Biological Molecules

Water Structure

• Covalently bonded
• Electrons not shared equally - slightly negative part and slightly positive part = dipole
• Hydrogen end slightly positive, oxygen slightly negative (electrons are pulled closer to oxygen)
• 104.5 degree angle between two hydrogen in the molecule
• Oxygen has 4 unpaired electron - form hydrogen bonds with other water molecules

Functions

• Polar solvent - many ionic and covalent substances will dissolve in water (do not in many other covalent substances) = good transport medium and reactions in cells occur in water
• Ice has a lower density than liquid water - floats on surface and acts as insulating layer which stops water underneath freezing = good habitat
• High specific heat capacity - lots of energy to seperate hydrogen bonds - large bodies of water do not change temperature much = good habitat
• Cohesive - forces between molecules mean they stick together - important in moving water
• High surface tension - stronger attraction in water molecules than to other molecules

Important anions - Negatively charged

• Nitrate - formation of amino acids, proteins and formation of DNA
• Phosphate - formation of ATP, ADP, and DNA&RNA
• Chloride - nerve impulses, sweating,secretory systems
• Hydrogen carbonate - buffering blood to stop it becoming too acidic

Important cations - Positively charged 

• Sodium - nerve impulses, sweating, secretory systems
• Calcium - Formation of calcium pectate for middle lamella in plant cell wall. Also for bone formation and muscle contraction in animals
• Hydrogen - cellular respiration and photosynthesis and in pumps and systems as well as pH balance
• Magnesium - production of chlorophyll in plants 

Useable energy sources e.g. glucose and sucrose

Monosaccharides

• Simplest form of carbohydrate
• Contain carbon hydrogen and oxygen in the ratio 1:2:1 (CH2O)n
• Hexose sugars (6 carbons) such as a-glucose and b-glucose and pentose sugars (5 sugars)  such as ribose and deoxyribose

Disaccharides

• Two monosaccharides joined together in a condensation reaction - molecule of water removed
• The covalent bond between them is a glycosidic bond
• If it is between carbon 1 and carbon 4 it is called a 1,4 Glycosidic bond
• Sucrose - a-glucose + a-fructose             (stored in plants)
• Lactose - a-glucose + b-galactose           (main carbohydrate in milk)
• Maltose  - a-glucose + a-glucose            (found in germinating seed)

Structure

• 11+ monosaccharides 
• No sweet taste
• Compact molecules
• Physically and chemically inactive
• Not very soluble so have little effect on water potential within a cell

Starch - alpha glucose

• Amylose - unbranched but coils to make it compact (1,4 glycosidic bonds)
• Amylopectin - branched so can be broken off quickly when energy is needed (1,4 and 1,6 glycosidic bonds)
• Amylose gives a slow release over a long period and amylopectin releases energy quickly = combination is good when playing sport

Glycogen - alpha glucose

• 1,4 and 1,6 glycosidic bonds so it is branched
  
• It can be broken down very rapidly. More glycogen is found in muscle and liver cells

Cellulose - beta glucose

• Structural material in plants - cell wall
• 1,4 glycosidic bonds
• Every other monomer unit is inverted so that bonding can take place
• This means hydroxyl groups will stick out on both sides of the molecule - hydrogen bonds can form between different chains = cross-linkages
• This holds neighbouring chains together
• Gives it high-tensil strength
• They do not coil or spiral and are therefore long linear molecules

Fats and Oils

• Fats = solid at room temp (saturated fatty acids) whereas oils = liquid (unsaturated )
• Less oxygen than carbohydrates
• Made of fatty acids (hydrocarbon chain and a carbonyl group) and glycerol
• Fatty acid = saturated or unsaturated (saturated single bonds between carbons, unsaturated has double bond between carbons - more than one = polyunsaturated)

Esterification

• Condensation reaction between carboxyl group on fatty acid and hydroxyl on glycerol
• Forms ester bonds and molecule of water removed
• Triglyceride = 3 molecules of water removed as 3 condensation reactions

Nature of Lipids

• More C-H bonds = 3x as much energy stored as carbohydrates in same mass
• Hydrophobic nature allows for waterproofing
• Good insulators = less heat loss & low density so help water mammals float
• Insoluble in water = don't interfere with reactions

Structure

• Glycerol, phosphate group and 2 fatty acids
• Slightly negative hydrophillic head
• Neutral hydrophobic tail

Monolayer

• Between aqueous solution and air
• Hydrophillic heads dissolve in solution and the hydrophobic tails in the air

Micelle

• In aqueous solution
• Hydrophillic heads point outwards into the solution and all the hydrophobic tails are inside

Bilayer

• Aqueous solutions both sides
• Hydrophillic heads dissolve in solutions on both sides leaving hydrophobic tails inside

Structure

• Long chain of amino acids
• Amino acid - amino group, hydrogen, carboxyl group and R group (20 different groups)
• Dipeptide - 2 amino acids
• Polypeptide - more than 2 amino acids
• Protein - 1 or more polypeptide chains
• Amino acids are joined in condensation reactions by peptide bonds

Levels of Structure

• Primary structure - sequence of amino acids in a polypeptide chain (Peptide bonds)
• Secondary structure - Repeating pattern in structure of peptide chains such as alpha helix or beta pleated sheet  (hydrogen bonding)
• Tertiary structure - The three dimensional further folding of the secondary structure (ionic bonding between negative and positive charges and disulfide bonds between two cysteine amino acids and hydrogen bonding)
• Quaternary Structure - three dimensional arrangement of more than one polypeptide (all of the bond types)

FIbrous

• polypeptide chains form long parallel strands with some cross-linkages (fibres), insoluble, repetitive regular sequence of amino acids they are for support and structure
• They have little/no tertiary structure
• Collagen - 3 alpha helices arranged in a triple helix held by hydrogen bonds, high tensil strength found in tendons

Globular

• polypeptide chain forms into spherical shape, irregular amino acid sequences, soluble, they are for metabolic functions
• Complex tertiary and sometimes quaternary structures
• Haemoglobin - 574 amino acids in 4 polypeptide chains held by disulfide bonds - contains a haem group 

Conjugated

• Protein joined with a prosthetic group which affects its performance and function
• E.g. glycoproteins (carbohydrate - hold more water etc) and lipoproteins (lipids) 

Structure

• Phosphate group, 5 carbon sugar (deoxyribose in DNA, ribose in RNA) and nitrogenous base
• Deoxyribose - no hyroxyl group on carbon 2
• Purine - 2 nitrogen containing rings - adenine and guanine
• Pyrimidines - 1 nitrogen containing ring - Uracil, cytosine and thymine

ATP

• 3 phosphate groups, ribose and adenine base
• Break off a phosphate bond in hydrolysis reaction to produce ADP and release energy 
• Energy is used in biological activity eg muscle contraction
• Formation and production of ATP requires ATPase

Structure

• Polynucleotide - carries all information for new cells
• DNA - double helix, 2 polynucleotide strands. RNA - single helix, 1 polynucleotide strand
• Nucleotides join in condensation reaction, forms phosphodiester bonds which makes up a sugar phosphate backbone
• Hydrogen bonds form between complementary base pairs (a purine and pyrimidine)
• AT/AU (in RNA) 2 hydrogen bonds
• CG - 3 hydrogen bonds
• 2 strands in DNA are anti-parallel, 5' prime and 3' prime strand
• Every turn in DNA contains 10 bases, 5 pairs

Gene

• Sequence of bases on DNA coding for a sequence of amino acids in a polypeptide

Triplet

• Bases are read in 3s (codons)

Non-Overlapping

• Codon before is seperate from the one after. Triplets do not share bases

Degenerate

• More combinations than there are amino acids (64 combos but 20 amino acids)
• If there is a mutation there is a chance it still codes for the same amino acid

Universal

• Same base triplet codes for the same amino acid in all organisms

Semi-Conservative Replication

• Each new double helix contains 1 strand of the original DNA and one new strand

Process

• DNA helicase unwinds DNA, hydrogen bonds are broken. The strands can act as templates for new DNA strands
• DNA polymerase lines up free complementary nucleotides to the template strand. Free floating DNA nucleotides form hydrogen bonds to the template
• DNA ligase catalyses the formation of phospodiester bonds between nucleotides

Two new strands are formed. Each DNA molecule has 1 strand of the original and one strand formed from free nucleotides

Hydrogen bonds cause DNA to coil automatically

Functions of RNA

• Carries instructions for polypeptide from nucleus to ribosome (mRNA)
• Pick up specific amino acids from the protoplasm (tRNA)
• Make up the bulk of ribosomes (rRNA)

Transcription

• RNA polymerase catalyses the unraveling of a DNA molecule
• Free complementary RNA nucleotides line up on the antisense strand and the mRNA strand is assembled with RNA polymerase catalysing the formation of phosphodiester bonds
• mRNA leaves the nucleus through a nuclear pore to the cytoplasm

Translation

• mRNA carries information the ribosome and attaches
• tRNA molecules with an anticodon which is complementary to mRNA carry an amino acid to it which binds by temporary hydrogen bonds (between anticodon and codon)
• More amino acids are brought by more tRNA molecules. The amino acids bind by peptide bonds. tRNA detaches to collect more amino acids. A completed polypeptide chain is left

A permanent change in the DNA of an organism

Types of Mutation

• Point - Change in one or a small number of nucleotides affecting a single gene
• Substitution - One base is swapped for another
• Insertion - a base is added (completely new or repeated). Deletion - base is lost. These are more likely to have an affect as affects whole gene by moving all of the codon positions

Chromosomal Mutation

• Change in position of gene in chromosome or whole chromosomal mutation - entire chromosome lost or duplicated in meiosis

Affects

• Cause of variation - can have no effect, be advantageous or disadvantageous
• Sickle cell disease - affects protein chain in haemoglobin (substitution mutation) - Makes red blood cells insufficient at carrying oxygen & can block capillaries - leads to pain or death

Enzymes are biological catalysts

• Globular proteins
• Tertiary structure is so specific that each enzyme will only catalyse a specific reaction 
• Contain an active site and can be extracellular or intracellular

How do they work

• Substrate binds to the active site of enzyme
• Lowers the activational energy for a reaction
• Speeds up the reaction without being used up themselves

Lock and Key Hypothesis

• Substrate fits like a key into active site, lock. Once reaction has occured, product does not fit and complex breaks up

Induced Fit theory (more accepted)

• Shape is distinctive but flexible, will modify to fit the substrate and relax to release products

Measuring rate of reaction

• Measure initial rate when variable is changed and have a large excess of substrate (to avoid limiting factors) compare rate at end to see the effect of variable

Substrate concentration

• As substrate conc. is increased rate of reaction increases until all active sites of enzymes are being used up (V MAX)
• To increase add more enzymes as all of the enzymes were saturated

Temperature

• Rate increases by double with each 10 degree C rise. However, above optimum the enzyme denatures as the active site changes due to breaking of hydrogen and disulfide bonds

pH

• Optimum and lower or higher changes the shape of the enzyme as it affects formation of hydrogen and disulfide bonds (hold 3D structure together)

Reversible - Competitive

• Shaped like substrate so bind to active site stopping the substrate from doing so
• If you increase substrate concentration it will overcome inhibition
• V MAX can still be reached but higher substrate concentrations are needed

Reversible - Non-competitive

• Binds to enzyme (not on active site) which changes shape of the active site
• Enzyme can't bind to substrate so can't catalyse reaction.
• Increasing substrate concentration has no effect

Irreversible

• Combines with enzyme by permanent covalent bonding - with a group vital to catalysis
• This change makes it permanently inactivated

End Product Inhibition

• One of the end products of a reaction inhibits enzyme catalysing reaction - prevents too many products beng formed