Linear Biopolymers and Central Dogma

Polymer

Covalent bond-linked chain of monomers
- Informational polymers have more than one kind of monomer, and the order of monomers is the information (DNA, RNA)

Joining Sites

The places where polymers can connect together, due to the chemistry of the monomers within.
- One joining site = no joining sites exposed at ends, no further side chain growth (only two monomers)
- Two joining sites = linear polymers of potentially infinite length
- Three joining sites = branched polymers (informational biopolymers are NOT branched)

Asymmetry of Informational Biopolymers

Made from asymmetric monomers, two joining sites but they are different
- asymmetry of monomers drives asymmetry of polymers
- DNA, RNA, and protein, growth of the chain occurs only at one end (unidirectional)

Nucleotides

Made of a polymer backbone (pentose sugar phosphate), with a characteristic heterocyclic base.
Join to each other on the 5' phosphate (negative) and 3' hydroxyl

DNA vs RNA Hydroxyl

Differ in the pentose sugar, Deoxyribose is missing the 2; hydroxyl of ribose. This makes DNA much more resistant to chain cleavage by hydrolysis - greater stability.

Heterocyclic Bases of Nucleotides

Purines: Adenine (A), Guanine (G)
Pyrimidines: uracil (U), Thyime (T), Cytosine (C)
Purines are larger, have the same basic ring structure but different add-ons. Pyrimidines have a single ring.
The methyl group on the 5' carbon of T makes it easier to repair mutations

Protein Monomers and Their Growth

The monomers are amino acids. The characteristic element is the amino acid side chain (R). The two joining sites are the amino (NH2) group and the carboxyl (COOH) group.
- Polymer growth is at the carboxyl end

Side Chains of Amino Acids

There are 20 different amino acid side chains, their chemical properities define three main classes of amino acid
1. Hydrophobic (8 amino acids)
2. Hydrophilic (includes acidic and basic, 9 amino acids)
3. Special (3 amino acids)

Adding Monomers to a growing Polymer Chain

The monomers need to be put in a higher energy state to be added to a chain
- nucleotide monomers are in the form of high-energy nucleotide triphosphates (NTPs)
- hydrolysis across the bond and the molecule is transferred to the chain, which is thermodynamically favourable. The outer two phosphates are "kicked out" when the NTP is incorporated into a growing nucleic acid chain
Even already energized monomers need an enzyme to catalyze the linkage reaction (ex. DNA polymerase)

tRNA

Amino acid monormers are in the form of high-energy amino-acyl-tRNA esters.
- the tRNA molecule is kicked out when the next amino acid is incorporated at the end of a growing polymer chain

DNA Structure

DNA strands are double-stranded (duplex DNA)
- held together by hydrogen bonds between complementary bases = watson-crick base pairs
- two strands are antiparallel
- they can be either left or right DNA (think about going up a spiral staircase, hand can be on the left or right)
- breaking these H-bonds allows the strands to separate, called denaturation

Uses of Major and Minor Grooves

DNA-binding proteins can make contact with BPs at major and minor grooves without having to separate the strands.

Denaturation and Tm

Tm is the temperature at which the DNA is one-half melted, which depends on its base composition
- DNA with a higher proportion of G-C BPs have a higher Tm, because they have more hydrogen bonds (3 H-bonds vs A-T having 2 H-bonds)

Central Dogma

DNA synthesizes DNA (heredity) -> RNA -> proteins
DNA synthesis is replication (making a perfect copy)
RNA synthesis is transcription (rewriting in a different nucleotide font, from dNTPs to rNTPs)
Protein Synthesis is Translation (rewriting in amino acids instead of nucleotides)

Transcription

Makes an RNA that is the same sequence as the non-template strand (both are complimentary to, and antiparallel with, the DNA template)
- DNA strand is exposed, this is the template strand
- RNA directly interacts with the template using the incoming monomer (rNTP) and only links if it forms a perfect pair
- RNA chain runs antiparallel to DNA, adding in the 3' direction

Transcription Bubble

Separates a small section of DNA at a time, where RNA polymerase binds to the promoter region and helicase locally separates the strands of DNA.
Moves along the DNA with RNA polymerase, transient unwinding.
When the original DNA duplex reforms, energy is released, allowing the newly-formed RNA to be taken off the template, and exit through a channel in the polymerase.

DNA Replication

Uses DNA as a template to make more DNA
DNA is unwound locally by helicase to expose the template and start sites, and the new strand is synthesized 5' to 3' antiparallel to the tempalte.
Monomers added are dNTP, interact directly with the template DNA with watson-crick base pairing.
Newly synthesized DNA does not unpair from the template strand.
- Start with one molecule of ds-DNA and end with two molecules of ds-DNA

Codons

The 3-character "words" that for amino acids, coded by nucleotides. Despite 64 possible combinations from the amino acids, there are 20 amino acids - many codons code for the same amino acids.

Protein Synthesis - Translation

Taking the nucleotide sequence and translating into an amino acid sequence.
Aminoacyl tRNAs adapt the nucleotide code into an amino acid.
The signal end binds to the mRNA (which it's complimentary to).
Ribosome makes the link between the amino acid and the terminal carbon (called a peptidyl transferase reaction), catalyzed by rRNA floating in ribosome

Summary Table of Transcription, Replication, and Translation