Unit 1 summary

What does DNA code for?

the sequence of amino acids in the primary structure of a protein

Diagram of the structure of a nucleotide

How are polynucleotides formed?

via condensation reactions b/w the deoxyribose sugar and the phosphate group

- creates a phosphodiester bond

(sugar-phosphate backbone)

How is the double helix formed?

- The hydrogen bonding between the polynucleotides (A-T/C-G)

- the coiling of the polynucleotides

What is complementary base pairing?

When base A always pairs up with base T, and base C always pairs up with base G

Which bases are purines?

Adenine (A) and Guanine (G)

they are 2-ring purine bases

Which bases are pyrimidines?

cytosine, thymine, uracil

they are 1 ring pyrimidine bases

How many H bonds are between A and T?

2 H bonds

How many H bonds are between C and G?

3 H bonds

what does complementary base pairing do?

complementary base pairing helps maintain the order of the genetic code once DNA is replicated

Explain why DNA replication is semi-conservative and its importance within the body.

• Produces 2 genetically identical DNA copies

• Each new DNA molecule contains 1 new strand and 1 original strand

• Ensures that new cells have identical genetic material to original cells

name 6 functions of DNA due to its structure

1.

stable structure due to the sugar-phosphate backbone and double helix

2. two stranded, so both strands can act as templates

3. weak hydrogen bonds between bases allow two strands to separate / unzip during DNA replication

4. double-stranded for semi-conservative replication

5. large molecule to carry lots of info

6. stable structure due to the sugar-phosphate backbone and double helix

stable structure due to the sugar-phosphate backbone and double helix

the role of the 2 enzymes in semi-conservative replication of DNA

• DNA helicase causes the breaking of H-bonds between DNA strands

• DNA polymerase joins the DNA nucleotides, forming phosphodiester bonds

contrast the structures of ATP and a nucleotide found in DNA

1. ATP has ribose whereas DNA nucleotide has deoxyribose

2. ATP has 3 phosphate groups whereas DNA nucleotide has 1 phosphate groups

3. ATP base is always adenine whereas the base in DNA nucleotide can vary (e.g. C,G and T)

explain how the active site of an enzyme causes a high rate of reaction

• lowers activation energy by weakening/bending bonds

• induced fit causes active site of an enzyme to change shape

• ESC causes bonds to weaken

Explain the induced fit model

Before reaction: enzymes active site not complementary to shape of substrate

1. Substrate binds to active site/enzyme
2. E-S complex forms
3. Active site changes shape, distorting/breaking bonds in the substrate
4. Active site changes shape so its complementary to substrate

Explain the effect of increasing the concentration of substrate on the rate of reaction without inhibitor

increasing the concentration of substrate increases the rate of reaction up until a certain point:

• rate of reaction will increase with increases substrate

• increasing substrate means that more molecules available to enter active site

• more substrate molecules enter active site

• more substrate binds to the enzyme active site

  • more successful collisions

  • forming more ESC

• however at a high concentration of substrates, it reaches a point where all the active sites are occupied

• no further increase in rate (of reaction)

• at high substrate concentration, the enzyme concentration is limiting

Explain the effect of increasing the concentration of substrate on the rate of reaction with inhibitor

• the inhibitor has a similar shape to substrate

• the inhibitor binds to the enzyme active site instead of the substrate, occupying it temporarily

• therefore fewer active sites for substrates

explain why different enzymes are involved in each stage of the digestion process

• enzymes are specific

• the substrates are different shapes

• active site and substrate are complementary

• so ESC forms

explain why the activity of an enzyme falls to zero at a pH of 7

the pH is too high/acidic

• change in pH alters charge distribution on enzyme molecule

• change in charge of active site and changes shape of active site

• H-bonds disrupted, which changes tertiary structure

• changes shape of active site

• substrate no longer fits active site

  • substrate cannot bind to active site

• ESC cannot form

• RoR decreases

explain why the initial rate of reaction with enzymes is greater than you may calculate

• conc. of substrate is higher at the start

• so more chance of substrate entering active site

• so most active sites become occupied

explain enzyme action at an optimum temperature

• molecules have kinetic energy

• frequent collisions between enzyme and substrate molecules

• more ESC formed

• max rate (of reaction) achieved

explain enzyme action at a temperature higher than the optimum temperature

• molecules have an increase in kinetic energy

• collisions occur more frequently and with more energy

• molecules vibrate

  • which breaks bonds

  • therefore hydrogen bonds broken

• tertiary structure/3D shape of enzyme changed/altered

• active site changes shape and loses its complementary shape

• enzymes are denatured

• substrate molecules no longer fits into active site

• will decrease rate (of reaction)

• may be irreversible

  • if this is the case then the reaction stops

suggest how plasmodium obtains amino acids from haemoglobin with red blood cells

• hydrolysis of haemoglobin by enzymes

• which breaks peptide bonds

Sucralose is a chemical that has been made from sucrose by replacing three of the hydroxyl (OH) groups with Chlorine (Cl) groups.

Suggest why sucralose cannot be digested in the body

• the Cl on the sucralose instead of OH gives it a different shape/structure

• enzymes are specific and only act on one substrate

• no suitable enzyme present in the body to digest sucralose

• so therefore no ESC formed

effect on enzyme concentration on rate of reaction

• reaction rate increases with increased enzyme

• more reaction sites available

• the rate (of reaction) will decrease as substrate is used up/becomes limiting

effect of competitive inhibitor on rate of reaction

• competitive inhibitor has similar shape to substrate

  • so it can fit/occupy active site

  • for a short period of time/temporarily/reversibly

• competitive inhibitor complementary to active site

• competitive inhibitor binds/attaches to enzyme active site instead of substrate

• prevents/blocks substrate from entering active site

• effects can be reversed by increasing substrate concentration

effect on non-competitive inhibitor on rate of reaction

• reduces rate (of reaction)

• fits into allosteric site/site other than active site

• alters/changes shape of active site

• substrate cannot fit/bind to allosteric site

• increasing substrate concentration has no effect

general structure of amino acid

describe how 2 amino acids are joined together to form a dipeptide.

- formed via condensation reaction

- water is removed

- peptide bond forms b/w the carboxylic group of one amino acid and the amine group of the other amino acid

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

• The structure of a protein is determined by the position of amino acids

• the primary structure is sequence of amino acids (in the polypeptide chain)

• the secondary structure is the folding of the polypeptide chain

  • H-bonds form between NH group of one amino acid and C=O group, to form alpha helix and beta-pleated sheets

• the tertiary structure is formed by interactions (ionic bonds, hydrogen bonds, disulfide bridges) between R groups

  • creates the active site in enzymes

• the quaternary structure contains more than 1 polypeptide chain

  • formed by bonds b/w polypeptides

  • may involve the addition of a prosthetic group

Each amino acid has a different R group.

Describe how these R groups can interact to determine the tertiary structure of a protein.

1. Some R groups attract

2. Disulfide bridges between S atoms

3. Ionic bonds between oppositely charged R groups

4. Hydrophyllic R groups on the outside of molecules

5. Hydropgobic R groups on the inside of molecule

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

Explain how.

• different sequence of AA

• forms ionic/hydrogen bonds in different places

structure of alpha glucose

structure of beta glucose

difference between alpha and beta glucose

Position of hydrogen and hydroxyl groups on carbon atom 1 inverted.

word equation of maltose

Glucose + Glucose -> Maltose + Water

word equation for lactose

glucose + galactose -> lactose + water

word equation for sucrose

glucose + fructose --> sucrose + water

ways in which starch molecules are adapted for their functions in plant cells

1. insoluble

   • doesnt affect water potential;

2. Helical

   • Compact

3. Large molecule

   • Cannot leave cell.

features of starch that make it a good storage molecule

1. Insoluble (in water)

   • so doesn’t affect water potential;

2. Branched / coiled / (α-)helix

   • so makes molecule compact/can fit many molecules in a small area

3. Polymer of α glucose

   • so provides glucose for respiration

4. Branched / more ends

   • for fast breakdown / enzyme action

describe the structure of a cellulose molecule and explain how cellulose molecules are adapted for their function in plant cells

• made from beta glucose

• joined by condensation reaction

• forms 1-4 glycosidic bonds

• Long and straight chains

• Become linked together by many hydrogen bonds to form

  fibrils

• Provide strength to cell walls

• cellulose makes cell walls strong and can resist turgor pressure

structure of glycogen

Polysaccharide/polymer of α-glucose

• joined by glycosidic bonds

branched structure

suggest how glycogen acts as a source of energy

hydrolysed to glucose

• glucose is used in respiration

describe the differences between the structure of a cellulose molecule and a glycogen molecule

1. Cellulose is made up of β-glucose (monomers) and glycogen is made up of α-glucose (monomers)

2. Cellulose molecule has straight chain and glycogen is branched

3. Cellulose molecule has straight chain and glycogen is coiled

4. 4. glycogen has 1,4- and 1,6- glycosidic bonds and cellulose has only 1,4- glycosidic bonds;

describe how the concentration of a reducing sugar can be measured using a calorimeter

1. using a known concentration of reducing sugar:

   • heat w benedcits solution

   • use same volume of solution each time

   • use an excess of Benedicts

2. solution changes colour to brick red

3. remove precipitate/obtain filtrate

4. calibrate using water/unreacted benedicts

5. use red filter

6. read the transmission/absorbance

   • more transmission/less absorbance = more sugar present

7. obtain calibration curve by plotting transmission/absorbance against reducing sugar concentration

8. use the reading of the unknown sugar solution and read off the graph to find the concentration

how should a procedure to test for reducing sugars be adapted to test for non-reducing sugars

hydrolyse non-reducing sugar w acid

Non-reducing sugar test

• So Benedict’s test: colour stays blue

• Boil with acid then add acid to neutralise

• Heat with Benedict’s solution

• Colour change from blue to red

what does the term electronegativity mean with regards to a water molecule?

oxygen is electronegative and pulls the shared electrons towards it

- the opposite side of the hydrogen becomes 𝛅+

- the opposite side of the oxygen becomes 𝛅-

diagram of water molecules bonded together

properties of water that help organisms survive in a pond

1. water has a high SHC

   • so water buffers changes to temperature

   • lots of energy required to break hydrogen bonds

   • so temperature doesn’t change much

   • can take a lot of heat without changing temperature

2. polar molecule

   • acts a universal solvent

3. Water is a solvent

   • so metabolic reactions can occur

   • water can act as a solvent for ions such as nitrates

4. water is reactive

   • takes places in hydrolysis

5. water is a metabolite in condensation/hydrolysis/photosynthesis/respiration

6. large latent heat of vaporisation

   • it takes a lot of energy to break the hydrogen bonds between the water molecules

   • a lot of energy is used up when water vaporises

   • so provides a cooling effect through evaporation

7. cohesion between water molecules

   • so supports columns of water in plants

   • so produces surface tension, supporting small organisms

   • gives support to large bodies

8. Ice floats

   • ice forms an insulating layer

   • so organisms don’t freeze and so organisms can still swim

9. water expands as it freezes

   • cooling allows max no. of hydrogen bonds to form

     • water molecules space out to allow this

10. water is transparent to light

    • so photosynthesis possible (in shallow waters)

explain how there's a strong cohesion b/w water molecules

water molecules are cohesive because they are polar

how does water help in control of body temperature?

heat energy is removed when water evaporates from the skin

- this lowers the internal temperature

monomer definition

a repeating unit from which larger molecules are made

polymer definition

lots of monomers bonded together

The chemical reactions involved in the conversion of monomers to polymers and polymers to monomers, including examples

a condensation reaction joins monomers together to form polymers and forms a chemical bond and releases water

• e.g. proteins are made from amino acids and are joined together via condensation reactions, forming a peptide bond

a hydrolysis reaction breaks the bond between monomers and uses water

• e.g. starch is made from glucose which are joined by condensation reaction, forming glycosidic bonds

What is the role of ATP?

an immediate energy source for biological processes

structure of ATP

How is ATP made?

Adenine, ribose and 3 phosphates join together by condensation reaction

- catalysed by ATP synthase

How is ATP broken down?

via hydrolysis:

- ATP can be hydrolysed to ADP and Pi (inorganic phosphate)

- catalysed by ATP hydrolase

what happens when ATP is hydrolysed?

a phosphate bond is broken and energy is released

Why is ATP an immediate energy source?

because only 1 bond has to be hydrolysed for energy to be released

give 4 reasons why ATP is suitable as the 'energy currency' of cell.

1. ATP has high energy bonds b/w the phosphate groups

2. only small amounts of energy are released at a time

- so less energy is wasted as heat

3. energy is available quickly due to single-step hydrolysis

4. ATP is readily resynthesised

explain how ATP can transfer energy to different compounds

the inorganic phosphate released during the hydrolysis of ATP can be bonded to different compounds to make them more reactive

- this is known as phosphorylation

explain 5 properties of ATP as an energy source, in comparison to glucose.

1. ATP releases energy in small, manageable amounts so that no energy is wasted

- prevents cells from overheating due to wasted thermal energy

Glucose releases large amounts of energy

- results in lots of wasted energy

2. ATP is a small and soluble molecule that can move around cytoplasm w ease

so it's easily transported around the cell

THIS IS THE SAME FOR GLUCOSE

3. ATP is an immediate energy resource b/c only 1 bond has to be hydrolysed for energy to be released

IN COMPARISON:

several glucose bonds have to be broken down for glucose to release energy

4. ATP can transfer energy to another compound by transferring one of it's phosphate groups

- this is bc ATP can enable phosphorylation

- this makes the compound more reactive

IN COMPARISON:

- glucose cannot do this bc it does not contain phosphate groups

5. ATP can't pass out of the cell, so the cell always has an immediate supply of energy

IN COMPARISON:

glucose can leave the cell via channel and carries proteins

- so a cell can run out of glucose but it can't run out of ATP

Describe how you would test a piece of food for the presence of lipid

• crush and dissolve in alcohol, then add water

• white emulsion would show presence of lipid

explain why triglycerides are not considered to be polymers

not made of monomers

Humans synthesise more than their body mass of ATP each day. Explain why it is necessary for them to synthesise such a large amount of ATP.

• ATP cannot be stored

• ATP only releases a small amount of energy at a time

describe how ATP is made in mitochondria

• ATP produced in krebs cycle

• krebs cycle produces NADH

• electrons released from NADH

• electrons pass through ETC, which releases energy

• ADP + Pi ——→ ATP

• by ATP synthase

Describe the part played by the inner membrane of a mitochondrion in producing ATP

• electrons transferred down ETC

• this provides energy to take protons into the space between the membranes

• protons pass back, through the membrane, into the matrix

• energy used to combine ADP + Pi

compare and contrast the structure and properties of triglycerides and phospholipids

• both contain ester bonds

• both contain glycerol

• the fatty acids on both may be either saturated or unsaturated

• both are insoluble in water

• both contain C,H and O

  • however, phospholipids also contain P

• triglyceride has 3 fatty acids and phospholipids have 2 fatty acids and phosphate group