1B: More Biological Molecules

DNA stores genetic information. RNA transfers genetic information from DNA to ribosomes. Ribosomes read RNA to make polypeptides in translation. Made from RNA and proteins.

Nucleotide structure: DNA and RNA are polymers of nucleotides (monomer). Pentose sugar (5 C atoms), nitrogen-containing organic base (contains C), phosphate group

Polynucleotide: Many nucleotides joined via condensation reaction between phosphate group of one nucleotide and sugar of another. Forms phosphodiester bond (phosphate group, 2 ester bonds). Chain is a sugar-phosphate backbone.

DNA: Double helix, 2 seperate strands (polynucleotides) wind around each other to form spiral, very long, coiled up very tightly so lots of genetic info can fit into small space of cell nucleus. Phosphate group, deoxyribose sugar, N-containing organic base of either A, T, C, G.

2 antiparallel strands that run in opposite directions joined by H bonds between bases. Each can only join with particular partner - complementary base pairing. Adenine>Thymine, Cytosine>Guanine. 2 H bonds>A+T, 3 H bonds>C+G. 

RNA: Shorter than DNA, single strand, ribose sugar, phosphate group, N-containing base of either A, U, C, G.

DNA 1st observed in 1800s but scientists doubted it carried genetic code because of simple structure. Argued that proteins carried it as more chemically varied. 1953: experiments determined DNA was carrier. Double helix was determined by James Watson and Francis Crick.

DNA copies itself before cell division so each cell has full DNA. Called semi-conservative because half strands in each new DNA are from original DNA. Means genetic continuinty between generations of cells.

1. DNA helicase breaks H bonds between bases on 2 polynuc DNA strands. Makes helix unwind to 2 single strands. 2.  Each OG strand acts as template for new strand. CBP means free-floating DNA nucleotides attracted to complementary exposed bases on OG strand. 3. Condensation joins nucleotides of new strand together, catalysed by DNA polymerase. H bonds form between bases on OG and new. Each new DNA molecule contains 1 strand from OG DNA and 1 new strand.

Each DNA end different. 3', 5'. During replication active site of DNA polymerase complementary to 3' end of new DNA strand. Enzyme can only add nucleotides to new strand at 3'. New strand made in 5' to 3' direction, DNA polymerase moves down template strand in 3' to 5' direction. DNA strands antiparallel so the DNA polymerase moves in opposite directions on each strand.

Watson and Crick also came up with theory of semi-conservative DNA replication. Meselson and Stahl validated this. People weren't sure if DNA was conservative (OG strands stay together, new DNA new strands) or not. 

Used 2 isotopes of N (DNA contains N), 15N (heavy), 14N (light). 2 samples of bacteria grown for many generations, 1 in nutrient broth of light N, 1 in heavy. As bacteria reproduced, took up N to help make nucleotides for new DNA. Samples were taken and spun in centrifuge. Heavy N settled lower than light N. Then bacteria grown in heavy N was put in broth of light N. Left for one round of replication, then spun in centrifuge. If replication was conservative, OG heavy DNA would settle at bottom and new light would settle at top. If semi-conservative, would contain one strand of heavy N and one strand of light, so DNA would settle between where heavy and light originally settled. DNA settled in middle, so DNA contained mixture of heavy and light N. It replicated semi-conservatively in light N. Other scientists carried out experiments to show replication was universal in all living things.

Plants and animals need energy for active transport (transport solutes from leaves, absorb glucose from ileum epithelium into bloodstream), DNA replication, cell division, protein synthesis. 

They release energy from glucose (respiration). Cell can't get energy directly from glucose. In respiration, energy released from glucose is used to make ATP. ATP is made from nucleotide base adenine, ribose sugar, 3 phosphate groups. Nucleotide derivative because modified form of nucleotide. Once made, it diffuses to the part of the cell that needs energy. Energy is stored in high energy bonds between phosphate groups. Its released via hydrolysis. ATP is broken into ADP and Pi (inorganic phosphate). Phosphate bond is broken and energy is released. Reaction is catalysed by enzyme ATP hydrolase. This reaction can be coupled to other energy requiring reactions in the cell rather than being lost as heat. Pi can be added to another compound to make it more reactive (phosphorylation). ATP can be synthesised in condensation: ADP + Pi (Catalysed by ATP synthase) = ATP.

Vital to living organisms. Makes up 80% of cells contents. Is a metabolite in many important metabolic reactions (condensation, hydrolysis). Is a solvent, means some substances dissolve in it. Most metabolic reactions take place in solution (cytoplasm) so is vital. Helps with temperature control because it has high latent heat of vaporisation (LHoV) and specific heat capacity (SHC). Very cohesive, which helps water transport in plants.

Structure: 1 O, 2 H, covalently bonded. The shared negative H electrons are pulled toward the O atom, so the other side of each H atom is left with a slight positive charge. The unshared negative electrons on the O atom give it a slight negative charge. This makes it a polar molecule; partial negative charge on 1 side and partial positive charge on the other. 

H bonds are weak bonds between a slightly positively charged H atom in 1 molecule and a slightly negatively charged atom in another molecule. H bonds form between water molecules because the slightly negatively charged O atoms of water attract the slightly positively charged H atoms of other water molecules. This H bonding gives water some of its useful properties. 

Important metabolite: Many metabolic reactions involve condensation/hydrolysis reaction. Hydrolysis requires a molecule of water to break a bond, condensation releases a molecule of water as a new bond is formed.

Good solvent: Lots of substances in biological reactions are ionic (made from 1 positively charged atom and 1 negatively charged atom). Water is polar so + end of water is attracted to - ion, and - end of water is attracted to + ion. Means ions get surrounded by water molecules so they dissolve. Living organisms can take up useful substances dissolved in water and these dissolved substances can be transported around the organisms body.

HLHoV: Water evaporates when H bonds are broken. Allows water molecules on the surface of water to escape into the air as gas. Takes a lot of energy to break H bonds so a lot of energy is used up when water evaporates. Water has high HLHoV; lots of heat is used to change from liquid to gas. Useful for living organisms as they can use water loss through evaporation to cool down without losing too much water. When it evaporates it carries away heat energy from a surface which cools the surface down and helps lower the temperature.

Can buffer changes in temperature: H bonds give water high SHC (energy needed to raise temperature of 1g by 1 celsius). When water is heated, a lot of heat energy is used to break H bonds between water molecules. Means there is less heat energy available to actually increase the temperature of the water. Takes a lot of energy to heat water up. Useful for living organisms as means water doesn't experience rapid temperature changes. Makes water a good habitat as temperature under water is more stable than land. Water inside organisms remains at stable temperature, maintains constant internal body temperature.

Very cohesive: Attraction between molecules of the same type. Water is very cohesive because its polar. It helps water flow, great for transporting substances. Its how water travels in columns up the xylem. Means water has high surface tension when it comes into contact with air. Is why sweat forms droplets, which evaporate to cool organism down. Reason why pond skaters can walk on surface of pond 

Ion is an atom or group of atoms that have an electric charge. + ion is cation, - ion is anion. Inorganic does not contain carbon (not always). Found in cytoplasm of cells and in body fluids of organisms. Each ion has a specific role, depending on properties. Role determines if found in high or low concentrations.

Iron ions in haemoglobin: Large protein that carries O2 around the body in red blood cells. 4 different polypeptide chains, each with Fe2+ in centre. That is what binds to oxygen. When it is bound, Fe2+ becomes Fe3+ until oxygen is released.

Hydrogen ions: pH is calculated based on the concentration of H ions in the environment. The more H+ present, the lower the pH. Enzyme-controlled reactions are all affected by pH.

Sodium: Glucose and amino acids need help crossing cell membranes. A molecule of glucose/amino acid can be transported into a cell alongside sodium ions. Co-transport.

Phosphate: When it attaches to another molecule, its a phosphate group (DNA, RNA, ATP). Bonds between phosphate groups store energy. The phosphate groups in DNA and RNA allow nucleotides to join up to form polynucleotides.