Biological Molecules

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  • Created by: _KatieR
  • Created on: 13-12-15 11:18


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


  • 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
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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 
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Useable energy sources e.g. glucose and sucrose


  • 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


  • 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)
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  • 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
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Polysaccharides continued

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
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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)


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


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


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


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


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Structure of Proteins

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)
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Globular, Fibrous and Conjugated proteins


  • 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


  • 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 


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


  • 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
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Nucleic Acids


  • 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
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Genetic Code


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


  • Bases are read in 3s (codons)


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


  • 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


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

Semi-Conservative Replication

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


  • 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

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Protein Synthesis

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)


  • 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


  • 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
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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


  • 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
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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
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Rate of Reaction

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


  • 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


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

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


  • 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
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