3.1 Biological Molecules💧 Flashcards
What are monomers
Smaller units from which larger molecules (polymers) are made
What are polymers
Molecules made from a large number of monomers joined together
Three examples of monomers
• Monosaccharides (polysaccharides)
• Amino Acids (polypeptides)
• Nucleotides
How are polymers formed
Polymerisation through a condensation reaction
Outline a condensation reaction
Joining two molecules together with the formation of a chemical bond, releasing water from the -OH group of one molecule and an -OH group on another
How are monomers formed
The hydrolysis of a polymer through a hydrolysis reaction
Outline a hydrolysis reaction
Breaks a chemical bond between two molecules and involves the use of a water molecule
What’s covalent bonding
Atoms share a pair of electrons in their outer shells, so both atoms have full outer shells forming a more stable compound
What’s ionic bonding
Electrostatic attraction where ions with opposite charges attract each other
• These are weaker than covalent bonds but stronger than hydrogen bonds
What’s hydrogen bonding
• A weak electrostatic bond forming important forces that alter the physical properties of molecules.
• The electrons within a molecule are polarised (not evenly distributed) but tend to spend more time at one position
What are monosaccharides
Smaller units (monomers) from which larger carbohydrates are made
What’s the formula for monosaccharides
(CH2O)n where n=3-7
Outline characteristics of monosaccharides
They’re sweet tasting and soluble and can be pentose sugars (ribose, deoxyribose) or hexose sugars (glucose, galactose, fructose)
State three common hexose monosaccharides
• Glucose
• Galactose
• Fructose
(C6 H12 O6)
What’s an isomer
Two molecules with the same molecular formula but differ structurally, so contain the same number of atoms of each element, but the atomic arrangement differs
What are the two types (isomers) of glucose
• Alpha glucose
• Beta glucose
Outline the characteristics of alpha glucose
• Found in food
• Hydrolysed from starch
• Used in respiration
• Has an -OH group below the hydrogen
Outline the characteristics of beta glucose
• Can’t be broken down by the human body
• Made in photosynthesis
• Produced by plants
• Has an -OH group above the hydrogen
What type of bonds joins carbohydrates
1,4 or 1,6-Glycosidic bond (from a condensation reaction)
What’s a glycosidic bond
A type of covalent bond that joins a carbohydrate molecule to another group (that may not be carbohydrate)
How are disaccharides formed
A condensation reaction of two monomers joined by a glycosidic bond
State three common disaccharides, where they’re produced and their monomers
• Maltose (2x alpha glucose)
• Sucrose (fructose and alpha glucose) produced
by plants
• Lactose (galactose and alpha glucose) produced
by mammals
(C12 H22 O11)
How are polysaccharides formed
By the condensation of many monosaccharides units
State three common polysaccharides
• Glycogen
• Starch
• Cellulose
Outline the characteristics of glycogen
• Polymer of alpha glucose
• Used in animals to store glucose
• Highly branched so has increased surface area
for fast breakdown and enzyme action
• 1,4-glycosidic bonds and 1,6-glycosidic bonds
Outline characteristics of starch
• Polymer of alpha glucose
• Used in plants to store glucose
• Large molecule that cannot leave the cell
• Insoluble in water (doesn’t affect water potential)
• Found in two forms; amylose and amylopectin
Why is starch a good storage molecule
• Large so it can’t cross the cell membrane
• Insoluble in water so doesn’t affect water potential
• Polymer of alpha glucose so provides glucose for respiration
• Branched so it makes the molecule compact and can fit many molecules in a small area
• Branched so has increased surface area for fast breakdown and enzyme action
Outline the characteristics of amylose
• Carbon 1,4-glycosidic bonds
• Compact helical structure to store lots of glucose
in a small space
• Hydrolysed into maltose by amylase enzyme
Outline the characteristics of amylopectin
• Carbon 1,4 and 1,6-glycosidic bonds
• Branched, so has increased surface area for enzyme action and releases glucose molecules faster than amylose
Describe the test for starch
Iodine/potassium iodine test:
- Add iodine solution, a positive result is a colour change from orange to blue-black
Outline the characteristics of cellulose
• Polymer of beta glucose
• Provides structure and support in plant cell
walls, preventing bursting under turgor pressure
and holds the stem up
• 1,4-glycosidic bonds
• Alternating glycosidic bonds due to the differing
-OH group placement in beta glucose than
alpha glucose, so it’s found in long straight chains
• These chains are joined together by hydrogen
bonds to form bundles of cellulose fibres
(microfibrils) that have high tensile strength
Differences between the structure of starch and cellulose
• Starch formed from alpha glucose, cellulose from beta glucose
• Position of hydrogen and hydroxyl groups on Carbon atom one are inverted
What biochemical test is used to test for carbohydrate/sugar
Benedict’s solution test
Outline the method of a Benedict’s test for reducing sugars
• Add an equal volume of Benedict’s solution to a
sample and heat in a water bath for 5 minutes
• A positive results indicated by a colour change of
the Benedict’s reagent from blue to brick red
What’s Benedict’s reagent
An alkaline solution of Copper (II) sulphate
How can the concentration of sugar be approximated in the Benedict’s test
Semi-quantitative use can approximate the concentration of sugar present by the colour of the Benedict’s reagent
Why can’t the Benedict’s test be used for non-reducing sugars, providing examples
• They can’t be oxidised as they can’t donate electrons, so must be hydrolysed into monosaccharides by breaking any glycosidic bonds
• Eg. Sucrose and all polysaccharides
Outline the method for testing for non-reducing sugars
• Negative Benedict’s test, reagent remains blue
• Add dilute hydrochloric acid and heat in a water
bath for 5 minutes and neutralise the solution with sodium hydrogen carbonate (NaHCO3)
• Can use an indicator (eg red litmus paper to
ensure neutralisation)
• Carry out Benedict’s test as normal
Outline how colorimetry could be used to give qualitative results for the presence of sugars and starch
• Make standard solutions with known concentrations, record absorbance or % transmission values
• Plot calibration curve: absorbance or % transmission on the y-axis and concentration on the x-axis
• Record absorbance or % transmission values of unknown samples. Use calibration curve to read off concentration
Identify properties of lipids
• Joined by ester bonds but don’t form polymers
• Insoluble in water but soluble in organic solvents (eg. alcohols and acetone)
• Found in two groups; triglycerides and phospholipids
Outline the roles of lipids
• Source of energy: when oxidised they provide more than twice the energy as the same mass of carbon judges and release water
• Waterproofing: lipids are insoluble in water and both pants and insects have waxy cuticles that conserve water while mammals produce an oily secretion from sebaceous glands
• Insulation: slow conductors of heat that when stored beneath the body surface help retain body heat. They also act as electrical insulators around the myelin sheath and nerve cells
• Protection; stored around the organs
What’s the difference between fats and oils
Fats are solid at room temperature (10-20°C) while oils are liquid
Outline the structure of triglycerides
• Formed by the condensation reaction of one molecule of glycerol and three molecules of fatty acid (RCOOH) forming an Ester bond
• Contains an R-group of a fatty acid that may be saturated or unsaturated
Outline the difference between saturated and unsaturated fatty acids (R-groups)
• Saturated fatty acids mean the chain has no ‘carbon-carbon’ double bonds because all carbon atoms are linked with the maximum possible number of hydrogen atoms
• Unsaturated fatty acids have one or more ‘carbon-carbon’ double bond and can be mono-unsaturated or poly-unsaturated
Outline properties of saturated fatty acids
• High melting point; solid at room temperature
• Energy dense animal fats
• Long straight chains tightly packed together, so more energy’s required to move them (high melting point)
Outline properties of unsaturated fatty acids
• Lower melting point
• Plant fats
• Not as tightly packed, so so are easier to move (lower melting point)
Identify functions of triglycerides
• High ratio of energy storing ‘C-H’ bonds to carbon atoms: excellent source of energy
• Low mass to energy ratio: good storage molecules so much energy can be stored in a small volume
• Large, non-polar, insoluble in water: storage doesn’t affect osmosis in cells or their water potential
• High ratio of hydrogen to oxygen atoms: release water when oxidised, providing an important source of water
Outline the structure of a phospholipid
• Formed by the condensation reaction of two fatty acids with a molecule of glycerol and a phosphate molecule
• Polar molecules: two poles that behave differently
- hydrophilic phosphate head that interacts with
water but not fat
- hydrophobic fatty acid tail consisting of a large
chain of hydrocarbons that repels water but
mixes readily with fat
Outline the function of a phospholipid
• Form a bilayer within cell-surface membranes, a hydrophobic barriers formed between inside and outside the cell
• Hydrophilic phosphate head that helps to hold at
the surface of the cell-surface membrane
• Forms glycolipids by combining with carbohydrates within the cell-surface membrane which is important in cell recognition
Identify the test for lipids
Emulsion test
Describe the method for the emulsion test
• Take a dry and grease free test tube for the sample
• Add ethanol
• Shake the test tube throughly to dissolve any lipids in the sample
• Add water and shake gently
• A milky white emulsion indicates the presence of lipids
• As a control, repeat procedures using water instead of a sample and the final solution should be clear
Why is a milky emulsion formed after the emulsion test
Lipids in the sample are finely dispersed in the water to form an emulsion
Light passing through this emulsions refracted as it passes from oil droplets to water droplets making it appear milky
Outline amino acids
• The monomers from which proteins are made that combine to form a polymer called a polypeptide
• Consist of an amine group (NH2), carboxyl group (COOH), Central Carbon and variable ‘R’ group (side chain)
• 20 amino acids are common in all organisms and differ only in their variable group.
Describe the formation of a dipeptide/polypeptide
A condensation reaction between two amino acids forms a peptide bond between the carbon atom from the carboxyl group of one amino acid and the nitrogen atom from the amine group of another amino acid
Describe protein structure
Can contain one or more polypeptide chains and is broken into primary, secondary, tertiary and quaternary structure
Outline primary protein structure
• The sequence of amino acids joined by peptide bonds
• The sequence determines the shape and function of the protein, the shape is very specific to the function and any change in shape will affect its function
• Determined by the sequence of DNA, and 20 different amino acids provide limitless number of possible combinations
Outline secondary protein structure
• A basic level of protein folding caused by many weak hydrogen bonds between the carboxyl (-) and amine groups (+)
• Forms either an alpha helix or beta sheet
Outline tertiary protein structure including examples
• More complex, specific and unique 3D structure making each protein distinctive, allowing it to recognise and be recognised by other molecules
• One polypeptide chain
• Bonding between variable groups of amino acids including hydrogen bonds, ionic bonds and disulphide bridges
• Can be globular (functional) proteins such as enzymes or Haemoglobin or fibrous (structural) proteins such as collagen, fibres or structural support proteins
Outline quaternary protein structure including examples
• Large complex molecule with more than one polypeptide chain, potentially including a prosthetic (non amino acid) group
• Eg. Haemoglobin/collagen
Describe the structure and function of haemaglobin
• A quaternary protein with 4 polypeptide chains, each associated with a ‘haem’ group containing a ferrous (Fe2+) ion
• Haemoglobin transports oxygen and each Haemoglobin can carry four O2 molecules and therefore 8 oxygen atoms as each Fe2+ can combine with a single oxygen
Describe the structure and function of collagen
• Has an unbranched primary structure and a tightly wound secondary structure. It’s tertiary structure is twisted into a second helix and it’s quaternary structure is made of three polypeptide chains wound together
• Found in tendons (join muscle to bone)
Identify the test for protein
Biuret test
Describe the biuret test
• Place a sample of the solution in a test tube with an equal volume of sodium hydroxide solution at room temperature
• Add a few drops of biuret reagent (very dilute (0.05%) Copper (II) sulphate solution) and mix gently
• A colour change from blue to purple indicates the presence of peptide bonds and hence a protein
Identify the functions of proteins
• Enzymes
• Antibodies
• Transport proteins
• Structural proteins
Outline the structure and function of an enzyme
• Protein with a 3D tertiary structure with an active site which has a specific shape that can only bind to a certain substrate
• Enzymes speed up the rage of chemical reactions in organisms by acting as catalysts, and don’t get used up in reactions. Each enzyme lowers the activation energy of the reaction it catalyses as described by the induced fit model of enzyme action
Describe how an enzyme catalyses a reaction through the induced fit model of enzyme action
• The active site of an enzyme changes shape as the substrate gets closer to become more complimentary
• The active site moulds itself around the substrate to form an enzyme substrate complex (ESC) because the specific tertiary structure of its active site is complimentary to that substrate
• The flexible active site puts strain on the bonds and lowers the activation energy, speeding up the rate of metabolic reactions
• The products leave the active site which goes back to its original shape and the enzyme goes on to make more enzyme substrate complexes as it isn’t used up
What factors affect the rate of enzyme-controlled reactions
• Enzyme concentration
• Substrate concentration
• Temperature
• pH
• Concentration of competitive and non-competitive inhibitors
Outline how enzyme concentration affects the rate of enzyme-controlled reactions
As enzyme concentration increases:
• Rate of reaction increases as there’s more active sites and enzyme substrate complexes
• Substrate concentration becomes the limiting factor
Outline how substrate concentration affects the rate of enzyme-controlled reactions
As substrate concentration increases:
• Rate of reaction increases as there’s more substrates attaching to active sites, more enzyme substrate complexes and more collisions
• Enzyme concentration becomes the limiting factor
Outline how temperature affects the rate of enzyme-controlled reactions
• As temperature increases rate of reaction increases due to more kinetic energy leading to more collisions and therefore enzyme substrate complexes
• As temperature exceeds the optimum, bonds between amino acids change shape so the substrates no longer complimentary, so there’s fewer enzyme substrate complexes
Outline how pH affects the rate of enzyme-controlled reactions
• At optimum pH, enzymes are at maximum activity
• A deviation will slow and eventually stop enzyme activity and can affect the shape of the substrate so enzymes and substrates are no longer complimentary, so less enzyme substrate complexes
Define competitive inhibitors and their effect on the rate of enzyme-controlled reactions
• Competitive inhibitors compete with the substrate to occupy the active site of an enzyme without causing a reaction as they have a similar shape to the substrate molecule
• reduces the amount of enzyme substrate complexes, decreasing rate of reaction
Define non-competitive inhibitors and their effect on the rate of enzyme-controlled reactions
• Non-competitive inhibitors bind to a different site on the enzyme, changing the shape of the enzyme so that it cannot bind to the substrate effectively.
• This slows down the reaction by making the enzyme less active.
Outline the structure of DNA
• Made up of deoxyribose (pentose) sugar, a phosphate group and one of the organic bases, adenine, cytosine, guanine or thymine
• The chain of sugars and phosphates are known as the sugar phosphate backbone
• Double helix with two polynucleotide chains held together by weak hydrogen bonds between specific complementary base pairs (Cytosine/Guanine joined by 3 H-bonds and Adenine/Thymine joined by 2 H-bonds)
• Antiparallel polynucleotide strands (running in opposite directions. As new DNA strands are produced, they can only be added in the 5’ to 3’ direction (carbon bonds 5 and 3)
• The 5-prime Carbon atom has an attached phosphate group while the 3-prime has a hydroxyl group
Outline the function of DNA
Important information carrying molecule that holds genetic information
Describe how DNA and RNA molecules are formed
• Polymers of nucleotides;
- A condensation reaction between two nucleotides forms a phosphodiester bond between the phosphate group of one nucleotide and the pentose sugar of another
Identify and explain the characteristics of DNA
• Stable structure
- Passes from generation to generation, rarely mutating
• Extremely large
- Carries an immense amount of genetic information
• Base pairing
- DNA can replicate and transfer information as mRNA
• Two strands joined only by hydrogen bonds
- Allows them to separate during DNA replication and protein synthesis
• Phosphodiester backbone
- Protects the more chemically reactive organic bases inside the double helix from chemical and physical forces
Outline the structure and function of RNA
• A relatively short (single stranded) polynucleotide chain
• Components include a ribose sugar, a phosphate group and one of the organic bases adenine, cytosine, guanine or uracil
• Formed by condensation reactions between nucleotides to form phosphodiester bonds
• Important information carrying molecule that transfers genetic information from DNA to ribosomes
Identify the structures of a nucleotide
• Pentose sugar
• Nitrogen-containing organic base
• Phosphate group
Compare and contrast DNA and RNA
• Both contain a phosphate group, nitrogenous base and pentose sugar
• DNA is double stranded while RNA is single stranded
• DNA contains deoxyribose while RNA contains ribose (pentose sugars)
• DNA contains bases adenine, cytosine, guanine and thymine, whereas RNA contains uracil instead of thymine
• DNA is self replicating while RNA is synthesised from DNA when required
• DNA is located in the nucleus of a cell and mitochondria while RNA is located in the cytoplasm, nucleus and ribosomes
Outline DNA replication
• DNA has to replicate itself every time a cell divides so both cells have identical copies of the entire genome to ensure genetic continuity between generations of cells
• This method of replication’s called semi-conservative replication because one strand of each new DNA molecule has come from the double helix of the original molecule and conserved by the parent cell
• The double helix structure of DNA and semi-conservative replication were discovered and proposed by James Watson and Francis Crick
Describe the process of semi-conservative replication
• The double helix of the original DNA molecules are unwound by the enzyme DNA helicase
• DNA helicase breaks hydrogen bonds between complimentary bases in the polynucleotide strands
• Two template strands have been produced and free DNA nucleotides form hydrogen bonds by complimentary base pairing
• The enzyme DNA polymerase catalyses the condensation reaction to join adjacent nucleotides by phosphodiester bonds
• Two identical strands of DNA are formed, each containing half of the original DNA
Describe the roles of DNA helicase and DNA polymerase in semi-conservative replication
• DNA helicase breaks hydrogen bonds between complementary nucleotides, it detaches from the lagging strand and has to go back
• DNA polymerase catalyses the condensation reaction to join nucleotides between the leading and lagging strands by phosphodiester bonds by completing a chunk on the leading strand and then going back and repeating it on the lagging strand
Describe the process that provides evidence for semi-conservative replication
• Grew bacteria in a culture containing Nitrogen 15
• Centrifuged it with a radioactive label
• Put them in a culture containing nitrogen 14 allowed them to divide once and centrifuged again
• Repeated with one more replication in Nitrogen 14 and centrifuged again
Describe the structure and function of adenosine triphosphate (ATP)
• Nucleotide derivative formed from a molecule of ribose, a molecule of adenine and three phosphate groups
• Acts as an energy currency of cells
Describe the reaction of ATP to release energy
• Hydrolysis of ATP to adenosine diphosphate (ADP) and an inorganic phosphate group (Pi) is catalysed by the enzyme ATP hydrolase
• Can be coupled to energy-requiring reactions within cells and the inorganic phosphate that’s released can be used to phosphorylate other compounds, often making them more reactive
• Eg. To provide energy for other reactions (named process) or to add phosphate to other substances to make them more reactive or change their shape
Describe how ATP is resynthesised
• Condensation reaction of ADP and Pi catalysed by the enzyme ATP synthase, during photosynthesis of respiration
• Eg. In chlorophyll during phosphorylation during photosynthesis
• Eg. During oxidative phosphorylation in respiration
Identify the differences between DNA and ATP
• ATP contains ribose sugar whereas DNA contains deoxyribose sugar
• ATP has 3 phosphate groups whereas DNA contains only 1 phosphate group
• ATP always contains the base adenine whereas the DNA base varies between adenine, cytosine, guanine and thymine
Identify the characteristics of ATP
• Small and soluble, so it can be transported around the cell
• ATP can’t pass out of the cell so cells always have an immediate supply of energy
• Hydrolysis is a single reaction, so energy’s released quickly and it rapidly resynthesises
• Low activation energy so it can release stored energy quickly
• Stores and releases small amounts of energy at a time, so no energy’s wasted
• Can transfer energy from one molecule to another by transferring one of its phosphate groups
Identify important biological properties of water
• Metabolite in many reactions:
- Required in hydrolysis and produced in condensation reactions
• Important solvent:
- In which metabolic reactions occur, and ionic compounds can dissolve in water because of its dipolarity (e.g. salt)
• High specific heat capacity:
- Buffers changes in temperature, making it a good habitat and helps organisms maintain a stable body temperature as temperature doesn’t rapidly change
• Large latent heat of vaporisation:
- Evaporates when hydrogen bonds are broken, which requires a relatively high amount of energy, so heat’s lost easily through evaporation which provides a cooling effect with little loss of water
• Strong cohesion between water molecules because they’re polar and therefore flow easily:
- Supports columns of water in tube-like transport cells of plants (xylem)
- Produces surface tension where water meets air, allowing some organisms to ‘walk on water’.
Outline the structure and function (in the body) of water
• (H2O) Dipolar molecule containing a slightly negative oxygen atom and a slightly positive hydrogen atom bonded with a hydrogen bond
• The body’s most critical nutrient where functional chemicals are dissolved and transported and chemical reactions take place
• Makes up about 70% of adult body mass and is the largest component of cells, blood and fluid between cells
• Helps regulate internal temperature
• Protects and lubricators joints and other body structures
Define specific heat capacity and latent heat of vaporisation
• SHC: The amount of energy required to raise the temperature of one kilogram of the substance by 1°C (4.2J raise 1 gram of water by 1°C - calorie)
• LHV: The amount of energy that must be added to a liquid substance to transform it into a gas
Describe inorganic ions, outlining key examples
• Atoms or molecules with an overall electric charge formed by the transfer of electrons, either positive (cations) or negative (anions) that don’t contain carbon
• Inorganic ions occur in solution in the cytoplasm and body fluids of organisms and have specific roles dependent on their properties E.G:
• Iron (Fe^2+) found in haemaglobin in red blood
cells that bind to oxygen
• Phosphate (Po4^3-) components of nucleic acids,
ATP and phospholipids in the cell membrane
• Sodium (Na+) involved in the co-transport of
glucose and amino acids
• Hydrogen (H+) maintain pH; the more H+, the lower the pH (more acidic)
Outline the main requirements for human life
• Oxygen is a key component of important chemical reactions (including ATP production).
The brain’s sensitive to lack of oxygen due to its requirement for high, steady ATP production
• Nutrients are substances in food and drink that are essential to human survival, they’re broken into water, macronutrients and micronutrients
Outline macronutrients
Macronutrients are:
• Energy yielding such as carbohydrates and lipids that are used in metabolic processes that convert them to ATP
• Body building such as proteins that supply the amino acids that are the building blocks of the body
Outline micronutrients
Vitamins and minerals,
• Vitamins are organic substances
• Minerals are inorganic compounds absorbed or consumed by animals
