B1 bio biological molecules

enzymes definition

Enzymes are biological catalysts , it alters the rate of a chemical reaction without undergoing permanent changes themselves

Activation energy

The initial amount of energy to statt rt the reaction

• enzymes work by lowering activation energy

• Or allowing reaction to occur quicker at the lower temp

Enzymes quantities

Tiny, as it retains its specific shape to form EScomplex

Enzyme Structure

• globular protein : specific 3D shape due to sequence of amino acids

• Hydrogen bonds : maintain enzyme shape

• Only active site functional : made form specific sequence of amino acids

Lock and key

1) enzymes have active sites : particular shape

2) the active site is specific to the substrate and is determined by protein stcurture —> order amino acids in polypeptide chains

3) active site is complementary shape to the substrate

4) the substrate fits into the active site : ES complex

Induced fit model

• active site has a general shape which is flexible

• Substrate gets near enzymes active site, it alters slightly to fit the substrate ( inducing a conformational change )

• As it changes shape : puts strains on substrate’s H bonds and distorting them, lowering the activation energy needed to break the bonds

Change in certain amino acids

• enzymes are specific, only 1 substrate fits active sites

• Active site is determined by the tertiary structure = determined by primary structure

• Altering an amino acid : affect hydrogen bonding in protein

• Changes tertiary structure : change active site shape

how temp affect enzyme rate of reaction

1) temp rises increase kinetic energy of molecules : molecules gain more kinetic energy and move more rapidly increasing the number of collision and more ES complex is formed — increasing rate of reaction

2) reaches optimum temp

3) high temp : collision rate too high causing hydrogen bonds in ES complex to break

—> changing specific tertiary structure and active site shape

4) 3D shape no longer held thus enzymes is denatured and no enzymes substrate complexes can be formed : no reaction

How PH affect enzyme

• enzymes have optimum pH

• At optimum pH : conc of H+ in solution gives the tertiary structure of enzyme the best overall shape

HOW damage enzymes :

• altering changes of amino acids that make up active sites

• Causes hydrogen and ionic bonds of the tertiary suture to break

• H+ ions can interfere with ionic bond in the enzymes

Why avoid touching chromatography paper with hand

• finger contains oil and dust that may contain amino acids

• Dissolve in solvents and mixed up with amino acids tested

Precautions for chromatography

1. Ninhydrin : flammable and use in fume cupboard

2. X use same capillary tube for multiple liquids

3. X touch with hand

Affinity

1. Absorption : how well amino acids soak in paper

2. Solubility : how all amino acids dissolve in solvent

High absorption: less movement

High solubility: move further away

Diff solvent in chromatography

Diff RF values as diff solvent diff properties affect how soluble amino acid is

Stationary phase

Paper

Mobile phase

solvent

RF formula

Distance moved by sample / distance move by solvent

— balance between 2 factors : paper liking or solvent liking

Chromatography

1. Pour solvent into talk beaker and cover with watch glass and allow the beaker to be saturated with vapour

2. Horizontal line and vertical lines above paper using pencil to seperate amino acid spots : vertical lines

3. bend paper with ruler and drop solution and put in beaker

4. Solvent reaches top of paper remove and dry

5. When dry spray with ninhydrin and beat for 5 min

Quaternary structure

• some protein ms consist more than 1 polypeptide chains cross held together in a 3D structure

• Polypeptide chains held by same type of forces responsible for tertiary

• Involve additional amino acids services group : prosthetic group ( globular protein )

Difference in tertiary structure cause

• unique sequence of polypeptides

• Aa in diff order

• Bonds formed in diff places

Secondary structure

• alpha helix and beta pleated sheet

• Secondary form as a result of hydrogen binding between diff amino acids in a chain ( CO of carboxyl group and NH of amine / OH of carboxyl)

• Shorter as it folds and coils polypeptide chain

primary structure

• peptide bond formed thru series condensation reaction : polymerisation

• Sequence of amino acids in a polypeptide chains cross held: unique

• The sequence of amino acid ( determined by DNA ) determines proteins ultimate shape thus function

• Change in one and make x function : shape very specific to function

Cause if change : DNA mutation : deletion substitution insertion

Test for protein

• place sample into test tube and add equal volume of biurets solution

• If it’s purple there is a presence of peptide bond

• Peptide bond more : intense colour

Biurets : alkali solution as it contains sodium hydroxide and copper sulfate

Solute solvent solution

• subtance dissolved in solvent

• Liquid medium for substances to dissolve into

• Mixture of solute and solvent

Dipeptide n polypeptide formation

• condensation reaction between x and y

• Loses water which is OH group from carboxyl group of x and H from amine group of y

• Remaining amine and carboxyl group form peptide and covalent bond

Structure of amino acid

Amine group + carboxyl group + H + R group

Function of protein

• structural : long polypeptide chains cross links compounds ( keratin and collagen)

• Enzymes that catalyse biochemical reactions : all are proteins

• Transport : Channel proteins in cell membrane transport substances into the cell

• Signaling : many hormones and receptors

• Immunological ; all antibodies

Proteins properties

• make up long chain of amino acids

• Properties determined by amino acid sequence

• 20 amino acids occur naturally in proteins

Cause if cloudy colour

1. Cloudy colour caused by any lipid droplets dispersed in water as they are insoluble in water

2. Light passing thru refracted by the droplets = cloudiness

Emulsion

Dispersion of droplet of a liquid un another

Control of emulsion

Ethanol and water

Emulsion process

1. 2cm sample and 5 ethanol

2. Shake the tube to dissolve any lipid in sample

3. Add 5 of water and shake

4. White milky lipid present

Formation of glycolipids

1. Combine with carbs within cell surface membrane

2. Carbs tail extends into water environment of cell

3. Recognition and receptor site for specific chemicals

Polar molecules

1. Electrons not equally shared so one part more negative than the other

2. Hydrophilic

Structural relations

1. Polar molecules

2. Formation of glycolipids

Phospholipid structure

One of the fatty acid substitutes by phosphate

Hydrophilic phosphate head

Hydrophobic fatty acids tail

Difference between phos and tri

2 fattty acids

1 fatty acids replaced by phosphate molecules

Similarity of phos and tri

• fatty acid tails and glycerols

• Ester bonds by condensation reaction

Unsaturated

Mono : 1 double cc bond causes a kink ( liquid )

Poly : more than 1 double bond less H and less Lipids

Saturated

Cc single bind

Maximum no of CH bonds in fatty acids

Structural relations of triglycerides

1. High ratio of energy storing CH bonds to C atoms

2. low mass to energy ratio ( energy stored in small volumes )

3. Large and non polar ( insoluble x affect water potential )

4. High ratio of HO atoms ( release water and oxidised improvise important source of water h

How form ester

Hydroxyl group from glycerol and OH from carboxyl group of fatty acids Properties determined lost during condensation reaction as water

Triglycerides structure

3 ester bond

3 fatty acids and a glycerol

Condensation reaction

Protection

Fat around organs

Insulation

Fat is a poor conductor of heat

Retains heat beneath the body surface for a long time

Waterproofing

Fat is soluble in water = waterproofing for fur ( x affect water potential )

Energy storage

long term energy storage as fat twice as much as carbs

Lipid cell membrane

Make membrane flexible and transfer lipid soluble substances across

Role

1. Cell membrane

2. Energy storage

3. Waterproofing

4. Insulation

5. Protection

Characteristics of lipids

1.C H O

2. Proportion of C ; OH is much smaller in carbs

3. Insoluble in H2O

4. Soluble in organic solvents

Monomer

One of the many small molecules that combines to form a larger one

Polymer

Large molecule made up of small repeating units

Isomer

Molecules that have the same molecular formulae but connected to each other in different ways

Monomer and polymer for nucleic acids

Nucleotides ; DNA

Reaction to firm disaccharides / poly

Condensation reaction joins 2 molecules together with the formation of a chemical bond and involves the elimination of a water molecule

Hydrolysis

Breaking down of a chemical bond between 2 molecules involving use of a water molecule

Monosaccharides and disaccharides name

Glucose + glucose = maltose

Glucose + fructose = sucrose

Glucose + galactose = lactose

Glucose isomers and their differences

Alpha glucose and beta

Alpha = H up

Difference = OH H positions flipped at 2 carbon

Name of bond formed by condensation reaction of monosaccharides

1,4 glycosidic bond

Test for reducing sugars

Benedict’s test ( cuso4)

1. equal volumes of Benedict’s reagent

2. Shake and heat for a few minutes at a 95C water bath

3. Precipitate = reducing sugar

Test for non reducing sugars

cannot reduce CUso4 so it is first hydrolysed to monosaccharide

1. Heat sample with excess Benedict’s reagent and gently put in water bath for 5 min

2. Stays blue

3. C reducing sugar present

4. use new sample + heat with dilute hydrochloric acid and neutralise by adding sodium hydrogen carbonate

5. Retest with Benedict’s

6. Brick red = non reducing sugar

Test for starch

Iodine test

Solution turns into blue black

Test in solid

Different colours in Benedict’s test

None : blue

Very low : green

Low : yellow

Medium : brown / orange

High : brick red

It is the result of mixing brick red precipitate with blue

Basic unit of living things

Atoms

Bonding and formation of molecules ways

Covalent ionic hydrogen

Kind of test Benedict’s test is

Semi qualitative

Determine result of experiment by looking at the Color

How to make Benedict’s more quantitative

Create calibration curve using series of known sugar concentration

How to find unknown conc of sugar Sol

Series dilution — equal amounts of Benedict’s

In water bath 5 min

Filter into colourimeter test tubes

Colourimeter low sugar conc

Not all cuso4 reduced to Cuo

Some blue remains

More red light will be absorbed = less transmitted

— higher conc lower absorbance

What happens is don’t filter the Benedict’s

Precipitate will block transmission of red light

Reversing result of colourimeter if not filtered

Starch properties

• Polysaccharides : found in plants : small grain

• Alpha glucose

• Important component of food and major energy source

• Formed by condensation reaction

Adaptations of starch

• insoluble x affect water potential so water cannot be drawn inside cell by osmosis

• Being larger and insoluble x diffuse out of cells

• Compare : unbranded chain : tightly coiled : stored in small spaces

• Hydrolyse to form alpha glucose : easily transported and readily used in respiration

• Highly branched : diff enzymes act on it simultaneously: glucose monomer released rapidly

Glycogen properties

• animals x in plant cells

• Alpha glucose

• shorter chain and more highly branched than starch

• Major carbs storage of animals

• Mass of carbs stored relatively small

Glycogen adaptation

• insoluble : x draw water into cell by osmosis x diffuse out of cells

• compact stored in small spaces

• More highly branched more ends that can be acted on simultaneously by enzymes— rapidly broken down to form glucose

• Animals have higher metabolic rate = respiratory rate increases

Cellulose properties

• Parallel unbranded straight b glucose

• Hydrogen bonds forms cross- linkages between adjacent chains

• Each individual H bond adds little strength — sheer overall no considerable contribution to strengthening

• Valuable structural material

• Cellulose : grouped to form microfibres : parallel group — fibres

Adaptations of cellulose

• Component of cell wall

• Provides rigidity to plant cells

• Prevents cell from bursting as water enters by osmosis

• Exerting inward pressure that stops any further influx of water

Enzyme conc

• enough substrate : increase in enzyme conc proportional increase in rate of reaction

• Limiting substrate — enzyme conc x effect on rate of reaction - rate stabilises graph levels off

Substrate concentration

• lower conc of substrate x all active sites occupied

• Saturation point : all active sites occupied

• All active sites occupied but spare substrate molecules : rate x further increase

Enzyme inhibitors types

Competitive / non competitive

Com inhibitors

• Interferes with active sites of enzyme so substrate x bind

• X EZ complex formed

• change of active site directly

• X permanent

Increase conc of inhibitor - rate of reaction decrease less EZ complex form

Conc of substrate increase

EZ complex’s can form as substrate outcompetes inhibitors increasing rate ( more substrates needed to reach same rate )

Non competitive inhibitors

• inhibitors attaches to a site other than active sites

• Alter shape of active site ( tertiary structure of enzyme changes specific 3D shape )

• Permanent damage

• X ez substrate complexes

Decrease inhibitor conc - less ES complex

Increase conc of substrate - no effect as active site changed alr enzyme cannot bind to it