Biological Molecules Flashcards
How do hydrogen bonds form between water molecules
Water is polar: O more electronegative than H, so attracts electron density in covalent bond more strongly
Forms O δ- and a H δ+
There are intermolecular forces of attraction between a lone pair on O δ- and H δ+ on an adjacent molecule
State 7 biologically important properties of water
Reaches maximum density at 4C
High surface tension
Incompressible
Metabolite / solvent for chemical reactions in the body
High specific heat capacity
High latent heat of vapourisation
Cohesion between molecules
Explain why ice floats on water. Why is this important for organisms?
Ice is less dense than water because H-bonds hold molecules in fixed positions further away from each other
Insulated water in arctic climates so aquatic organisms can survive
Water acts as a habitat
Why is the high surface tension of water important for organisms?
Slows water loss due to transpiration in plants
Water rises unusually high in narrow tubes lowering demand on root pressure
Some insects can ‘skim’ across the surface of water
Why is water an important solvent for organisms
Polar universal solvent dissolves and transports charged particles involved in intra and extra cellular reactions e.g.[PO4]3+ for DNA synthesis
Why are the high latent heat of vaporisation and high specific heat capacity of water important for organisms
Cooling effect when water evaporates from skin surface as sweat / from mouth when panting
Acts as a temperature buffer which enables endotherms to resist fluctuations in core temperature to maintain optimum enzyme activity
Define monomer and give some examples
Monomer: smaller units that join together to form larger molecules
- Monosaccharides
- Amino acids
- Nucleotides
Define polymer and give some examples
Polymer: Molecules formed when many monomers join together
- Polysaccharides
- Proteins
- DNA / RNA
What happens in condensation reactions?
Chemical bond forms between 2 molecules and a molecule of water is produced
What happens in a hydrolysis reaction?
A water molecule is used to break a chemical bond between two molecules
Name the elements found in carbohydrates and lipids
C, H, O
Name the elements found in Proteins
C, H, O, N, S
Name the elements found in nucleic acids
C, H, O, N, P
Describe the properties of alpha glucose
Small and water soluble
Complementary shape to antiport for co-transport for absorption in gut
Complementary shape to enzymes for glycolysis = respiratory substrate
What type of bond forms when monosaccharides react
(1,4 or 1,6) glycosidic bond
2 Monomers = one chemical bond = disaccharide
Multiple monomers = many chemical bonds = polysaccharide
Name 3 disaccharides. Describe how they form
Condensation reaction forms glycosidic bond between 2 monosaccharides
- Maltose: glucose + glucose
- Sucrose: glucose + fructose
- Lactose: glucose +galactose
All have molecular formula C12H22O11
Describe the function of starch
Storage polymer of alpha glucose in plant cells
Insoluble so no osmotic effect on cells
Large so does not diffuse out of cells
Describe the structure of amylase
- 1,4 glycosidic bonds
- Helix with intermolecular H-bonds = compact
Describe the structure of amylopectin
1,4 and 1,6 glycosidic bonds
branched so many terminal end for hydrolysis into glucose
Describe the function of glycogen
Main storage polymer of a alpha glucose in animal cells (but also found in plant cells)
Describe the structure of glycogen
1,4 and 1,6 glycosidic bonds
Branched so many terminal ends for hydrolysis
insoluble so no osmotic effect and does not diffuse out of cells
Compact
Describe the function of cellulose
Polymer of Beta glucose gives rigidity to plant cell walls (prevents bursting under turgor pressure, holds stem up)
Describe the structure of cellulose
1,4 glycosidic bonds
Straight chain, unbranched molecules
Alternate glucose molecules are rotated 180 degrees
H-bond crosslinks between parallel strands form microfibrils = high tensile strength
How do triglycerides form
Condensation reaction between 1 molecule of glycerol and 3 fatty acids which forms ester bonds
Describe the features of a saturated fatty acid
Contain only single bonds
Straight chain molecules have many contact points
Higher melting point = solid at room temperature
Found in animal fats
Describe the features of an unsaturated fatty acid
Contain C=C double bonds
Kinked molecules have fewer contact points
Lower melting points = liquid at room temperature
Found in plant oils
Relate the structure of triglycerides to their function
High energy : Mass ratio = high calorific value from oxidation
Insoluble hydrocarbon chain = no effect on water potential of cells and used for waterproofing
Slow conductor of heat = thermal insulation
Less dense than water = buoyancy of aquatic animals
Describe the function of phospholipids
Forms phospholipid bilayer in water = component of membranes
Tails can splay outwards = waterproofing e.g. for skin
Describe the structure of phospholipids
Amphipathic: glycerol backbone attached to 2 hydrophobic fatty acid tails and one hydrophilic polar phosphate head
Are phospholipids and triglycerides polymers
No; they are not made from a small repeating unit. They are macromolecules
Describe the structure of cholesterol
Steroid structure of 4 hydrocarbons rings
Hydrocarbon tail on one side, hydroxyl (-OH) group on the other side
Describe the function of cholesterol
Adds stability to cell surface phospholipid bilayer by connecting molecules and reducing fluidity
What is the general structure of an amino acid
-COOH carboxyl / carboxylic acid group
-R variable side group consists of carbon chain and may include other function groups e.g. benzene ring or -OH group
-NH2 amine / amino group
How do polypeptides form
Condensation reactions between amino acids form peptide bonds (-CONH-)
There are 4 levels of protein structure
Define primary structure of proteins
Sequence, number and type of amino acids in the polypeptide, determined by the sequence of codons on mRNA
Describe secondary structure of proteins
Hydrogen bonds form between O δ- attached in -C=O and H δ+ attached to -NH
Describe the 2 types of secondary protein structure
Alpha helix
- All N-H bonds on same side of protein chain
- Spiral shape
- H-bonds parallel to helical axis
Beta pleated sheets
- N-H and C=O groups alternate from one side to the other
Describe the tertiary structure of a protein
Describe the bonds present
3D structure formed by further folding
- Disulphide bridges : strong covalent S-S bonds between molecules of the amino acid Cysteine
- Ionic bonds: relatively strong bonds between charged R groups (pH changes cause these bonds to break)
- H-bonds: numerous and easily broken
Describe the quaternary structure of a protein
Functional proteins may consist of more than one polypeptide
Precise 3D structure held together by the same types of bond as tertiary structure
May involve addition of prosthetic groups e.g. metal ions or phosphate groups
Describe the structure of globular proteins
Spherical and compact
Hydrophilic R groups face outwards and hydrophobic R groups face inwards - usually water soluble
Describe the function of globular proteins
Involved in metabolic processes e.g. enzymes such as amylase, insulin (2 polypeptide chains linked by 2 disulphide bonds), Haemoglobin
Describe the structure of haemoglobin
Globular conjugated protein with prosthetic group
2 alpha chains and 2 beta chains, 4 prosthetic haem groups
Water soluble so dissolves in plasma
Fe2+ haem group forms coordinate bond with O2
Tertiary structure changes so it is easier for subsequent O2 molecules to bind (cooperative binding)
Describe the structure and function of fibrous proteins
Can form long chains or fibres
Insoluble in water
Useful for structure and support e.g. collagen in skin
What is the function of collagen
Component of bones, cartilage, connective tissues and tendons
What is the function of elastin
Provides elasticity to connective tissue, arteries, skin, lungs, cartilage and ligaments
What is the function of keratin
Structural component of hair. nails, hooves, claws and epithelial cells of outer layer of skin
Describe how to test for proteins in a sample
Biuret test confirms presence of peptide bond
1. Add equal volume sodium hydroxide to sample at room temperature
2. Add drops of dilute copper (II) sulfate solution. Swirl to mix. (Steps 1 and 2 make Biuret reagent).
3. Positive result: colour changes from blue to purple
Negative result: Solution remains blue
Describe how to test for lipids in a sample
- Dissolve solid samples in ethanol
- Add an equal volume of water and shake
- Positive result: milky white emulsion forms
Describe how to test for reducing sugars
- Add an equal volume of Benedict’s reagent to a sample
- Heat the mixture in an electric water bath at 100 *C for 5 mins
- Positive result: colour changes from blue to orange and brick red precipitate forms
Or use test strip coated in a reagent that changes colour if reducing sugar is present
Describe the Benedicts test for non-reducing sugars
- Negative result: Benedicts reagent remains blue
- Hydrolyse non-reducing sugars e.g. sucrose into their monomers by adding 1cm3 of HCl. Heat in a boiling water bath for 5 mins
- Neutralise the mixture using sodium carbonate solution
- Proceed with the Benedict’s test as usual
Describe the test for starch
- Add iodine solution
- Positive result: colour changes from orange to blue-black
State the role and chemical symbol of Nitrates
(NO3)- is used to make DNA, amino acids, NADP for photosynthesis and NAD for respiration
State the role and chemical symbol of ammonium
(NH4)+ can be converted to (NO3)- by saprobionts during nitrogen cycle. Produced by deaminated of amino acids during ornithine cycle in liver
State the role and chemical symbol of hydroxide ions
OH- ions affect pH and can interact with bonds in tertiary protein structure to cause denaturation
State the role and chemical symbol of phosphate ions
(PO4)3- is a component of ATP/ADP for energy release and NADP
State the role and chemical symbols of Potassium and Sodium ions
Na+ and K+ are involved in maintenance of resting potential of neurones and generation of action potentials
Na+ is also involved in the co-transport mechanisms
State the role and chemical symbol of chlorine ions
Cl- is involved in inhibitory synapses to cause hyperpolarisation
State the role and chemical symbol of Hydrogen ions
Forms in organisms when CO2 dissolves in water
H+ regulates pH and can interact with bonds in tertiary protein structure to cause denaturation. H+ pump is involved in chemiosmosis and active loading in translocation
State the role and chemical symbol of hydrogen carbonate ions
(HCO3)- forms in organisms when CO2 dissolves in water
State the role and chemical symbol of calcium ions
Ca2+ is used to make calcium pectate to add stability to middle lamella of plant walls
Regulates exocytosis of neurotransmitter
Binds to troponin to stimulate muscle contraction
How can the concentration of a solution be measured quantitatively
• Use colorimetry to measure absorbance / % transmission. Interpolate a calibration curve from solutions of known concentrations
• Use biosensors. A bioreceptor detects the presence of a chemical. A transducer converts the response into a detectable electrical signal
Outline the principles and process of thin layer spectroscopy
- Use capillary tube to spot solution onto pencil start line (origin) 1cm from the bottom of the paper
- Place chromatography paper into solvent (origin should be above solvent level)
- Allow solvent to run until it almost touches the other end of the paper. Molecules in mixture move different distances based on relative solubility in solvent / attraction to paper
What are Rf values
Ratios that allow comparison of how far molecules have moved in chromatograms
How do you calculate Rf values
Rf value = distance between origin and centre of pigment spot / distance between origin and solvent front
