2.2 biological molecules
Condensation
2 molecules are joined together with the removal/releasing/elimination of water. A covalent bond is formed.
Insulin structure
2 polypeptide chains. The A chain begins with a section of alpha helix and the B chain ends with a section of beta pleat sheet. These are folded into the tertiary structure and joined by disulfide links.
Collagen structure
3 polypeptides in a closely packed triple helix with many hydrogen bonds. Long fibrils that can cross link to make strong fibres. Flexibility and mechanical strength.
Phospholipid bilayer
A 2-layered fluid sheet of phospholipids with tails inside and heads outside. They are free to move but within keeping the orientation of the tails not exposed to water, giving stability. In the membrane, they separate the aqueous external environment from the cytosol. Selectively permeable to control the passage of substances. Can be saturated or unsaturated fatty acids.
Stigmasterol
A cholesterol derivative in plant membranes. Only different due to the one extra double bond between carbon 22 and 23.
Alpha helix
A coil shape held in place by hydrogen bonds between NH and CO of amino acids 4 monomers apart in the polypeptide chain chain. There are 3.6 amino acids per turn.
Ab initio modelling Comparative protein modelling
A model is built based on the atoms in the amino acids' physical and electrical properties. Gives multiple solutions which need other methods to reduce the number. Protein threading. Scans the sequence against a database of known structures to produce a set of possible models.
Hydrolysis
A molecule is split into two with the addition/using up/supply of water. A covalent bond is broken.
Isomer
A molecule that has the same molecular formula as another but it has a different arrangement of atoms in space (not including rotations).
Monomer Polymer
A small single unit that can bind to many other identical molecules. A large molecule made of many repeating monomers.
Ionic bonds in proteins
A strong attraction between oppositely charged R groups or at the ends of polypeptide chains where the groups have joined to NH₃⁺ and COO⁻. Sometimes these types of ionised groups are part of R groups. Or there may be other ionised groups in the R groups. Affected by pH and temperature.
Iodine test for starch
Add a few drops of iodine which is in potassium iodide solution. If it is present it turns from yellow/brown to blue/black. When dissolved in KI, I₂ forma a triiodide ion I₃⁻. This slips into the middle of the long amylose helix. Shorter chains (not starch) give no change or a weak red-purple.
Biuret test for proteins
Add the reagent- alkaline Cu²⁺ solution. Light blue to lilac/mauve. The reagents may be separate: Biuret A- sodium hydroxide. Biuret B- copper sulfate. A complex forms between the 4 nitrogen atoms that are in the peptide bonds of 2 adjacent peptides and the Cu²⁺ ions.
Condensation of beta glucose
Alternating B glucose molecules are rotated forward by 180° (we say this even though it's not true). Turned upside down inverted. Its a reflection horizontally. They are now close enough to react. Forms a 1-4 glycosidic bond through a condensation reaction, making straight chains.
Cellulose straight chains
Alternating rotated B and the 1-4 glycosidic bond makes a different kind of polysaccharide to whats seen with alpha that prevents spiralling of the chain. Hydrogen bonds form within the chain due to the rotated monomers. These prevent spiralling also and stabilise the structure.
Protein ionisation
Amino acids ionise in water due to the polarity making them soluble. The H⁺ moves from the carboxyl to the amino group to make NH₃⁺ and COO−. Whole proteins can also be ionised because the H⁺ can move from the COOH group at one end all the way to the NH₂ group to give it a positive and negative end.
Phospholipid ends
Amphipathic due to the long length of the molecule. The phosphate head is charged and hydrophilic. It interacts with and is attracted to water. The fatty acid chains are hydrophobic and non-polar. They repel water but mix readily with fat.
Glycerol
An alcohol with free OH groups. 3 carbon atoms. 3 OH groups. C₃H₈O₃.
essential amino acids
Animals can make some amino acids but others must be ingested from our diet. Of the 20 amino acids 5 are non-essential and can be made. 9 are essential and need to be eaten. 6 are conditionally essential and are needed only by children.
Protection
Around delicate vital organs to act as a shock absorber for cushioning. In some bacteria, they have a waxy cuticle which is a lipid rich coat on the outer peptidoglycan wall for protection.
Other cell walls
Bacterial cell walls are made of peptidoglycan which are made of polysaccharide chains that are long, parallel and cross-linked with short peptide chains. Exoskeletons- chitin is an acetyl amino group (NH.COCH₃). on carbon 2 instead of the OH group, crosslinks of short peptide chains between long parallel chains of acyetylglucosamine.
Test for non-reducing sugars
Benedict's gives a negative. New sample and boil it with acid (hydrochloric). This hydrolyses the sugar, breaking the glycosidic bond to release monosaccharides which are reducing. Cool. Neutralise with sodium hydrogencarbonate. Heat with Benedict's again. A positive red result.
Hydrogen bonds in proteins
Between δ+ H and δ- O or δ- N in carbonyl, hydroxyl and amino groups OR between polar areas on the R groups of different amino acids. Relatively weak but because so many form they make strong, stable structures. Are strongly affected by temperature and pH.
Lipids Source of energy
Broken down in respiration to generate ATP. The ester bonds are hydrolysed and the glycerol and fatty acids are broken down into carbon dioxide, water + energy. Respiration of lipids makes more water and twice energy than sugars. There is a higher proportion of hydrogens and fewer Oxygens.
Lipids
C, H ,O. Low proportion of O. soluble in non-polar solvents. Insoluble in water. No δ+ and δ- to attract molecules. Even distribution of electrons in outer orbitals. Macromolecules- very large, complex organic molecules. Not polymers- not repeating regular monomers, different bonded components.
Fatty acids
CH₃(CH₂)nCOOH. A carboxyl group attached to a hydrocarbon chain. A carboxylic acid. It is an acid because the carboxyl group ionises in solution to produce free H+. COOH → H⁺ + COO⁻. 2 - 20 carbon atoms in the long hydrocarbon chain. Many C-H bonds.
Nucleic acids (elements monomers polymers)
Carbon Hydrogen Oxygen Nitrogen Phosphorus Nucleotides DNA/ RNA
Proteins (elements monomers polymers)
Carbon Hydrogen Oxygen Nitrogen Sometimes sulfur. Amino acids polypeptides and proteins
Beta pleated sheet
Chains fold slightly into a zig-zag structure due to the pattern formed by the individual amino acids. These long chains fold over themselves forming the sheet held together by hydrogen bonds between NH and CO but much further down the chain in adjacent sections.
Primary structure 2
Changing just 1 amino acid can alter the protein function because of the change in shape. There are many possible combinations of amino acid sequences due to the 20 amino acid variants. The only bonding involved is peptide bonds between monomers.
Collagen function
Connective tissue, skin, ligaments, cartilage, nervous system. Artery Walls- prevents bursting when withstanding high pressure. Tendons- bundles of fibres to connect muscles to bones so they can pull on bones. Bones- made of collagen reinforced with calcium phosphate to make it hard.
Conjugated proteins
Contain a prosthetic group- a non protein component. these can be lipids, carbohydrates, metal ion, molecules derived from vitamins.
Test strips for reducing sugars
Contain immobilised enzymes. Dip the stick and compare the colour change with the calibration card. Commercially manufactured. It is semi quantitative because the concentration can be determined.
Qualitative tests
Determine the presence or absence of a particular biological molecule without telling you how much is present. The molecules have to pass into solution to be tested on. Grind and squash food sample and mix vigorously with a solvent.
shape = function
Different amino acids have different sequences resulting in different structures that make different shapes which are specific for the function.
Peptide breaking If 4 amino acids bond together-
Dipeptides are broken down into amino acid monomers by hydrolysis reactions and water is used up. Protease does this in digestion or to break down enzymes. 3 peptide bonds form and 3 water molecules are produced.
Disulfide bridges bonds links
Double covalent bonds between R groups that contain sulfur atoms. Very strong. Unaffected by heat and pH. Affected by reducing agents.
Haemoglobin function
Each of the subunits has space in which the haem group is held . Oxygen reversibly bonds to the iron ion haem to transport it as oxyhaemoglobin from the lungs to the cells where it is needed.
Pepsin
Enzyme that digests protein in the stomach. One polypeptide chain that folds into a symmetrical tertiary structure. Hydrogen bonds and disulfide bridges. High proportion acidic R groups, stable in stomach. Few basic groups to accept H+ ions so this doesn't affect the structure much
Catalase
Enzyme. Catalyses the breakdown of hydrogen peroxide-prevents damage to cells caused by its build up. 4 haem prosthetic groups Fe²⁺ ions interact with H₂O₂.
Buoyancy
Fat is less dense than water allowing aquatic mammals to float.
Essential fatty acids
Fatty acids that can't be synthesised and need to be ingested compete.
Globular proteins
Fold to be near spherical.compact, water soluble. Hydrophobic units inside and hydrophilic units outside so water can cluster and bind. Important for functions in regulating major life processes. Very specific shapes.
Saturated fatty acids
General formula CnH₂n+1COOH. No double c=c bonds. Carbon atoms form the maximum number of bonds possible with hydrogen. Forms straight chains. Animals tend to have saturated triglycerides
Keratin functions
Hair skin nails, hoofs, horns, scales, fur, feathers. Degree of disulfide bonds determines the flexibility. Hair less, nails more.
Insulation
Heat insulation- adipose tissue in mammals as blubber for hibernation. Electrical insulation- in nerve cells for impulse transmission.
Quaternary structure
How multiple polypeptides are arranged to make the complete protein molecule. 3D arranged subunits. Same or different chains. Can have a non-protein part. Held together by bonds between polypeptides. Enzymes- 2 same subunits. Insulin- 2 different. Haemoglobin- 2 sets of 2 same subunits.
Microfibrils Macrofibirls
Hydrogen bonds form between many chains (60+). They combine to form macrofibrils. Macrofibrils have 400 Microfibrils. Macrofibrils are embedded in pectins - a polysaccharide glue of substances- in the wall. They criss-cross for extra strength. Macrofibrils combine to make the cellulose fibres.
Cellulose parallel chains
Hydrogen bonds form between the parallel chains. The hydroxyl group on C2 sticks out. Carbon 6 is part of CH₂OH. They form between -OH group on C2 and the -OH on C6. O of the glycosidic bond and -OH C6 group. they stabilise the structure, adding additional strength. Stops spiralling.
Increasing strength of protein bonding at RTP
Hydrophilic and hydrophobic interactions Hydrogen bonds Ionic bonds Disulfide bonds Peptide bonds
Hydrophobic and hydrophilic interactions 2
Hydrophobic parts associate together in the centre of the structure to avoid water creating interactions between non polar groups. Hydrophilic parts go to the edge outside to be close to water creating interactions between polar groups.
Functional groups
Hydroxyl -OH Carboxyl -COOH Amine -NH2 Phosphate Carbonyl
Esterification
Hydroxyl groups interact- in the COOH of the fatty acid and the OH group of glycerol. Condensation reaction. Up to 3 fatty acids can bond due to the 3 available OH groups. 3 ester bonds are made and 3 water molecules are produced. The fatty acids that bond can be different to each other.
Protein bonding
In different amino acids, different R groups interact and this forms different types of intermolecular forces and bonds which means long polypeptides fold into complex 3D structures with different shapes that are specific for the function. Crucial in creating tertiary and quaternary structure.
Elastin functions
In elastic fibres. Skin- stretch around bones and muscles. Manipulative. Lungs- alveoli can expand and return to inflate or deflate. Bladder- expand to hold urine. Blood vessels- stretch and recoil to maintain pressure. Flexibility to expand when needed and return to shape.
Cellulose
In plant cell walls. Tough, insoluble, fibrous. Hard to break down into monomers. It is a homopolysaccharide as it has long chains of beta glucose molecules joined by 1 - 4 glycosidic bonds where every alternative Beta glucose is inverted.Straight chains, unbranched. Multiple chains lie side by side.
Lipids Energy store
Insoluble in water so they can be stored without affecting the water potential in the cell. Fats are used instead of sugars due to the energy source. Adipose tissue is stored under the skin in mammals.
Hydrogen bonds (definition)
Intermolecular attractions between molecules that have a slightly positively charged hydrogen atom and another slightly negatively charged one (that is highly electronegative).
Fibrous proteins
Long, strong, regular sequences. Insoluble, high % of hydrophobic Rs. Small range of amino acids. Small R groups. Repetitive sequences make organised structures and form fibres, good for roles in structure. Not folded into complex 3D shapes. Supercoiled tertiary structure.
Keratin structure and properties
Lots of cysteine so disulfide bridges form between sulfur containing R groups as well as many Hydrogen bonds. Very strong, insoluble, inflexible. Mechanical protection and an impermeable barrier to infection. Waterproof so it prevents the entry of water-borne pollutants.
Steroid hormones
Made from cholesterol. small and (mostly) hydrophobic to pass through membranes without needing a receptor or protein on the outside. Goes straight into cells to be received on DNA.Testosterone, oestrogen, vitamin D.
Emulsion test for lipids
Mix the sample thoroughly with ethanol and it will dissolve. Filter. Pour the solution into a test tube containing water. A cloudy white emulsion. Small liquid droplets that come out of the solution with water.
Phospholipids
Modified triglycerides. One of the 3 fatty acid chains is replaced with a phosphate group. A condensation reaction happens between the OH group of phosphoric acid (H₃PO₄) with one of the 3 OH groups on glycerol. They commonly have an even number of carbons in the fatty acid chain. One chain is saturated and one chain is unsaturated.
Amino acids
Monomers of proteins with the same structure of an N-C-C backbone. 500 exist but only 20 are proteinogenic- found in proteins. They have: Amino group- NH₂ Carboxyl group- COOH R group- variable. a range of chemical groups different in each amino acid. Vary by size, polarity and hydrophilic/phobic.
Triglycerides
One glycerol and 3 fatty acid chains held together by ester bonds.
Unsaturated fatty acids
One or more double bonds between carbon atoms. Fewer hydrogens bonded to the molecule so it has less H than the general formula for saturated fatty acids. Plants tend to have unsaturated triglycerides. Monounsaturated- 1 C=C bond - Oleic acid. Polyunsaturated- multiple C=C bonds - Linoleic acid.
Water polarity
Oxygen has a greater attraction for the shared pair of electrons than hydrogen because it has more protons. O is slightly negative and H is slightly positive, so the bond is polar. There is a charge difference across the bond and molecule because the two permanent dipoles don't cancel out.
Proteins
Peptides- short chains of amino acids making a polymer. Proteins- much longer chains of amino acids (50+) that are able to fold into a 3D fixed structure for a certain function. Can be one or more polypeptides arranged as complex macromolecules.
Computer modelling of protein structure
Predicting the shapes of protein molecules from their primary structure. This is done through predicting their secondary structure or their tertiary structure (Ab initio or comparative modelling).
Proteins and digestion
Proteins get broken down into amino acids in digestion by protease enzymes like pepsin in the stomach. They cannot be stored as builds up would make them toxic. In deamination the liver prevents this by removing the amino group.
Haemoglobin structure
Quaternary structure 4 polypeptide chains joined by bonds. 2 alpha-globin sub-units and 2 beta-globin sub-units. These two types have their own tertiary structure. Interactions between polypeptides give a very strong specific shape.
Insulin uses
Regulation of blood glucose concentration. It is a hormone so it is transported dissolved blood plasma. Insulin binds to glycogen receptors on muscle and fat cells to increase the uptake to increase the rate of consumption of glucose. The specific receptors need to work so precise shapes.
Cholesterol
Small, very hydrophobic molecule. Made in the liver and intestines. In membranes, it's in the hydrophobic core, apart from the polar OH which sticks out to the outside. gives stability and regulates fluidity so not too fluid at high temperatures and not too stiff at low.
fatty acids and health
Some evidence suggests that unsaturated are more healthy than saturated. Saturated in excess cause coronary artery disease and obesity although this is inconclusive.
Lipids Functions
Source of energy Energy store Insulation Buoyancy Protection Waterproofing Cell membranes Absorption of fat soluble vitamins Waterproofing hormones
Sterols
Steroid alcohols. Complex alcohol molecules. Lipids with a different structure to triglycerides. 4 isoprene units (carbon rings) with a branched side chain and a hydroxyl group at one end. They are dually hydrophilic and hydrophobic. The OH group is polar and the rest is non-polar.
Function of cellulose in cell walls
Strength- each strong to support the whole plant. Prevents bursting when turgid. Turgid apply pressure to one another to support the structure. Protects the delicate membrane. Permeability- water and mineral ions can pass in and out. Macrofibrils can be reinforced with other substances for waterproofing and protection- cutin, suberin, lignin.
Elastin structure
Stretchy tropoelastin molecules cross link and coil to make a molecule that is large, stable, insoluble and extensible. Allows stretching for when a body part needs to reversibly adapt it's shape as part of a life process..
Cellulose properties
Strong fibrils have a high tensile strength due to the glycosidic bonds and the hydrogen bonds between chains. Hard to digest because it is hard to break all the glycosidic bonds. Wrong enzymes. Form fibre. Freely permeable in water due to the space in between fibrils. Insoluble in water so can be a structural unit.
Functions of proteins
Structural components such as muscle in animals. Enzymes, antibodies and hormones, which adopt specific shapes for function Movement across cell membranes as protein carriers or channels for active transport and facilitated diffusion. Specialist roles like myofibrils and in the cytoskeleton.
A sample containing both reducing and non-reducing sugars
Take some of the sample. Benedict's. Positive. Filter off and measure the mass of the precipitate. Take some more of the sample. Test for non-reducing sugars. filter and weight. The precipitate from the second sample (non-reducing) will have more ass than the precipitate from the first (reducing).
Catabolic reactions Anabolic reactions
The breaking down of larger molecules. The building up of molecules from smaller ones.
Secondary structure
The coiling or folding of an amino acid chain as a result of interactions between the atoms in the amino acids at different parts of the chain. Hydrogen bonds create them when they form within the chain and O, H and N interact. Common between NH group and CO group on another.
Unsaturated fatty acids 2
The double bond causes the chain to kink and bend. The acids can't pack together so closely and this pushes the molecules apart. In cell membranes, this makes them more fluid. Have a lower melting point. Makes them liquid at room temperature so they are oils. In membranes they help main fluidity even in cold environments.
Tertiary structure
The overall 3D shape of a protein molecule caused by the specific folding/coiling of sections of secondary structure with the further folding of α and β. It's held together by bonds from the interactions of the different R groups that have been brought together.
Properties of phospholipids in water
The phosphate group has a negative charge and so polar water is attracted to it. However, the non-polar tails still repel. They can form a layer on the surface of water with heads in and tails sticking up and out. They are surfactants- surface active agents.
Predicting secondary structure Predicting tertiary structure
The probability of an amino acid or sequence to be in a particular secondary structure. Based on already known protein molecular structures. More useful to know as this is what determines its bioactive function.
Glycine Cysteine
The simplest amino acid.The R group is a hydrogen atom. the R group contains sulfur. CH₂SH.
Primary structure
The specific sequence of amino acids which are joined by peptide bonds to form the protein molecule. It depends on amino acid type, number and order, determined by DNA. These make the sequence unique which determines how the polypeptide folds through further structures.
vitamin D plant steroids Digitalis
Vitamin D is synthesised in the cholesterol of the skin using sunlight. Helps calcium absorption from the gut. Plant steroids are ingested by animals and upon absorption become animal hormones. Digitalis. A cardiac poison made of steroids. Used in smaller quantities to treat heart problems.
Waterproofing
Waxes have these properties, different to triglycerides. Fatty acids and alcohols that allow disease protection as they prevent the entry of water-borne diseases.
Hydrophobic and hydrophilic interactions
Weak between polar and non-polar R groups. The way it folds depends on if/which R groups are hydrophilic or hydrophobic. Cause the twisting of the amino acid chain determine shape. Important influence. Not affected by heat. Could be affected by pH or a change in solvent.
Reacting beta glucose problem
When neighbouring B glucose molecules line up the hydroxyl groups on C1 and C4 are too far away to interact and react.
Types of secondary structure.
Which type of secondary structure forms is depends on which R groups interact with other R groups and the formation of hydrogen bonds. Multiple types of secondary structure can form in the same primary structure at different parts. Strong stable structures at optimum conditions for the H bonds.
Benedict's test for reducing sugars
a alkaline solution of copper(II) sulfate. Add equal volumes. Heat gently in a water bath at 80°C for 3 minutes. After the colour changes, a brick-red precipitate forms. blue Cu²⁺ ions from CuSO₄ are reduced to Cu⁺ ions in red Cu₂O. the reducing sugar donates the electron.
Amino acids as buffers
amphoteric- have both acidic and basic properties so they can act as buffers- help to resist large changes in pH. Low pH- high concentration of H+ . amino acids accept H+ ions- have basic properties. High pH- low concentration of H+. amino acids donate H+ ions - have acidic properties.
Carbohydrates (elements monomers polymers general formula)
hydrated carbon. Carbon Hydrogen Oxygen Monosaccarides Polysaccarides. C 1 : H 2: O 1 Cn(H2O)n (+ same elements for lipids)
reducing sugar concentration (colour and quant)
if the solution is in excess, the intensity of the red colour is proportional to he concentration of the sugar. More reducing sugar means more precipitate and less unreacted blue supernatant. Less means less precipitate and more unreacted blue supernatant and ions.
Peptide synthesis
the H of the amino and the OH of the carboxyl groups react A condensation reaction forms a peptide bond C-N and releases water. Peptide bonds are shorter than a normal C-N bond. This inhibits rotation around the bond for a rigid chain. Catalysed by the enzyme peptidyl transferase in ribosomes.
Micelles
tiny balls of phospholipids with heads pointing out and tails tucked away. an aggregate of surfactant molecules dispersed in a liquid colloid. Micelles form spontaneously in water due to the amphipathic nature of the molecule. The driving force for this arrangement is the hydrophobic interactions the molecules experience.
