2.2 biological molecules Flashcards
what is a hydrogen bond?
a weak interaction that can occur wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom
how does hydrogen bonding occur in the case of water?
- water is a polar molecule - there is an uneven distribution of charges
- the attraction between the dipoles of hydrogen (slightly positively charged) and oxygen (slightly negatively charged) creates hydrogen bonds between the water molecules
why is the incompressible nature of water important for organisms?
- provides turgidity for plant cells
- provides hydrostatic skeleton for some small animals (e.g. earthworms)
explain why its density is an important property of water
- water becomes less dense upon freezing, so ice floats
- this is because H-bonds holds molecules in fixed positions further away from each other
- this insulates the water below and reduces the rate of heat loss, which allows aquatic animals to survive in the winter
explain why cohesion and adhesion is an important property of water
- H-bonds pull water molecules together to form a skin, which gives water good surface tension
- cohesion and adhesion are both factors in slowing down the rate of water loss in transpiration
why is water an important solvent?
- it is polar, so it is a good solvent for polar substances such as salts and other ionic compounds
- this means that molecules and ions can move around and react with each other
- also means substances can be transported while dissolved
explain why its SHC is an important property of water
- water has a relatively high SHC, so it does not heat up or cool down quickly (thermostability)
- this means it provides a stable habitat for aquatic organisms, and a temperature-controlled environment for enzyme-controlled reactions to happen (major component of tissues)
explain why high latent heat of vaporization is an important property of water
- requires a lot of energy to vaporize, so it can be used as a coolant
what is a monomer? (+examples)
- a small molecule which binds to many other identical molecules to from larger molecules
e.g. monosaccharides, amino acids, nucleiotides
what is a polymer? (+examples)
- a large molecule formed from many repeating units (monomers)
e.g. polysaccharides, proteins, DNA
what is a condensation reaction?
a reaction that occurs when two molecules are joined together with the removal of water
what is a hydrolysis reaction?
a reaction that occurs when a molecule it split into two smaller molecules with the addition of water
what atoms are carbohydrates made of?
C, H, O
what is the formula and function of triose?
C3H6O3
- important in cellular respiration
what is the formula and function of pentose?
C5H10O5
- ribose for RNA - ring structure
- deoxyribose - DNA - ring structure
what is the formula and function of hexose?
C6H12O6
- glucose, galactose, fructose
what is an isomer?
- compounds that have the same molecular formula but are structurally different
- this affects their taste, digestibility and overall shape formed
what is the structure of a-glucose?
(practice drawing the entire thing)
H
|
OH
what is structure of b-glucose?
(practice drawing the entire thing)
OH
|
H
describe the properties of glucose
- dissolves in water - has polar hydroxyl groups that interact with the polar water molecules
- small (and water soluble) - easily transported in bloodstream
- sweet in taste
- reducing sugar
what type of bond and reaction occurs when monosaccharides react?
condensation reaction - (1,4 or 1,6) glycosidic bonds
what is a disaccharide (+examples of maltose, sucrose and lactose + formula)?
- a disaccharide is when a glycosidic bond forms between 2 monosaccharides
- maltose - glucose + glucose (found in barley)
- lactose - glucose + galactose (found in milk)
- sucrose - glucose + fructose (found in sugar cane)
- maltose, sucrose and fructose all have the formula C12H22O11
describe the structure and function of amylose
- made of a-glucose
- makes up starch (plant cells)
- 1,4 glycosidic bonds - helix shape held in spiral shape by H-bonds
- hydroxyl groups on inside of structure, making it less soluble
describe the structure and function of amylopectin
- made of a-glucose
- makes up starch (plant cells)
- 1,4 and 1,6 glycosidic bonds - many branches
- branching makes it more compact
- branching also means there are many glucose molecules on the ends of branches which can easily be broken off by hydrolysis for respiration, so it can provide a rapid supply of energy
describe the structure and function of glycogen
- made of a-glucose
- main storage polymer of glucose in animal cells (but also found in plant cells)
- 1,4 and 1,6 glycosidic bonds - many branches (more than amylopectin), less tendency to coil
- branching makes it more compact (energy dense)
- large and insoluble - no osmotic effect (will not effect water potential of cell) and will not diffuse out of cells
- branching also means there are many glucose molecules on the ends of branches which can easily be broken off by hydrolysis for respiration, so it can provide a rapid supply of energy
describe the structure and function of cellulose
- made of b-glucose
- 1,4 glycosidic bonds - straight, unbranched chain
- b-glucose gives rigidity to plant cell walls, to support cells against turgor pressure
- alternate glucose molecules are rotated 180 degrees
- H-bonds crosslinks between parallel strands of microfibrils create high tensile strength
- space between macrofibrils for water and mineral ions to pass through, making it fully permeable, and so it des act as a barrier to the cell membrane
what atoms are lipids made of?
C, H, O
structure of saturated vs. unsatured fatty acids?
saturated:
- only single bonds
- straight chain molecule, many contact points
- high MP (solid at RTP)
- found in animal fats
unsaturated:
- C=C double bonds (can be mono-unsaturated or poly-unsaturated)
- ‘kinked’ molecule, fewer contact points
- lower MP - liquid at RTP
- found in plant oils
how do triglycerides form?
- condensation reaction between 1 molecule of glycerol and 3 fatty acid chains
- forms ester bonds
how does the structure of triglycerides relate to their function?
- high energy : mass ratio (energy dense) - used to store energy
- insoluble - will not affect cell’s water potential
- slow conductor of heat - used for thermal insulation
- less dense than water - buoyancy
how do phospholipids form?
- condensation reaction between phosphoric acid and glycerol
- forms an ester bond
- glycerol backbone attached to 2 hydrophobic fatty acid tails and 1 hydrophilic polar phosphate head
how does the structure of phospholipids relate to its function?
- forms micelle in aqueous solution
- forms phospholipid bilayer in cell membranes to act as a barrier protecting the cell
- tails can be used for waterproofing
how does cholesterol form?
- sterol - a type of lipid not formed by glycerol or fatty acids
- 4 carbon rings and hydrocarbon tail
- small and non-polar (hydrophobic)
how does the structure of cholesterol relate to its function?
- situated in the cell membrane in between the phospholipids. the rigid rings of the cholesterol molecule interact with the hydrophobic tails of the phospholipids. this stabilizes them and makes them more rigid as well. this makes the cell membrane less permeable to small molecules.
- also used to make hormones (estrogen, progesterone)
what atoms are proteins made of?
C, H, O, N, S
what is the general structure of an amino acid? (practice drawing the entire thing)
- COOH carboxyl group
- variable R group
- amino group
why can amino acids not be stored in the body?
- the amine group contains nitrogen - it is toxic
- it is converted to urea via deamination and removed
how can amino acids act as buffers?
- when dissolved in water both the amino and carboxyl group can ionise (H+ and NH3+)
- in low pHs the amino acid accepts H+ ions and in high pHs it produces them (amphoteric) - this helps resist large changes in pH
how do polypeptides form? (practice drawing)
- condensation reaction between amino acids that form peptide bonds (-CONH-)
what is the primary structure of a protein?
the specific sequence of amino acids in the polypeptide chain
what is the secondary structure of a protein?
- regular 3D structure of the protein backbone, stabilised by hydrogen bonding
what are the two types of secondary structure?
- a-helix - helix shape, held by H-bonds parallel to the helical axis - the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain
- B-pleated sheet - two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds
what is the tertiary structure of a protein?
the folding of the secondary structure to form an irregular 3D shape
what are the 3 types of bonds that maintain the tertiary structure?
- disulfide bridge - strong covalent between S-S atoms
- ionic bonds - relatively strong bonds between the charged R groups
- hydrogen bonds - weak and numerous, affected by pH and temp
- sometimes hydrophobic and hydrophilic interactions
what is the quaternary structure of a protein?
when complex proteins may consist of more than one polypeptide chain, which becomes linked by bonds
- may involve the addition of prosthetic (non-protein) groups, e.g. metal ions or phosphate groups
what are the general functions of proteins?
- enzymes
- hormones
- contractile
- storage
- transport
- protection
- buffers
- toxins
- osmotic pressure
describe the structure and function of globular proteins
- spherical and compact
- hydrophilic R groups face outwards and hydrophobic face inwards to the centre of the molecule
- usually water soluble, because water molecules can easily cluster around and bind to them
- very susceptible to changes in temp. and pH
- specific shape for specific roles - hormones, enzymes, haemoglobin, etc.
describe the structure and function of fibrous proteins
- regular, repetitive structure of amino acids
- do not dissolve in water
- unaffected by pH and temp. changes
- form fibers, which tend to have a structural function, providing support to tissues
- e.g. collagen, elastin, keratin
describe the properties and functions of collagen
- fibrous protein
- provides mechanical strength
- in artery walls, a layer of collagen prevents the artery bursting from high pressure
- tendons, bones and cartilage are made from collagen
describe the properties and functions of keratin
- fibrous proteins
- hydrogen bonding and disulfide bridges make the molecule very strong
- structural component of hair, nails, claws, horns, etc.
- mechanical protection, impermeable barrier to infection, waterproof
describe the properties and functions of elastin
- fibrous protein
- cross-linking and coiling makes elastin strong and extensible
- provides elasticity to connective tissue, arteries, skin, lungs, cartilage, ligaments
describe the structure, properties and function of haemoglobin
- globular protein
- 2 a-chains and 2 B-chains, 4 prosthetic haem groups (conjugated protein)
- water-soluble - dissolves in plasma
- carries oxygen from the lungs to the tissues - iron haem groups form coordinate bonds with oxygen
- tertiary structure changes so it easier for the oxygen molecules to bind
describe the structure, properties and function of insulin
- A chain begins with section of a-helix, and B chain ends with a section of B-pleat
- hydrophilic R groups on the outside, so water soluble
- binds to glycoprotein receptors on the outside of the muscle and fat cells to increase their uptake of glucose from the blood
describe the structure, properties and function of pepsin
- enzyme that digests protein in the stomach
- single chain of 327 amino acids, folds into symmetrical tertiary structure
- more acidic R groups - stable in acidic environment of the stomach
role and chemical symbol of nitrates
NO3-
- used to make DNA, amino acids, vitamins and chlorophyll for photosynthesis
- a component of nitrogen cycle
role and chemical symbol of ammonium
NH4+
- used to make DNA, amino acids, vitamins and chlorophyll for photosynthesis
- involved in the maintenance of pH
- a component of the nitrogen cycle
role and chemical symbol of hydroxide ions
OH-
- affect pH
- interact with hydrogen bonds to cause denaturation
role and chemical symbol of phosphate ions
(PO4)3-
- component of ATP/ADP for energy release
role and chemical symbol of sodium ions
Na+
- regulation of osmotic pressure, water levels and pH
- constituent of vacuole
role and chemical symbol of potassium ions
K+
- regulation of water levels and pH
- constituent of vacuole
- generates healthy leaves and flowers
role and chemical symbol of chloride ions
Cl-
- involved in inhibitory synapses to cause hyperpolarisation
role and chemical symbol of hydrogen and hydrogencarbonate ions
H+, HCO3-
- involved in transport of oxygen and carbon dioxide in the blood
- involved in regulation of blood pH
role and chemical symbol of calcium ions
Ca2+
- rigidity of bone, teeth and cartilage
- blood clotting and muscle contraction
- formation of middle lamella in cell walls
describe how to test for proteins
- biuret’s test to test for presence of peptide bond
- positive result: blue to lilac
describe how to test for lipids
- dissolve solid sample in ethanol
- add equal volume of water and shake
- positive result: milky white emulsion
what are reducing sugars?
- sugars that can reduce, or give electrons to, other molecules
- includes all monosaccharides and some disaccharides
describe how to test for reducing sugars
- heat a reducing sugar with benedict’s reagent
- positive result: blue to green to yellow to orange, and brick-red precipitate
describe how to test for non-reducing sugars
- first check for reducing sugars to make sure none are there
- boil with HCl to hydrolyze the sucrose into glucose and fructose
- neutralize the solution with sodium hydrogencarbonate solution
- test for reducing sugars again
describe how to test for starch
- add iodine solution
- positive result: orange to blue-black
