Biology SL - Chapter 2 - Molecular Biology

Semi-conservative replication

- The two strands of DNA molecule are separated by breaking the hydrogen bonds between their bases by helicase - DNA polymerase links nucleotides together to form new strands, using the pre-existing standards as templates - The daughter DNA molecules each rewind into a double helix Note: Each new strand has the same base sequence as the old strand. Each molecule produced has an old and a new strand (semi conservative)

Metabolism

- The web of all enzyme catalysed reactions in a cell or organism - Most metabolic pathways consist of chains of reactions, but some may also be cycles of reactions

Theory of vitalism

- Theory that living organisms only used organic chemicals available to them - Falsified by the synthesis of urea

Transport in blood

- Transport of substances in blood depend on the type of substance they are: Oxygen is non polar and the amount that dissolves in the plasma is insufficient, so hemoglobin is needed Cholesterol and fats are non polar, so they are transported in small droplets called lipoproteins Glucose and amino acids are polar, so they can be dissolved in the plasma Sodium chloride is soluble in water, transported in the plasma as Na and Cl ions

Condensation reactions

- Two molecules are joined together to form a larger molecule plus a molecule of water - Pairs of monomers bonded together are a dimer - A chain of monomers is a polymer - i.e: Two amino acids can be joined together to form a dipeptide by a condensation reaction. Further condensation forms a polypeptide. In this case, the bonds would be called peptide bonds - Condensation reactions are used to build up carbohydrates and lipids

Energy storage

- Two ways of energy storage: fats or oils and glycogen or starch -Lipids: more energy released from use of fats or oils (double the amount than that of carbohydrates) - Adipose tissue has no water associated in its storage, but glycogen does

Aerobic cell respiration

- Use of oxygen - Glucose or lipids as substrate - Yield of ATP per glucose is large -Products: CO2 and H20 (Pyruvate ---------> CO2, H2O, ATP)

Natural selection

- What distinguishes living organisms from non-living matter

Using yeast in brewing and baking

1- CO2 and the baking industry: When yeast is mixed into dough and put in oven, it forms bubbles which make the dough rise 2- Ethanol and the brewing and biofuel industries: Yeast is cultured in a liquid with sugar and other nutrients, but not oxygen. This yields ethanol, which can be used in biofuel and brewing industries

RNA polymerase and transcription

1- RNA polymerase moves along the gene separating the DNA into two single strands 2- RNA nucleotides are assembled along one of the two strands of DNA. Complementary base pairing (except that uracil pairs with adenine) 3- RNA nucleotides are linked together by covalent bonds between the pentose sugar of one nucleotide and the phosphate of the other 4- RNA strand separates from the DNA strand as it is produced and is released completely when the end of the gene is reached 5- The DNA strands pair up again and twist back into a double helix (Sense strand is the DNA strand not being transcribed, and the transcribed strand is the anti sense strand)

Chromatography of pigments

1- Tear up a leaf into small fragments 2- Grind pieces and mix with propanone 3- Transfer sample of extract to a watch glass 4- Evaporate to dryness with hair dryer 5- Add a few drops of propanone to dissolve the pigments 6- Build up concentrated sport of pigment at end of strip of paper 7- Suspend strip in a tube with base dripping into running solvent 8- Remove strip from the tube when the solvent has nearly reached the top 9- Calculate Rf values for each pigment spot ((distance moved by spot)/(distance moved by solvent))

Factors affecting enzyme activity

1- Temperature: At first, if temperature is increased, activity rises. This is owed to more collisions. After, enzymes are denatured and stop working. 2- pH: Enzyme activity is reduced as pH decreases from the optimum because the conformation of the enzyme is altered more and more. At optimum pH, enzyme activity is fastest. Enzyme activity is reduced as pH increases from the optimum because once more, conformation is altered. 3- Substrate concentration: Initially increases, but eventually reaches plateau given that there are no more substrates for enzymes to react with any more.

Ethical implications of cell respiration experiments

1- Will the animal suffer? 2- Any risks for the animals? (i.e: contact with the alkali) 3- Will the animals have to be removed from their habitat? Can they return to their habitat afterwards 4- Is it necessary to use animals in the experiment?

Molecular biology

- Aims to explain living processes in terms of the chemical substances involved

Peptide bonds and polypeptides

- Amino acids are linked together by condensation reactions - Bonds between the two are called peptide bonds - Two amino acids bonded together: dipeptide - Multiple amino acids linked together: polypeptides

Atoms and molecules

- An atom is a single particle of an element, consisting of a positively charged nucleus surrounded by a cloud of negatively charged electrons - A molecule is a group of two or more atoms held together by covalent bonds - Molecules used by living organisms are based on carbon - Each carbon atom forms four covalent bonds - Covalent bonds are relatively strong - Bonds between molecules (intermolecular bonds) are much weaker) - Main types of molecules used by living organisms are carbohydrates, lipids, proteins and nucleic acids

Energy for muscles

- Anaerobic produces less ATP, but it can supply ATP at a faster rate as it isn't limited by how fast oxygen is supplied - Therefore: Anaerobic cell respiration is used in muscles carrying out very vigorous exercise - It maximises the power of muscle contraction as lactate and hydrogen ions are produced - Can only be used for around 2 minutes, after that, H ions make pH of blood too low

Condensation reactions of carbohydrates

- Basic sub unit of carbohydrates are monosaccharides - Two monosaccharides linked form disaccharide plus water, and more saccharides together form polysaccharide(s)

Substrates and active sites

- Biological catalysts = enzymes - Enzymes are globular proteins - Reactant in an enzyme catalysed reaction is known as a substrate - Enzyme catalyse reactions in the active site - Enzymes only work in liquids, where random collisions are possible - Collisions may lead to binding (note: enzymes are substrate-specific) - After catalysis: products are released from the active site

Catabolism

- Breakdown of complex molecules into simpler molecules (i.e: hydrolysis of macromolecules into monomers - Hydrolysis reactions are reactions where water molecules are split

Lipids

- Carbon compounds made by living organisms that are mostly or entirely hydrophobic Three main types of lipids: 1- Triglycerides: made from three fatty acids and one glycerol molecule. Three hydrocarbon tails (i.e: Fats and oils) 2- Phospholipids: only two fatty acids linked to glycerol, and a phosphate group instead of the third fatty acid. (partly hydrophobic) 3- Steroids: Four fused rings in their molecule (i.e: testosterone, cholesterol, progesterone, estrogen)

Absorption spectra

- Chlorophyl a and b - They absorb mostly red and blue, so we perceive them as green

Rejected theories

- Conservative replication - Dispersive replication

Amino acids

- Contain: hydrogen atom, amine group (NH2), carboxyl group (COOH), R groups (R) - R groups vary (20 different combinations) Anomalies: selenocysteine and pyrrolysine

Meselson and Stahl experiments

- Cultured ^15N bacteria and finally ^14N bacteria - After one generation, the DNA was intermediate in density between ^15N and ^14N

Structure of RNA and DNA

- DNA has two strands, while RNA has one strand - Covalent bonds between pentose sugar of one nucleotide and the phosphate of the next one - Antiparallel strands, both linked by hydrogen bonding - ATCG complementary base pairs - Forms a helix

Action spectra

- Efficiency of photosynthesis is not the same in all wavelengths of light - Maximum rates are blue and red light - Shows that some use of green in photosynthesis, but its mainly red and blue light

Energy and cells

- Every cell produces its own ATP through cell respiration - Organic compounds broken down and the energy released by doing this is used to make ATP - Cell respiration is defined as the controlled release of energy from organic compounds to produce ATP - ATP can easily diffuse to any part of the cell and release its energy within a fraction of a second

Condensation reactions of lipids

- Fatty acids can be linked with glycerol to form glycerides (+ water) - Maximum is a triglyceride, as glycerol can have a maximum of three fatty acids attached

Synthesis of urea

- Friedrich Wöhler synthesised urea in 1828 using silver isocyanate and ammonium chloride

Production of human insulin in bacteria

- Gene for insulin transferred to bacteria - Bacteria begins producing insulin - Same sequence insulin thanks to the universality of the genetic code

Hydrogen bonding in water

- Hydrogen bonds: When a bond forms between the positive pole of one molecule and the negative pole of another (in water) - Energy released when bond is made - Energy used when bond breaks (explains the use of water as a coolant)

Solubility in water

- Hydrophilic substances: Substances that are attracted to water and form intermolecular bonds with water molecules (soluble in water) - Hydrophobic substances: When water molecules are more attracted to each other than to the non-polar molecules of hydrophobic substances (insoluble in water) - Polar molecules are hydrophilic

Production of lactose free milk

- Lactose ----lactase----> glucose + galactose - Can be made by adding free lactase to milk - Can also be made by passing milk through immobilised lactase Benefits: - Many people are intolerant to lactose - Galactose and glucose are sweeter than lactose, meaning less sugar has to be added to milk shakes/fruit yoghurt - Bacteria and glucose and galactose ferment quicker than lactose

Anaerobic cell respiration

- No oxygen - Glucose as substrate - Small yield of ATP - Products: lactate in humans, and CO2 and ethanol in yeast (Glucose ---------> ATP + Pyruvate)

Photosynthesis and the atmosphere

- Oxygen is waste product of photosynthesis - Produced when water is split by photolysis to provide the electrons needed to convert CO2 into carbohydrates and other carbon compounds

Polypeptides and proteins

- Polypeptide is an unbranched chain of amino acids - Can be up to 10,000 amino acids, but they usually have between 50 and 2,000 - Chains of fewer than 40 amino acids are usually called peptides -20^100 possible sequences - They are coded by a gene - A protein consists of either a single polypeptide, or multiple polypeptides bonded together

BMI

BMI = (mass in kg)/(height in metres)^2

Photosynthesis

- Production of carbon compounds in cells using light energy - Substrates for photosynthesis are simple inorganic substances including CO2 and H2O Example (synthesis of glucose) CO2 + Water + Light energy ----> glucose + oxygen Stages of photosynthesis 1- CO2 is converted into carbohydrates and other carbon compounds (energy needed) 2- Energy obtained in the form of light. Light is absorbed by photosynthetic pigments 3- Electrons are needed to convert CO2 into carbohydrates. They are obtained by photolysis, which is the splitting of water molecules. Oxygen is a waste product from photolysis.

Proteins and proteomes

- Proteomes: All of the proteins produced by a cell, tissue or organism - Proteome of an individual is fixed - Proteome is variable

Nucleotides

- RNA and DNA are nucleic acids - Pentose sugar, phosphate group and a base - Ribose in RNA and deoxyribose in DNA - Four possible bases for each, but thymine is replaced by uracil in RNA

Respirometers and respiration rates

- Respirometer: any device used to measure respiration rates (note: not ventilation rate) Examples: A sealed glass or container in which the organism or tissue if placed An alkali which absorbs CO2 produced by cell respiration. Volume of air decreases as a result of oxygen being used in cell respiration by the organisms in the respirometer Capillary tube with fluid, connected to the container, which allows the volume of air inside the respirometer to be monitored

Hydrolysis reactions

- Reverse of condensation reactions - Large molecule is broken down into smaller molecules, and water is used up in the process Polypeptides + water -> dipeptides or amino acids Polysaccharids + water -> disaccharides or monosaccharides Glycerides + water -> fatty acids + glycerol

Polarity of water

- Sometimes in molecules with multiple covalent bonds, electrons are not shared equally, so one part of the molecule has a slight positive charge, and another part has a slight negative charge - This feature is called polarity - Water molecules are polar, as hydrogen nuclei are less attractive to electrons than oxygen nuclei, so the two hydrogen atoms have a slight positive charge and the oxygen atom has a slight negative charge - Dipolarity (two poles)

Monosaccharides

- Sugars that consist of a single sub-unit (monomer) - Contain carbon, hydrogen and oxygen in the ratio of 1:2:1 - Examples: Ribose and Glucose

Polysaccharides

- Sugars that consist of multiple monosaccharides: Cellulose: unbranched polymer of beta-d-glucose. Glucose units alternate up-down-up-down, so the polymer is straight rather than curved. Allows for other cellulose molecules to be arranged in parallel with hydrogen bonds forming cross links Starch: polymer of alpha-d-glucose (branched), all glucose units have same orientation, which gives the polymer a helical shape. Types of starch are amylose and amyloceptin Glycogen: branched polymer of alpha-d-glucose, more branched than amyloceptin. Used by mammals to store glucose in the liver (insoluble)

Disaccharides

- Sugars that consist of two monosaccharides - Examples: maltose, lactose, sucrose

Polymerase chain reaction

- Taq DNA polymerase used to replicate DNA artificially - Use of enzymes and high temperatures to speed up reaction - Millions of copies of the DNA can be produced in just a few hours thanks to the high temperatures

Protein conformations

- The conformation of a protein is its three dimensional structure - Polypeptides of most proteins are folded up to produce a globular shape - The sequence of amino acids in a polypeptide determines how this folding is done, and thus, it determines the conformation of a protein - Each time a polypeptide with a particular sequence of amino acid is synthesised on a ribosome, it will have the same conformation always - The structure is stabilised by intramolecular bonds between the amino acids in the polypeptides that are brought together by the folding process

Anabolism

- The synthesis of complex molecules from simples molecules (i.e: synthesis macromolecules from monomers) - Condensation reactions (water is produced)

Properties of water

Cohesive: Water molecules cohere (stick to each other) because of the hydrogen bonds Adhesive: Dipolarity of water molecules makes them adhere to surfaces that are polar/hydrophilic Thermal: Due to hydrogen bonding, water has high melting and boiling points, high latent heat of vaporisation, high specific heat capaticy Solvent: Many substances dissolve in water due to its polarity, including those composed of ions or polar molecules

Immobilised enzymes

Enzymes that are immobilised have many benefits: - Catalysis can be controlled by adding or removing enzymes from reaction mixture - Enzyme concentrations can be higher - Recycle - Enzymes are resistant to denaturation over greater ranges of pH and temperature - Products not contaminated with enzymes Methods of immobilisation: - Glass - Gel/membrane

Denaturation

Factors: 1. Heat: causes vibrations within the molecule which may lead to broken bonds (almost always irreversible: egg white) 2. pH: if pH is decreased or increased dramatically, conformation of molecule with disintegrate too

Limiting factors of photosynthesis

Light intensity CO2 concentration Temperature

Crick and Watson

Model making helped to figure out the structure of DNA. Once they did, they figured out that it wraps into a double helix

Translation

The synthesis of polypeptides on ribosomes, using mRNA and tRNA Use of codon (three bases) Process: 1- mRNA binds to a site on the small sub unit of the ribosome. It contains a series of codons consisting of three bases, each of which code for one amino acid 2- tRNA molecules are present around the ribosome, and each has a special triplet of bases called an anticodon, which carries the amino acid corresponding to this anticodon 3- There are three binding sites for tRNA molecules in the ribosome, but only two bind at once. tRNA can only bind if it has the anticodon that is complementary to the codon on the mRNA. The bases on the codon and anticodon link together by forming hydrogen bonds, following the same rules of complementary base pairing 4- Amino acids carried by the tRNA molecules are bonded together by a peptide bond. A dipeptide forms, and the tRNA on the left detaches. The ribosome moves along the mRNA to the next codon. Another tRNA carrying an amino acid binds, and a chain of three amino acids is formed. (Stage three repeated until a polypeptide is formed)

Health risks of trans fats and saturated fatty acids

Trans fats - may lead to coronary heart disease Saturated fatty acids - may also lead to coronary heart disease, but there are anomalies, such as the Maasai people of Kenya

Functions of proteins

Various functions: - enzyme - hormone - antibody - pigment - structural protein

Types of fatty acids

Saturated: all of the carbon atoms in the chain are connected by single covalent bonds (no more hydrogen links can be made) Unsaturated: one or more double bonds between carbon atoms in the chain, so more hydrogen could be bonded to the carbons if a double bond was replaced by a single bond Monounsaturated: only one double bond Polyunsaturated: two or more double bonds Cis unsaturated: hydrogen atoms are bonded to the carbon atoms on the same side of a double bond Trans unsaturated: hydrogen atoms are bonded to the carbon atoms on the opposite side of a double bond