topic 1

although the variety of life, both past and present is extensive but what is the same

the biochemical basis of life is similar for all living things

what are monomers

smaller units from which larger molecules are made

polymers

polymers are molecules made from a large number of monomers joined together

what are examples of monomers

-monosaccharides

-amino acids

-nucleotides

condensation reaction

a condensation reaction joins two molecules together with the formation of a new chemical bond and involve the elimination of a molecule of water

hydrolysis reaction

breaks a chemical bond between two molecules and involves the use of a water molecule

monosaccharides

are monomers from which larger carbohydrates are made

examples of common monosaccharides

glucose

galactose

fructose

carbohydrates

most are polymers

-they are made of the elements C,H,O

-the monomers they are made from are monosaccharides

condensation reaction

a condensation reaction between two monosaccharides forms a glycosidic bond

disaccharides

are formed by the condensation of two monosaccharides

maltose

maltose is a disaccharide formed by condensation of two glucose molecules

sucrose

is a disaccharide formed by the condensation reaction of a glucose molecule and fructose molecule

lactose

is a disaccharide formed by the condensation of a glucose molecule and galactose moelcule

two isomers of glucose and with structures

(glucose fructose and galactose are isomers meaning same molecular formulae but a different arrangement of atoms in space)

polysaccharides

are formed by the condensation of many glucose monomers

how are glycogen and starch formed

by the condensation of alpha glucose

how is cellulose formed

condensation.of beta glucose

how to test non-reducing sugars

-add acid and boil (acid hydrolysis)

-cool solution and then add alkali to neutralise

-add benedict’s reagant and heat

-a positive test means solution from blue to red (precipitation)

a-glucose

-main substrate for respiration

-the form in which carbonhdyrate is transported in mammalian blood

-forms the polysaccharides starch and glycogen

b-glucose

forms the polysaccharide cellulose

fructose

-found in nectar and many fruits, it is sweeter than glucose and helps to attract animals for polination and fruit dispersal

galactose

with glucose, forms disaccharides lactose

maltose

formed from the breakdown of starch in germinating seeds where it provides energy for the growing embryo

sucrose

forms in which sugars are transported in phloem in plants

lactose

sugar found in milk;energy source for suckling mammals

starch

-monomer

-bond between monomer

-function

-location

-structure

-explanation of how structure leads to function

-formed by the condensation of alpha glucose

-1-4 glycosidic bonds in amylose and 1-4 and 1-6 in amylopectin ( in starch formation molecules of alpha glucose can be synthesised into amylose and amylopectin)

-storage for excess glucose in plants- main carbohydrate in plants

-plant cells

-made of 2 polymers amylose-an unbranched helix of alpha glucose. it gets its helical structure from the bond angles of the glycosidic bonds. amylopectin-a long branched molecule of alpha glucose

-compact due to the helical structure of amylose lots of glucose can be stored in a small space. this can make it an efficient energy store

many branches( in amylopectin) increases number of points where enzymes can attach meaning many glucose monomers can be released rapidly

insoluble= doesnt affect water potential so water isnt drawn into or out of cells by osmosis

cellulose

-monomer

-bond between monomers

-function

-location

-structure

-explanation of how structure leads to function

-beta glucose-made of long unbranched chains of beta glucose. the bonding of beta glucose forms a straight chan

-1-4 glycosidic bonds

-supports and strenghten the cells

-cell wall

-these chains run in parallel to each other and are linked by hydrogen bonds to form microfibrils. many microfibrils are arranged in parallel groups called fibres

-many hydrogen bonds provide collection strength, insoluble-wont affect water potential

glycogen

-monomer

-bond between monomers

-function

-location

-structure

-explanation of how structure leads to function

-alpha glucose

-1-4 and 1-6 glycosidic bonds ( mostly 1-6 glycosidic bonds)

-energy storage in animals (storage in animals) - same structure as amylopectin just more brnaches

-liver and muscle cells

-highly branched molecule

-many branches- increases number of points where enzymes can attach so many glucose monomers can be released rapidly

compact=lots of it can be stored in a small space efficient energy store

why can benedict’s reagent can be used for the presence of reducing sugars

because reducing sugars can donate an electron to the benedict’s reagent - add benedicts solution and heat in a water bath thats been brought to boil for 2 mins and positive result (coloured brick-red precipitate forms)

which are reducing sugars and how to test for them

all monosaccharides and some disaccharides are reducing sugars ( sucrose is non reducing)

-do benedicts test (solution stays blue) then add dilute HCl acid and heat in a water bath thats been brought to boil

-add sodium hydrogen carbonate to neutralise

-repeat benedicts test

positive result -a brick red precipitate

( we need to add the acid at the start to hydrolyse the non reducing sugar into its monosaccharides. only then can these reduce cu2 ions to cu+ ions giving us the brick red precipitate

how to separate a mixture of monosaccharides and identify their compounds

-could use chromotography with known standard solutions

how to test for starch

add iodine dissolved in potassium iodide solution

-solution changes colour from brown-orange to blue/black

how could students identify the unknown concentration of glucose in an unknown substancce

-produce a dilution series of glucose solution and use colorimetric techniques to produce a calibration curve with which to identify the concentration of glucose in an unknown solution

lipids

-non polar and hydrophobic

-contains C,H,O atoms only(and sometimes P and N)

what are the two groups of lipids

triglyceride (main component of fats and oils)

phospolipids (type of lipid molecule that is a major component of cell membranes)

how are triglycerides formed

formed by the condensation of one molecule of glycerol and three molecules of fatty acid

-act mainly as energy stores in plants and animals

-fatty acids have general formula of RCOOH so are carboxylic acids and glycerol is an alcohol (-OH functional group)

condensation reaction between glycerol and a fatty acid (RCOOH) what type of bond does it form

an ester bond

why are lipids insoluble in water

the hydrocarbon tails of fatty acids are hydrophobic making it insoluble

the R-group of a fatty acid can be what

saturated or unsaturated

what is the difference between triglyceride and phospholipid

In phospholipids, one of the fatty acids of a triglyceride is substituted by a phosphate-containing group.

how does triglyecerides structure relates to function

-mainly used as energy storage molecules

insoluble-dont affect water potential which could cause water to move into or out of cells by osmosis which could cause cells to swell burst shrink

-high ratio of energy-storing C-H bonds to carbon atoms and are therefore excellent sources of energy

-low mass to energy ration good storage molecules as much energy can be stored in a small volume

high ration of H to O atoms-release water when oxidised and therefore providing an important source of water especially for organisms living in dry deserts

phospholipid

• a hydrophilic head

• hydrophobic tails

• make up the bilyaer of cell membranes this what can enter and leave the cell

• polar molecules( hydrophobic and hydrophillic ends) forms a bilayer in an aqueous environmentn

-this forms a hydrophobic barrier at the centre of the bilayer so water-soluble substances cannot pass through

• phsopholipid structurea allows to form glycolipids by combining with carbohydrates within the cell surface membrane. glycolipids are important in cell recognition

structure

• A typical phospholipid consists of:

  • one glycerol molecule

  • two fatty acid chains

    • These are non-polar and hydrophobic

  • one phosphate group

    • This is polar and hydrophilic

    • Sometimes attached to an additional polar group (e.g. choline)

• The fatty acids are bonded to glycerol by ester bonds, while the phosphate group is attached to glycerol via a phosphoester bond

The structure of a phospholipid

monolayers and bilayers

• As a result of having hydrophobic and hydrophilic parts, phospholipid molecules form monolayers or bilayers in water

In the presence of water, due to the hydrophobic and hydrophilic parts, phospholipids will form monolayers or bilayers.

Function of phospholipids

• Hydrophobic fatty acid tails create a hydrophobic core when a phospholipid bilayer forms

  • This acts as a barrier to water-soluble molecules

• The hydrophilic phosphate heads form H-bonds with water, allowing the cell membrane to be used to compartmentalise

  • This enables the cells to organise specific roles into organelles, helping with efficiency

• The composition of phospholipids contributes to the fluidity of the cell membrane

  • If there are mainly saturated fatty acid tails, then the membrane will be less fluid

  • If there are mainly unsaturated fatty acid tails, then the membrane will be more fluid

• Phospholipids control membrane protein orientation

  • Weak hydrophobic interactions between the phospholipids and membrane proteins hold the proteins within the membrane but still allow movement within the layer

benefit of carrying out an emulsion test

• The emulsion test can be carried out quickly and easily in a lab to determine if a sample contains lipids

drawback of carrying out an emulsion test

• This test is qualitative so it does not give a quantitative value as to how much lipid may be present in a sample

emulsion test steps

-shake sample with ethanol

filter the liquid into a test tube of water leaving any solids behind

positive result- lipid will precipitate forming a white emulsion

proteins

polymers made from the monomers of amino acids. amino acids contains C H O and N atoms and sometimes S

proteins are essential in cells because they form the following

• Enzymes

• Cell membrane proteins (e.g. carrier)

• Hormones

• Immunoproteins (e.g. immunoglobulins)

• Transport proteins (e.g. haemoglobin)

• Structural proteins (e.g. keratin, collagen)

• Contractile proteins (e.g. myosin)

amino acids

• Amino acids are the monomers of proteins

• There are 20 amino acids found in proteins common to all living organisms

the general structure of an amino acid

how do the twenty amino acids that are common in all organisms differ

The twenty amino acids that are common in all organisms differ only in their side group.

what does a condensation reaction between two amino acids form

a peptide bond

dipeptide

Dipeptides are formed by the condensation of two amino acids

Polypeptides

• Polypeptides are formed by the condensation of many amino acids. The bonds formed between amino acids are called peptide bond s

what may a functional protein may contain

one or more polypeptide

chromotography of amino acids

1. A spot of the unknown amino acid sample mixture is placed on a line at the bottom of the chromatography paper

2. Spots of known standard solutions of different amino acids are then placed on the line beside the unknown sample spot

3. The chromatography paper is then suspended in a solvent

   • Each amino acid will be more or less soluble in the mobile phase than others and will therefore separate, travelling with the solvent at different times/distances from the line, depending on their:

     • charge

     • size

identification of amino acids

• The unknown amino acid(s) can then be identified by comparing and matching them with the chromatograms of the known standard solutions of different amino acids

  • If a spot from the amino acid mixture travels the same distance as a spot from a known standard, it indicates that the mixture contains that amino acid

• To view the spots from the different amino acids, it may be necessary to first dry the chromatography paper and then spray it with ninhydrin solution; this chemical reacts with amino acids, producing an easily visible blue-violet colour

protein structure

• There are four levels of structure in proteins

  • Three are related to a single polypeptide chain

  • The fourth level relates to a protein that has two or more polypeptide chains

• 
  

primary structure of proteins

• The sequence of amino acids bonded by peptide bonds is the primary structure of a protein

• DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence, during translation. This affects the shape and, therefore, the function of the protein

• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

secondary structure

• The secondary structure of a protein is held together by hydrogen bonds that form between the -NH region of one amino acid and the -C=O region of another

  • The hydrogen of -NH has an overall positive charge, while the oxygen of -C=O has an overall negative charge

• Hydrogen bonds are relatively weak, so they can be broken easily by high temperatures and pH changes

• Two shapes can form within proteins due to the hydrogen bonds:

  • α-helix

  • β-pleated sheet

• The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond

• The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other, enabling hydrogen bonds to form between the folded layers

tertiary structure

• Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)

• The additional bonds are:

  • hydrogen bonds between R groups

  • disulfide bonds between cysteine amino acids

  • ionic bonds between charged R groups

  • weak hydrophobic interactions between non-polar R groups

• This structure is common in globular proteins such as enzymes and antibodies

quaternary structure

• Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin

• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

functions of proteins

• Proteins perform a wide range of essential roles in all living organisms due to their diverse structures

• They are therefore vital for structure, transport, communication, defence, movement, and catalysis in all living cells:

  • Enzymes – biological catalysts that speed up metabolic reactions (e.g. amylase, DNA polymerase)

  • Transport proteins – carry substances (e.g. haemoglobin transports oxygen; channel proteins in membranes)

  • Structural proteins – provide support (e.g. collagen in connective tissues; keratin in hair and nails)

  • Hormones – regulate processes (e.g. insulin controls blood glucose levels)

  • Antibodies – part of the immune response, recognising and neutralising pathogens

  • Contractile proteins – enable movement (e.g. actin and myosin in muscles)

disulfide

• Disulfide bonds (also known as disulfide bridges) are strong covalent bonds that form between two cysteine R groups (this is the only amino acid with an available sulfur atom in its R group)

• These bonds are the strongest within a protein, but occur less frequently, and help stabilise the proteins

• They can be broken by reduction

• Disulfide bonds are common in proteins that are secreted from cells e.g. insulin

ionic bonds

• Ionic bonds form between positively charged (amine group -NH₃⁺) and negatively charged (carboxylic acid -COO^-) R groups

• Ionic bonds are stronger than hydrogen bonds, but they are not common

• These bonds are broken by pH changes

hydrogen

• Hydrogen bonds form between strongly polar R groups

• These are the weakest bonds that form, but the most common, as they form between a wide variety of R groups

biochemical test; proteins

a few drops of biuret solution

a blue ring forms at the surface of the solution which disappeares upon shaking and turn lilac purple

this test can be used for enzymes as they are proteins

enzymes

are globular proteins

each enzyme lowers the activation energy of the reaction it catalyses they do that by providing an alternative reaction pathway of lower activation energy

lock and key model for enzymes

the tertiary structure of the enzyme is such that the shape of the enzymes active site is complementary to that of the substrate so the substrate can fit into the enzyme’s active site to form an enzyme-substrate complex

what is the specifity of an enzyme determined by

• The specificity of an enzyme is a result of the complementary nature between the shape of the active site on the enzyme and its substrate(s)

• The active site of an enzyme has a specific shape to fit a specific substrate

  • Extremes of heat or pH can change the shape of the active site, preventing substrate binding – this is called denaturation

the properties of an enzyme related to the tertiaty structure of its active site and its ability to combine with complimentary substrate to form enzyme-substrate complex

• The shape of the active site is determined by the complex tertiary structure of the protein that makes up the enzyme:

  • Proteins are formed from chains of amino acids held together by peptide bonds

  • The order of amino acids determines the shape of an enzyme

  • If the order is altered, the resulting three-dimensional shape changes

induced fit model

in order to completely form an enzyme substrate complext the enzyme and substrate have to alter their shape slightly. this weakens specific bonds in the substrate needing to be broken, which lowers the activation energy required for the reaction to happen increasing the rate of reaction

development of induced fit model

• Scientists often use models to explain their observations from experiments

• As technology and research advances within a field, new models can be developed and old ones disproven

• The lock and key model covered at GCSE was originally thought to be an accurate model of enzyme action

  • It was suggested that the rigid shape of the active site of the enzyme is a precise fit for the specific shape of the substrate

• New techniques have allowed scientists to discover that proteins are not rigid structures

  • Experiments showed that multiple regions of an enzyme molecule moved in response to the environment

  • Many of these movements were minimal, but some of them were more significant

  • The larger movements occurred when the substrate bound to the enzyme

• These findings led to the now widely accepted induced fit model

• There is evidence to support the induced fit model:

  • X-ray diffraction techniques allow for 3D pictures of molecules to be formed

  • This technique was used to produce pictures of the enzyme hexokinase before and after it bound to its substrate glucose

  • The images confirmed that the active site of the enzyme changed shape after the substrate bound

the effect of temperature

as the temperature increases the rate of reaction increases

this is because enzyme and substrate molecules have more kinetic energy so frequency of collisions between these molecules increases so more enzyme-substrate complexes are formed per unit time

however after optimum temperature the rate begins to decrease. this is because the rise in temperature causes hydrogen and ionic bonds (which holds the enzymes tertiary structure in place to break altering the tertiary structure of the enzyme changing the shape of the active site too

after a certain temperature the shape of the active site is no longer complementary to that of the substrate. the enzyme is said to be denatured

the effect of ph

as you move away from the optimum pH rate of reaction begins to decrease

this is because the change in concentration of H plus and OH minus ions interferes with hydrogen and ionic bonds that hold the enzyme’s tertiary structure in place, altering the shape of the active site too

if Ph deviates too far from the optimum ph the shape of the active site is changed too much that it is no longer complementary to that of the susbtrate. the enzyme is said to be denatured

the effect of enzyme concentration

the more enzymes that are in a solution the more likely a substrate molecule is to collide with one to form an ES complex

af first enzyme conc is directly proportional to rate of reaction

however, after a certain point the amount of substrate becomes limiting so increasing the enzyme concentration has no further efect on increasing the rate of reaction so rate levels off and remains constant

effect of substrate concentration

the more substrate there is in a solution the more likely an enzyme is to collide with one and form an enzyme substrate complex

at first substrate concentration is directly proportional to rate of reaction

however after a certain point the amount of enzymes becomes limiting because all active sites are occupied and therefore increasing the substrate concentration will have no further effect on increasing the rate pf reaction the rate levels off and remains constant

competitive inhibitors

are molecules that have a similar shape to that of the enzymes normal substrate=they can ft into the enzyme’s active site to form an enzyme-inhibitor complex. this prevents substrate molecules from b inding to the active site

competitive inhibitors compete with substrate molecules for available active sites. the difference in concentrations of the inhibitor and substrate molecules determines how many enzymes are inhibited

-the higher the concentration of competitive inhibitor the lower the rate of reaction because there is more competition for available active sites so fewer es complexses formed

non competitive inhibitors

work by binding to enzymes in a place other than the active site. this changes the tertiary structure of the enzyme altering the shape of the active site too meaning that it is no longer complementary to that of the substrate. substrate molecules can therefore no longer bind to the active site

-they are often foreign to the body and toxic. this is an irreversible reaction and the active site shape is changed forever

-rate of reaction is decreased as non competitive inhibitors reduce the number of functional enzymes available. substrate and inhibitor do not compete for the active site so increasing the substrate concentration has no influence on the effect of the inhibior

DNA

Deoxyribonucleic acid

holds genetic information in all living cells

RNA

ribonucleic acid

transfers genetic information from DNA to ribosomes

similarities of DNA and RNA

polynucleotides

-phosphate group

pentose sugar

nitrogenous containing organic base (2:02)

how to do nucleotides be joined together

nucleotides themselves can be joined togethere by a condensation reaction between a phosphate group of one nucleotide and the pentose sugar of another

this forms phosphodiester bond between twoo nucleotides which consissts of one phosphate group and two ester bonds

structure of dna

• two DNA polynucleotide strands which are joined together by H bonds between complementary base pairs

• complementary means specific base pair with each other

• Adenine (A) complementary Thymine (T) two hydrogen bonds form between these bases

• Cytosine is complementary with Guanine 3 hydrogen bonds

• due to the complementary base pairing the quantity of A is same as T and the wuantity of C is the same as G

• the two DNA strands are antiparallel=they run in opposite directions (one strand runs in the 5’ to 3’ direction and whilst the other runs in the 3’ to 5’ direction

why did scientists at first doubt the DNA could carry the genetic code

because it had a simple chemical composition

-some argued that genetic information must be carried by proteins which are chemical varied. however in 1953 experiments showed that dna was the true carrier of the genetic code

how does DNA structure relate to function

The two DNA polynucleotide strands are only joined together by relatively weak H bonds meaning that the strands can sepearate during DNA replication

base pairs are protected from being corrupted by being within the helical cylinder of the sugar-phosphate backbone

very large molecule so can carry lots of genetic information

RNA

much shorter than DNA

made from. single polynucleotide chain

3 main types of RNA that we need to know about:

-mRNA =transfers genetc information from DNA to ribosomes

tRNA=involved in protein synthesis

rRNA =make up part of the ribsome structure