Topic 2

• The rate of gas exchange by diffusion is increased by:


  •Surface area exchanged across increase

  ● Diffusion distance decrease

  ● Diffusion gradient made more steep
• Fick's Law


  the larger the surface area, difference in concentration and shorter the diffusion distance the quicker the rate.
• Rate of diffusion


  Surface area x concentration difference/ distance
• in mammals, lungs are adapted for rapid gas exchange in the following ways:


  ● They have a large surface area due to the presence of many alveoli which increase the surface area

  ● Good supply of circulating blood to the lungs which carries carbon dioxide to the lungs and oxygen away from them ensures that the concentration gradient is steep - high concentration of oxygen and low concentration of carbon dioxide is maintained by mechanical ventilation

  - They have a short diffusion distance as the alveoli are just one cell thick thus reducing the diffusion distance
• All cells and organelles are surrounded by a partially permeable membrane


  - composed of a sea of phospholipids with protein molecules between phospholipid molecules. Membrane proteins consist of transport proteins, receptor proteins, enzymes, structural and recognition proteins
• The main function of the membrane:


  controlling the movement of substances in and out of the cell/organelle. It also contains receptors for other molecules such as hormones, and enables adjacent cells to stick together

  - the fluidity of the membrane and the mosaic arrangement of the protein give the structure of them membrane its name - fluid mosaic model
• Diffusion


  the passive movement of small, non-polar, lipid-soluble molecules, such as carbon dioxide and oxygen, from an area of high concentration to an area of low concentration. The molecules move directly through the phospholipid bilayer
• The rate of gas exchange by diffusion becomes more rapid as:


  - the surface area increases

  - the diffusion distance decreases

  - the diffusion gradient becomes more steep.
• Facilitated diffusion


  requires a channel protein in the cell membrane to transport polar, charged and water-soluble molecules across the membrane.
• Osmosis


  the movement of water molecules from an area of low solute concentration to an area to high solute concentration through a partially permeable membrane.
• Active transport


  - can transport all types of molecules through carrier proteins. Movement may be either down the concentration gradient, as with diffusion, or against the concentration gradient (such as in many neurones).

  - This process requires energy in the form of ATP. Hydrolysis of ATP provides an accessible store of energy for biological processes. - - Phosphorylation of ATP requires energy.
• Endocytosis/exocytosis


  - transport large particles

  - In endocytosis, particles are enclosed in vesicles made from cell surface membrane and transported into the cell

  - In exocytosis, vesicles containing large parcles are fused with the cell surface membrane and transported out of the cells. These are both active processes.
• DNA: structure of a mono nucleotide


  - Bases:

  o Purine (two nitrogen-containing rings): adenine, guanine

  o Pyrimidine (one nitrogen-containing rings): cytosine, thymine

  - Pairing:

  A & T, G & C

  - Sugar:

  deoxyribose (hydroxyl group replaced by hydrogen on Carbon-2)

  - Bonding:

  o Phosphodiester bonds between phosphate group and Carbon-5 o Hydrogen bonds between the bases

  - Structure: double-stranded, alpha double helix with a sugar-phosphate backbone on each strand
• mRNA


  - Bases:

  o Purine: adenine, guanine

  o Pyrimidine: cytosine, uracil

  - ● Pairing:

  o A-U

  o C-G

  - ● Sugar: ribose

  - ● Bonding: same as DNA

  - ● Structure: single-stranded, not usually folded, carries codons (triplets of bases)

  which attach to tRNA via hydrogen bonds
• tRNA


  - Bases:

  o Purine: adenine, guanine

  o Pyrimidine: cytosine, uracil

  - Pairing:

  o A-U

  o C-G

  - Sugar: ribose

  - Bonding: same as DNA

  - Structure: single-stranded, folded into a specific pattern held together by hydrogen bonds, carries anticodons complementary to mRNA codons, bonded via hydrogen bonds
• Transcription


  - which occurs in the nucleus and involves DNA and mRNA and translation, which occurs at the ribosomes and involves mRNA and tRNA. During transcripon the DNA strand is transcribed into mRNA and during translation the amino acids are assembled together to form a polypeptide chain/protein.
• steps of transcription


  1. The hydrogen bonds between the complementary bases break and DNA uncoils, thus separating the two strands.

  2. One of the DNA strands is used as a template to make the mRNA molecule. The template is called the antisense strand.

  - Free nucleotides line up by complementary base pairing and adjacent nucleotides are joined by phosphodiester bonds, thus forming a molecule of mRNA. This is catalysed by RNA polymerase.

  3. mRNA then moves out of the nucleus through a pore and attaches to a ribosome in the cytoplasm which is the site of the next stage of protein synthesis.
• steps of translation


  During translation amino acids join together to form a polypepde chain:

  ● mRNA attaches to a ribosome tRNA is a single stranded molecule with an amino acid binding site. tRNA binds to specific amino acids from the cytoplasm depending on its anti-codon, this is known as activation.

  ● Complementary anticodons of tRNA bind to mRNA codons and are held in place by hydrogen bonds.

  ● The ribosome joins the amino acids attached to two tRNA molecules by a peptide bond and then tRNA molecules detach from the amino acids.

  This process is repeated thus leading to the formation of a polypeptide chain until a stop codon is reached on mRNA.
• Gene


  - a series of bases on a DNA molecule which codes for a series of amino acids in a polypeptide chain
• Genetic code


  - the order of bases on DNA which consists of triplet bases

  - Each triplet of bases codes for a particular amino acid. The amino acids are then joined together by peptide bonds and form a polypeptide chain

  - However, not all of the genome codes for proteins - the non-coding sections of DNA are called introns and the coding regions are called exons.
• Features of the genetic code


  - The genetic code is non-overlapping, meaning that each triplet is only read once and triplets

  don't share any bases.

  - The genetic code is degenerate, meaning that more than one triplet codes for the same

  amino acid.

  - The genetic code is a triplet code - each three bases codes for one amino acid.

  It also contains start and stop codons which either start or stop protein synthesis.
• Amino acids


  - the monomers from which proteins are made.

  - Amino acids contain an amino group, a carboxyl group, and a variable R group which is a carbon-containing chain.

  - There are 20 different amino acids with different R groups.

  - Amino acids are joined by peptide bonds formed in condensation reactions

  - a dipeptide contains two amino acids and polypeptides contain three or more amino acids
• The structure of proteins is determined by the order and number of amino acids as this determines the bonding present and the shape of the protein:


  -Primary structure of a protein is the sequence of amino acids in a protein.

  - The secondary structure is the 2D arrangement of the chain of amino acids- either

  alpha helix or beta pleated sheet.

  - Tertiary structure of a protein is the 3D folding of the secondary structure into a complex shape. The shape is determined by the type of bonding present, namely: hydrogen bonding (forces of aracon between parally charged atoms in R groups), ionic bonds (salt bridges, form between oppositely charged groups on the R groups) and disulphide bridges (covalent bonds between sulphur atoms in cysteine).

  - quaternary structure: the 3D arrangement of more than one polypeptide. Not all proteins have the same level of structure
• Fibrous proteins


  - Long parallel polypeptides

  - Very little tertiary/quaternary structure

  - Occasional cross-linkages which form microfibres for tensile strength

  - Insoluble

  - Used for structural purposes - such as collagen.
• globular proteins


  - Complex tertiary/quaternary structures

  - Form colloids in water

  - Many uses e.g. hormones, antibodies, carrier proteins, for example haemoglobin.
• Collagen


  - an example of a fibrous protein. I

  - it has high tensile strength due to presence of both hydrogen and covalent bonds in the structure.

  - Collagen molecules are made up of three polypeptides which forms an alpha triple helix which forms fibrils and strong collagen fibres

  - collagen forms the structure of bones, cartilage and connective tissue and is a main component oof tendons which connect muscles to bones
• Haemoglobin


  - a water soluble globular protein which consists of four beta polypeptide chains and a haem group.

  - It carries oxygen in the blood as oxygen can bind to the haem (Fe2+) group and oxygen is then released when required.
• Enzymes


  - biological catalysts and increase the rate of reaction by lowering the activation energy of the reactions they catalyse, including both anabolic and catabolic, intracellular and extracellular reactions.
• Active site


  - the area of the enzyme where the substrate binds.

  - Enzymes are specific to substrates they bind to, as only one type of substrate fits into the active site of the enzyme

  - lock and key model
• Induced fit theory


  - When the enzyme and substrate form a complex, the structure of the enzyme is distorted so that the active site of the enzyme fits the substrate
• substrate concentration


  - the rate of reaction increases as enzyme concentration increases as there are more active sites for substrates to bind to.

  - However, increasing the enzyme concentration beyond a certain point has no effect on the rate of reaction as there are more active sites than substrates so substrate concentration becomes the liming factor.
• enzyme concentration


  - as concentration of substrate increases, rate of reaction increases as more enzyme-substrate complexes are formed

  - However, beyond a certain point the rate of reaction no longer increases as enzyme concentration becomes the liming factor
• temperature


  rate of reaction increases up to the optimum temperature which is the temperature enzymes work best at.

  - rate of reaction decreases beyond the optimum temperature because enzymes denature
• pH


  - enzymes work within a narrow range of a specific pH value, values above or below this alter the bonds within its structure, hence the shape of its active site.
• The semi-conservative replication of DNA


  - ensures genetic continuity between generations of cells meaning that genetic information is passed on from one generation from the next.
• conservative replication


  - which conserves both strands of parent DNA
• dispersive replication


  - where individual strands. are a mixture of old and new DNA
• Mesehlson and Stahl


  - originally grew DNA in a culture containing N15 - (an isotope of nitrogen) for several generations, so all the bases contained this isotope

  - They then grew the DNA in a culture of N14 for one generation. After this generation, the DNA contained one strand containing 15-N and one strand containing 14-N

  - After another generation, half of the DNA molecules were the same as in generation one, and the other half contained entirely 14-N (where the 14-N strand from generation one had been used as a template).

  - this provides evidence for the semi conservative model
• The steps of semi conservation


  1. The double helix unwinds and the hydrogen bonds between the complementary

  bases break, catalysed by DNA helicase, thus separating the two strands of DNA

  2. One of the strands is used as the template and complementary base pairing occurs between the template strand and free nucleotides.

  3. Adjacent nucleotides are joined by phosphodiester bonds formed in condensation reactions, catalysed by DNA polymerase.
• mutations


  permanent changes in the DNA of an organism.