Unit 1 Flashcards
Monomer
Single units that are joined together to create a chain.
Polymer
Large molecules made up of repeating smaller molecules.
Condensation Reaction
A chemical process in which two molecules combine to form complex structures like polysaccharides and polypeptides. Usually eliminates water.
Hydrolysis Reaction
The breaking down of large molecules into smaller molecules by the addition of water.
3 types of carbohydrates:
Monosaccharides, disaccharides, polysaccharides.
Bond between monosaccharides:
Glycosidic!!!
Bond between amino acids:
Peptide
Bond between glycerol and fatty acid within a lipid:
Ester bond
Bond between DNA/RNA bases:
Phosphodiester.
Monosaccharide examples:
-Glucose
-Fructose
-Galactose
Two isomers of glucose:
-Alpha-glucose (draw it!)
-Beta-glucose (draw it!!)
How is a glycosidic bond formed?
Two hydroxl (-OH) groups react together forming a covalent bond (-O-) and water comes away. Condensation reaction.
Disaccharide examples:
-Maltose
-Sucrose
-Lactose
Glucose + Glucose –>
Maltose
Glucose + Fructose –>
Sucrose
Glucose + Galactose –>
Lactose
Starch contains:
-Amylose
-Amylopectin
Amylose
-1-4 glycosidic bonds, straight chains.
-Helix structure enables it to be more compact and resistant to digestion.
Amylopectin
-1-4 glycosidic bonds but ALSO 1-6 glycosidic bonds creating branched molecules.
-Branches mean more terminals which can be hydrolysed to use for respiration or to be added to for storage.
Glycogen
-Highly branched
-More compacts so animals can store more energy.
-The branching means more free ends to which glucose molecules can either be added or removed.
-The storage or release of glucose can suit the demands of the cell.
Cellulose chains can be:
-Branched and unbranched
-Folded (can be made compact)
-Straight or coiled
-Insoluble
Cellulose Structure
-Long chain of beta glucose joined by 1-4 glycosidic bonds.
-Rotated 180 degrees and each monomer is inverted.
-Bc of inversion, hydrogen bonds form between the chains.
Cellulose Function
-Cell walls because hydrogen bonds between parallel chains creating microfibrils.
-High tensile strength allows it to be stretched.
-Cellulose fibres are permeable.
Test for reducing sugars:
-Add Benedict’s Reagent to the sample.
-Heat in water bath at 80 degrees
-Will turn brick red if reducing sugars are present.
(Benedict’s Reagent has Copper Sulfate ions making it a pale blue colour. When reducing sugars are present, the CuSO4 is reduced to CuO.)
Test for non-reducing sugars:
-Add dilute HCl.
-Heat in water bath.
-Neutralise using Sodium Hydrogencarbonate (use indicator to check).
-Carry out Benedicts test as normal.
Test for starch:
-Add iodine to potassium iodide solution.
-Add that to the sample of food.
-Colour change from orange/yellow to blue/black.
Saturated fatty acid
Single covalent bonds between carbon atoms.
Unsaturated fatty acid
Double covalent bonds between carbon atoms.
Triglyceride
Contains 1 glycerol molecule and 3 fatty acids.
Ester link between hydroxyl on glycerol and carboxylic group on fatty acid. O-C=O
Condensation reaction.
Water molecule comes away.
Triglyceride functions:
-Energy store
-Insulation
-Buoyancy
-Protection
Phospholipid
1 glycerol, 1 phosphate group, 2 fatty acids
‘Heads’ and ‘tails’
Role of phospholipids
-Cell membrane
-Barrier to water-soluble molecules
-Saturated fatty acid tails- less fluid.
-Unsaturated fatty aid tails- more fluid.
Test for lipids:
-Qualititive test
-Add ethanol to food sample.
-Add water
-Cloudy/milky emulsion- lipids present.
Amino acid general formula
NH2-CHR-COOH
Draw
Condensation reaction of amino acids
-Peptide bond between H fron NH2 and OH from COOH.
-H2O formed.
Primary structure of protein
-Sequence of amino acids bonded together by peptide bonds forming a polypeptide chain.
-DNA affects sequence and therefore protein.
Secondary structure of a protein
-Weak hydrogen bonds between partially negative N and O and partially positive H.
-Forms alpha-helix or beta-pleated sheet.
-Fibrous proteins typically have secondary structure.
-Secondary structure refers to the hydrogen bond between the amino acid and carboxyl group.
Alpha-helix bonding
Hydrogen bond between every fourth peptide bond.
Beta-pleated sheet bonding
Protein folds and polypeptide chains are parallel enabling hydrogen bonds to form between parallel peptide bonds.
Tertiary structure of protein
-Bonds form between R groups (side chain).
-Hydrogen bonding
-Ionic bonding
-Disulphide bridges
-Weak hydrophobic interactions
-Often in globular proteins
Disulphide Bonds
-Form between 2 cysteine R groups
-Stabilise the protein
-Broken by reduction
-Common in proteins secreted by cells.
Ionic Bonds
-Form between + charged (amine group) and - charged (carboxylic acid) R groups.
-Broken by pH changes
Hydrogen Bonds
-Between strongly polar R groups.
-Most common.
Hydrophobic Interaction
Forms between hydrophobic, non-polar R groups in the interior of proteins.
Quaternary structure of proteins:
Multiple polypeptide chains joined together by peptide bonds.
Globular vs fibrous proteins
Globular proteins (e.g. enzymes) are compact.
Fibrous proteins (e.g. keratin) are long forming fibres.
Test for proteins
-Add NaOH or KOH to make sample alkaline.
-Add Copper(II) Sulfate to the solution
-(Biuret’s Reagent contains both these.)
-Colour change from blue to purple indicates the presence of proteins.
Enzymes
-Act as a catalyst by lowering activation energy needed to start a reaction.
-Globular protein that has a specific region called an active site.
-Substrates bind to the active site forming an enzyme-substrate complex.
Induced fit model
-Proposes the idea that the active site changes shape slightly to accommodate the substrate.
-As it changes shape, the enzyme puts a strain on the substrate molecule.
-The strain distorts bonds in the substrate and consequently lowers the activation energy needed to break the bond.
Lock and key model
-Each key fits and operates only a single lock (one substrate only fits one specific enzyme).
-A limitation of this is that enzymes are considered a rigid structure.
-Enzymes are actually flexible so therefore the induced fit model was developed.
Factors affecting the rate of enzyme reactions
-Temperature
-pH
-Enzyme concentration
-Substrate concentration
Temperature
-As temperature increases so does the rate of reaction.
-This is because there is more kinetic energy so therefore molecules move more and there are more collisions and more successful enzyme substrate complexes.
-After the optimum temperature is reached, the rate of reaction decreases.
-At high temps, the enzymes vibrate too much and the bonds that maintain tertiary structure are broken.
-Active site changes shape and no more ES complexes so enzyme is denatured.
pH
-All enzymes have optimum pH.
-Above and below the optimum, the H+ and OH- ions disrupt the ionic and hydrogen bonds in the tertiary structure of the enzyme.
-Active site changes shape, no more ES complexes so enzyme is denatured.
Enzyme Concentration
-Increases number of active sites for collisions.
-More ES complexes form.
-Rate of reaction increases until amount of substrate becomes the limiting factor then the graph plateaus.
-Increasing the enzyme concentration after this will not have an effect.
Substrate Concentration
-Increases rate of reaction as there is more chance of successful collisions so more ES complexes form.
-Rate of reaction will slow as enzyme conc becomes a limiting factor. All active sites are occupied.
-Increasing the substrate concentration will no longer have an effect on the rate.
Competitive inhibitors
-Have a molecular shape similar to that of the substrate.
-Occupies the active site of an enzyme.
-Prevents substrates from binding and forming enzyme-substrate complexes.
-Reduces rate of reaction.
-Can overcome this by increasing the concentration of the substrate so it increases the likelihood of enzyme-substrate complexes forming.
Non-competitive inhibitors
-They attach at the allosteric site.
-When they attach they alter the shape of the active site.
-This decreases the rate of reaction as the enzyme can therefore not be used so no enzyme-substrate complexes will form.
RNA
-Transfers genetic material from nucleus to ribosomes.
-Nucleotides contain: ribose sugar, phosphate group and a nitrogenous base.
-Uses uracil instead of thymine.
DNA
-Holds genetic information.
-Nucleotides contains: deoxyribose sugar, phosphate group and a nitrogenous base (A=T, C3-G).
Stability of DNA
-Phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.
-Hydrogen bonds link the organic base pairs forming bridges between the phosphodiester uprights.
-There are 3 hydrogen bonds between C and G so therefore a higher proportion of C-G bonds, the more stable.
Prime location
-3’ is the hydroxyl group
-5’ is the phosphate group
-In double helix, one strand runs 5’ to 3’ and the other runs 3’ to 5’. Referred to as ‘antiparallel’.
4 differences of DNA and RNA
-Double strand vs single strand.
-Hydrogen bonds vs no hydrogen bonds.
-Uses thymine vs uses uracil.
-Long vs short.
-Deoxyribose sugar vs ribose sugar.
DNA is stable because:
-Phosphodiester backbone protects the highly reactive nitrogen base in the helix.
-Hydrogen bonds form bridges between phosphodiester uprights.
-More C-G bonding= more stable due to 3 hydrogen bonds.
Semi-conservative replication needs:
-Each types of bases (A, T, C, G).
-Enzyme of DNA Polymerase.
-Chemical energy source.
-Both strands of DNA act as a template for attachment of nucleotides.
Semi-conservative replication
-DNA helicase breaks the hydrogen bonds between the bases causing the helix to unwind.
-Free nucleotides enter and use one strand as a template and complementary bases pairing occurs.
-DNA Polymerase joins the nucleotides forming phosphodiester bonds.
-Two strands of DNA are formed.
Meselson-Stahl Experiment of Semi-conservative replication
Draw it!!!!!!
Transcription
-DNA helix unwinds to expose bases to act as a template.
-Only one chain of the DNA acts as a template.
-Catalysed by DNA helicase.
- DNA helicase breaks hydrogen bonds between bases.
-Free mRNA nucleotides in the nucleus align with opposite exposed complementary bases.
- Enzyme RNA polymerase bonds together the RNA nucleotides creating RNA polymer chain. one gene is copied (pre-mRNA).
-Splicing- introns are ‘spliced out’ (by protein- splicesome) as they don’t code for proteins.
Translation
-Once the modified mRNA leaves the nucleus, attaches to ribosomes.
- Ribosomes attach to start codon.
-tRNA with complementary anticodon to codon aligns opposite mRNA.
-Ribosome will move along the mRNA reading it in triplets.
-Amino acids brought by tRNA form peptide bond (catalysed by enzymes and requires ATP).
-Continues to stop codon (doesn’t code for amino acid) so ribosome detaches and ends.
ATP
-Consists of ribose, adenine, and three phosphate groups.
-ATP—> ADP + Pi (condensation catalysed by ATP hydrolase)
-ADP + Pi —> ATP (hydrolysis catalysed by ATP synthase)
-Pi can phosphorylate other molecules making them more reactive.
3 ways that ATP is synthesised:
-In chlorophyll-containing plant cells during photosynthesis (photophosphorylation).
-In plant and animal cells during respiration (oxidative phosphorylation).
-In plant and animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation).
Roles of ATP:
-Metabolic processes- provides energy to build up macromolecules from basic units.
-Movement- energy for muscle contraction, filaments of muscle slide past one another to shorten overall length of muscle fibre.
-Active transport- change shape of carrier proteins in membrane, allows molecules to be moved against a conc gradient.
-Secretion- form lysosomes needed for secretion of cell products.
-Activation of molecules- Pi can make molecules more reactive, lowering the activation in enzyme-catalysed reactions. E.g. Pi+glucose at start of glycolysis.
Water structure
-Dipolar
-2 hydrogen atoms and 1 oxygen.
-Oxygen is partially negative and hydrogen is partially positive.
Specific heat capacity of water
-Hydrogen bonding means that molecules stick together and therefore more energy is needed to separate them.
-Acts as a buffer against sudden temperature variations.
-Makes aquatic environments more temperature-stable.
-Buffers organisms against sudden temperature changes in terrestrial environments.
Latent heat of vaporisation of water
-Hydrogen bonding between water molecules means that it required a lot of energy to evaporate 1 gram of water.
-Sweating in thermoregulation provides a cooling effect through evaporation.
Cohesion and surface tension of water
-Tendency for molecules to stick together is cohesion.
-Due to hydrogen bonding, water has high cohesion forces which allows it to be pulled through a tube.
-ST is a force that means that when water molecules meet air, they tend to be pulled back into the body of water rather than escaping from it.
Water in metabolism
-Break down and build up molecules (condensation and hydrolysis).
-Chemical reactions take place in an aqueous medium.
-Raw material in photosynthesis.
Water as a solvent
Readily dissolve:
-Gases such as O2 and CO2.
-Wastes such as ammonia and urea.
-Inorganic ions and small hydrophilic molecules such as amino acids, monosaccharides and ATP.
-Enzymes whose reactions take place in solution.
Other properties of water
-Evaporation cools organisms and allows them to control temperature.
-Not easily compressed and therefore provides support.
-Transparent so photosynthesis can occur and also light rays penetrate jelly fluid in eye so light rays reach retina.
Inorganic ions
-Fe+ ions- found in haemoglobin and play a role in transport of oxygen.
-Phosphate ions- structural role in DNA and storing energy in ATP molecules.
-H+ ions- determining pH of solutions and functioning of enzymes.
-Na+ ions- important in transport of glucose and amino acids across plasma membrane.
