OCR Biology - F212 - Module 1 (In progress)

1. Metabolism

   Annotations:

   • Metabolism is the sum total of all the chemical reaction taking place in an organism. Catabolic reactions are reactions that involve breaking down bigger molecules into smaller ones, such as digestion. Anabolic reactions involved making bigger molecules from smaller ones, such as muscle growth.
2. You are what you eat

   Annotations:

   • After consuming something, it will either become part of you or will be used to provide energy in metabolism. If something cannot be digested, it will pass through you.

1. Condensation

   Annotations:

   • The making of covalent bonds, produces a water molecule 
   1. Glycosidic

      Annotations:

      • Carbohydrates
   2. Peptide
      1. A bond between two amino acids
      2. Between carboxylic acid of one amino acid and amine group of another, H of amine and OH of carboxylic acid
   3. Ester

      Annotations:

      • Fatty acids
2. Hydrolysis

   Annotations:

   • The breaking of bonds, requires a water molecule

Annotations:

• Have a ration of Cn(H20)n  Their group is saccharides.

1. Simple sugars

   Annotations:

   • Glycosidic bonds form between glucose molecules to form maltose, which is a disaccharide.
   • Simple sugars are usually soluble in water, sweet tasting and from crystals. Simple sugars exist as different numbers of carbon. 3 = triose sugar 5 = pentose 6 = hexose.
2. Polymers

   Annotations:

   • Polysaccharides are made from beta glucose (cellulose) and alpha glucose (Starch and glycogen)
   1. Storage

      Annotations:

      • Storage of carbohydrates involve glucose glycosidicaly bonded to form a multiple ended mass of glucose. They are used for a quick release of energy as enzymes can remove multiple glucose molecules at different ends by enzymes.
      • This is called starch in plants and glycogen in animals (Multiple ended) Amylose is similar but only have 1,4 carbon bonds and not 1,6. It is often coiled up for a slow release of energy at there are only 2 ends where enzymes can break the bonds.
      • Alpha glucose is for storage as it can be respired, Beta cannot.
      1. Glucose

         Annotations:

         • Soluble, so can be transported around organism. Small so can diffuse through membranes. Can easily be broken down to ATP
         1. Alpha
         2. Beta
         3. Ring
         4. Straight
   2. Structural

      1. Annotations:

         • Multiple of these chains hydrogen bond together to form microfibrils, which then hydogen bond further to make macrofibrils. This is the formation of cellulose
         • The hydrogen bonds are staggared to ensure a weak point is not mad and it is the same strength the whole way through.

Annotations:

• The monomer of proteins, some can be hydrophobic and some can be hydrophilic. There are 20 types of amino acid occurring naturally. 
• Animals cannot store excess amino acids, so the process of deamination occurs in the liver to turn them unto urea to be removed.

1. Proteins

   Annotations:

   • Make up 50% of all organic matter in a cell, containing C, H, O, N and S
   1. Structure
      1. Primary

         Annotations:

         • A single chain of amino acids
      2. Secondary

         Annotations:

         • This is when the polypeptide is coiled and pleated. There is the alpha helix or beta-pleated sheet. This is where hydrogen bonds appear
      3. Tertiary
         1. Disulfide bonds
         2. Hydrogen bonds
         3. Ionic bonds between oppositely charged R groups
         4. Hydrophobic/hydrophilic interactions
         5. 3D structure
      4. Quaternary

         Annotations:

         • Multiple polypeptide chains are used to make this structure, either the same or different chain.
   2. Uses

      Annotations:

      • Functions of proteins are structural, membrane carriers, Enzymes, hormones and antibodies. It is also used for growth and repair in an organism, also metabolic reaction
      1. Globular

         Annotations:

         • Globular proteins such as haemoglobin have a structure as follows: Made of 4 chains of polypeptides and 2 of the subunits are different, they are alpha helixes. They have a wider range of amino acids in them than fibrous proteins such as collagen.
      2. Fibrous

         Annotations:

         • The structure of a fibrous protein such as collagen is important as it is strong, tough and insoluble.
         • The structure of collagen is a polypeptide with peptide bonds between the amino acids, it is an alpha helix coil made of 3 polypeptide chains which are hydrogen bonded together. Every 3rd amino acid is glycine allows close twisting of the polypeptide chains. Adjacent molecules are crosslinked which are staggered so there is no weak point.

2. Annotations:

   • When 2 join together, it is called a dipeptide,
   1. How R groups interact
      1. Some attract or repel
      2. Hydrophobic R group will be inside of molecule, shielded
      3. Hydrophilic R groups will be on the outside of the molecule

1. Lipids

   Annotations:

   • Lipids are a group of chemicals that dissolve in organic solvents. Roles of lipids are: Thermal insulation Energy storage Protection Membranes  Steroid hormones Buoyancy  Water proofing  Source of water from respiration Electrical insulation around neurons Aids absorption of fat soluble vitamins 
   • Lipids are different in plants and animals as animal lipids are saturated and plants are unsaturated, This is due to animal fats having more double bonds at room temperature
   • The hydrolysis of lipids can make water and CO2, and also releases energy by forming ATP. 1g of lipid gives out twice as much energy as 1g of carbohydrate. This means they are good storage molecules as they can be stored without affecting water potential.
   1. Triglyceride

      1. Annotations:

         • Top shows the ester bonds being formed, bottom shows full triglyceride
         • Triglyceride has 1 glycerol/glyceride moleule connected via ester bonds to 3 fatty acids 
2. Cholesterol

   Annotations:

   • 4 carbon based rings with an alcohol group attached. Regulated fluidity of membranes. It is also used to make steroid hormones such as testosterone and oestrogen.  Waterproofs skin Makes bile salts Makes vitamin D

1. Hydrogen bonds

   Annotations:

   • Found in: Protein secondary structure, Alpha helix and beta pleated sheet.  Protein tertiary structure Between polypeptide chains in quaternary structure, between adjacent chains in collagen. Between chains of cellulose Between DNA bases Between enzyme and substrate. Between mRNA and tRNA
2. Properties
   1. Large amount of heat is needed to evaporate it. Evaporation is an efficient cooling mechanism, e.g. panting or sweating
   2. Thermally stable e.g. the ocean doesnt really change temperature. Aquatic organisms don't have to regulate temperature well, so less energy is used for an organism. Meaning temperature of organisms change only slowly so biological reactions function properly
   3. Ice floats on water, due to molecules spreading out forming crystal lattice, providing a habitat for organisms such as penguins
      1. The water beneath the ice is insulated and is warmer, so organisms do not freeze can survive and still swim. Also allows currents with nutrients to circulate
   4. Organisms can obtain O2, food, CO2 and minerals from it.
   5. Water has a high density so can allow things to float.
   6. Water is an effective solvent and is a medium for reactions/transport. Cohesion/adhesion e.g. transpiration stream up xylem.
   7. Surface tension, habitat for insects

1. Biuret reagent

   Annotations:

   • Test for proteins, turns from a blue to purple if present
2. Iodine

   Annotations:

   • Tests for starched, turns a dark brown from a yellow if present
3. Ethanol emulsion

   Annotations:

   • Test for lipids, a white emulsion is formed near the top.
   • Add ethanol to sample, stir well, add to water.
4. Benedict
   1. For reducing sugars
      1. Add benedicts reagent, heat to 80'C, this forms a precipitate, colour change form blue to orange
      2. Amount of reducing sugar can be predicted by filtering and weighing precipitate, greater mass means more sugar present
   2. For Non-reducing sugars
      1. Add HCl and boil, neutralise with sodium carbonate then carry out reducing sugar test again

1. DNA

   Annotations:

   • The different parts are held together by condensation reactions.
   • phosphate is C5, base is C1 of deoxyribose.
   1. Phosphate group
   2. Deoxtribose
   3. Nitrogenous base
   4. Differences for RNA
      1. U instead of T
      2. Ribose sugar
      3. Single stranded
      4. 3 forms
   5. Double stranded
   6. One form
2. Bases

   Annotations:

   • The different nitrogenous bases available in DNA
   1. Purines

      Annotations:

      • The larger of the bases
      1. Adenine
      2. Guanine
   2. Pyrimidines

      Annotations:

      • The smaller of the bases
      1. Thymine
      2. Cytosine
      3. Uracil
3. Bonding
   1. G-C

      Annotations:

      • 3 hydrogen bonds
   2. A-T/U

      Annotations:

      • 2 Hydrogen bonds
4. DNA replication
   1. DNA unwinds
      1. DNA unzips via enzyme helicase
         1. Unzips via H bonds breaking
            1. Both stands act as a template
               1. Free DNA nucleotides align complementary to the aposing bases, C to G, A to T, Purine to pyrimidine
                  1. Hydrogen bonds form, C-G 3 H bonds A-T 2 H bonds via DNA polymerase
                     1. Sugar phosphate back bone forms using covalent bond via ligase enzyme
                        1. This is semi conservative replication
5. Making proteins
   1. Different sequence of nucleotides
      1. Different sequence of amino acids
         1. Different protein produced
            1. Gives a different function
6. RNA

   Annotations:

   • Differences between RNA and DNA are: Length, RNA is shorter as it holds one copy of a gene, whereas DNA contains many genes  Bases (Uracil present in RNA, Thymine present in DNA) Helix shape single and double strand RNA contains ribose and DNA contains deoxyribose 
   • Plasma cells also contain RNA as antibodies are proteins and DNA to make the proteins cannot leave the nucleus. mRNA contains a copy of a gene which can leave through the nuclear pores into the cytoplasm, where at the ribosome (Made of rRNA) rRNA is needed for protein synthesis, and tRNA brings the amino acids to the ribosome
   1. transfer

      Annotations:

      • Carries RNA to the ribosomes 
   2. messenger

      Annotations:

      • Made complimentary to DNA and is small enough to leave the nucleus.
   3. ribosomal

      Annotations:

      • Found in ribosomes
7. A gene

   Annotations:

   • A sequence of amino acids that code a protein 

Annotations:

• 1 enzyme will be able to break down 2 different molecules of they have a similar structure, such as a molecule at the end that is the same, which would mean that they are able to fit into the complementary shape of the active site.

1. Inhibitors

   Annotations:

   • Any substance/molecule that slows down the rate of an enzyme controled reaction by affecting the enzyme in some way
   • Inhibition of enzymes are used to control the rate of reaction
   1. Competitive
      2. This is reversible as the inhibitor unbinds after a short period of time. The amount of inhibition is dependent on the concentration of substrate and inhibitor
      3. Something is an inhibitor if:
         1. The substrate and inhibitor have a similar shape
         2. The shape of the inhibitor is complimentory to the active site
         3. Both inhibitor and substrate have same functional group
         4. The inhibitor can block the active site
   2. Non-competitive

      Annotations:

      • This is permanent as the tertiary structure is denatured the active site.

      1. Annotations:

         • The inhibitor enters the allosteric site
   3. 1. Without inhibitor
         1. More substrate enter the active site
         2. More enzyme substrate complexes form
         3. Achieves max turnover rate, V max
         4. At low concentrations of substrate, not all active sites are occupied, visa versa
         5. At high substrate concentration, enzyme concentration is limiting factor
      2. With competitive inhibitor
         1. Inhibitor binds to binding site, temporary
         2. Fewer active sites available for substrate
         3. With more substrate, there is a higher chance of the substrate forming an ESC
2. Rate of reaction

   Annotations:

   • Rate of reaction will always be fastest at the start and slow down as there is less substrate over a period of time as it has been broken down to product. These answers always involve: rate of collision with the active site and forming ESCs
   1. Temperature

      Annotations:

      • As temperature increases, so does rate of reaction due to the increase of kinetic energy, so more successful collisions occur with the active site to form enzyme substrate complexes. If the temperature is above the optimum temperature, the enzyme denatures and the active site loses its specific shape as the bonds themselves gain kinetic energy making them vibrate, so the enzyme is denatured
      • At low temperatures the enzyme and substrate have little kinetic energy so little/less ESC are formed, slowing down the rate of reaction.
   2. pH

      Annotations:

      • Enzymes have an optimum pH, if the enzyme is in the wrong pH, the H+ ions will react with the hydrogen bonds in the tertiary structure of the enzyme, meaning the bonds are broken and the complementary shape is lost.
   3. Concentration
      1. Of enzyme

         Annotations:

         • With more enzymes, more ESC can be formed per second so the rate of reaction increases
      2. Of substrate

         Annotations:

         • More substrate leads to faster rate of reaction, but once every active site is occupied, the rate of reaction stays the same rate.
         • If the substrate is the limiting factor, the reaction will continue to get faster.
   4. Time
3. Cofactors/coenzymes

   Annotations:

   • A cofactor 
   1. Prosthetic groups

      Annotations:

      • A permanent coenzyme attached to the enzyme
4. Interfering

   Annotations:

   • A biosensor uses enzyme controlled reactions to detect the presence of substances in a highly sensitive way. If a substance is there, a reation will occur and the biosenser will reveal of the product has been made
   1. Poisons
   2. Drugs
5. Experiments

   Annotations:

   • Basics of an experiment: Constant pH/temperature constant. Keep concentration of enzyme and substrate the same. Use a control. Use different concentrations of substrate. Do a minimum of 2 repeats on top of the original. Time at fixed intervals or at the end point. 
   1. Hydrogen peroxide w/ catalase
6. Metabolism

   Annotations:

   • Turnover number is the number of reactions an enzyme can catalyse a second.
   • Controlling metabolic pathways is possible due to a sequence of reactions of the same substrate being catalysed into a new substrate by different enzymes, then the final product is a competitive inhibitor of the first enzyme used, meaning as the concentration of final product increases, the over all production of that product slows down until the concentration lowers so more needs to be made.
   • Inborn errors of metabolism is when the DNA for an enzyme is mutated, so the enzyme is faulty.
7. Lock and key model

   Annotations:

   • An enzyme has a specific complementary shape for specific molecules
   1. Simple representation to show people how the process works
8. Induced fit

   Annotations:

   • The substrate is attracted to the active site due to opposite charges. The substrate binds to active site. the active site fits more close around the substrate, forming more bonds between substrate and active site. This has formed an enzyme substrate complex, this change in shape puts strain on the substrate which destabilises it, meaning the reaction can occur more easily by reducing the activation energy. Once the product is made it is called an enzyme product complex. The substrate no longer fits the active site as the shape has been changed, so they move away, leaving the enzyme to catalyse another reaction.
   1. Fits the evidence more closely than the lock and key model
9. Location

   Annotations:

   • Enzymes work in different places, inside cells (intrinsic) and outside cells (extrinsic)
10. Hot and cold enzymes
    1. More flexible membrane at lower temperatures
       1. Increased chance of substrate entering active site
       2. More bonds can form between active site and substrate
       3. Easier for active site to change shape as part of induced fit
       4. Induced fit will be easier
    2. Different structures
       1. Different amino acid sequence
       2. Different R group orientation
       3. Different co enzymes
       4. Different bonds, e,g, hydrogen
    3. Different DNA
       1. Different nucleotide sequence
       2. Different number of nucleotides
       3. Different gene would code for the polypeptide

Annotations:

• The key biological molecules are Carbohydrates, lipids, proteins and nucleic acids.  The key elements in biological molecules are carbon, hydrogen, oxygen and nitrogen, these make up 99% of all organisms. the other 1% include elements such as sulfur and phosphorus. Other elements such as iron, magnesium, sodium and iodine are considered separate.

1. Annotations:

   • The chemicals include: 1% DNA 2% Phospholipids 2% Polysaccharides 4% Ions,small molecules 6% RNA 15% Proteins 

1. Glycogen
   1. 1. Structure
         1. Carbohydrate/polysaccharide
         2. Alpha glucose units
         3. All units are identical
         4. Glycosidic bonds
         5. Branched
         6. Non-helical
         7. One chain per molecule
         8. No cross links
         9. Contains C H O
2. Collagen
   1. 1. Structure
         1. Protein/polypeptide
         2. Amino acid units
         3. Different units
         4. Peptide bonds
         5. Unbranched
         6. Helical
         7. Three chains per molecule
         8. Crosslinks between chains
         9. Contains C H O N
      2. Properties
         1. Flexable
         2. High tensile strength
         3. Does not stretch
         4. Insoluble
3. Haemoglobin
4. Amylose
   1. 1. Structure
         1. Only 1-4 glycosidic bonds
         2. Only one monosaccharide repeating unit
         3. Helix/coiled chain
5. Cellulose
6. DNA
7. RNA
8. Lipids
9. Triglycerides