proteins,enzymes,nucleic acids,DNA exam qs

describe the induced fit model of enzyme action and how enzymes act as a catalyst

Substrate binds to active site/enzyme, enzyme-substrate complexes are formed, active site changes shape to be complementary to the substrate

suggest and explain a procedure scientists can use to stop an enzyme reaction

boil/add strong acid/alkali, enzyme is denatured

what is a reason an enzyme reaction graph may plateau?

all active sites are occupied

a competitive inhibitor decreases the rate of an enzyme-controlled reaction. explain how

inhibitor similar shape to substrate, binds to active site, prevents enzyme-substrate complexes forming

Describe how the structure of a protein depends on the amino acids it contains.

structure determined by position of amino acids/R group

primary structure is sequence of amino acids

secondary structure is formed by hydrogen bonding between amino acids.

tertiary structure is formed by interactions between R groups, creates an active site in enzymes

Explain how the induced fit in an active site of an enzyme causes a high rate of reaction.

lowers activation energy- induced fit causes active site of enzyme to change shape, so formation of an enzyme-substrate complex causes these bonds to break

describe a biochemical test to confirm the presence of proteins

add biurets solution, positive result is purple/lilac

A dipeptide consists of two amino acids joined by a peptide bond. Dipeptides may differ in the type of amino acids they contain. Describe two other ways in which all dipeptides are similar and one way in which they might differ.

Similar: amine/NH2 group at end, carboxyl/COOH group at end but variable groups are different

How many R groups do all dipeptides have?

2

Describe how a peptide bond is formed between two amino acids to form a dipeptide.

condensation reaction between amine and carboxyl group

The secondary structure of a polypeptide is produced by bonds between amino acids. Describe how.

Hydrogen bonds between NH and C=O

Two proteins have the same number and type of amino acids but different tertiary structures. Explain why.

different sequence of amino acids forms hydrogen, ionic and disulphide bonds in different places

Formation of an enzyme-substrate complex increases the rate of reaction. Explain how.

reduces activation energy due to bending bonds

what is an R group?

variable side chain-determines what amino acid it is

how many amino acids in human body?

20

what 3 things can the R group be

hydrogen atom, carbon chain, more complex stucture

what 4 elements are amino acids generally made up of?

carbon hydrogen oxygen nitrogen

what element do only some amino acids contain?

sulphur

basic formula of amine group

nh2

formula of carboxyl group

COOH

what reaction causes formation of dipeptides?

condensation reaction

how many h20s does one formation of a dipeptide make?

1

what is formed from a dipeptide bond?

OH and H forms water, C and N bond

are hydrophilic molecules charged or uncharged?

uncharged

are hydrophobic molecules charged or uncharged?

charged

primary structure of a protein?

The sequence of amino acids in the polypeptide chain, determined by the DNA base sequence of the gene

secondar structure of a protein?

The amino acid chain spontaneously forms one of two secondary structures- alpha helices and beta pleated sheets

what is a secondary structure protein stabilised by

Hydrogen bonds between C=O and NH sections

A tertiary protein structure is established by 3 types of bond. Describe them and put them in the order of strength

Hydrogen bonds- attractions between slightly positive and slightly negative R-groups.

Ionic bonds between positive and negative R-groups.

Disulphide bridge- covalent bonds between R-groups that contain sulphur.

Bacteria living in hot water springs (thermophiles) have more cysteine + methionine. Why?

They have more disulphide bridge covalent bonds which are very strong, so it’s less likely the proteins will denature

what is a quaternary protein structure?

More than one polypeptide chain held together by hydrogen, ionic and disulphide bonds.

2 examples of quaternary structure proteins

haemoglobin, antibodies

what are the bonds in antibodies?

disulphide bonds

how many heavy chains and how many light chains in antibody molecule

2 heavy chains, 2 light chains

what does antibody molecule look like

Y

what is haemoglobin as a quaternary protein structure?

2 alpha chains and 2 beta chains each containing a haem group to which O2 can bind

what causes molecules to always fold in the same shape in a protein?

protein has a primary structure therefore bonds form in the same position

what are enzymes

globular proteins that act as biological catalysts

why is tertiary structure of an enzyme important

active site must be complementary in shape to the substrate

each enzyme is ….. to one particular substrate or functional group

specific

why is activation energy required

energy needed to start a reaction- some bonds in reactants need to be broken even in an exothermic reaction, to form new bonds in the products

how do enzymes speed up metabolic reactions?

reduce activation energy

lock and key theory

Substrate has a complementary shape and so it fits perfectly into the active site of the enzyme, to form an enzyme-substrate complex.

induced fit theory

Enzyme has to alter its tertiary structure slightly to form an enzyme-substrate complex. This weakens the bond that needs to be broken in the substrate so activation energy is reduced.

explain why bond is weakened in induced fit theory

active site has changed shape to fit the substrate, which puts stress on this bond and weakens it. so, if the reactants collide, there’s a greater chance of a chemical reaction.

What factors affect the rate of an enzyme controlled reaction?

temperature, PH, substrate concentration

how does temperature affect enzyme action

as temp increases, enzyme +substrate molecules = more KE

more collisions occur, more enzyme-substrate complexes are formed, ROR increases.

at even higher temperatures, polypeptide chain vibrates so much that hydrogen/ionic bonds pulled apart, enzyme loses its tertiary structure, denatured

active site changes shape , so no enzyme-substrate complexes can form.

explain how PH affects enzyme action

each enzyme has optimum PH where tertiary structure is stable.

If the PH moves away from optimum, excess H+ or OH- ions can disrupt ionic + hydrogen bonds in the enzyme, loses its tertiary structure.

active site changes shape, no enzyme-substrate complexes can be formed, ROR decreases

how doe substrate concentration affect enzyme action?

as substrate conc increases, ROR increases proportionally as more enzyme-substrate complexes are formed.

at high substrate concentrations, enzymes working at maximum rate, adding more substrate =no effect on ROR, something else has to become the limiting factor.

how does enzyme concentration affect enzyme action

As enzyme conc increases, ROR increases proportionally. Double enzyme conc means double reaction rate because twice the enzyme-substrate complexes are formed.

Why are enzymes never in excess?

They are reusable, therefore present in small numbers

how to perform iodine test?

Put 2cm cubed test solution into test tube, add 2 drops iodine solution, positive result = blue/black

what tests for starch

iodine test

test for sugars

benedicts test

how to test for reducing sugars

2cm cubed test solution into test tube, add equal quantity benedict’s reagent, shake + heat for a few minutes in 95 degree water bath, positive result = green, brown or red

how to test for non reducing sugars

2cm cubed test solution into test tube, add equal quantity of dilute HCL, boil for a few mins to hydrolyse glycosidic bonds, neutralise- add small amounts of solid sodium-hydrogen-carbonate until it stops fizzing, positive result = green, brown or red

what does emulsion test test for

lipids

how to perform emulsion test

Shake some test material with 4cm cubed ethanol, filter liquid into test tube of water, leaving any solids behind, positive result: lipids precipitate in water, cloudy-white emulsion

what does biurets test test for?

proteins

how to perform biurets test

2cm cubed test solution into test tube, add equal volume biuret solution down side of test tube, POSITIVE RESULT = blue ring at surface, disappears upon shaking, solution turns lilac-purple

What are competitive inhibitors and what do they do?

molecule, has shape similar to enzyme’s normal substrate, can fit into the active site and form an enzyme-inhibitor complex

Is the action of a competitive inhibitor reversible?

Yes, the inhibitor can leave the active site

Describe what a competitive inhibitor looks like on a graph when added to a reaction, compared to no inhibitor

Increases at a slower rate, however eventually reaches the same point as no inhibitor

What is a non-competitive inhibitor and what does it do?

binds to the enzyme in a place other than the active site. this changes the tertiary structure of the molecule, also altering the shape of the active site

Is the action of a non-competitive inhibitor reversible?

no- no more enzyme-substrate complexes can be formed because the tertiary structure has been altered

When using a non-competitive inhibitor, why does the reaction plateau at a lower rate?

active sites no longer complementary, so increasing the substrate concentration has no effect as they are still not complementary

Describe how monomers join to form the primary structure of a protein.

Condensation reaction between amino acids form peptide bonds, creating specific sequences of amino acids

nucleic acids

polymers of repeating nucleotide monomers

what do nucleotides consist of?

pentose sugar, phosphate, nitrogenous base

how are nucleotides joined together and what does it make?

phosphodiester bonds formed by a condensation reaction between the -OH on C3 of one nucleotide and an OH- on the phosphate, forming a polynucleotide chain

What does DNA contain?

the pentose deoxyribose and one of four bases: cytosine, guanine, adonine, thymine

in dna, what are 2 polynucleotide chains held together by?

hydrogen bonds between base pairs to form a double helix. these are antiparallel (parallel but run in opposite directions)

what is eukaryotic dna associated with?

histones- proteins which protect the fragile dna and have a role in the control of dna expression

what is this?

deoxyribose

what is this?

ribose

what is the purple part?

nucleotide

what is the pink part?

deoxyribose

what is the green part?

phosphate

what is the blue part?

base pair

what are the 4 base pairs and which goes with which?

cytosine and guanine, thymine and adenine

what 3 things are nucleotides made up of?

pentose sugar, phosphate group, nitrogenous base (cysotine, thymine, uracil, adenine, guanine

a pentose sugar, phosphate group and an organic base use what reaction to form a mononucleotide?

condensation

how do 2 mononucleotides join together and what bond does it form?

condensation reaction

between deoxyribose sugar of one nucleotide, phosphate group of another

forming a dinucleotide

forms a phosphodiester bond

what does the continued linking of mononucleotides make?

a long chain called a polynucleotide

what is RNA and what is it made up of?

a single, relatively short polynucleotide chain (polymer). made of pentose sugar ribose and organic bases are adenine, guanine, cytocine and uracil

explain how organic bases help to stabilise the structure of dna

hydrogen bonds between base pairs hold polynucleotide chains together to form double helix

held in antiparallel directions

what is the pentose of dna?

deoxyribose

what is the sugar in dna?

deoxyribose

what is the sugar in rna?

ribose

4 differences between DNA and RNA.

in DNA, bases are CGAT whereas in RNA, bases are CGAU

DNA double stranded, RNA is single stranded.

in DNA, deoxyribose is the pentose whereas in RNA, ribose is the pentose.

DNA is long molecule, whereas RNA is shorter.

dna replication (4 stages)

1. dna helicase unzips dna, exposing free base.

2. free complementary nucleotides bind to the exposed bases and DNA polymerase makes a complementary polynucleotide chain, adding 1 nucleotide at a time.

3. other strand uses another dna polymerase because this new dna strand needs to be made in the opposite direction.

4. eventually, each strand has been copied and 2 new identical strands of DNA are produced

what are the 2 stages of protein synthesis?

transcription, translation

what bonds are the two strands in dna joined by?

hydrogen bonds formed by certain bases

are matching base pairs always in the same quantity?

yes, however the ratio of adenine and thymine to cytosine and guanine varies from species to species

what makes up the structural backbone of a dna molecule?

phosphate and deoxyribose wind around each other alongside the base pairs to form a double helix

why is dna a stable molecule? 3 reasons

phosphodiester backbone protects the chemically reactive organic bases inside the double helix

hydrogen bonds link the organic base pairs forming bridges (rungs) between the phosphodiester uprights

three hydrogen bonds between cytosine + guanine, so higher the proportion of C-G pairings, the more stable the DNA molecule

what is dna

hereditary material responsible for passing genetic information from cell to cell and generation to generation.

5 ways dna is adapted to its function (number them)

stable structure,normally passes from generation to generation without significant change. most mutations are repaired, so persistent mutations are rare

2 separate strands joined by hydrogen bonds so can separate for dna replication/ protein synthesis.

large molecule- carries lots of genetic information.

base pairs in helical cylinder of deoxyribose-phosphodiester backbone, so genetic information protected from outside chemical/physical forces

base pairing leads to dna being able to replicate and transfer information as mRNA