Flashcards in Biological Molecules Deck (41):
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Molar solution
Contains 1 mole of solute in each litre of solution
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Covalent bonding
Shared pair of electrons, the attraction between the nuclei and the shared electrons
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Ionic bond
Ions with opposite charge have electrostatic forces of attraction between them
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Hydrogen bonds
Uneven distribution of electrons cause a dipole induced dipole where the less electron dense areas of a molecule are elctrostatically bonded to a less electron dense area; a polar bond
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The main organic polymers
Polysaccharides, polypeptides, polynucleotides
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Condensation reaction
Polymerisation; each new sub-unit which is attached, H2O is formed
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Hydrolysis reaction
Breaking polymers into its constituent parts; broken down by the addition of H2O
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Metabolism
All chemical processes that take place in living organisms
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Lipids
-Contain carbon hydrogen and oxygen
-the proportion of oxygen to carbon and hydrogen is smaller than carbohydrates
-insoluble in water
-soluble in organic solvents (alcohol/acetone)
*main group of lipids are triglycerides (fats and oils) and phospholipids
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Roles of lipids
-form the phospholipid bilayer that makes up the cell membrane
-source of energy - when oxidised they provide more than twice the energy provided by the same mass of carbohydrates
-Waterproofing - insoluble in water; used by plants and insects for waterproofing (waxy,lipid cuticles) to conserve water; mammals produce an oily secretion from the sebaceous glands in the skin
-insulation - fats are slow conductors of heat so when stored beneath body surface they help retain body heat. Also act as electrical insulators in the myelin sheath around nerve cells
-protection - stored around delicate organs (e.g. kidney)
*fats are solid at room temperature whereas oils are liquids
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Triglycerides
Have three fatty acids combined with glycerol. The fatty acid forms an ester bond with glycerol in a condensation reaction.
The glycerol molecule is the same in all triglycerides, so the different fats and oils come from variations in the fatty acids (there are over 70 different fatty acids and all have a carboxyl group attached with a hydrocarbon chain attached
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Saturated
No carbon-carbon double bonds
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Mono-/poly-unsaturated
Mono-single double bond present
Poly-more than one double bond is present
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Structure of triglycerides related to properties
- high carbon-hydrogen bonds : carbon atoms ratio so an excellent source of energy
- have a low mass:energy ratio so great storage molecules (much energy is stored in small vol)
- being large non-polar molecules, they are insoluble in water so do not affect osmosis in cells or the water potential of them
-high hydrogen:oxygen atoms and they release water when oxidised so provide an important soured of water, especially for organism in dry environments
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Phospholipids
Similar to triglycerides but one fatty acid molecule is replaced by a phosphate molecule. The fatty acid molecules repel water (hydrophobic tails), phosphate molecules attract water (hydrophilic heads)
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The structure of phospholipids related to their properties
-Having a hydrophobic end and a hydrophilic end, in an aqueous environment, they form a bilayer within cell-membranes and so a hydrophobic barrier is formed between the inside and outside of a cell
-the hydrophobic phosphate heads help hold at the surface of the cell-surface membrane
-the phospholipid structure allows them to form glycolipids by combining with carbohydrates within the cell surface membrane which is important in cell recognition
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Test for lipids
-add 5cm^3 of ethanol to 2cm^3 of sample being tested
-shake the tube thoroughly to dissolves any lipid sample
- add 5cm^3 of water and shake gently
-a cloudy-white colour indicates the presence of a lipid
-repeat the experiment with water as a control and the final solution should remain clear
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Proteins
complex large molecules which all have different in shape and have lots of different functions. Their monomer unit is amino acids
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Structure of amino acids
•amino group - a basic (alkaline) group
•carboxyl group- an acidic group
•hydrogen atom
•R group - a variety of different chemical groups; each amino acid has a different R group. The 20 naturally occurring amino acids which occur in all living organisms only differ in their R group
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The formation of a peptide bond
A condensation reaction occurs between amino acids; a OH from the carboxyl group of one amino acid with a H from the amino group of another amino acid form a water molecule; a peptide bond forms between the carbon atom of the carboxyl group on one amino acid and the nitrogen atom of amino group on another amino acid
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Primary structure of proteins - polypeptides
The sequence of amino acids in a polypeptide chain forms the primary structure of any protein. This sequence is determined by DNA.
As polypeptides have many of the 20 naturally occurring amino acids joined in different sequences it follows that there is an almost limitless number of possible combinations and, therefore, primary structures. A change in even one amino acid can result in a change in the proteins shape and may stop it carrying out its function
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Secondary structure of proteins
Hydrogen bonds form between Oxygen on the C-_O (which has a negative charge) and the hydrogen on the N-H (which has a positive charge) on either side of each amino acid. This causes the long polypeptide chain to be twisted into a 3D shape (e.g. an alpha helix)
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Tertiary structure of proteins
The alpha helices can be twisted further to form a even more complex tertiary structure. This occurs due to different types of bonds:
- disulfide bridges - which are fairly strong and not easily broken
- ionic bonds - formed between any carboxyl and amino groups that are not involved in forming peptide bonds; they are weaker than disulfide bonds and are easily broken by changes in the pH
-hydrogen bonds - numerous but easily broken
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The importance of the 3D structure of proteins
It makes each protein distinctive and allows it to recognise, and be recognised by, other molecules and can then interact with them in a very specific way
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Quaternary structure
Large proteins often form complex molecules containing a number of individual polypeptide chains that are linked in various ways. Prosthetic groups can also be attached with the molecules such as the haem group in haemoglobin
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Test for proteins
-Place sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide at RTP
-Add a few drops of very dilute copper sulphate solution and mix gently
-A purple coloration indicates the presence of peptide bonds. If no protein is present the solution will remain blue
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Enzyme action
Enzymes are globular proteins which act as catalysts lowering activation energy which allows reactions to occur at lower temperatures which allows metabolic processes occur at body temp;
The reactant molecules must collide wit sufficient energy to alter the arrangement of their arrangement of their atoms to form the products. Many reactions require an initial amount of energy to start. The minimum amount of energy required to start a reaction is called activation energy
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Enzyme structure
Being globular proteins they have a specific 3D shape that is the result of their sequence of amino acids, a specific region of the enzyme is functional, this is known as the active site. The substrate fits neatly into this depression and forms an enzyme-substrate complex. The substrate is held within the active site by bonds that temporarily form between certain amino acids of the active site and groups on the substrate molecule
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Induced fit model
The active site forms as the enzyme and substrate interact; the enzyme is flexible and can mould itself around the substrate. As the enzyme changes shape it puts strain on the substrate molecule which distorts a particular bond/bonds in the substrate and consequently lowers the activation energy needed to break bond
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Factors affecting enzyme action
Temperature
pH
Enzymes concentration
Substrate concentration
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Temperature
- an increase in temperature increases the kinetic energy of molecules - the substrates and enzymes move around more rapidly and collide more frequently, so there are more effective collision resulting in more SUBSTRATE-ENZYME COMPLEXES being formed and so the rate of reaction INCREASES
-however if the temperature INCREASES MORE (45°C) this causes hydrogen, and other binds to break in the enzyme and so the enzyme changes shape and therefore the active site changes shape, so the substrate fits less easily SLOWING the rate of reaction
- at around 60°C the enzyme becomes so disrupted that it stops working all together - DENATURATION
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pH
- change in pH alters the charges on amino acids that make up the active site - this means the substrate can no longer become attached so the enzyme-substrate complex can't be formed.
- and significant changes in pH may cause the bonds maintaining the enzymes tertiary structure to break - changing the shape of the active site
*different enzyme work best at different pH's and many enzymes are very specific in the pH (this is why the stomach is acidic, the small ingesting is more neutral etc)
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Enzyme concentration
-An increase in the amount of enzymes leads to a proportionate increase in the rate of reaction
-if the substrate is limiting (there is not a sufficient supply to fill all the enzymes active sites at one time) then an increase in enzyme concentration will have no effect on the rate of reaction (the graph at high enzyme concentration is a straight line due to the substrate being limiting
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Substrate concentration
-If the concentration of enzymes is fixed and the substrate concentration is increased slowly the RoR increases in proportion to the concentration of substrate;
This is because at low substrate concentrations the enzymes lave a muted amount of substrates to collide with so the active sites are not working to full capacity. As it increases, the active sites become gradually filled to the point where all of them are working as fast as they can, this means the RoR is at maximum so anymore substrate will have no effect
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Competitive inhibitors
-have a molecular shape similar to the substrate which allows them to occupy active site.
-if substrate concentration is increased the effect of the inhibitor is reduced
-the inhibitor is not permanently bonded to the active site so images it leaves another molecule can take its place
-sooner or later all the substrate molecules will occupy an active site but the greater the concentration of the inhibitor the longer this will take
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Non-competitive inhibitor
-attach themselves to the enzyme at a binding site which isn't the active site, which alters the shape of the enzyme and thus it's active site in such a way that the substrate molecules can no longer occult it so the enzyme cannot function
-as the substrate and the inhibitor are not competing for the same site, an increase in substrate concentration does not decrease the effect of the inhibitor
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Nucleotide structure
•Pentose sugar
•phosphate group
•organic base - a nitrogen containing an organic base; cytosine, thymine, uracil, adenine and guanine
These are joined together as a result of condensation reactions
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Polynucleotide
-2 mononucleotide can join together by a condensation reaction between the deoxyribose sugar of one and the phosphate group of another -this bond is called a phosphodiester bond
-this repeated many time forms a long chain of nucleotides - polynucleotide
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RNA structure
-A single, (relatively) short chain of polynucleotides. The pentose sugar is ribose and the bases are guanine, cytosine, adenine, and uracil
-can be in the form of:
•tRNA - transfer genetic info from DNA to ribosomes
•mRNA
•rRNA - protein synthesis
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DNA structure
-2 extremely long strands of polynucleotides, pentose sugar is deoxyribose.
-The strands are joined together by hydrogen bonds between certain bases
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