Section 1 2 Nucleic acids + Section 4 8 DNA, genes and protein synthesis

Compare the structure of DNA and RNA

Differences

• DNA is double stranded, RNA is single stranded

• DNA contains deoxyribose sugar, RNA contains ribose sugar

• DNA is a larger molecule, RNA is a smaller molecule

• DNA contains the bases: Thymine, Guanine, Adenine, Cytosine. RNA contains the bases: Uracil, Guanine, Adenine, Cytosine. [AT//AU]

Similarities:

• Both via condensation reaction form phosphodiester bonds (reaction between the sugar and phosphate group)

• Both contain phosphates

• Both are polymer of nucleotides

How the DNA molecule is a stable molecule?

• Forms a double helix

• Phosphodiester bonds, protect the chemically more reactive organic bases

• Between the C-G bonds there are 3 hydrogen bonds, so more C-G the more stable the DNA structure is.

The function of DNA:

• Two seperate strands are joined via hydrogen bonding, so easy to separate during DNA replication and protein synthesis.

• Large molecule so contains lots of information

• Complementary base pairing, allows for DNA to replicate and transfer information

• Very stable structure, which is able to pased down from generation without change (only rarely mutates)

• The double helix structure allows for molecule to be compact in small space

• The double helix structure allows to protect the reactive organic bases not to damages.

The steps for DNA replication:

• Enzyme DNA helicase, attaches to the DNA molecule and breaks hydrogen bonding between complementary base pairs. Causing the two DNA strands to separate from each other

• Free activated nucleotides form complementary base pairs on the open DNA strand (activated nucleotides have 3 phosphate ions) and hydrogen bonding between them

• DNA polymerase, moves along the DNA stand, catalysing the formation of phosphodiester bonds (using the 2 phosphate ions as energy)

• This is called semi-conservative model.

What is the semi-conservative model:

• The model forms two copies of DNA

• Where one strand acts as a template

• Where there is a newly synthesised strand and an original strand.

The semi-conservative model vs the conservative model

• Semi-conservative where there is a new strand of DNA and original strand of DNA, conservative model where there is the two strands of original DNA molecule and the new DNA molecule, two strands of new DNA molecule.

Experiment to prove semi-conservative model:

• All four bases contain nitrogen, they exist as two isotopes N14(light, less dense) and N15(heavy, more dense)

ATP and energy

• The structure of ATP is 3 phosphate ions connected to a ribose sugar and adenine.

• It only requires a small amount of energy (activation energy) to break the last phosphate which releases energy, which can be used in cellular processes.

• AMP (adenine mono phosphate)

• ADP (adenine diphosphate)

• ATP (adenine triphosphate)

• The enzyme ATP hydrolase (ATP —→ ADP) [metabloic processes, active transport, movement]

• The enzyme ATP synthase (ADP —→ ATP) [respiration and photosynthesis]

Water and its’ functions

• Forms a dipole, with oxygen partially negative and hydrogen partially positive, so hydrogen bonding

• High specific heat capacity, because of hydrogen bonding, so takes more energy to heat a given mass of water

• High latent heat of evaporation, more energy to evaporate water

• High cohesion forces, due to hydrogen bonding (for water to move up a the xylem)

The importance of water in living organisms:

• Metabolism: hydrolysis reactions, reactant for photosynthesis

• Solvent (readily dissolves substances): O2 and CO2, waste products ammonia and urea, hydrophillic molecules such as amino acids, monosaccarides.

• Evaporation to cool organisms (sweating)

• Not easily compressed, so provides support (hydrostatic skeleton of animals, tugor)

• Transparent for photosynthesis to occur for aquatic life

What is a gene?

A section of DNA that codes for making proteins and functional RNA.

Allele

An alternative form of gene.

Homologous chromosomes:

• One chromosome from mother, one from the father

• Carry the same genes, but not the same alleles of gene

Genome vs Protenome

• Genome: The complete set of genes in a call

• Protenome: Full range of proteins formed from the genome

The genetic code and its’ features:

• Degenerate: more than one triplet codes for the same amino acid

• Non-overlapping: Each base is only read once

• Universal: Each triplet codes for the same amino acid in all organisms

• There are start and stop codons

Differences in DNA in prokaryotic and Eukaryotic

• Prokaryotic: DNA is shorter and circular, no histones so no chromosomes, no introns

• Eukaryotic: DNA is longer and linear, associates with histones to form chromosomes, introns and exons

• DNA in mitrocondria and chloroplasts is similar to prokaryotic DNA by being cirular and short

DNA and histones:

DNA and histones coil together to form chromosomes, during replication of DNA there are two chromatids jointed together by centromere.

The structure of mRNA

• Single-stranded chain folded into a clover leaf

• At one end of tRNA amino acid attached

• At another end anti-codon (DNA bases and complementary to codon)

Transcription and splicing steps:

• RNA helicase enzyme attaches to a specific region of DNA, causing the two strands to separate exposing nucleotide bases.

• The free RNA nucleotides form complementary base pairs with the DNA and form hydrogen bonding.

• RNA polymerase moves along the nucleotides to form phosphodiester bonds. Once RNA polymerase detaches pre-RNA is formed.

• Pre-RNA to RNA is formed via splicing removing introns (non-coding regions of the gene)

• The RNA then moves out of the nucleus pore

Translation steps:

• Ribosome binds with mRNA at start codon

• A tRNA molecule that is complementary to mRNA attaches, and held together by hydrogen bonds between the complementary base pair.

• A second tRNA moves into place, complementary to the mRNA.

• A peptide bond is formed between the amino acids

• The ribosome moves along while peptide bonds between amino acids are being formed.

• When reaching a stop codon the polypeptide chain is released.

• The protein is formed which can be used in the cell.