RNA.
- Ribosomes translate RNA to proteins.
Key structural difference beween RNA and DNA
- RiboNucleic Acid has an OH group on the 2’ carbon of its sugar.
- DeoxyriboNucleic Acid has a H on the 2’ carbon of its sugar (aka deoxidized).
Nucleotides are comprised of…
- a base (a purine or pyrimidine)
- a (deoxy) ribose, aka a sugar
- and phosphate PO4 (one or more)
Nucleotides are joined together through…
Nucleotides are joined together through phosphodiester bonds between the 3’ oxygen on each nucleotide’s sugar and the phosphate group of the neighboring nucleotide attached to its sugar’s 5’ carbon.
These phosphodiester bonds form the “backbone” of the polynucleotide.
Polynucleotides structures of one-strand and 2-strand DNA are stabilized through…
base stacking.
purine (A, G) and pyrimidine (T/U, C) pair via…
Hydrogen bonds.
The conformation of the base can affect H-bonding.
“sugar pucker” conformation…
The “sugar pucker” conformation affects nucleic acid’s tertiary structure by influencing whether it is tightly or loosely compacted.
It determines the distances between phosphates in the phosphodiester backbone.
The conformation of the base (syn vs. anti) determines how nucleotide bases interact.
DNA and RNA favor DIFFERENT sugar pucker conformations.
Z-form DNA includes both anti and syn conformations.
DNA structure basics
Typically 2-stranded in cells.
The two strands run antiparallel (3’ and 5’ on opposite ends).
Turns right-handed.
RNA structure basics
Typically single-stranded in cells.
Widely variable secondary structures.
Multi-functional molecule.
In forming nucleotide chains (polynucleotides), which end serves as nucleophile?
The 3’ hydroxyl is deprotonoated and acts as nucleophile, attacking the phophate off of the 5’ C on the next nucleotide.
Because of this, nucleotides are always added in a 5’ to 3’ manner.
nucleoside
A nucleoSIDE is a base connected to a pentose (5 carbon) sugar.
(no phosphate group)
glycosidic bond
The glycosidic bond links the base and the sugar to form a nucleoSIDE.
Occurs between the 1’ position carbon on the sugar and a nitrogen on the purine or pyrimidine base.
nucleoside monophosphate
A nucleotide with 1 phosphate group.
(phosphate-sugar-base)
This is what the final nucleic acid polymer is composed of.
nucleoside triphosphate
A nucleotide with 3 phosphate groups.
(phosphate-phosphate-phosphate-sugar-base)
These serve as high-energy building blocks used by the cells to synthesize the nucleic acid polymer.
Core chemical mechanism of joining nucleotides to form DNA:
1) Oxygen on 3’ carbon activated via deprotonation by a base.
2) 3’ O acts as nucleophile, attacking alpha phosphate of a nucleoside triphosphate.
3) Pyrophosphate (2 of the 3 phosphates) acts as a leaving group to drive the reaction forward.
The nucleotides always add to the 3’ end, so the strands are always extended from 5’ to 3’.
most common nucleotide base pairing pattern
H-bonds occur between the amino and carbonyl groups.
In Watson-Crick-Franklin base-pairing, H-bonds occur between the bases of two strands running anti-parallel to each other.
A-T (2-H bonds between adenine and thymine)
C-G (3 H-bonds between guanine and cytosine)
B-form double-stranded DNA helix
- Right-handed helix.
- Strands are antiparallel (maximizing WCF base-pairing).
- Sugar-phosphate backbone is oriented to the outside.
- Nucleobases are oriented to the inside.
Does B-form DNA need to unwind to interact?
NO! There is a wide, deep MAJOR groove
and a shallow, narrow MINOR groove in the B-form double helix.
Hoogsteen base pairs
When anti/syn-conformation nucleotides form base pairs.
(vs. traditional Watson-Crick-Franklin anti/anti base pairs)
Only the purine nucleotides (A, G) can take on syn conformation.
Linking Number
Linking number defines the topology of DNA twists.
LK=TW+Wr.
Linking number = sum of its twist and writhe.
Twist and writhe are inversely proportional.
B-form geometry, with equal numbers of Tw and Wr is very energetically favorable!
supercoiling
changing twists in DNA molecule.
(recall yoyo string example).
Supercoiled DNA is more compact.
If delta Lk=0, then DNA is relaxed.
If delta Lk<0, then DNA is unwound and negative supercoiling occurs. (most common in cells)
If delta Lk>0, then DNA is overwound and positive supercoiling will occur.
Topoisomerases
Topoisomerases are enzymes that change DNA topology by changing the linking number of DNA. This involves cutting, rearranging, and resealing the structure.
Help DNA compact and deal with disruptive structures that might form during replication and transcription.
Melting Temperature of DNA
Tmelting = the temperature at which the helix is half double-stranded and half-single-stranded.
(aka 50% denatured)
Stable helix = high Tm
Unstable helix = low Tm
Nucleosome
DNA wrapped around histone proteins.
The fundamental unit of eucharyothic genome packaging.
DNA must be unwrapped from around histone before a gene can be transcribed.
Chromatin
A form of DNA packaging. Tight and very compact, but not very accessible.
Histone acetylation
Marker that makes DNA MORE ACCESSIBLE. Found in euchromatic regions.
Histone methylation
Marker making DNA INACCESSIBLE. Found in heterochromatic regions. Also marked by binding of heterochromatin proteins.
What is the preferred sugar-pucker conformation of DNA nucleotides?
C2 endo conformation; dominates B-strand DNA.
C3 endo conformation can be adapted by A-strand DNA.
phosphodiester bond
phosphodiester bond occurs between the 3’ OH and the phospho group on the 5’ C. Links the nucleotides in the polynucleotide strand.
A base activates the OH for nucleophilic attack of the dNTP (deoxyribonucleotide 5’-triphosphates). diphosphates act as leaving group.
Why is DNA the principal storage, and not RNA?
RNA is more suseptible to degradation than DNA. The 2’ OH makes it more reactive and can break down the chain.
DNA Polymerase
the enzyme (and protein) that catalyzes nucleotide addition for replication.
Requires a primer–a short double-stranded segment–to start replication.
Uses metal ions (Mg2+) to interact with triphosphate groups of incoming nucleotides, stabilizing neg charged transition state.
Why does DNA polymerase require a primer?
base-pairing provides a portion of the stability; the primer facilitates base STACKING, which is energetically favorable.
exonuclease
When DNA polymerase makes mistakes and its own proofreading doesn’t catch it, it can cause instability that leads the DNA strand to the exonuclease site on the polymerase.
The exonuclease removes the erroneous base, and polymerase has another chance to add the correct base. Cleaves 1 nucleotide at a time from the END of a strand.
frequency of DNA mistakes
DNA polymerase error rate is about every 1 in 100,000 to 10,000,000 additions
What happens at the DNA replication fork?
leading strand and lagging strand split in opposite directions.
The leading strand undergoes continuous synthesis 5’ to 3’.
The lagging strand requires a series of primers to synthesize 5’ to 3’. Therefore, it is made of a series of discontinuous Okazaki fragments, linked together by DNA ligase.
Telomerase
prevents shortening at the end of the lagging strand during DNA replication.
