2.1.2 Biological Molecules Flashcards
Define a carbohydrate
- Contains carbon, hydrogen, and oxygen
Explain how carbohydrates are classified and give examples
Sugars
- monosaccharides - glucose, fructose, galactose
- disaccharides - sucrose, maltose, lactose
Polysaccharides
- storage - glycogen, starch
- structural - cellulose
Characteristics of a monosaccharide?
- are soluble in water
- have a sweet taste
- form crystals
Explain how the amount of carbons ina sugar correlates to the type of monosaccharide
- if they have 3 carbons they are triose sugars
- 5 carbons = pentose sugar
- 6 carbons = hexose sugar
What is the general formula of a monosaccharide?
(CHO2O)n, where n is >= to 3
Explain how you distinguish between a-glucose and b-glucose
- In a-glucose the OH group on carbon 1 is below the plane of the ring
- In b-glucose the OH group on carbon 1 is above the plane of the ring
How does glucose contasing lots of bonds relate to it’s function?
It can contain lots of energy
What is a disaccharide?
Sugars composde of two monosaccharides bopnded together by a glycosidic bond
What monosaccharides make up:
- maltose
- sucrose
- lactose
- maltose = glucose + glucose
- sucrose = glucose + fructose
- lactose = glucose + galactose
How is a a-1,4-glycosidic bond formed?
- between carbon 1 of one glucose molecule and carbon 4 of another glucose molecule
- two OH groups bond to form a water molecule (H2O)
- O boned to carbon in one molecule and carbon in another
- C-O-C link formed
What are the two types of storage polysaccharides and in which species are they found
- starch - plants
- glycogen - animals
What are the two different polysaccharides that make up starch?
- amylose (coiled)
- amylopectin (coiled and branched)
What bonds do amylose and amylopectin use?
- amylose = a-1.4-glycosidic bonds
- amylopectin = a-1,4glycosidic + a-1,6 glycosidic bonds
Give key points about starch
- carbohydrate consiting of two polysacchardies, amylose and amylopectin
- stored in chloroplast and elsewhere in plants
- stored in cells as starch grains
- can be broken down into a-glucose which are respired to produce ATP
Explain the structure of glycogen
- a-1,4glycosidic + a-1,6 glycosidic bonds
- same overall satrucutre as amylopectin, but signifficantly more branching and 1,4 chains are smaller
Where and how is glucose stored?
- stored as glycogen granules
- found in large amounts in the liver + skeletal muscles
Give key points about glycogen
- polymer of a-1,4 glycosidic bonds
- many side chains due to a-1,6 glycosidic bonds
- insoluble, compact, energy dense
- does not affect water poetion of cell
- branches for rapid hydrolysis by enzymes
How do storage polysacchrides’s structures and properties relate to their function?
Structure
- both are made by bonding thousands of a-glucose molecules together (condenstation reactions)
- a-glucose stored is used in respiration
Function
- compact - lots of energy stored in small volume (energy dense)
- metagbolically inactive (doesn’t take part in metabolic reactions)
- insoluble in water - do not dissolve in water, so does not affect cell water potential
- chain molecules - glkucose held by chains which can be hydrolysed by enzymes
- branched - branches ahve ends where enzymes can add or remove glucose - can be quickly hydrolysed
Give an example of a structural polysaccharide and it’s properties
cellulose - high tensdile strength + insoluble
Explain the structure of the cell wall, and the glucose used
- beta glucose
- forms cellulose fibres, which form microfibril, which form macrofibril, which form the wall
- alternate beta glucose molectules roatet 180 degress - forms hydrogen bonds between OH groups
Give examples of lipids
triglycerides, phospholipids and steroid alcohols
Explain the key functions of lipids
Triglycerides
- enmergy storage and source
- insulation
- protection of organms
Phospholipds
- plasma membrane
Sterols
- make up some hormones
Explain the structure of a triglyceride
- made from 1 glyercol + 3 fatty acids
- not built from repeating units - not a polymer
- macromlecule - a large molecule
Why is water a polar molecule?
- more positive protons in its nucleus
- uneven distribution of electrons
- oxygen atoms become partially negative
- hydrogen atoms become partially positive
Give key aspects of hydrogen bonds
- weak electrostatic interaction
- molecules contain a partially negativley charged atom (N,O,F) bonded to partially positivley charged hydrogen atom
- weaker than a covalent bond
- thousands of hydrogen bonds can stabalise structures
Define metabolism
All the biochemical reactions happening inside the cells of an organism
What are catabolic and anabolic reactions?
Catabolic reactions: Breaking down large molecules (hydrolysis reactions)
Anabolic reactions: Building large molecules (condensation reactions)
What are the functions of carbohydrates?
- energy storage and supply
- structure (plant cellulose cell wall)
What are the functions of proteins?
- structure (keratin in hair, collagen in skin)
- transport (channel and carrier)
- enymes
- antibodies
- most hormones
What are the functions of lipids?
- plasma membranes
- energy storage and supply
- insulation of animals
- nerve cell insulation
- some hormones (steroid hormones)
What are the functions of vitamins and minerals?
- form parts of larger molecules
- vitamins used as co-enzymes
- minerals used as inorganic cofactors + prosthetic groups
What are the functions of nucleic acids?
- contain genes that code the amino acid sequence of proteins
What are the functions of water?
- support plants
- solvent for metabolic reactions
- transport medium
Give key aspects of carbon
- 4 electrons in its outer shell
- becomes stable via sharing 4 outer electrons with other atoms (8 electrons in outer shell)
- forms covalent bonds (single or double)
What is the difference between a monomer and a polymer?
Monomer: Single molecule units repeated to make polymers
Polymers: Large molecules made from joining monomers together (Monomers must be of the same type)
Give examples of monomers and polymers of carbohydrates
Monomer: Monosaccharide e.g. glucose/fructose/galactose
Polymer: Polysaccharide e.g. starch/cellulose/glycogen
Give examples of monomers and polymers of proteins
Monomer: Amino acids e.g. Glycine/Tyrosine
Polymer: Polypeptides + proteins e.g. haemoglobin/enzymes
Give examples of monomers and polymers of nucleic acids
Monomer: Nucleotides
Polymer: Polynucleotides e.g. DNA & RNA
Give key aspects of hydrolysis
- water molecule used
- covalent bond breaks
- monomer molecules from polymer
- normally requires an enzyme
- e.g. digestion
Give key aspects of condensation
- water molecule is released
- covalent bond forms
- polymer molecules from monomers
- normally requires an enzyme
- e.g. protein synthesis
Give key aspects of water
- polar molecules
- the oxygen attracts the pair of electrons in the O-H bond more strongly thean the hydrogen atom
- oxygen atom has delta negatie charge
- hydrogen atom has delta positive charge
- hydrogen bonds ^
Give important properties of water that play important roles in living organisms
- water is a liquid
- water is a solvent
- there are cohesive forces between H20 molecules in water
- density when water freezes
- water has thermal stability
- water is a reactant
Explain why water is a liquid at room temperature and the biological importance of it.
Why
- hydrogen bonds form between water molecules, forming a network that allows the molecules to move around, continually making + breaking hydrogen bonds
Importance
- used as a transport medium in animal blood
- used as a transport medium in vascular tissues in plants
- used as a habitat by prokaryotic organsisms e.g. Cholera
Explain why polar molecules are able to dissolve in water and the biological importance of it
Why
- polar ions are soluble in water - water is attracted to the ions/polar molecules, clusters around them and seperates them
Importance
- allows ionic compounds to seperate
- medium for metabolic reactions
- repsiration + photosynthesis relies on reactants dissolved in water to react
- liquid transport medium
- organisms can take in dissolved mineral ions
- dissolves toxic substances
Explain why there is cohesion between water molecules biological importance of it.
Why
- hydrogen bonds force water molecules to stick to each other
Importance
- water can move up xylem in transpiration stream by forming strong water collumns
- creates surface tension on water surface - habitat for invertebrates
Explain why water density decreases under 0 degrees and the biological importance of it.
Why
- as water cools its density decreaes - molecules spread out more
- due to more and longer hydrogen bonds forming between H20 molecules, creating an oppen lattice structure
- ice is less dense than water so floats on liquid water
Importance
- forms ice on the surface of the water
- creates a habitat + insulates water below causing aquatic organisms no to freeze
Explain why water has a high specific heat capacity and the biological importance of it.
Why
- a large amount of energy is needed to raise the temperature of water
- many stable hydrogen bonds between water molecules that need to be broken
Importance
- temperatue of large bodies of water (lakes + oceans) remains stable even when outsaide temperature changes dramatically
- provides thermally stable environment for aquatic + prokaryotic organisms
- temperatues change very slowly so organisms use less energy on temperature control
- prevents internal temperature inside organisms changing quickly so enzymes can function properly
Explain why water has a high latent heat of vaporisation and the biological importance of it.
Why
- the evaporation of water uses up a large amount of energy
- many stable hydrogen bonds between water molecules that need to be broken
Importance
- water evaporating from the surface ‘removes’ heat, cooling the organism down
- organisms usae water as an efficient cooling mechanism (panting, transporation, sweating)
Water has thermal stability - explain the difference between high specific heat capacity and high latent heat of vaporisation
High specific heat capacity: A relativley large amount of energy is needed to raise the temperature of the water
High latent heat of vaporisation: The evaporation of water (liquid to gas) uses up a relativley large amount of energy
Explain the biological importance of water being a reactant in chemical proccesses inside cells (metabolism)?
- water used in photosynthesis
- water molecules used in hydrolysis reactations
Explain the structure of an amino acid
- amino groups
- R group
- carboxyl group
Give key aspects of amino acids
- 20 amino acids due to 20 different R-groups
- you make 12
- 8 ‘essential’ amino acids needed in your diet
- some R-groups are polar so are hydrophillic (water loving)
- some R-groups are non-polar so are hydrophobic (water repelling)
What is a dipeptide and polypeptide
Dipeptide: Two polypeptides bonded together
Polypeptide: More than two polypeptides bonded together
How is a dipeptide formed?
- condensation reaction
- peptide bond formed
- OH group of carboxyl group of one amino acids bonds with H atom of amino group of another acid to form H20
- C + N atoms bond
How is dipeptide broken down?
- hydrolysis reaction
- peptide bond broken
- amino acids made from the dipeptide
- water used up
- C-N bond of peptide bond breaks
- OH group of water joins to C of peptide bond to reform carboxyl group
- H atom left over from h20 bonds to the N of the peptide bond to reform the amino group
What are the 4 levels of protein structure?
- primary structure
- secondary structure
- tertiary structure
- quaternary structure
Define primary structure
The specific sequence of amino acids in the protein chain
How is an alpha helix formed
- when polypeptide chains coil to for ma helix
- shape is held together via hydrogen bonds
Define secondary structure and the twp types
The coiling and pleating of parts of the polypeptide chain
- alpha helix - the most common secondary structure
- beta pleated sheets
- both are held together via hydrogen bonds
How is tertiary structure held in place?
- hydrogen bonds between polar groups
- disulphide bonds (covalent) form between sulphurs in R groups of the amino acids cysteine
- ionic bonds between positively + negatively charged R groups of amino acids
- hydrophobic interactions between non-polar R groups which cluster together towards the centre of the molecule]0 hydrophilic interactions outside of molecule with contact with water
Define tertiary structure
When secondary A helix + B pleated sheets gold further to give a complex and specific 3-D shape
How are Beta pleated sheets formed
- polypeptide chain folds so sections of the chain are parallel
- held together via hydrogen bonds
- pattern formed by the individual amino acids causing the structure to look pleated
Give examples of proteins with tertiary structure
- antibodies
- antigens
- enzymes
- their tertiary structures are specific shape to only one substance
How are tertiary structures denatured?
Heat gives kinetic energy (vibrations) which cause hydrogen bonds to break first, and then ionic bonds
- disulphide bonds will eventually break due to heat but only at 1000s degrees
Define Quaternary structure
Proteins with more than one polypeptide chain
Give an example of a Quaternary structure
Haemoglobin
- 4 polypeptide chains
- 2 a chains + 2 b chains
- each chain has a haem prosthetic group which contains a Fe2+ ion (conjugated)
- carries oxygen from lungs to respiring tissue for aerobic respiration
Give other examples of proteins with quaternary structure
Catalase + Collagen
What are the two types of 3-D shape molecules can be?
Globular or Fibrous
Give key details about globular proteins
- folds into a compact ball-shaped spherical structure
- hydrophobic R-groups turn inwards to centre of protein
- hydrophilic R-groups on the outside means they’re more water soluble as water molecules can cluster around the protein
- have metabolic roles e.g. enzymes, plasma proteins, antibodies
- water soluble
Give key aspects of Catalase
- globular protein
- enzyme (speeds up metabolic reactions)
- specific shaped active site for a specific substrate molecule
- quaternary structure with 4 haem prosthetic groups
- presence of Fe2+ ions allows increased sped breaking down hydrogen peroxide
- hydrogen peroxide made in metabolic reactions and can damage cells if allowed to accumulate
Give key aspects of Insulin
- globular protein
- transported in blood
- hormone regulating blood glucose concentration
- fits into binding sites in specific receptors on cell surface membrane of muscle/liver cells
- needs precise + specific 3D shape
- secreted as pro-insulin
Give key aspects of fibrous proteins
- formed from long chains of amino acids + are insoluble molecules
- high proportion of amino acids with hydrophobic R-groups in primary structure
- limited range of amino acids - usually have small R-groups
- regular, repetitive sequences of amino acids
- little tertiary structure
- very organised structure
- structural roles e.g. myosin in muscles, keratin in hair, collagen in skin
Give key aspects of keratin
- group of fibrous proteins present in hair, skin + nails
- a helixes held together by many cysteine amino acids forming many disulphide bonds
- forms strong, inflexible, insoluble molecules
- more cysteine amino acids = more disulphide bonds = stronger the structure
- nails have more disulphide bonds than hair so less flexible
Where is collagen found?
- walls of arteries
- tendons
- bones
- cartilage
- cosmetic treatments
Give key aspects of collagen
- made up of three polypeptide chains wound around each other to form a triple helix
- forms a long, rope like structure
- some flexibility
- each polypeptide chain itself is a helix
Give key aspects of elastin
- fibrous protein found in elastic fibres
- found in blood vessels + alveoli
- give structure flexibility to expand when needed, nut return to normal size afterwards
- allows for stretch + recoil
- quaternary protein made of many stretchy molecules called tropoelastin
What is qualitative test?
Tests for the presence or absence of a particular biological molecules
- does not tell you the concentration of a particular biological molecule in the solution
What can you qualitative test for?
- starch - iodine solution
- reducing sugar (e.g. glucose) - Benedicts solution + heat
- protein - Biuret solution
- lipid - alcohol emulsion test
Explain the test for starch and the positive + negative results
- add one drop of iodine solution
Positive result: Blue/black
Negative result: Yellow colour
Explain the test for reducing sugar and the positive + negative results
- Uses Benedict’s solution
1. Add Benedict’s solution to sample in test tube
2. Shake mixture + heat - don’t boil (80 degrees)
Positive result: Red precipitate
Negative result: Blue precipitate - can be a range of colours - semi-quantitative
How do you edit the test for reducing sugar for non-reducing sugars and the positive + negative results
- non-reducing sugars do not give a positive with Benedict’s reagent
1. Boil with dilute hydrochloric acid
2. Neutralise with sodium carbonate
3. Repeat Benedict’s test
What can be used to test for reducing sugars?
Diastix + Clinistix
What are the advantages + disadvantages of Diastix & Clinstix
Advantages
- quick
- just need urine sample
- may tests can be done at once
- no labs required
Disadvantages
- subjective in terms of colour
- colour blindness
- not many intermediate values
Explain the test for protein and the positive + negative results
- uses Biruet solution
1. Add Biuret solution
2. Shake thoroughly
Positive result: Lilac colour
Negative result: Blue colour
Explain the test for lipids and the positive + negative results
- uses Ethanol & water
1. Crush sample (if needed)
2. Add ethanol to sample
3. Shake
4. Pour into water
Positive result: White emulsion obtained
Negative result: No cloudy white emulsion
Give key aspects of a colorimeter
- device that shines a beam of light through a sample
- a photoelectric cell picks up the light that has passed through
- sample of the solution placed between the light and photoelectric cell in a cuvette
- advantage of using a colorimeter is that is is not subjective + less affected by human error
What is a colorimeter absorbance & transmission?
- colorimeters can be set to absorbance or transmission
- before they are used they are set to 0% absorbance/transmission
- 0% absorbance to record absorbance
- 0% transmission to record transmission
What is a blank?
A blank is used to calibrate a colorimeter
- distilled water for absorbance
- unreacted benedicts for transmission
Why is a red filter used in the colorimeter
- the filter absorbs all parts of the visible spectrum apart from red (including blue)
- this will only transmit red light to the blue solution in the cuvette, no blue light will be transmitted
How is a calibration curve constructed?
- known concentrations of glucose are used and a Benedict’s test is carried out on each known concentration of glucose
- the precipitate is filtered out of the solution + a red filter is used
- a colorimeter is used to give readintgs of light passing through light/absorbed
- the readings are plotted on a graph to show transmission or absorbance on y-axis against sugar concentration on x-axis
What variables need to be controlled when measurring the concentration of a reducing sugar
- same volume of glucose solution
- same volume of Benedcit’s solution
- same concentration of Benedict’s solution
- Heat to 80 degrees for same length of time
- calibrate colorimeter
- same red filter/colorimeter
What other quantitative methods can be used to determine glucose concentration
- use biosensor
- use clinistix/diastix
What is TLC?
Thin layer chromatography - used to seperate vitamins, amino acids, carbohydrates, proteins, amino acids and pigments
What is the stationary phase?
The chromatography strip
What is the mobile phase?
The liquid solvent
How is TLC carried out?
The mobile phase flows through the stationary phase and carries the components of the mixture with it
What are the stationary phase made of?
A thin, uniform layer of silica gel or alumina coated on to a piece of glass, metal or rigid plasticW
In TLC, waht is the distance travelled determined by?
- solubility of the compound moving in the solvent
- the interaction between the compound moving and the silica gel
How is the Rf value for a compound worked out?
R1 = distance travelled by component/distance travelled by solvent
Where should TLC be measured from?
The baseline, not the endo f the chromatogram
What rule should Rf values be?
Should always be less than 1
(Jf greater than 1, probably completed the divison wrong way round)
