Topic 6: Infection, Immunity & Forensics

The areas covered in this topic are:

• The Genetic Code
• Protein Synthesis
• DNA Profiling
• Viral Infections
• Bacterial Infections
• Infection
• Non-Specific Immune Response
• Specific Immune Response
• Developing Immunity
• Antibiotics
• Microbial Decomposition
• Time of Death

Protein Synthesis

• DNA molecules are found in the nucleus of the cell, but the ribosomes needed in protein synthesis are found in the cytoplasm.
• The DNA is too large to move out of the nucleus.
• Instead a section is copied into RNA.
• This process is called transcription.
• The RNA leaves the nucleus and joins with a ribosome, where it can be used to synthesise a protein.
• This process is called translation.

There are 2 types of RNA:

1. Messenger RNA (mRNA):

• This carries the genetic code from the DNA in the nucleus to the cytoplasm.
• It's 3 adjacent bases are called a codon.

     2.  Transfer RNA (tRNA):

• This carries the amino acids to the ribosomes.
• It has an amino acid building site at one end and a sequence of 3 bases at the other end called an anticodon.

Transcription

• RNA polymerase attaches to the DNA double helix at the beginning of a gene.
• This causes the hydrogen bonds between the 2 DNA strands to break, separating the strands, and uncoiling the DNA molecule.
• One of the strands is then used as a template to make an mRNA copy, the strand is called the antisense strand.
• The RNA polymerase lines up free RNA nucleotides alongside the template strand.
• Complementary base pairing means that the mRNA strand is a reverse copy of the antisense strand.
• Except that the base T on the antisense strand is replaced by base U in RNA.
• As soon as the RNA nucleotides have paired with their complementary bases, they're joined together, forming an mRNA molecule.
• RNA polymerase moves along the DNA strand, separating the strands and assembling the mRNA strand.
• The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strands coil back into a double helix.
• RNA polymerase stops making mRNA and detaches from the DNA once is reaches a stop codon.
• The mRNA then moves out of the nucleus through a nuclear pore and attaches itself to a ribosome in the cytoplasm.

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mRNA Modification

• Genes contain sections that don't code for amino acids, called introns.
• All the sections that do code for amino acids are called exons.
• During transcription, both introns and exons are copied into mRNA.
• A process then occurs called splicing, this is when introns are removed and exons are joined forming mRNA strands.
• This takes place in the nucleus.
• The exons are then joined together in different orders to form different mRNA strands.
• This means more than 1 amino acid sequence, and therefore, more than 1 protein, can be produced from 1 gene.
• After splicing the mRNA leaves the nucleus for the next stage of protein synthesis.

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Translation

• The mRNA attaches itself to a ribosome.
• A tRNA molecule carrying an amino acid, with an anticodon that's complementary to the 1st codon on the mRNA, attaches itself to the mRNA by complementary base pairing.
• A 2nd tRNA molecule attaches itself to the next codon on the mRNA in the same way.
• The 2 amino acids attached to the tRNA molecules are joined by a peptide bond.
• The 1st tRNA molecule moves away, leaving its amino acid behind.
• A 3rd tRNA molecule binds to the next codon on the mRNA.
• Its amino acid binds to the first 2 and the 2nd tRNA molecule moves away.
• This process continues, producing a chain of linked amino acids (a polypeptide chain), until there's a stop codon on the mRNA molecule.
• The polypeptide chain (protein) then moves away from the ribosome.

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Light-Independent Reactions

Calvin Cycle

• CO2 enters the leaf through the stomata and diffuses into the stroma of the chloroplast.
• The CO2 then combines with a 5-carbon compound called ribulose biphosphate (RuBP).
• This reaction is catalysed by an enzyme called ribulose biphosphate carboxylase (RuBISCO).
• The 6-carbon compound formed is unstable and quickly breaks down into 2 molecules of a 3-carbon compound called glycerate 3-phosphate (GP).
• Now ATP, from the light-dependent reactions, provides the energy to reduce GP to a 3-carbon sugar phosphate called glyceraldehyde 3-phosphate (GALP).
• This reduction reaction also requires H ions, which come from the reduced NADP, also from the light-dependent reactions.
• The reduced NADP is then recycled to NADP.
• 2 out of every 12 GALPs formed are involved in the creation of a 6-carbon sugar which can be converted into other organic compounds, such as, amino acids.
• 10 out of every 12 GALPs are used to regenerate RuBP.
• The 10 GALP molecules rearrange to form 6 5-carbon compounds.
• Then, using the last of the ATP, phosphorylation takes place to form RuBP.

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Light-Dependent Reactions

• Light hits a chlorophyll molecule, transferring the energy to the electrons of the molecule.
• The electrons become excited and are raised to a higher energy level.
• If the electrons' energy level is raised significantly it will leave the chlorophyll molecule completely.
• The excited electron will then be picked up by an electron acceptor and is used in the synthesis of ATP via either cyclic or non-cyclic photophosphorylation.

Cyclic Photophosphorylation

• This involves only photosystem I and will only produce small amounts of ATP.
• The light hits the chlorophyll molecule in PSI, exciting the electron and causing it to leave the molecule.
• it's taken up by an electron acceptor and passed directly along an electron transport chain to create ATP.
• The electron then returns to the chlorophyll molecule in PSI and cna be excited in the same way.
• The electrons are recycled and can repeatedly flow through PSI.

Non-Cyclic Photophosphorylation

• Light energy is absorbed by PSII and excites the electrons in the chlorophyll, moving it to a higher energy level.
• The electrons are then able to leave the chlorophyll and be taken up by an electron acceptor.
• The electrons that leave the chlorophyll in PSII, must be replaced.
• light energy will then split water into protons (H ions), electrons and oxygen.
• The electrons that have been take up by the electron acceptor then move along the electron transport chain, causing them to loose energy.
• The energy that is released is used to convert ADP and Pi into ATP.
• These electrons will enter another chlorophyll molecule in PSI, where they become excited to an even higher level by more light energy.
• Eventually they pass to NADP, and with the hydrogen from water form reduced NADP.

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Photosynthesis

Overview

• Photosynthesis is the process where energy from light is used to break apart strong bonds in H2O molecules.
• It involves the reduction of CO2 to carbohydrates.
• The hydrogen is combined with CO2 to form glucose and O2 is released into the atmosphere.
• The hydrogen comes from the photolysis of H2O.
• The energy for photolysis is at first trapped by a pigment molecule called chlorophyll.
• This process happens 3x, to produce C6H12O6, glucose.
• Therefore, photosynthesis stores energy in glucose.
• The process occurs in 2 linked stages called the light-dependent and light-independent reactions

Key Words

• Phosphorylation - adding phosphate to a molecule
• Photophosphorylation - adding phosphate to a molecule using light 
• Photolysis - the splitting of a molecules using light energy
• Hydrolysis - the splitting of a molecule using water
• Redox Reactions - reactions that involves oxidation and reduction; the oxidation of 1 molecule always involves the reduction of another, and vice versa
• Oxidation - when something loses electrons
• Reduction - when something gains electrons

Topic 5: On The Wild Side

The specification includes these topics:

• Ecosystems
• Abiotic Factors
• Biotic Factors
• Anthropogenic Factors
• Succession
• Photosynthesis
• Light-Dependent Reaction
• Light-Independent Reaction
• Location of Photosynthesis
• Energy Transfer
• Efficiency of Energy Transfer
• Evidence of Climate Change
• Greenhouse Effect/Gases
• Global Warming Debate
• Global Warming Models
• Coping With Climate Change
• Adaptation
• Evidence For Evolution
• Speciation
• Environmental Balance