biological molecules

TOPIC 1

what is the structure of ATP?

one adenine base, one ribose sugar and three phosphate groups

what are the products of a hydrolysis reaction to ATP?

one ADP and one inorganic phosphate ion

what is a coupled reaction?

reactions that link an exergonic reaction to an endergonic process

what is phosphorylation?

when an inorganic phosphate ion is added to an organic molecule, changing its shape and making it more reactive

how does phosphorylation make molecules more reactive?

the electrons of the phosphate push against and strain the molecule’s existing bonds, causing the activation energy to lower

what are some ways ATP is effective?

realeases small, manageable energy
is immediately available
rapidly regenerates
can lower other molecule’s activation energy

what monomer is carbohydrate made of?

monosaccharides

what do two monosaccharides form?

a disaccharide

what bond is formed between two monosaccharides?

glycosidic bond

what reaction bonds two monosaccharides?

condensation reaction

what reaction separates two bonded monosaccharides?

hydrolysis reaction

what is the difference between an alpha and a beta glucose?

the hydroxide group and hydrogens (of the first carbons) are inverted in a beta glucose

how are two monosaccharides bonded (which molecules?)

the first carbons and fourth carbons, or the first the sixth

how are two monosaccharides bonded vertically?

the first carbon and sixth carbons hydroxide groups bond, producing water

what is the structure of starch?

a mix of straight-chain amylose and branched amylopectin

what is the structure of glycogen?

long, branched chain with side branches, made by 1st to 6th glycosidic bonds

what is the structure of cellulose?

unbranched straight chains, linked by hydrogen bonds

what is the name of the thicker fibres of cellulose formed by hydrogen bonds?

microfibrils

advantages of amylose

can be coiled up to be more compact and more of it can be stored

advantages of amylopectin

side branches increase its surface area, meaning more enzymes can hydrolyse the glycosidic bonds for glucose releasing.

advantages of glycogen

side branches increase its surface area, meaning more enzymes can hydrolyse the glycosidic bonds for glucose releasing.
the molecule is compact, meaning it is good for storage

where is starch found?

plants

where is glycogen found?

animals

where is cellulose found?

plants

what kind of glucose is starch made of?

alpha

what kind of glucose is glycogen made of?

alpha

what kind of glucose is cellulose made of?

beta

what is starch used for?

energy storage

what is glycogen used for?

energy storage

what is cellulose used for?

structure

what is a feature of starch useful for its purpose?

it is insoluble, meaning it will not affect the water potential of the plants

what is a feature of glycogen that is useful for its purpose?

it is soluble, meaning it can be hydrolysed for quick glycogen releasing

what is a feature of cellulose that is useful for its purpose?

it is insoluble, meaning it can give plant cell walls structural support without dissolving

what makes maltose?

glucose + glucose

what makes lactose?

glucose + galactose

what makes sucrose?

glucose + fructose

what monomer makes up protein?

amino acids

what bond is found between two amino acids?

peptide bond

what is the term for two bonded amino acids?

dipeptide

what is the term for several bonded amino acids?

polypeptide

what reaction bonds two amino acids?

condensation reaction

what reaction separates two bonded amino acids?

hydrolysis

what three components do all amino acids have?

amino group, carboxyl group, R group

what is the primary structure of a protein?

a chain of amino acids (a polypeptide chain)

what is the secondary structure of a protein?

hydrogen bonds form between the amino acids, causing folding into a beta-pleat, or coil into an alpha-helix

what is the tertiary structure of a protein?

this is when interactions between R-groups cause a 3D shape

what kinds of interaction between R groups are there?

hydrophobic and hydrophilic interactions
hydrogen bonds
ionic bonds
disulphide bonds

what are hydrophobic interactions?

non-polar side chains cluster inwards towards the protein core to avoid surrounding water, which is the main drive of the folding force

what are hydrophilic interactions?

polar side chains are hydrophilic, and form hydrogen bonds with the surrounding water, which helps refine its 3D shape

what are ionic bonds?

bonds that are formed between oppositely charged side chains

what are disulphide bonds?

bonds that are formed between R groups that contain sulphur - the sulphur molecules covalently bond

what is the quartenery structure?

this is the final 3D structure of a protein containing more than one joint polypeptide chains

how does the primary structure affect the tertiary structure?

if the primary structure differs, then the tertiary interactions would form in different places, changing the 3D shape of the protein

what external factors can affect the tertiary structures?

temperature and pH

how does temperature affect the tertiary structure?

higher temperature massively increase the kinetic energy of the R group H+ ions, which can cause them to vibrate and break the hydrogen or ionic bonds.

how does low pH affect the tertiary structure?

low pH means high concentration of H+ ions, which can neutralise the negative R groups, meaning less ionic bonds can be made

how does high pH affect the tertiary structure?

high pH means low concentration of H+ ions, which can cause the R groups to releaase their own H+ ions, destroying ionic bonds.

what molecules make up a lipid?

a glycerol molecule and up to three fatty acids

what kind of molecule is a lipid?

macromolecule

what is a lipid with one fatty acid called?

a monoglyceride

what is a lipid with two fatty acids called?

a diglyceride

what is a lipid with three fatty acids called?

a triglyceride

what is a lipid with two fatty acids and a phosphate molecule called?

a phospholipid

what makes up a phospholipid?

a glycerol molecule, two fatty acids and a phosphate molecule

what do lipids provide?

energy, insulation, waterproofing, membranes and hormones

what is the name of the bond in a lipid?

ester bond

what is a saturated fatty acid?

a fatty acid, where every carbon atom is bonded to as many hydrogen atoms as possible

what is an unsaturated fatty acid?

a fatty acid, where some carbon atoms are double bonded to each other

what is the structure of a saturated fatty acid?

a straight chain, which is tightly packed

what is the structure of an unsaturated fatty acid?

has kinks in it, the number depends on how many double bonds there are

what state of matter is a saturated lipid at room temperature?

solid

what state of matter is an unsaturated lipid at room temperature?

liquid

why are lipids a good energy source?

they have a high proportion of carbon-hydrogen bonds, which can be broken down to release energy

do saturated fats or unsaturated fats have a higher melting point?

saturated

why do saturated fats have a higher melting point?

they have no double bonds, meaning they are more tightly packed and require more energy to break the bonds

what makes up the cell membrane?

a double layer of phospholipid molecules/ phospholipid bilayer

how is a phospholipid bilayer made

the hydrophilic heads with face towards water and the hydrophobic tails face away, creating a hydrophobic centre

what is an enzyme?

proteins with a tertiary structure, and an active site, which is specific to a certain substrate

what are the two enzyme-substrate complex models?

lock-and-key and the induced fit model

how do enzymes catalyse reactions?

they either put pressure on the bonds, or hold molecules together to decrease replusion

how does substrate concentration affect enzyme action?

they will speed it up, as more ES complexes can be made quicker, until the enzymes are all occupied, causing a plateau

how does temperature affect enzyme action?

they will give the enzymes and substrates more kinetic energy, which will increase the likelyhood of more collisions to make ES complexes
once the optimum temperature is passed, the enzymes denature and activity drops

after the optimum temperature is surpassed, the enzymes will denature, causing the activity to fall down to zero

how does pH level affect the activity of enzymes?

above and below the optimum pH, the H+ and OH- will disrupt the ionic and hydrogen bonds, meaning the tertiary structure and active site will change

what is a competitive inhibitor?

a molecule with a similar shape to the substrate, which will try to bind to the active site and block substrates from binding to form ES complexes

what is a non-competitve inhibitor?

a molecule, which binds to an eznymes allosteric site, which will cause the active site to change shape

how can you stop competitive inhibitors?

increasing substrate concentration, so that they out-compete the inhibitors

how can you stop non-competitve inhibitors?

you cannot

what is DNA made of?

a strand of repeating nucleotides

what is a nucleotide made of?

a phosphate molecule, a pentose sugar and a base

how do nucleotides bond together?

by a phosphodiester bond - the 3' carbon of the pentose sugar will bond to the phosphate molecule of the next nucleotide

what is the structure of DNA?

two sugar-phosphate anti-parallel backbones and base pairs bonded in the middle

what does anti-parallel mean?

one backbone is 5' to 3', and the other is 3' to 5'

what are the structural differences between DNA and RNA?

deoxyribose vs ribose sugar, thymine vs uracil, two strands vs one strand

why can RNA not have two strands?

the extra oxygen molecule can make it too awkward for a helical shape, disrupting the ideal van der waal spacing

which bases are purine?

adenine and guanine

which bases are pyrimidine?

thymine, cytosine and uracil

which base pairs have three bonds?

guanine and cytosine

which base pairs have two bonds?

adenine and thymine/uracil

what enzymes are involved in DNA replication?

DNA helicase and polymerase