3.1 biological molecules Flashcards
what is meant by poly?
many
what is meant by penta?
five
what is meant by di?
two
what is meant by tetra?
four
what is meant by mono?
one
what is meant by hexa?
six
what is meant by tri?
three
what elements do carbohydrates contain?
carbon, hydrogen, oxygen
what are the monosaccharides?
glucose, galactose, fructose
what are the disaccharides?
maltose, lactose, sucrose
what are the polysaccharides?
starch, glycogen, cellulose
what are monosaccharides?
simple sugars
what is the general formula for monosaccharides?
Cn(H2O)n
how are disaccharides formed?
two monosaccharides joined by a 1 4 glycosidic bond through a condensation reaction
what is maltose made up of?
glucose+glucose
what is sucrose made up of?
glucose+fructose
what is lactose made up of?
glucose+galactose
how are glucose fructose and galactose all structural isomers?
same molecular formula, different structures/arrangement of atoms
what is always given off/lost in a condensation reaction?
water
what is starch and glycogen made up of?
long chain of alpha glucose
what is cellulose made up of?
long chain of beta glucose
what is starch?
a polysaccharide
how is starch used?
plants use it as a storage molecule in the form of granules or grains
how many glucose monomers make up starch?
200-100,000
what is the test for starch?
in the presence of starch iodine goes black from brown
what are reducing sugars?
simple sugars
what are the the reducing sugars?
all monosaccharides and lactose and maltose
what is the test for reducing sugars?
benedicts solution, heat in a water bath, blue to brick red
what does semi quantitative mean?
the colour range of precipitate in Benedict’s test means of can be used to estimate the amount of reducing sugar
what is an amino acid?
the monomers that form the polymers called polypeptides, polypeptides join together to form proteins
how many amino acids occur naturally in proteins?
20
what does it mean that the same 20 amino acids occur in every living organism?
this is proof of evolution
what is a dipeptide?
2 amino acids linked by a peptide bond
what is a tripeptide?
three amino acids linked by peptide bonds
what is a polypeptide?
many amino acids linked by peptide bonds
what are proteins?
one or more polypeptide chains
what do R group (side chains) contain?
mainly hydrogen, carbon and oxygen atoms, some amino acids have sulphur or nitrogen atoms in their R groups
how are the 20 amino acids different?
they all have different side chain structures
what are the functions of proteins?
structure, enzymes, some hormones, membrane transport, antibodies, mass transport, receptors, cell recognition
what are the examples of proteins for structure?
collagen and keratin
what are the examples of proteins for enzymes?
amylase, carbohydrase, protease, lipase
what is an example of a hormone that is a protein?
insulin
what is an example of a protein for mass transport?
haemoglobin
what is the primary structure of protein?
many amino acids can be joined together through condensation reactions called polymerisation, many 100s of amino acids are linked in this way
what makes the variety in primary structure?
polypeptides have many of the 20 naturally occurring amino acids, huge number of possible combinations, huge variety of primary protein structures, primary structure determines the shape of the protein
how can a change in primary structure affect the function of the protein?
a change in a single amino acid in the primary structure can change the shape of the protein, this could lead to it being unable to carry out its function, a proteins shape is very specific to its function, a protein can be a single polypeptide but it is more common for a protein to be made of a number of polypeptide chains
what is secondary structure of protein?
the linked amino acids that make up a polypeptide each have -NH and -C=O on either side of the peptide bond, the H of the -NH group has a positive charge the O of the -C=O has a negative charge, these two groups therefore easily form weak hydrogen bonds, this causes the long polypeptide chain to twist i.e. alpha helix
how can the secondary structure in proteins be arranged?
alpha-helix (spiral), beta-pleated sheet (zig zag)
what is tertiary structure in proteins?
the alpha helix of the secondary structure can be twisted and folded even more, this forms a complex and often unique 3D structure known as tertiary structure maintained by a number of bonds (disulphide bridges, ionic bonds, hydrogen bonds)
what are the bonds in tertiary structure of protein?
disulphide bonds (strong), ionic bonds (between carboxyl and amino groups not involved in forming the peptide bonds, weaker than disulphide bonds and easily broken by pH changes), hydrogen bonds (lots of them and easily broken)
what is quaternary protein structure?
large proteins can form complex molecules consisting of many individual polypeptide chains
what is different about haemoglobin from other proteins?
there can also be non-protein (prosthetic) groups associated with the molecules e.g. iron carrying haem groups in haemoglobin, the protein that carries oxygen in red blood cells
how do you test for proteins?
the biuret test detects peptide bonds, place the test solution in a boiling tube, add an equal amount of biuret reagent, gently mix, if it turns purple this indicates the presence of peptide bonds and therefore protein, if it remains blue, the test is negative for protein
what is the role of proteins dependent on?
their shape
what are the two basic types of protein?
fibrous (collagen, structure) and globular (haemoglobin, enzymes, metabolic functions)
what are fibrous proteins?
from long chains parallel to each other, linked by cross bridges, form very stable molecules e.g. collagen
how are tendons formed?
made of collagen (fibrous protein), individual collagen polypeptide chains are linked together by cross linkages between amino acids of adjacent chains, the points where one collagen molecule ends and the next begins is staggered, this increases strength.
what are examples of lipids?
triglycerides, phospholipids, cholesterol, steroids
what are the functions of lipids?
substrate for respiration, storage on energy, insulation, protection of organs, buoyancy and streamlining in aquatic mammals, cell membranes, steroid hormones, waterproofing
how are lipids used for insulation?
slow conductors of heat and electrical insulators in the myelin sheath
how are lipids used in cell membranes?
phospholipids and cholesterol
what is an example of a lipid steroid hormone?
oestrogen
what are hydrophilic molecules/groups?
are polar or charged and can mix/dissolve in water
what are hydrophobic molecules/groups?
are not polar or charged so do not dissolve in or mix with water
what does saturated mean?
a hydrocarbon chain with no C=C double bonds
what does unsaturated mean?
a hydrocarbon chain that contains one or more C=C double bond
what are the main characteristics of lipids?
varied group, contain carbon, hydrogen and oxygen, insoluble in water, soluble in organic substances (alcohol and acetone)
what are the main lipid groups?
triglycerides (fats and oils) and phospholipids
what is the difference between fats and oils?
fats are solid at room temperature, oils are liquid
what are triglycerides (fats and oils) formed from?
glycerol and three fatty acids
how are triglycerides formed?
a triglyceride in which three fatty acids have reacted with three -OH groups, contains three ester bonds, each fatty acid forms an ester bond with glycerol in a condensation reaction, hydrolysis produces glycerol and three fatty acids
what is similar in all triglycerides?
the glycerol is the same
where does the difference in properties of fats and oils come from?
the over 70 different fatty acids that all have a carboxyl group with a hydrocarbon tail attached (-COOH)
what is the impact of double bonds?
they cause the molecule to bend, cannot pack as tightly together, liquid at room temperature
how does the high ratio of energy storing C-H bonds to C atoms relate to the function of triglycerides?
excellent energy store
how does the low mass to energy ratio relate to the function of triglycerides?
large amount of energy stored in a small space (animals carry less weight)
how does triglycerides being large, non polar, insoluble relate to the function?
storage does not affect osmosis/ water potential in cells
how does the high hydrogen to oxygen atoms ratio relate to the function of triglycerides?
release water when oxidised, desert animals
how are phospholipids similar to triglycerides?
they both contain a glycerol linked by ester bonds to hydrophobic fatty acids
how are phospholipids different to triglycerides?
they have two fatty acids not three, the third replaced by a polar (hydrophilic) phosphate containing group giving the phospholipid molecule a hydrophilic head and a hydrophobic tail
what is the hydrophilic head in phospholipids?
interacts with water (attracted to it) but not with fat
what is the hydrophobic tail in phospholipids?
orientates itself away from water, mixes readily with fat
what are polar molecules?
have two poles that behave differently
what are phospholipids like in solution?
form spherical structures called micelles, hydrophobic tails pointing inwards and the hydrophilic heads on the outside
what is the test for lipids?
the emulsion test
how do you carry out the emulsion test?
crush solid samples and place in a dry test tube (or add a few drops of liquid sample), add ethanol to 2cm3 above the level of sample and shake, allow to settle, decant ethanol into another test tube leaving the solid behind, use a pipettes to remove the ethanol without disrupting the solid, add 2cm3 of deionised/distilled water to the second test tube, is the ethanol becomes cloudy on adding the distilled water an emulsion has formed indicator presence of lipids
What are enzymes?
Proteins that speed up chemical reactions by acting as biological catalysts, they catalyse metabolic reactions both at cellular level and for the organism as a whole, they can affect structures in an organism as well as functions, enzyme action can be intracellular or extracellular
What is a catalyst?
A catalyst is a substance that speeds up a chemical reaction without being used up in the reaction itself
What is the structure of an enzyme?
They have an active site, which has a specific shape to bind with the substrate, they are specific due to their tertiary structure
How do enzymes catalyse reactions?
Enzymes lower the activation energy needed, often making reactions happen at a lower temperature than they could without an enzyme to speed up the rate of reaction
What is an enzyme substrate complex?
When a substrate fits into the enzymes action site
How does an enzyme substrate complex lower the activation energy?
If two substrates need to be joined (condensation reaction) being attached to an enzyme holds them close together and reduce repulsion so they can bond more easily. If the enzyme is catalysing a hydrolysis reaction fitting into the active site puts a strain on the bonds in the substrate so it breaks up more easily
What is the lock and key model?
Enzymes only work with substrates that fit their active site, the lock and key model is where the substrate fits into the enzyme the way that a key fits into a lock
What is the induced fit model?
active site changes shape as the substrate bonds causing a change in shape of the substrate, results in a tight fit where the active site is now complementary to the altered substrate, change in substrate shape induced strain in the substrate bones which lowers the activation energy by lowering the energy to break the bonds
How are the properties of an enzyme determined?
Related to their tertiary structure, determined by the primary protein structure. The tertiary structure can be altered by changes in pH or temperature and the primary structure is determined by a gene, a mutation in the gene can change the primary structure and therefore the tertiary structure
what are the advantages of the induced fit model?
explains how the enzyme substrate complex lowers the activation energy, explains how products are released because active site is complementary to the transition state not products, flexibility of active site explains how an enzyme may act on two similar but non-identical substrates, flexibility of protein also provides better explanation on non competitive inhibition
what are enzyme inhibitors?
substrates that directly or indirectly interfere with the active site of an enzyme, sometimes it will bind so strongly that it will block the site and permanently prevent the enzymes from working, most inhibitors are temporary and will only occupy the active site for a short time
what are competitive inhibitors?
competitive inhibitor molecules have a similar shape to that of the substrate molecules, they compete with the substrate molecules to bind to the active site, but no reaction takes place, instead they block the active site, so no substrate molecules can fit in
how much do competitive inhibitors decrease the enzyme activity?
How much the enzyme is inhibited depends on the relative concentrations of the inhibitor and the substrate, if there is a high concentration of the inhibitor it will take up nearly all the active site and hardly any of the substrate will get to the enzyme, but if there is a higher concentration of substrate then the substrates chances of getting to an active site before the inhibitor increase, so increasing the concentration of substrate will increase the rate of reaction up to a point
how do non competitive inhibitors affect enzyme activity?
Non-competitive inhibitor molecules bind to the enzyme away from its active site, this causes the active site to change shape so the substrate molecules can no longer bind to it, they don’t compete with the substrate molecules to bind to the active site because they are a different shape, increasing the concentration of substrate won’t make any difference to the reaction rate - enzyme activity will still be inhibited
how does temperature affect enzyme activity?
as temperature increases as does the rate of reaction, as more kinetic energy, molecules move faster so more frequent collisions, more collisions result in a reaction due to the higher energy. Past optimum temperature the rate of the reaction decreases and stops as the enzymes molecules vibrate more which breaks the bonds that hold enzymes together and the shape of the active site changes so it is no longer complementary to the substrate, the enzyme has become denatured
how does pH affect enzyme activity?
above and below optimum pH level the H+ and OH- ions found in acids and alkalis can mess up the ionic bonds and hydrogen bonds that hold the enzymes tertiary structure in place, this changes the shape of the active site so the enzyme is denatured
how does enzyme concentration affect the rate of reaction?
the more enzyme molecules there are in solution, the more likely a substrate molecule is to collide with one and form an enzyme substrate complex, so increasing the concentration of the enzyme increases the rate of reaction. if the amount of substrate is limited, there comes a point when there’s more than enough enzyme molecules to deal with all the available substrate, so adding more enzymes has no further affect
how does the substrate concentration affect the rate of an enzyme control reaction?
the higher the substrate concentration, the faster the reaction - as collisions between substrate and enzyme is more likely so more active sites will be used. this is only true up to the point of saturation as after that all the active sites are full so adding more substrate makes no difference. substrate concentration decreases with time during a reaction so if no other variables are changed, the rate of reaction will decrease over time. this makes the initial rate of reaction the highest
what is covalent bonding?
atoms share a pair of electrons in their outer shells, as a result, the outer shell of both atoms is filled and a more stable compound, called a molecule is formed
what is ionic bonding?
ions with opposite charges attract one another, this electrostatic attraction is known as an ionic bond, for example, positively charged Na+ ions and negatively charged Cl- ions form an ionic bond to make sodium chloride, ionic bonds are weaker than covalent bonds
what is hydrogen bonding?
the electrons within a molecule are not evenly distributed but tend to spend more time in one position, this region is more negatively charged, a molecule with an uneven distribution of charge is said to be polarised - it is a polar molecule, the negative region of one polarised molecule and the positive region of another attract each other. a weak electrostatic bond is formed, although each bond is individually weak, they can collectively form important forces that alter the physical properties of molecules , this is especially true for water
what are monomers?
individual units that bond together to form polymers, usually based on carbon e.g. monosaccharaides such as glucose
what is a polymer?
large molecule that is made up of a long chain of monomers e.g. polysaccharides and polyesters
what is polymerisation?
the process by which monomers undergo condensation reactions to form a polymer
what is a mole?
the SI unit for measuring the amount of a substance and is abbreviated to mol, one mole contains the same number of particles as there are in 12g of carbon-12 atoms which contains 6.022x10^23 carbon atoms (the Avogadro number/constant)
what is a molar solution?
a solution that contains one mole of solute in each litre of solution, a mole is the molecular mass (molecular weight) expressed as grams
what are atoms?
the smallest units of a chemical element that can exist independently, comprises of a nucleus that contains protons and neutrons and electrons orbit the nucleus
what are neutrons?
occur in the nucleus of an atom and have the same mass as protons but no charge
what are protons?
occur in the nucleus of an atom and have the same mass as neutrons but are positively charged
what are electrons?
orbit in shells around the nucleus, have very little mass and are negatively charged, their number determines the chemical properties of an atom
what is the charge of an atom?
the number of protons and electrons are the same so there is no overall charge
what is the atomic number?
proton number
what is the mass number?
number of protons and neutrons
what are isotopes?
different types of atom produced due to a variation in neutron number, isotopes of an element have the same chemical properties but different masses, isotopes, especially radioactive ones, are useful for tracing the route of certain elements in biological processes and for dating fossils
how are ions formed?
an atom becomes an ion if it loses or gains an electron, losing an electron becomes positively charged, gaining an electron becomes negatively charged, more than one electron may be lost or received, ions may be made of more than one type of atom
what are monosaccharides?
a single monomer that makes up carbohydrate polymers, they are sweet tasting, soluble substances that have the general formula (CH2O)n’ where n can be any number from three to seven e.g. glucose (C6H12O6), galactose and fructose
what are disaccharides?
formed when monosaccharides are joined in pairs e.g glucose + glucose = maltose, glucose + fructose = sucrose, glucose + galactose = lactose
what are polysaccharides?
polymers formed by combining together many monosaccharide monomers, joined by glycosidic bonds formed through condensation reactions, polysaccharides are very large molecules making them insoluble, meaning they are suitable for storage as when hydrolysed they break down into monosaccharides or disaccharides e.g. cellulose and starch
what is hydrolysis?
when water is added to a disaccharide under suitable conditions, it breaks the glycosidic bond releasing the constituent monosaccharides, the addition of water that causes breakdown
what is the structure of starch?
a mixture of two polysaccharides of alpha glucose; amlylose which is a long unbranched chain, the angles of glycosidic bonds give it a coiled structure making it compact and good for storage, and amylopectin which is a long branches chain, the side branches allow enzymes to break it down easily as they can get to the glycosidic bonds easily, it is insoluble so doesn’t effect the water potential in cells so it is good for storage
what is the structure of glycogen?
polysaccharide of alpha glucose, long branched chain with more side branches than amylopectin, stored glucose can be released quickly, important for energy release in animals, also compact so good for storage
what is the structure of cellulose?
long unbranched chains of beta glucose, when beta glucose molecules bond, they form straight cellulose chains, which link together by hydrogen bonds to form strong fibres called micro fibrils, provide structural support for cells in the cell wall.
triglycerides have a hydrophobic tail, explain how this feature of a lipid is important for its function.
The hydrophobic tails force them to clump together in the cytoplasm as insoluble droplets this means they can be stored in cells as a source of energy without affecting the cells water potential
describe the induced fit model of enzyme action
The complimentary substrate binds to the active site of the enzyme to form an enzyme substrate complex as the substrate binds the active site changes shape slightly which provides a better fit the substrate is broken down/join together to form the product
Explain how a change in the amino acid sequence of an enzyme may prevent it from functioning properly
A change in the amino acid sequence of an enzyme may alter its tertiary structure this changes the shape of the active site so that the substrate can’t bind to it
Which groups to all amino acid molecules have in common?
anime and carboxyl groups
What are the functions of proteins?
Enzymes, antibodies, transport proteins, structural proteins
Describe how you would test for the presence of protein in a sample
The test solution needs to be alkaline so first you add a few drops of sodium hydroxide solution, then you add some copper(II) sulfate solution OR add biuret reagent and mix gently, positive result turns blue to purple
describe how a dipeptide is formed (3 marks)
A peptide bond forms between the carboxyl group of one amino acid and the amino group of the other amino acid, a molecule of water is released/a condensation reaction takes place
Describe the tertiary structure of a protein (2marks)
The secondary structure is coiled and folders further to form the proteins final 3-D structure, more bonds including hydrogen bonds ionic bonds and disulphide bridges bond between different parts of the polypeptide chain
what did meselson and stahl provide?
Evidence for semiconservative replication they validated Crick and Watsons semiconservative DNA replication theory their experiment used to isotopes of nitrogen heavy nitrogen and light nitrogen
describe Meselson and Stahl’s experiment
Two samples of bacteria were grown one in the nutrient containing light nitrogen and one in a broth with heavy nitrogen, as the bacteria reproduced they took up nitrogen from the broth to help make nucleotides fo new DNA so the nitrogen gradually became part of the bacterias DNA, a sample of DNA was taken from each batch of bacteria and spun in a centrifuge the DNA from the heavy nitrogen bacteria settled lower down the centrifuge tube than the DNA from the light nitrogen bacteria because it’s heavier, then the bacteria growing in the heavy nitrogen broth were taken out and put in a broth containing only light nitrogen the bacteria were left for one round of DNA replication and then another DNA sample was taken out and spun in the centrifuge if replication was conservative the original heavy DNA which would still be together would settle at the bottom and the new light DNA would settle at the top if replication was semiconservative the new bacterial DNA molecules which contain one strand of the old DNA containing heavy nitrogen and one strand of the new DNA containing light nitrogen so the DNA would settle out between where the light nitrogen DNA settled out and where the heavy nitrogen DNA settled out, as it turned out the DNA settled out in the middle showing that the DNA molecules contain a mixture of heavy and light nitrogen. The bacterial DNA had replicated semiconservatively in the light nitrogen
what is the structure of an amino acid?
