Biology Paper 2 - 2.3 Nucleic Acids

Double helix, polynucleotide, macromolecule.

In eukaryotes - in the nucleus, wound around histone proteins, held as chromosomes.
Mitochondria and chloroplasts have prokaryote like plasmids, single, double stranded loop of DNA.
In prokaryotes - free in the cytoplasm, single, double stranded loop, no histones, naked DNA.
Plasmids free in cytoplasm.

Monomers of DNA and RNA.

Phosphorylated nucleotides contain more than one phosphate group, e.g. adenosine di/triphosphate - the universal energy currency.
Regulation of biochemical pathways, e.g. cAMP.
Component of coenzymes, e.g. NAD - electron/proton carrier in respiration.

Deoxyribose (DNA), ribose (RNA).
Pentose sugar and phosphate group joined by a phosphodiester bond in a condensation reaction.
An organic nitrogenous base joined to the pentose sugar by a covalent bond formed in a condensation reaction.

Adenine, Thymine, Uracil, Cytosine, Guanine.

Guanine and adenine. Double nitrogenous ring.

Cytosine, thymine and uracil (uracil replaces thymine in RNA). Single nitrogenous ring.

A pyrimidine always pairs with a purine.
A always pairs with T (or U in RNA).
C always pairs with G.
A and T form two hydrogen bonds.
C and G form three hydrogen bonds.

The sugar phosphate backbones of each strand in DNA run in opposite directions.
The 5th carbon of the pentose is attached to the phosphate group This is the 5’ end of the molecule.
The third carbon on the pentose ring is free to bond with the 5th carbon of the next nucleotide.
This is the 3’ end of the molecule.
Nucleotides are added 5’ to 3’.

Long - can hold lots of information.
Coiled - compact so can store a lot of information in a small space.
Sugar phosphate backbone - strong bonds make DNA stable.
Many hydrogen bonds between complementary bases - give stability but easily broken to allow enzymes access for replication and transcription.
Code is universal.

DNA is the same in all living organisms.

Ribose sugar and phosphate backbone.
Organic nitrogenous bases, U replaces T.
Single stranded.

Messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA).

DNA: long molecule; found in the nucleus; pentose sugar is deoxyribose; adenine, thymine, cytosine and guanine; double stranded, replicates to produce two identical molecules - semiconservative replication.
mRNA: shorter molecule; found in the nucleus and cytoplasm; pentose sugar is ribose; adenine, cytosine and guanine, uracil replaces thymine; single stranded; does not replicate, exists only for polypeptide synthesis then destroyed.

During interphase, before cell division. DNA in mitochondria and chloroplasts also replicates.

Gyrase untwists the double helix. Helicase breaks the hydrogen bonds between nitrogenous bases. DNA nucleotide nitrogenous are exposed. Free phosphorylated nucleotides, present in the nucleus, form complementary base pairs with the exposed nucleotides. DNA polymerase catalyses the formation of the phosphodiester bonds in a 5’ to 3’ direction. Energy to form this bonds comes from the hydrolysis of the extra phosphate group on the activated nucleotides. The leading strand is synthesised continuously in the 5’ to 3’ direction. The lagging strand is synthesised in smaller 5’ to 3’ fragments called Okazaki fragments. Ligase joins the fragments together. Two identical strands are formed. Each strand contains one strand from the parent molecule and one new strand. This is semiconservative replication.

Universal - present in almost all living things; the same triplet bases of DNA code for the same amino acid in almost all living things.
Degenerate - there is more than one base triplet code for all amino acids except methionine and tryptophan.
Non-overlapping - read in sequence, starting from a fixed point.

A stretch of DNA that carries the code to make a polypeptide.

3 DNA nucleotide bases = 1 DNA base triplet.
3 mRNA nucleotides = 1 mRNA base triplet = 1 codon.
Each tRNA base triplet = 1 anticodon = 1 specific amino acid.

The production of mRNA from DNA using RNA polymerase.

Takes place in the nucleus.
Gene unwinds and unzips.
Hydrogen bonds between nitrogenous bases break, exposing DNA nucleotide nitrogenous bases.
Free RNA nucleotides in nucleus form complementary base pairs with exposed DNA nucleotides - C with G, A with U.
RNA polymerase catalyses formation of phosphodiester bond in 5’ to 3’ direction on one strand only forming mRNA, the transcript.
This DNA strand is the template strand.
mRNA passes out of the nucleus into the cytoplasm, via a nuclear pore.
The opposite DNA strand is the coding strand; this does not produce mRNA.

rRNA is synthesised in nucleus. Single stranded rRNA folded to form rRNA in nucleus. 2 subunits, one larger, one smaller. Subunits move through nuclear pore into cytoplasm.

tRNA is synthesis in nucleus. Single stranded tRNA folded to form tRNA in nucleolus. tRNA moves through nuclear pore into cytoplasm.

tRNA is folded into cloverleaf shape held together with hydrogen bonds between complementary bases. tRNA contains an anticodon at one end of the hairpin. tRNA has three unpaired bases at the other end of the hairpin, an amino acid binding site.

The production of polypeptides from the sequence of codons carried by mRNA.

mRNA attaches to ribosome at the start codon, AUG, and moves along the mRNA to next codon.
tRNA, carrying a specific amino acid, forms temporary hydrogen bonds between mRNA codon and tRNA RNA codon.
First and second tRNA anticodon attaches to complementary mRNA.
The two amino acids attached to tRNA are joined together by a peptide bond, this requires energy in the form of ATP.
tRNA leaves the ribosome.
Ribosome moves along and cycle repeats with next tRNA.
Polypeptide produced until stop codon reached.
Polypeptide chain folded into 3D shape using chaperon proteins.

DNA replication: Takes place in nucleus; catalysed by DNA polymerase; uses helicase, gyrase and ligase; produces two identical chromosomes; uses free phosphorylated DNA nucleotides A,T,C,G; requires energy from the hydrolysis of extra phosphate group on free DNA nucleotides; takes place only during interphase.
Transcription: Takes place in nucleus; catalysed by RNA polymerase; produces one mRNA transcript per gene; uses free RNA nucleotides A,U,C,G; requires energy in form of ATP; takes place throughout cell cycle.
Translation: Takes place in cytoplasm; uses ribosomes, tRNA, chaperone proteins; produces a polypeptide; uses amino acids; requires energy in the form of ATP; takes place following transcription, throughout cell cycle.