Chapter 1: Biological Molecules Flashcards
What is molecular biology? (1.1)
The study of biological molecules
What is hydrogen bonding? (1.1)
- where electrons are unevenly distributed
- creating an uneven charge which is said to be polarised
- this is called a polar molecule
- form weak electrostatic forces
- such as water molecules
What is polymerisation? (1.1)
The formation of polymers from sub units called monomers
What is condensation? (1.1)
A reaction where water is formed as a bi-product of polymerisation
What is hydrolysis (1.1)
The splitting of a polymer into its constituent parts by adding water molecules
What are macromolecules? (1.1)
- very large molecules formed from many condensation reactions
- contain 1000 or more atoms, therefore have a high molecular mass
- the four main ones are carbohydrates, proteins, lipids and nucleic acids
What is a mole? (1.1)
- SI unit for measuring amount of a substance
- one mole of a substance contains 6.022 X 10^23 particles
- the atomic number of an element is the weight of one mole of that element
What is a molar solution? (1.1)
A solution containing 1 mole of solute per litre of solution
What are organic molecules? (1.2)
Molecules based on carbon
- life on earth is made from molecules with a carbon ”backbone”
- this is because carbon reacts readily with each other
- this leads to lots of different molecules, based on the versatile carbon atom
What is a monosaccharide? (1.2)
A sweet tasting, soluble substance, which are carbohydrates
- a general formula of (CH₂O)ₙ where ‘n’ is 3 - 7
- such as glucose (isomers), fructose and galactose
Examples of monomers (1.2)
- monosaccharides, nucleotides, amino acids
Examples of the formation of disaccharides (1.3)
- glucose + glucose = maltose
- glucose + fructose = sucrose
- glucose + galactose = lactose
Examples of the formation of polysaccharides (1.3)
- glycogen and starch are formed from α-glucose condensation
- cellulose is formed from β-glucose condensation
How does glucose bond to form starch? (1.4)
- starch is found in plants in the form of small grains
- seeds and storage organs, such as tubers
- food and energy in diets
- chains of glucose may be branched or unbranched
- the unbranched chain is wound in a tight coil using intramolecular bonds, making the molecule large and compact
-> ideal for storing energy as lots fits in small space - the branched chain has many loose ends
-> meaning enzymes can act simultaneously, releasing monomers at a faster rateAmylase Maltase Starch - maltose - glucose
How is starch suited for energy storage? (1.4)
- insoluble, meaning it doesn’t alter water potential due to osmosis
- large, meaning it doesn’t diffuse out of cells
- compact, so lots can be stored
- forms α-glucose, which is easily transported and readily used in respiration
- branching allows increased rate of enzymes
How is glycogen bonded? (1.4)
- glycogen is found in animals and bacteria
- stored as granules in the liver and muscle cells
- a small storage as animals mainly use fats
- it has shorter chains and is more highly branched
-> more rapidly broken down as animals have a higher metabolic rate and therefore faster respiratory rate - a 1:6 bond occurs more often, 8 - 12 units
How is glycogen suited to energy storage? (1.4)
- insoluble: doesn’t affect water potential, osmosis
- insoluble: doesn’t diffuse out of cells
- compact: lots stored in small surface area
- highly branched: more simultaneous enzyme activity
How does glucose bond to form cellulose? (1.4)
- straight, unbranched chains, which run parallel to each other
-> this allows for hydrogen bonding in the for of cross linkages, which are intermolecular - these are collectively strong
- they form fibres, which are harder for the enzymes to break down
- provide rigidity for the cell wall
- exerts inward pressure
-> makes non woody part of a plant semi-rigid - makes them turgid, meaning there is maximum surface area for photosynthesis
- makes up 40% - 60% cell wall
- made of 100 - 15000 glucose
How does cellulose function for structure? (1.4)
- cross linkage hydrogen bonds
- parallel runs of fibres
- every other β-glucose molecule flips
What are the characteristics of lipids? (1.5)
- contain C, H, O
- insoluble in water
- soluble in organic solvents like alcohol and acetone
- fatty acids may be saturated or unsaturated
What are the roles of lipids? (1.5)
- cell membranes (phospholipids flexibility and transfer of lipid-soluble substances)
- source of energy (release water more energy than carbohydrates when oxidised)
- waterproofing (waxy cuticles and oil secretion from sebaceous glands)
- insulation (slow conductors of heat and electricity, like with the myelin sheath)
- protection (kidney)
How are triglycerides structured to fit their function? (1.5)
- each fatty acid forms an ester bond with the glycerol via condensation (hydrolysis can occur)
- fats and oils vary due to the fatty acid (there are over 70 types)
- have a high proportion of C-H bonds to store energy compared to carbon atoms
- low mass: energy, especially good for animals
- do not affect water potential as they are large and non-polar (they’re insoluble)
- release water when oxidised (camel hump storage)
How are phospholipids structured to fit their function? (1.5)
- phosphate group attracts water
- fatty acids repel water
-> a hydrophilic ‘head’, and a hydrophobic ‘tail’ - in an aqueous environment, they form a bilayer within cell surface membranes, (hydrophobic barrier created)
- the ‘heads’ help hold the surface together
- phospholipids allow the formation of glycolipids by combining with carbohydrates. These are helpful with cell recognition
Describe the test for lipids (1.5)
1) take a dry, grease-free test tube
2) add 5 cm³ ethanol to 2 cm³ food sample
3) shake vigorously to dissolve any lipid
4) add 5 cm³ water and shake gently, forming the milky white emulsion
5) do a control with water only
What are proteins? (1.6)
- large molecules formed from amino acids
- vary from organism to organism
- ‘of first importance’
- enzymes are part of almost every living process
What is an amino acid? (1.6)
- monomers
- form polymers called polypeptides
- 100 have been identifies, 20 of which are in nature (indirect evidence for evolution)
- have a central carbon with four groups attached
- amino group (—NH₂)
- carboxyl group (—COOH), the acidic group
- hydrogen (—H)
- R group, a variety of different chemical groups which cause amino acids to differ
How do amino acids combine to form a dipeptide? (1.6)
- condensation reactions
- the carbon from one amino acid is bonded to a nitrogen of another
- called a peptide link
What are the different structures of proteins? (1.6)
- primary structure
-> a single polypeptide
-> based on the sequence of amino acids determines shape and function
-> proteins can be a single chain or multiple - secondary structure
-> a polypeptide has both —NH and —C=O on either side
-> forming an attractive hydrogen bond
-> twists into an α-helix or β-pleated sheets - tertiary structure
-> can become even more folded into 3-D, leading to function
-> different bonds, depending on primary structure
-> disulphide bridges (strong), ionic bonds (broken by pH change), hydrogen bonds - quaternary structure
-> multiple polypeptides, and non-protein (prosthetic) groups (haemoglobin)
What is the test for proteins? (1.6)
The Biuret test identifies peptide bonding
1) add equal sample and sodium hydroxide solution at room temp into a test tube
2) add a few drops of dilute copper(II) sulphate solution and mix gently
3) a lilac indicates protein is present
What are fibrous and globular proteins? (1.6)
- forms of protein structure
- fibrous
-> structural, long chains which run in parallel, linked by cross bridges
-> collagen, three unbranched polypeptide chains wound tightly into a double helix using glycine (it is found in tendons) - globular
-> enzymes and haemoglobin, metabolic function
What are enzymes? (1.7)
Globular proteins that act as biological catalysts. They provide an alternate pathway in chemical reaction, and lower the activation energy without being used up themselves
- catalyse intracellular and extracellular reactions
What are the conditions for a reaction to occur naturally? (1.7)
- the two molecules must collide with sufficient energy to alter the arrangement of their atoms
- free energy (the energy available to perform work) of the products must be less that that of the substrates
- the activation energy must be met
What is activation energy? (1.7)
- energy barrier needed to be overcome for a reaction to start
- enzymes lower the activation energy
- this means reaction that occur in the body can happen rapidly at lower temperatures (37°C)
What is the structure of an enzyme? (1.7)
- globular proteins with 3D shape dependant of the primary structure of amino acids
- active site is made of a small number of animo acids, which forms a depression
- the substrate is temporarily held in place by bonds that occur between the amino acids of the active site and the groups of the substrate
What is the induced fit model of enzyme action? (1.7)
- proposes that the active site forms as the enzyme and substrate interact
- this is due to the proximity of the substrate, and forms a functional active site on the enzyme - the enzyme is a certain general shape, but moulds around the substrate
- the change of shape puts strain on the substrate’s bonds, lowering the activation energy enough for it to break
What is the lock and key model of enzyme action? (1.7)
- stated that a particular enzyme fitted one substrate
- it was supported as some enzymes were specific to certain reactions
- one drawback was that thus enzymes would have to have a rigid structure, which was proved false as molecules binding to other sites of the enzyme altered its activity, meaning it had to be flexible
How would you measure an enzyme catalysed reaction? (1.8)
- usually measured time against either:
-> the appearance of the products
-> the disappearance of the substrate - at first there is lots of substrate, hence not much product
- it is hence easy for substrate molecules to come into contact with empty active sites
- active sites become filled and the rate of product formed increases rapidly
- amount of substrate decreases, hence the amount of product increases
- fewer substrate molecules means more difficulty colliding (product may also get in the way)
- graph flattens off
How does temperature affect rate of reaction? (1.8)
- increases the particles kinetic energy, meaning they collide more frequently, increasing rate
- enzymes begin to denature (45°C), meaning substrate can’t fit as easily
- completely denature (60°C) and no new product is formed
- despite human enzymes having an optimum temperature of 40°C, the human body has evolves to work at 37°C for a few different reasons:
-> a higher temperature would mean more food is needed to maintain that
-> higher temperatures due to illness may start denaturing our enzymes
-> other proteins may denature at higher temperatures
How does pH affect rate of reaction? (1.8)
- pH is a measure of H+ ion concentration
- it can be calculated as pH = -log₁₀[H+]
- pH affects enzymes as follows:
-> a change in pH alters the charges of the amino acids forming the active site, affecting attachment of substrates
-> may affect the bonds in the enzyme’s tertiary structure, leading to a change in shape
-> the change in H+ ions affects bonding between —NH₂ and —COOH groups of the polypeptides, causing the active site to change
How does concentration affect rate of reaction? (1.8)
- is enzyme concentration increases, rate will proportionally increase if there is a limitless supply of substrate
-> if substrate is limited, and increase in enzyme concentration will have no effect, as there will be unoccupied active sites - this is the same for substrate concentration, rate will increase if there is an excess of enzymes, otherwise all active sites will be occupied, and there will be substrates left not being broken down
-> more substrates also mean more opportunities for collision
What are enzyme inhibitors? (1.9)
- substances that directly or indirectly interfere with the functioning of the active site, hence reducing its activity
What are competitive inhibitors? (1.9)
- molecules with a shape similar to that of the substrate
-> is substrate concentration increased, effect of inhibitors is decreased, vice versa - it does not permanently bind
- eg: succinate being prevented from binding by malonate
What are non-competitive inhibitors? (1.9)
- molecules that attach to another binding site of an enzyme
- this affects the shape of the active site, preventing the substrates to bind
-> as they are not competing for the same site, increasing substrate concentration will have no effect in activity
