1.2 Biological molecules 1 (and 1.1 water) Flashcards
what is the general formula for monosaccharides
(CH2O)n
name 5 monosaccharides
Galactose, fructose, alpha-glucose, beta-glucose
describe triose sugars
-have 3 carbon atoms
-molecular formula C3H6O3
-important in the mitochondria where glucose is broken down into triose sugars during respiration
describe pentose sugars
-have 5 carbon atoms
-molecular formula C5H10O5
-E.G. ribose and deoxyribose
describe hexose sugars
-have 6 carbon atoms
-molecular formula C6H12O6
-E.G. glucose, fructose, galactose
how are disaccharides formed
2 monosaccharides join together in a condensation reaction
a glycosidic bond (type of covalent bond) forms between the 2 monosaccharides
forming a disaccharide and 1 molecule of water is removed
there can be a 1,4-glycosidic bond or a 1,6-glycosidic bond
name 3 disaccharides
maltose
sucrose
lactose
all have the molecular formula C12H22O11
what 2 monosaccharides form the disaccharide maltose
2 alpha glucose
what 2 monosaccharides form the disaccharide sucrose
alpha glucose + fructose
what 2 monosaccharides form the disaccharide lactose
alpha glucose + beta galactose
how are polysaccharides formed
many monosaccharides join during a condensation reaction, where glycosidic bonds form and water molecules are lost
why are polysaccharides good storage molecules
-polysaccharides are very compact, so many can fit inside a cell
-glycosidic bonds are easily broken, so monosaccharide units can be easily released
-not very water soluble, so have little affect on water potential and cause no osmotic water movements
what happens during hydrolysis
-the opposite of a condensation reaction
-a water molecule is added to break the bonds
what are the 2 types of polysaccharides
oligosaccharides - have 3-10 sugar units
true polysaccharides - have 11 or more sugar units
properties of starch
what is starch made up off
-insoluble, so doesn’t affect water potential and creates no osmotic water movements
-compact
-can release glucose, so is an energy store
-large, so doesn’t diffuse out of cells
alpha glucose in the form of the 2 compounds: amylose + amylopectin
describe amylose
-made up of only alpha-glucose joined by 1,4-glycosidic bonds
-forming a coiled chain and an alpha-helical structure, making it harder for hydrolysis to occur
-the coiled shape makes it compact
describe amylopectin
-made up of only alpha-glucose joined by both 1,4-glycosidic bonds and 1,6-glycosidic bonds
-forming branching chains, but this leaves many terminal glucose molecules so hydrolysis can happen easily (a water molecule can join on)
describe glycogen
a polysaccharide and polymer
glycogen is the only carboydrate energy store found in animals (but also found in some plants)
made up of only alpha-glucose units
both 1,4-glycosidic bonds and 1,6-glycosidic bonds
(has more 1,6-glycosidic bonds than amylopectin)
many branched chains, so can release glucose rapidly
compact like starch
how is cellulose formed
-made up of only beta-glucose monomer units
-bonded together by only 1,4-glycosidic bonds, formed during condensation where a water molecule is lost
-each beta glucose molecule must be inverted 180 degrees from the previous beta glucose molecule
-hydrogen bonds form between the hydroxyl groups on adjacent chains
-as oxygen is more electronegative than hydrogen, it attracts the pair of electrons closer to itself
-causing hydrogen bonds to form between the delta negative oxygen atom and delta positive hydrogen atom
-this crosslinking between cellulose chains holds them strongly together
-cellulose chains bundle together to form microfibrils, these bundle together to form fibers
what are the properties of cellulose within the cell wall
-the hydrogen bonds hold cellulose chains together and make cellulose very strong
-strong to prevent cell lysis, maintain turdigity, and resist turgor pressure
-cellulose molecules remain as very long, straight chains
-can’t be broken down by most animals
-beta glucose monomers in cellulose are polar, so water and minerals can diffuse through the cell wall
why can’t cellulose be broken down by most animals
Because most animals don’t contain the enzymes needed to break the 1,4-glycosidic bonds between molecules of beta-glucose, so cannot digest cellulose.
Therefore cellulose is a type of fibre.
why is water a polar molecule
-in a water molecule there is a covalent bond between the oxygen and hydrogen atoms.
-oxygen is more electronegative so pulls the shared pair of electrons in the covalent bond more towards itself.
(oxygen is more electronegative because it has a larger nucleus, so the pair of electrons are attracted to the larger number of positively charged protons)
-the oxygen atom becomes slightly δ−
(delta negative) and the hydrogen becomes slightly δ+ (delta positive)
-water has a permanent dipole
how do water molecules take part in hydrogen bonding
-the slightly negative oxygen atom on one water molecule will attract the slightly positive hydrogen molecule on another water molecule, forming a hydrogen bond between them (a weak electrostatic intermolecular force)
-although each hydrogen bond is weak, there are many of them, giving water a relatively high melting and boiling point compared to other molecules the same size, because it takes a lot of energy to break all the hydrogen bonds.
what are the 7 important properties of water
-is a polar solvent
-it’s maximum density is at 4 degrees celcius
-high specific heat capacity
-incompressible
-high surface tension
-cohesive
-adhesive
what is the meaning of dipole
the separation of charge when the pair of electrons in a covalent bond are not evenly shared
a polar molecule contains a dipole
describe how water is a polar solvent and why this is important
-water is a polar molecule allowing it to easily dissolve ionic and polar molecules
-water molecules are attracted to the ions in contact with the water
-water molecules cluster around each ion, separating them from the ionic lattice
-the delta positve hydrogen atoms are attracted to the negative ions
-and delta negative oxygen atoms are attracted to the positive ions
describe why water’s maximum density is 4 degrees celcius and why this is important
-as water condenses from a gas to a liquid it becomes more dense because more hydrogen bonds form between water molecules pulling them closer
-at 4 degrees celcius water is at it’s maximum density
-as water cools down further, water molecules form the maximum 4 hydrogen bonds each, to do this the water molecules must move apart into a regular structure
-ice is less dense than water
-ice forms an insulating layer above water, preventing water underneath from freezing
-protecting aquatic organisms
-as ice floats ontop off water it’s exposed to sunlight so melts quickly
describe how water has a high specific heat capacity and why this is important
-water has high specific heat capacity
-so releases and absorbs heat very slowly
-because the hydrogen bonds between molecules need a lot of energy to be broken
-the temperature of lakes and seas is stable throughout the year, making the habitats of aquatic organisms a stable environment
-water has a high melting point becuase the hydrogen bonds between molecules need a lot of energy to break
-they type of intermolecular force water has is hydrogen bonds, these are the strongest intermolecular force
why is water incompressible
it is a liquid
what is meant by “water molecules are cohesive” and why is this important
-cohesion is the attraction between molecules of the same type
-water molecules are attracted to eachother due to hydrogen bonds formed between molecules
-allowing for the movement of water from the roots to the leaves
what is meant by cohesion and adhesion
cohesion - the attraction between molecules of the same type
adhesion - the attraction of molecules of different types
what is meant by “water molecules are adhesive” and why is this important
-water molecules are attracted to molecules of different types
-only when the molecules are polar or charged
-allowing surface tension and capillary action
describe why water has high surface tension and why this is important
-water molecules at the surface of water are more attracted to eachother than to molecules in the air
-this uneven attraction pulls the water molecules towards the rest of the water molecules below
-so theres lots of tension at the surface of water
-important for plant transport systems and animals which can walk on the surface of water
describe the basic structure of an amino acid
-1 central carbon atom bonded to
-an amine group (NH2)
-a carboxyl group (COOH)
-a hydrogen atom
-a R group
how is a dipeptide made
-2 amino acid monomers join to make 1 dipeptide.
-1 of the amino acids is inverted, so the amine group and carboxyl group are next to eachother and can react together
-in a condensation reaction, where 1 molecule of water is lost.
-a peptide bond forms between the 2 amino acids, forming a dipeptide
how is a polypeptide chain made
2 amino acid monomers react to form a dipeptide.
More amino acids react with the dipeptide forming a polypeptide.
When the polypeptide folds, coils, or associates with other polypeptide chain, a protein is formed.
what is the primary structure of a protein
the sequence of amino acids that make up the polypeptide held together by peptide bonds
what is the secondary structure of a protein
-the polypeptide chain curl and fold into a regular repeating structure held together by hydrogen bonds
-either in an alpha helix or beta pleated sheet
how does a protein form the secondary structure alpha helix
-the polypeptide chain coils
-the hydrogen in the amine group (NH2) is slightly positive
-the oxygen in the carboxyl group (COOH) is slightly negative
-a hydrogen bond forms between the hydrogen on one amino acid and the oxygen on another amino acid
-the hydrogen bonds keeps the coil stable
how does a protein form the secondary structure beta pleated sheet
-the polypeptide chains form a zig-zag and fold over themselves
-the hydrogen in the amino group (NH2) is slightly positive
-the oxygen in the carboxyl group (COOH) is slightly negative
-a hydrogen bond forms between the hydrogen on one amino acid and the oxygen on another amino acid
-the hydrogen bonds keeps the folded zig-zag shape stable
what is the tertiary structure of a protein
the overall specific 3-D shape of a protein, determined by interactions between the R-groups and properties of R-groups
how does the tertiary structure of a protein form
-the alpha-helices and beta pleated sheets twist to form a protein with a specific structure
-the structure is held in place by bonds formed between the R-groups of the amino acids
-these can be hydrogen, disulfide or ionic bonds or van der walls forces
-the structure is also determined by whether the R-groups are hydrophilic or hydrophobic
describe the hydrogen bonds formed in the tertiary structure of a protein
-hydrogen bonds form between polar R-groups
-between any delta positive and delta negative atom
describe the ionic bonds formed in the tertiary structure of a protein
-ionic bonds form between any positively and negatively charged R-groups
describe the disulphide bonds formed in the tertiary structure of a protein
-disulphide bonds form between 2 sulfur atoms in cysteine groups
-the 2 cysteine groups are oxidised, forming a disulphide bond
describe how R-groups being either hydrophilic or hydrophobic influences the structure of a protein
-amino acids with hydrophobic R-groups are found in the middle of the protein
-amino acids with hydrophilic R-groups are found on the outside of proteins
what is the quaternary structure of a protein
the specific 3-D shape of a protein, determined by multiple polypeptide chains, and/or prosthetic groups bonded together
how are proteins with quaternary structures formed
-multiple polypeptide chains with tertiary structures are bonded together by the same type of bonds in their tertiary structure
-prosthetic groups (non-protein groups) can be associated with the polypeptide chains, forming conjugated proteins
what are 3 properties of all fibrous proteins
-contain long polypeptide chains with repeating sequences of amino acids
-the amino acids have non-polar R groups, so fibrous proteins are insoluble in water (the amino acids can’t interact with water)
-main uses are for structure
-fairly unreactive
describe the structure of collagen
-the primary structure is a repeating sequence of 3 amino acids
-every 3rd amino acid is glycine
-glycine is the smallest R group (just H) of any amino acid
-allowing the polypeptides to wrap tightly
-made up of 3 alpha polypeptide chains
-this first forms a procollagen (triple helix with lose ends)
-procollagen peptidases remove the loose ends, creating a collagen molecule
-multiple collagen molecules come together to make a collagen fibril
-in the fibril the collagen molecules are staggered so there are no weak spots
-many fibrils form collagen fibers
what is the main function of collagen
for strength - collagen has high tensile strength
where is collagen found in the body, and what is it’s function
-collagen is found in artery walls to prevent vessels from bursting from high pressure
-collagen is used to make tendons
-tendons connect muscle to bone, allowing movement
-collagen is found in muscle, bone and skin
what are the properties of all globular proteins
-spherical shape, with hydrophobic R-groups on the inside and hydrophilic R-groups on the outside
-soluble in water, hydrophilic R-groups react with water
-have very specific shapes to carry out specific functions e.g. enzymes
-reactive
-irregular amino acid sequences
-main uses are functional
describe the structure of haemoglobin
-4 polypeptide chains (2 alpha globin and 2 beta globin)
-haemoglobin is a conjugated protein, it has 4 prosthetic haem groups (1 haem group for each polypeptide chain)
-a heam group contains an iron ion (Fe2+)
what is the function of haemoglobin
-one haem group binds to one oxygen molecule, allowing haemoglobin to bind to 4 oxygen molecules at a time, maximising the amount of oxygen being carried through the blood
-oxygen is delivered to cells to be used for respiration
name 3 globular proteins
haemoglobin
insulin
lysozyme
name 3 fibrous proteins
collagen
keratin
elastin
how does cellulose arrange itself around plant cells
cellulose fibres wrap around plant cells in many layers and at different angles
describe Van der Walls forces in the tertiary structure of a protein
-weak forces of attraction between non-polar groups
-only occurs when atoms/molecules are very close to eachother
-caused by changing charges due to movements of electrons
explain how the structure of glycogen is related to its function
3 marks
-branched chains leave many terminal glucose molecules so can easily undergo hydrolysis
-compact for its function as an energy storage molecule
-insoluble so doesn’t affect osmosis/water potential + large molecules so don’t leave cells
what are glycoproteins
-conjugated proteins
-a protein with a carbohydrate prosthetic group
explain how and why glycoproteins are useful in the body
-the carbohydrate prosthetic group on the molecule holds onto lots of water and makes it harder for protease to digest it
-so the water-holding properties of glycoproteins make them slippery, reducing friction
-useful in mucus which lines the stomach, protecting the protein walls from being digested
what are lipoprotiens
-conjugated proteins
-proteins with a lipid prosthetic group
explain how and why lipoproteins are useful in the body
-the lipid prosthetic groups binds to cholesterol (also a lipid)
-so lipoproteins transport cholesterol in the blood
-there are 2 main forms of lipoproteins in the blood: low density lipoporoteins and high density lipoproteins
-HDLs contain more protein than LDLs, making HDLs denser because proteins are more compact than lipids
describe the test for proteins
-add biuret reagent (sodium hydroxide solution and copper sulfate solution) to the sample in a test tube
-a positive test will turn from blue to purple
-this indicates the presence of peptide bonds, therefore the sample is a protein
describe the test for lipids
-emulsion test for lipids
-add ethanol to the test tube with the sample
-mix till the lipid has dissolved
-add distilled water and mix the mixture
-for a positive test, the mixture will turn from colourless to a cloudy white precipitate
-the cloudy white precipitate if formed because lipids are insoluble in water so they come out of the solution to form an emulsion
what 2 organic chemicals are fats and oils made up off
glycerol (propane-1,2,3-triol) and fatty acids
what 2 ways do fatty acids differ
-the length of the carbon chain (depending on the size of the R group)
-fatty acids can be saturated or unsaturated
what are saturated fatty acids, what sate are they at room temperature and where are they found
-carbon atoms are joined together by single covalent bonds
-mostly solid at room temperature
-mostly meat and dairy sources
what are unsaturated fatty acids
-the carbon chain has one or more double covalent bond
-mostly liquid at room temperature
-mostly plant sources
-a monounsaturated fatty acid has 1 double covalent bond
-a polyunsaturated fatty acid has 2 or more double covalent bonds
how is a triglyceride formed
-through esterification (type of condensation reaction)
what is esterification
-a type of condensation reaction where ester bonds are formed
-between the carboxyl group (-COOH) of a fatty acid and 1 of the hydroxyl groups (-OH) on the glycerol
-a water molecule is lost for every ester bond formed
how is a triglyceride formed
-1 glycerol molecule + 3 fatty acids
- esterification happens between the carboxyl group on 1 of the fatty acids and 1 of the hydroxyl groups on the glycerol
-3 ester bonds are formed
-3 water molecules are lost
how much more energy do lipids store compared to carbohydrates
lipids store 3 times as much energy as the same mass of carbohydrates
what are the functions of lipids
energy stores
waterproofing
good insulators
all lipids dissolve in organic solvents
low density
how is the structure of lipids adapted to its function of waterproofing
lipids are hydrophobic
2 examples of how lipids are good insulators
-a fatty sheath insulates nerves so electrical impulses can travel faster
-they prevent heat loss in animals, like the thick layer of blubber in whales
an example of why the low density property of lipids is useful
-the body fat in water mammals is made from lipids which are low density, helping them float on water easily
an example of why lipids’ unique dissolving properties are useful
-lipids dissolve in organic solvents
-but are insoluble in water
-so lipids don’t affect water-based chemical reactions in the cytoplasm or affect water potential of cells
how are phospholipids formed
-esterificstion
-inorganic phosphate ions (-PO4^3-) are present in the cytoplasm
-one of the hydroxyl groups on glycerol undergoes esterification with a phosphate group instead of a 3rd fatty acid
-phospholipids are made up of: 1 phosphate group, 1 glycerol, 2 fatty acids
describe insulin as a globular protein
structure and function
-2 polypeptide chains: 1 alpha-helix 1 beta pleated sheet
-these 2 chains are held together by disulfide bonds
-the globular shape of insulin allows it to be specifically binded to receptors on cell membranes
-insulin travels in the blood, so it has hydrophilic R groups on the outside, so it is soluble
-insulin is a hormone used to lower blood glucose levels
describe the structure of the globular protein lysozyme
-made of 1 polypeptide chain (can be either alpha helix or beta pleated sheet)
-it is a bacterial enzyme so the specific shape of the active site means it has a complementary fit with the substrate molecule in the bacterial cell wall
describe the function of lysozyme
-an enzyme which catalyses the breakdown of a molecule found in the bacterial cell wall
-helping defend the body from bacteria
why are globular proteins soluble
globular proteins have amino acids with hydrophilic r groups on their surface and amino acids with hydrophobic amino acids in the center
so the hydrophilic amino acids can interact with water molecules
what is the function and structure of keratin
-found in skin, hair and nails
-strong
-insoluble
-contains a large proportion of cysteine
-cysteine is a sulfur containing amino acid which forms disulfide bonds
-so keratin has a large proportion of disulfide bonds, making it very strong
-the amound
what is the function and structure of elastin
-found in skin, making it elastic
-found in artery walls, as blood flows through the artery wall stretches and then recoils back to its original shape
-the hydrophobic regions on elastin molecules associate causing elastin molecules to group together
-when stretched the molecules move apart but remain attached at the crosslink
-after stretching the elsatin molecules reassociate making elastin elastic
how does the ration of C:H:O compare in carbohydrates and lipids
in carbohydrates: 1:2:1
in lipids: 1:2: less than 1
so in lipids there are very few oxygen atoms and many hydrogen atoms
