3 - Biological Molecules

Front 1

one positive inorganic ion important in human metabolism

Back 1

K *high +* --> potassium

Front 2

one negative inorganic ion available to plant roots in the soil

Back 2

NO *mini 3-* --> nitrate

Front 3

state one functional difference between lipids and carbs

Back 3

lipids are used for thermal insulation while carbs are used for cell walls and short term energy store

Front 4

what food could a positive result on a non-reducing sugar test be?

Back 4

ripe banana

Front 5

what food could a positive result on a non-reducing sugar test be?

Back 5

ripe banana

Front 6

what food could a negative result on a non-reducing sugar test be?

Back 6

potato flour

Front 7

what food could a positive result on a reducing sugar test be?

Back 7

ripe banana

Front 8

what food could a positive result on a emulsion test be?

Back 8

olive oil

Front 9

what food could a positive result on a biuret test be?

Back 9

egg whites

Front 10

what is a macromolecule of the monomer beta glucose

Back 10

cellulose

Front 11

what is a monomer of the macromolecule triglyceride lipid?

Back 11

fatty acids and glycerol

Front 12

which bonds occur in primary structure but not secondary?

Back 12

hydrogen

Front 13

which bonds occur in primary structure?

Back 13

peptide and a sequence of amino acids

Front 14

state what structural detail of a polypeptide is altered by gene mutations

Back 14

sequence of amino acids

Front 15

explain how pairing of nitrogenous bases allows identical copies of DNA to be made

Back 15

A and T with 2 hydrogen bonds and C and G with 3 hydrogen bonds. a purine and pyrimidine have to go together because they are different sizes.

Front 16

which nucleotide bases are common to DNA and RNA

Back 16

A, C and G

Front 17

name the bond that joins the units in a molecule of sucrose

Back 17

glycosidic bond.

Front 18

what % of humans are water?

Back 18

70%

Front 19

glucose general formula

Back 19

CnH2nOn

Front 20

Hydrolysis recation of glucose

Back 20

C12H22O11 + H2O --> O6H12O6 + O6H12O6

Front 21

Pentoses and hexoses – sugars of DNA

Back 21

pentose monosaccharides contain five carbon atoms and form a ring. Hexose monosaccharides have six carbon atoms. Ribose and deoxyribose and important constitutes of RNA and DNA.

Front 22

what monosaccharides make up the dissaccharide lactose

Back 22

glucose + galactose

Front 23

Reduction

Back 23

a reaction involving the gain of electrons. All monosaccharides and some disaccharides are reducing sugars. This means they can donate electrons, or reduce another molecule or chemical.

Front 24

Hydrolysis reactions

Back 24

are used to break polysaccharides and disaccharides into monosaccharides. Hydrolysis reactionsare the opposite to condensation reactions.

Front 25

What type of reactions join monosaccharides?

Back 25

condensation

Front 26

State the reaction that breaks down maltose?

Back 26

hydrolysis

Front 27

Passive

Back 27

no energy needed – particles from higher to lower concentration gradient – osmosis and simple and facilitated diffusion (facilitated doesn’t need energy but requires help by carrier proteins and membrane structures).

Front 28

Equilibrium

Back 28

molecules or ions evenly spread out within a given space or volume. It doesn’t mean the particles stop moving, just that the movements are equal in both directions.

Front 29

Net movement

Back 29

overall movement

Front 30

Helixcase in DNA replication

Back 30

break down hydrogen bonds holding the bases together.

Front 31

DNA polymerase in DNA replication

Back 31

joins the free nucleotide.

Front 32

Semi conservative replication- DNA replication

Back 32

where one strand is old and the other is new.

Front 33

Suggest how changing the sequence of DNA nucleotides could affect the final product the DNA codes for

Back 33

different folding, different proteins created

Front 34

Conjugated proteins

Back 34

globular proteins that contain a non-protein component called a prosthetic group. There are different types of prosthetic groups. Lipids or carbs can combine with proteins forming lipoproteins or glycoproteins. Metal ions and molecules derived from vitamins also form prosthetic groups. Haem groups are examples of prosthetic groups. They contain an Iron II ion (Fe2+). Catalase and haemoglobin both contain haem groups.

Front 35

Simple proteins

Back 35

proteins without a prosthetic group.

Front 36

Differences between RNA and DNA nucleotides

Back 36

in RNA the pentose sugar is ribose rather than deoxyribose and thymine base is replaced with uracil (a pyrimidine that forms two hydrogen bonds with adenine).

Front 37

Similarities between RNA and DNA nucleotides

Back 37

both form polymers by the formation of phosphodiester bonds in condensation reactions.

Front 38

Energy in the form of ATP is required for....

Back 38

movement of cells along the cytoskeleton, changing the shape of cells to engulf materials and the fusion of cell membranes as vesicles form or as they meet the cell surface membrane.

Front 39

To prevent cytoltsis and crenation, multicellular animals usually......

Back 39

have control mechanisms to make sure their cells are continuously surrounded by aqueous solutions with an equal water potential. In blood the aqueous solution is blood plasma.

Front 40

what is the shape of a fibrous protein?

Back 40

Long and narrow with little to no tertiary structure

Front 41

what is the shape of a globular protein?

Back 41

round/spherical

Front 42

what is the amino acid sequencing of a fibrous protein?

Back 42

repetitive amino acid sequences

Front 43

what is the amino acid sequencing of a globular protein?

Back 43

Irregular amino acid sequances

Front 44

examples of fibrous proteins

Back 44

collagen, myosin, fibrin, actin and keratin

Front 45

examples of globular proteins

Back 45

enzymes, haemoglobin, insulin

Front 46

Solubility of fibrous proteins

Back 46

insoluble in water

Front 47

Solubility of globular proteins

Back 47

soluble in water

Front 48

atomic number

Back 48

amount of protons, neutrons and electrons

Front 49

atomic number of carbon atom

Back 49

6

Front 50

mass number of carbon

Back 50

12

Front 51

atomic number in an oxygen atom

Back 51

8

Front 52

mass number of oxygen

Back 52

16

Front 53

how many bonds can carbon atoms form with other atoms

Back 53

4

Front 54

how many bonds can nitrogen atoms form with other atoms

Back 54

3

Front 55

how many bonds can oxygen atoms form with other atoms

Back 55

2

Front 56

how many bonds can hydrogen atoms form with other atoms

Back 56

1

Front 57

what elements are in lipids

Back 57

C, H and O

Front 58

what elements are in proteins

Back 58

C, H, O, N, and S

Front 59

what elements are in nucleic acids

Back 59

C, O, H, N, P

Front 60

mRNA in transcription

Back 60

single stranded not double stranded, contains ribose instead of deoxyribose, contains uracil instead of thymine, small enough to leave the nuclear pores, easily broken down, only exists whilst it is needed to manufacture a protein.

Front 61

Transcription

Back 61

proteins synthesis occurs in the cytoplasm at ribosomes but a chromosomal DNA molecules is too large to leave the nucleus to supply the coding information needed to determine the proteins amino acid sequence. To get around this problem, the base sequences of genes have to be copied and transported to the site of protein synthesis, a ribosome. Shorter molecules of RNA are made to get through the nucleus, DNA to RNA.

Front 62

Similarities between transcription and DNA replication

Back 62

start at a start codon, DNA unwinds and unzips under the control of DNA helicase (hydrogen bonds at the bases).

Front 63

Differences between transcription and DNA replication

Back 63

in transcription only one of the strands (the antisense strand) is used as a template, whereas on DNA, both strands are used; in transcription thymine is replaced with uracil.

Front 64

Transcription sense and anti-sense strands

Back 64

only one of the two strands of DNA contains the code for the protein to be synthesised. This is the sense strand, and it runs from 5’ to 3’. The other strand, 3’ to 5’, is a complimentary copy of the sense strand and does not code for a protein. This is the antisense strand, and it acts as a template strand during transcription, so that the complementary RNA strand formed carries the same base sequence as the sense strand.

Front 65

Transcription steps: DNA molecule unwinds and unzips by DNA helicase

Back 65

hydrogen bonds broken at the bases, exposed base pairs, beginning at a start codon. RNA polymerases join the base pairs with their complementary bases exposed on the antisense strands. Thymine in RNA is replaced with the base uracil. Phosphodiester bonds are formed between the RNA nucleotides by the enzyme RNA polymerase. Stops at the end of the gene and the completed short strand of RNA is called messenger RNA. It is the same base sequence as the bases making up the gene on the DNA, except uracil replaces thymine. mRNA detaches from the DNA template and leaves through the nucleus, through the nuclear pore (DNA double helix reforms), mRNA molecule travels to a ribosome in the cell cytoplasm for the next step in protein synthesis.

Front 66

rRNA translation

Back 66

ribosomes are made up of two subunits, one large and one small. These subunits are composed of almost equal amounts of protein and a form of RNA known as ribosomal RNA. It is important in maintaining the structural stability of the protein synthesis sequence and plays a biochemical role in catalysing the reaction.

Front 67

mRNA translation

Back 67

after leaving the nucleus, the mRNA binds to a specific site on the small subunit of a ribosome which holds the mRNA in position while it is decoded, or translated, into a sequence of amino acids. This process is called translation.

Front 68

tRNA translation

Back 68

another form of RNA that is necessary for the translation of RNA. It is composed of a strand of RNA folded in such a way that three bases, called the anticodon will bind to a complementary codon on mRNA following the normal base pairing rules. The tRNA molecules carry an amino acid corresponding to that codon. When the tRNA binds to complementary codon along the mRNA the amino acids are brought together in the correct sequence to form the primary structure of the protein coded for by the mRNA. This cannot happen all at once. Instead, amino acids are added one at a time and the polypeptide chain (protein) grows as this happens.

Front 69

Ribosomes in translation

Back 69

act as the binding site for mRNA and tRNA and catalyse the assembly of the protein

Front 70

Steps of translation

Back 70

the mRNA binds to the small subunit of the ribosome at its start codon (AUG) a tRNA with the complementary anticodon (UAC) binds to the mRNA start codon. This tRNA carries amino acid methionine. Another tRNA with the anticodon UGC and carrying the corresponding amino acid, threonine, then binds to the next codon on the mRNA. A maximum of three tRNAs can be bound at the same time. The first amino acid methionine is transferred to the amino acids threonine on the second tRNA by the formation of a peptide bond, this is catalysed by the enzyme peptidyl transferase, which is a tRNA component of this ribosome. The ribosome then moves along the mRNA, releasing the first tRNA. The second tRNA becomes the first. Stages 3-5 are completed with another amino acid added to the chain each time. This process continues until the ribosome reaches the end of the mRNA at a stop codon and the polypeptide is released. The amino acids are joined together forming the primary, secondary and then tertiary structures of the protein. The folding and bonds are determined by the sequence of the amino acids in the primary structure. The protein may be modified in the Golgi apparatus before it is fully functional and ready to carry out its specific role for which it has been synthesised. Multiple identical polypeptides can be synthesised simultaneously.

Front 71

Why do cells require energy

Back 71

synthesis, transport, and movement e.g., muscle contraction, cell division, the transmission of nerve impulses, and even memory formation.

Front 72

Forms of energy

Back 72

Energy comes in many forms, such as heat, light, and the energy in chemical bonds. Energy has to be supplied in the right form and quantity to the processes that require it.

Front 73

Three main types of activity cells require energy for

Back 73

synthesis - for example of large molecules such as proteins transport - for example pumping molecules or ions across cell membranes by active transport movement - for example protein fibres in muscle cells that cause muscle contraction.

Front 74

Structure of ATP

Back 74

in cells, molecules of adenosine triphosphate (ATP) are able to supply energy in such a way that it can be used. An ATP molecule is composed of a nitrogenous base, a pentose sugar and three phosphate groups- it is a nucleotide. You will notice that the structure of ATP is very similar to that of the nucleotides involved in the structure of DNA and RNA. However, in ATP the base is always adenine and there are three phosphate groups instead of one. The sugar in ATP is ribose, as in RNA nucleotides.

Front 75

ATP as a universal energy currency

Back 75

ATP is used for energy transfer in all cells of all living things. Hence it is known as the universal energy currency.

Front 76

How ATP releases energy

Back 76

Energy is needed to break bonds and is released when bonds are formed. A small amount of energy is needed to break the relatively weak bond holding the last phosphate group in ATP. However, a large amount of energy is then released when the liberated phosphate undergoes other reactions involving bond formation. Overall, a lot more energy is released than used, approximately 30.6kJ mol.

Front 77

Hydrolysis of ATP

Back 77

As water is involved in the removal of the phosphate group this is another example of a hydrolysis reaction. The hydrolysis of ATP does not happen in isolation but in association with energy-requiring reactions. The reactions are said to be coupled' as they happen simultaneously. ATP is hydrolysed into adenosine diphosphate (ADP) and a phosphate ion, releasing energy.

Front 78

Instability of ATP

Back 78

The instability of the phosphate bonds in ATP, however, means that it is not a good long-term energy store. Fats and carbohydrates are much better for this. The energy released in the breakdown of these molecules (a process called cellular respiration) is used to create ATP. This occurs by reattaching a phosphate group to an ADP molecule. The process is called phosphorylation. As water is removed in this process, the reaction is another example of a condensation reaction.

Front 79

Three biological processes which require energy

Back 79

muscle contraction, cell division and transmission of nerve impulses

Front 80

Why ATP is a good immediate energy store

Back 80

Due to the instability of ATP, cells do not store large amounts of it. However, ATP is rapidly reformed by the phosphorylation of ADP. This interconversion of ATP and ADP is happening constantly in all living cells, meaning cells do not need a large store of ATP. ATP is therefore a good immediate energy store.

Front 81

Properties of ATP

Back 81

The structure and properties of ATP mean that it is ideally suited to carry out its function in energy transfer: Small - moves easily into, out of and within cells. Water soluble - energy-requiring processes happen in aqueous environments. Contains bonds between phosphates with intermediate energy: large enough to be useful for cellular reactions but not so large that energy is wasted as heat. Releases energy in small quantities- quantities are suitable to most cellular needs, so that energy is not wasted as heat. Easily regenerated - can be recharged with energy.

Front 82

Nucleotides and nucleic acids

Back 82

Nucleic acids are large molecules that were discovered in cell nuclei - hence their name. There are two types of nucleic acid – DNA and RNA, and both have roles in the storage and transfer of genetic information and the synthesis of polypeptides (proteins). They are the basis for heredity. Nucleic acids contain the elements carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are large polymers formed from many nucleotides (the monomers) linked together in a chain.

Front 83

An individual nucleotide is made up of three components

Back 83

a pentose monosaccharide (sugar), containing five carbon atoms a phosphate group, -PO,, an inorganic molecule that is acidic and negatively charged a nitrogenous base a complex organic molecule containing one or two carbon rings in its structure as well as nitrogen.

Front 84

Bonding of nucleic acids

Back 84

Nucleotides are linked together by condensation reactions to form a polymer called a polynucleotide. The phosphate group at the fifth carbon of the pentose sugar (5) of one nucleotide forms a covalent bond with the hydroxyl (OH) group at the third carbon (3) of the pentose sugar of an adjacent nucleotide. These bonds are called phosphodiester bonds. This forms a long. strong sugar-phosphate backbone' with a base attached to each sugar. The phosphodiester bonds are broken by hydrolysis, the reverse of condensation, releasing the individual nucleotides.

Front 85

Deoxyribonucleic acid (DNA)

Back 85

As the name suggests, the sugar in deoxyribonucleic acid (DNA) is deoxyribose - a sugar with one fewer oxygen atoms than ribose.

Front 86

Nucleotide bases

Back 86

The nucleotides in DNA each have one of four different bases. This means there are four different DNA nucleotides. The four bases can be divided into two groups: Pyrimidines - the smaller bases, which contain single carbon ring structures - thymine (T) and cytosine (C) Purines - the larger bases, which contain double carbon ring structures - adenine (A) and guanine (G).

Front 87

The double helix

Back 87

The DNA molecule varies in length from a few nucleotides to millions of nucleotides. It is made up of two strands of polynucleotides coiled into a helix, known as the DNA double helix. The two strands of the double helix are held together by hydrogen bonds between the bases, much like the rungs of a ladder. Each strand has a phosphate group (5') at one end and a hydroxyl group (3’) at the other end. The two parallel strands are arranged so that they run in opposite directions – they are said to be antiparallel.

Front 88

Base pairing rules

Back 88

The pairing between the bases allows DNA to be copied and transcribed - key properties required of the molecule of heredity. The bases bind in a very specific way. Adenine and thymine are both able to form wo hydrogen bonds and always join with each other. Cytosine and guanine form three hydrogen bonds and so also only bind to each other. This is known as complementary base pairing. These rules mean that a small pyrimidine base always binds to a larger purine base. This arrangement maintains a constant distance between the DNA backbones', resulting in parallel polynucleotide chains. Complementary base pairing means that DNA always has equal amounts of adenine and thymine and equal amounts of cytosine and guanine. It is the sequence of bases along a DNA strand that carries the genetic information of an organism in the form of a code.

Front 89

RNA

Back 89

Ribonucleic acid (RNA) plays an essential role in the transfer of genetic information from DNA to the proteins that make up the enzymes and tissues of the body. DNA stores all of the genetic information needed by an organism, which is passed on from generation to generation. However, the DNA of each eukaryotic chromosome is a very long molecule, comprising many hundreds of genes, and is unable to leave the nucleus in order to supply the information directly to the sites of protein synthesis.

Front 90

How DNA is able to leave the nucleus

Back 90

To get around this problem, the relatively short section of the long DNA molecule corresponding to a single gene is transcribed into a similarly short messenger RNA (mRNA) molecule. Each individual mRNA is therefore much shorter than the whole chromosome of DNA. It is a polymer composed of many nucleotide monomers. RNA nucleotides are different to DNA nucleotides as the pentose sugar is ribose rather than deoxyribose and the thymine base is replaced with the base uracil (U). Like thymine, uracil is a pyrimidine that forms two hydrogen bonds with adenine. Therefore, the base pairing rules still apply when RNA nucleotides bind to DNA to make copies of particular sections of DNA. The RNA nucleotides form polymers in the same way as DNA nucleotides - by the formation of phosphodiester bonds in condensation reactions. The RNA polymers formed are small enough to leave the nucleus and travel to the ribosomes, where they are central in the process of protein synthesis. After protein synthesis the RNA molecules are degraded in the cytoplasm. The phosphodiester bonds are hydrolysed, and the RNA nucleotides are released and reused.

Front 91

DNA extraction from plant material

Back 91

Grind sample in a mortar and pestle - this breaks down the cell walls. Mix sample with detergent-this breaks down the cell membrane, releasing the cel contents into solution Add salt -this breaks the hydrogen bonds between the DNA and water molecules. Add protease enzyme - this will break down the proteins associated with the DNA in the nuclei. Add a layer of alcohol (ethanol) on top of the sample - alcohol causes the DNA to precipitate out of solution. The DNA will be seen as white strands forming between the layer of sample and layer of alcohol. The DNA can be picked up by 'spoiling' it onto a glass rod.

Front 92

Why does DNA need to replicate?

Back 92

cell division, new cells need new DNA for growth and tissue repair; reproduction, gametes require DNA to pass on genetic information

Front 93

Continuous and discontinuous replication

Back 93

continuous replication is where polymerase joins the free nucleotides without stopping until the end, while discontinuous does sections at a time.

Front 94

Helicase

Back 94

break down hydrogen bonds holding the bases together during DNA replication.

Front 95

DNA polymerase

Back 95

joins the free nucleotides during DNA replication.

Front 96

Semi-conservative replication

Back 96

where one strand is old, and the other is new.

Front 97

State how many different types of nucleotide are found in DNA and name components of one of these nucleotides

Back 97

4 and a base, a phosphate, and a pentose monosaccharide

Front 98

Suggest hoe changing the sequence of DNA nucleotides could affect the final product the DNA codes for

Back 98

different folding, different proteins created.

Front 99

State what genes code for

Back 99

a sequence of amino acid

Front 100

Summary of DNA replication

Back 100

DNA polymerase always moves along the template strand in the same direction. It can only bind to the 3 ends, so travels in the direction of 3’ to 5’. As DNA only unwinds and unzips in one direction, DNA polymerase has to replicate each of the template strands in opposite directions. The strand that is unzipped from the 3 end can be continuously replicated as the strands unzip. This strand is called the leading strand and is said to undergo continuous replication. The other strand is unzipped from the 5’ end, so DNA polymerase has to wait until a section of the strand has unzipped and then work back along the strand. This results in DNA being produced in sections, which then have to be joined. This strand is called the lagging strand and is said to undergo discontinuous replication.

Front 101

Step by step process of DNA replication

Back 101

Gyrase enzymes unwind the DNA and DNA helicase enzyme unzips separating into two parts by breaking the hydrogen bonds holding the bases together Free nucleotides from the cytoplasm match up with their complementary base pairs which have been exposed (template strand) as the strands separate. Hydrogen bonds are formed between them, and DNA polymerase joins the free nucleotides through strong covalent phosphodiester bonds, forming the phosphate-sugar backbone. All of the bonds from a complete polynucleotide chain. This process results in two DNA molecules, each with one new synthesised strand of DNA and one strand from the original (semi-conservative).

Front 102

Replication error/mutations

Back 102

sequences of bases are not always matched exactly, and an incorrect sequence may occur in the newly copied strand. These errors occur randomly and spontaneously and lead to a change in the sequence bases, known as mutation.

Front 103

Genetic code

Back 103

DNA codes for a sequence of amino acids

Front 104

Triplet code

Back 104

the instructions the DNA carries are contained in the sequence of bases along the chains of nucleotides that make up the strand of DNA. The code in the bases sequence is a simple triplet code. It is a sequence of three bases called a codon. Each codon codes for an amino acid. A section of DNA that contains the complete sequence of bases to code for an entire protein called a gene. The genetic code is universal – all organisms use this same code, although the sequence will be different for each individual protein.

Front 105

Degenerate code

Back 105

there are four different bases which means 64 different base triplets or codons are possible 4^3 (4 bases and a codon is 3 bases).

Front 106

Start codon

Back 106

comes at the beginning of the gene, signalling the start of a sequence that codes for a protein. If it is in the middle of the gene, it codes for the amino acid methionine. Having a single codon to signal the start of a sequence ensures codons are read ‘in frame’, read from base 1 not 2 or 3 etc, so that the genetic code is non-overlapping.

Front 107

Degenerate

Back 107

there are only 20 different amino acids that regularly occur in biological proteins, so there are a lot more codons than amino acids. Therefore, many amino acids can be coded for by more than one codon. Due to this, the code is known as degenerate.

Front 108

Stop codons

Back 108

there are 3 stop codons that do not code for any amino acids and signal the end of a sequence.

Front 109

Meselson and Stahl (1958)

Back 109

proved the semi-conservative hypothesis to be the true mechanism of DNA replication. They grew the bacteria Escherichia coli with different isotopes of nitrogen. The bacteria was exposed to M15 for several generations until it was exposed to a lighter N14. Scientists could then distinguish between the different DNA densities by centrifying them. They knew all the bases in DNA contain nitrogen; nitrogen has two forms: light (14N) and heavy isotope (15N); bacteria will incorporate nitrogen from their growing medium into any new DNA they make.

Front 110

Similarities between DNA replication and transcription

Back 110

nucleotides line up along an exposed DNA strand, A tRNA triplet pairs with an exposed codon, adjacent nucleotides bond- forming a sugar – phosphate backbone

Front 111

Differences between DNA replication and transcription

Back 111

with DNA replication the whole of the double helix ‘unzips’ – in transcription is does not. In transcription uracil pairs with adenine, but in DNA replication adenine pairs with thymine.

Front 112

Proving DNA replication is semi-conservative

Back 112

the 15N strand is heavy so makes a band low down the tube. High density (heavy) sinks further down the tube. Afte 1 generation there was only 1 band – this was the 14/15 hybrid. After another generation there were two bands – a light chain and a 14/15 level.

Front 113

Roles of proteins

Back 113

transport across membranes, metabolic reactions (enzymes), structural support, transport in the blood and immunity.

Front 114

Proteins

Back 114

Peptides are polymers made up of amino acid molecules (the monomers). Proteins consist of one or more polypeptides arranged as complex macromolecules and they have specific biological functions. All proteins contain the elements carbon, hydrogen, oxygen, and nitrogen.

Front 115

Amino acids

Back 115

All amino acids have the same basic structure. Different R-groups (variable groups) result in different amino acids. Twenty different amino acids are commonly found in cells. Five of these are said to be non-essential as our bodies are able to make them from other amino acids. Nine are essential and can only be obtained from what we eat. A further six are said to be conditionally essential as they are only needed by infants and growing children.

Front 116

Synthesis of peptides

Back 116

Amino acids join when the amine and carboxylic acid groups connected to the central carbon atoms react. The R-groups are not involved at this point. The hydroxyl in the carboxylic acid group of one amino acid reacts with a hydrogen in the amine group of another amino acid. A peptide bond is formed between the amino acids and water is produced. The resulting compound is a dipeptide. When many amino acids are joined together by peptide bonds a polypeptide is formed. This reaction is catalysed by the peptidyl transferase present in ribosomes, the sites of protein synthesis. The different R-groups of the amino acids making up a protein are able to interact with each other (R-group interactions) forming different types of bond. These bonds lead to the long chains of amino acids (polypeptides) folding into complex structures (proteins).

Front 117

Different sequences of amino acids

Back 117

The presence of different sequences of amino acids leads to different structures with different shapes being produced. The very specific shapes of proteins are vital for the many functions proteins have within living organisms.

Front 118

Thin layer chromatography

Back 118

thin layer chromatography (TLC] is a technique used to separate the individual components of a mixture. The technique can be used to separate and identify a mixture of amino acids in solution. There are two phases, the stationary phase and the mobile phase which involves an organic solvent.

Front 119

Mobile and stationary phases of chromatography

Back 119

The mobile phase picks up the acids and moves through the stationary phase and the amino acids are separated. In the stationary phase a thin layer of silica gel (or another adhesive substance) is applied toa rigid surface, for example a sheet of glass or metal. Amino acids are then added to one end of the gel. This end is then submerged in organic solvent. The organic solvent then moves through the silica gel, this is known as the mobile phase. The rate at which the different amino acids in the organic solvent move through the silica gel depends on the interactions (hydrogen bonds) they have with the silica in the stationary phase, and their solubility in the mobile phase. This results in different amino acids moving different distances in the same time period resulting in them separating out from each other.

Front 120

Procedure of separating and identifying amino acids in solution

Back 120

Remember, when working with chemicals to take care, wear safety glasses and report any spillages/ breakages to the teacher: Wearing gloves, the student drew a pencil line on the chromatography plate about 2 cm from the bottom edge. The plate was only handled by the edges. Four equally spaced points were marked at along the pencil line. The amino acid solution was spotted onto the first pencil mark using a capillary tube. The spot was allowed to dry and then spotted again. The spot was labelled using a pencil. The three remaining marks were spotted with solutions of three known amino acids. The plate was then placed into a jar containing the solvent. The solvent was no more than 1 cm deep. The jar was then closed. The plate was left in the solvent until it had reached about 2 cm from the top. The plate was then removed, and a pencil line drawn along the solvent front. The plate was then allowed to dry. The plate was then sprayed, in a fume cupboard, with ninhydrin spray. Amino acids react with ninhydrin and a purple/brown colour is produced. The centre of each spot present was then marked with a pencil.

Front 121

Rf

Back 121

distance travelled by component/distance travelled by solvent

Front 122

Primary structure

Back 122

this is the sequence in which the amino acids are joined. It is directed by information carried within DNA. The particular amino acids in the sequence will influence how the polypeptide folds to give the protein's final shape. This in turn determines its function. The only bonds involved in the primary structure of a protein are peptide bonds.

Front 123

Secondary structure

Back 123

the oxygen, hydrogen, and nitrogen atoms of the basic, repeating structure of the amino acids (the variable groups are not involved at this stage) interact. Hydrogen bonds may form within the amino acid chain, pulling it into a coil shape called an alpha helix. Polypeptide chains can also lie parallel to one another joined by hydrogen bonds, forming sheet-like structures. The pattern formed by the individual amino acids causes the structure to appear pleated, hence the name beta pleated sheet. Secondary structure is the result of hydrogen bonds and forms at regions along long protein molecules depending on the amino sequences.

Front 124

Tertiary structure

Back 124

this is the folding of a protein into its final shape. It often includes sections of secondary structure. The coiling or folding of sections of proteins into their secondary structures brings R-groups of different amino acids closer together so they are close enough to interact and further folding of these sections will occur.

Front 125

Interactions which occur between the R-groups in tertiary structure

Back 125

hydrophobic and hydrophilic interactions - weak interactions between polar and non-polar R-groups hydrogen bonds - these are weakest of the bonds formed ionic bonds - these are stronger than hydrogen bonds and form between oppositely charged R-groups disulfide bonds (also known as disulfide bridges) these are covalent and the strongest of the bonds but only form between R-groups that contain sulfur atoms. This produces a variety of complex-shaped proteins, with specialised characteristics and functions.

Front 126

Quaternary structure

Back 126

this results from the association of two or more individual proteins called subunits. The interactions between the subunits are the same as in the tertiary structure except that they are between different protein molecules rather than within one molecule. The protein subunits can be identical or different. Enzymes often consist of two identical subunits whereas insulin (a hormone) has two different subunits. E.g., Haemoglobin, a protein required for oxygen transport in the blood, has four subunits, made up of two sets of two identical subunits.

Front 127

Hydrophilic and hydrophobic interactions in proteins

Back 127

Proteins are assembled in the aqueous environment of the cytoplasm. So, the way in which a protein folds will also depend on whether the R-groups are hydrophilic or hydrophobic. Hydrophilic groups are on the outside of the protein while hydrophobic groups are on the inside of the molecule shielded from the water in the cytoplasm.

Front 128

Breakdown of peptides

Back 128

peptides are created by amino acids linking together in condensation reactions to form peptide bonds. Proteases are enzymes that catalyse the reverse reaction - turning peptides back into their constituent amino acids. A water molecule is used to break the peptide bond in a hydrolysis reaction, reforming the amine and carboxylic acid groups.

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identification of proteins - Biuret test

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Peptide bonds form violet-coloured complexes with copper ions in alkaline solutions. A mixture of an alkali and copper sulfate solution is called biuret reagent and can be used instead of adding the solutions individually. Safety - Remember, when working with chemicals, take care, wear safety glasses and report any spillages/breakages to the teacher. Carrying out the following procedure to test a sample for the presence of protein: 3cm² of a liquid sample was mixed with an equal volume of 10% sodium hydroxide solution. 1% copper sulfate solution was then added a few drops at a time until the sample solution turned blue. The solution was mixed and left to stand for five minutes.

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The two main groups of proteins

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globular proteins and fibrous proteins.

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Globular proteins

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Globular proteins are compact, water soluble, and usually roughly spherical in shape. They form when proteins fold into their tertiary structures in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment. The hydrophilic R-groups are on the outside of the protein. This means the proteins are soluble in water. This solubility is important for the many different functions of globular proteins. They are essential for regulating many of the processes necessary to life. These include processes such as chemical reactions, immunity, muscle contraction, and many more.

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Insulin

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Insulin is a globular protein. It is a hormone involved in the regulation of blood glucose concentration. Hormones are transported in the bloodstream so need to be soluble. Hormones also have to fit into specific receptors on cell-surface membranes to have their effect and therefore need to have precise shapes.

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Conjugated proteins

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Conjugated proteins are globular proteins that contain a non-protein component called a prosthetic group. Proteins without prosthetic groups are called simple proteins. There are different types of prosthetic groups. Lipids or carbohydrates can combine with proteins forming lipoproteins or glycoproteins. Metal ions and molecules derived from vitamins also form prosthetic groups. These are called cofactors when they are necessary for the proteins to carry out their functions. Haem groups are examples of prosthetic groups. They contain an iron ion (Fe2+). Catalase and haemoglobin both contain haem groups.

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Haemoglobin

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Haemoglobin is the red, oxygen-carrying pigment found in red blood cells. It is a quaternary protein made from four polypeptides, two alpha and two beta subunits. Each subunit contains a prosthetic haem group. The iron ions present in the haem groups are each able to combine reversibly with an oxygen molecule. This is what enables haemoglobin to transport oxygen around the body. It can pick oxygen up in the lungs and transport it to the cells that need it, where it is released.

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Catalase

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Catalase is an enzyme. Enzymes catalyse reactions, meaning they increase reaction rates, and each enzyme is specific to a particular reaction or type of reaction. Catalase is a quaternary protein containing four haem prosthetic groups. The presence of the iron |I ions in the prosthetic groups allow catalase to interact with hydrogen peroxide and speed up its breakdown. Hydrogen peroxide is a common by-product of metabolism but is damaging to cells and cell components if allowed to accumulate. Catalase makes sure this doesn't happen.

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Fibrous proteins

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Fibrous proteins are formed from long. insoluble molecules. This is due to the presence of a high proportion of amino acids with hydrophobic R-groups in their primary structures. They contain a limited range of amino acids, usually with small R-groups. The amino acid sequence in the primary structure is usually quite repetitive. This leads to very organised structures reflected in the roles fibrous proteins often have. Keratin, elastin, and collagen are examples of fibrous proteins. Fibrous proteins tend to make strong. long molecules which are not folded into complex three-dimensional shapes like globular proteins.

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Keratin

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Keratin is a group of fibrous proteins present in hair, skin, and nails. It has a large proportion of the sulfur-containing amino acid, cysteine. This results in many strong disulfide bonds (disulfide bridges) forming strong, inflexible, and insoluble materials. The degree of disulfide bonds determines the flexibility - hair contains fewer bonds making it more flexible than nails, which contain more bonds. The unpleasant smell produced when hair or skin is burnt is due to the presence of relatively large quantities of sulfur in these proteins.

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Elastin

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Elastin is a fibrous protein found in elastic fibres (along with small protein fibres). Elastic fibres are present in the walls of blood vessels and in the alveoli of the lungs - they give these structures the flexibility to expand when needed, but also to return to their normal size. Elastin is a quaternary protein made from many stretchy molecules called tropoelastin.

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Collagen

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Collagen is another fibrous protein. It is a connective tissue found in skin, tendons, ligaments, and the nervous system. There are a number of different forms, but all are made up of three polypeptides wound together in a long and strong rope-like structure. Like rope, collagen has flexibility (see the Extension, The structure of fibrous proteins, for further detail of structure).

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The structure of Elastin

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Elastin is made by linking many soluble tropoelastin protein molecules to make a very large, insoluble, and stable, cross-linked structure. Tropoelastin molecules are able to stretch and recoil without breaking, acting like small springs. They contain alternate hydrophobic and iodine-rich areas. Elastin is formed when multiple tropoelastin molecules aggregate via interactions between the hydrophobic areas. The structure is stabilised by cross-linking covalent bonds involving the amino acid lysine, but the polypeptide structure still has flexibility. Elastin confers strength and elasticity to the skin and other tissues and organs in the body.

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The structure of Collagen

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Collagen molecules have three polypeptide chains wound around each other in a triple helix structure to form a tough, rope-like protein. Every third amino acid in the polypeptide chains is glycine, which is a small amino acid. Its small size allows the three protein molecules to form a closely packed triple helix. Many hydrogen bonds form between the polypeptide chains forming long quaternary proteins with staggered ends. These allow the proteins to join end to end, forming long fibrils called tropocollagen. The tropocollagen fibrils cross-link to produce strong fibres. Collagen also contains high proportions of the amino acids proline and hydroxyproline. The R-groups in these amino acids repel each other and this adds to the stability of collagen. In some tissues, multiple fibres of collagen aggregate into larger bundles. This is the structure found in ligaments and tendons. In skin, collagen fibres form a mesh that is resistant to tearing.

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Lipids

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commonly known as fats and oils, are molecules containing the elements carbon, hydrogen, and oxygen. Generally, fats are lipids that are solid at room temperature and oils are lipids that are liquid at room temperature. Lipids are non-polar molecules as the electrons in the outer orbitals that form the bonds are more evenly distributed than in polar molecules. This means there are no positive or negative areas within the molecules and for this reason lipids are not soluble in water. Oil and water do not mix. Lipids are large complex molecules known as macromolecules, which are not built from repeating units, or monomers, like polysaccharides.

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Roles of lipids

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cushioning to protect vital organs, creation of hydrophobic barriers, hormone production, electrical insulation necessary for impulse transmission, waterproofing, long term energy storage, thermal insulation to reduce heat loss, buoyancy for aquatic animals like whales

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Triglycerides

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A triglyceride is made by combining one glycerol molecule with three fatty acids. Glycerol is a member of a group of molecules called alcohols. Fatty acids belong to a group of molecules called carboxylic acids - they consist of a carboxyl group (-CooH) with a hydrocarbon chain attached. Both of these molecules contain hydroxyl (OH) groups. The hydroxyl groups interact, leading to the formation of three water molecules and bonds between the fatty acids and the glycerol molecule. These are called ester bonds and this reaction is called esterification. Esterification is another example of a condensation reaction.

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Breaking down of triglycerides

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When triglycerides are broken down, three water molecules need to be supplied to reverse the reaction that formed the triglyceride. This is another example of a hydrolysis reaction.

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Saturated

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Fatty acid chains that have no double bonds present between the carbon atoms are called saturated, because all the carbon atoms form the maximum number of bonds with hydrogen atoms (i.e., they are saturated with hydrogen atoms).

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Unsaturated

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A fatty acid with double bonds between some of the carbon atoms is called unsaturated.

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Mono and poly saturated

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If there is just one double bond between carbon atoms it is called monounsaturated. If there are two or more double bonds between carbon atoms it is called polyunsaturated. The presence of double bonds causes the molecule to kink or bend and they therefore cannot pack so closely together. This makes them liquid at room temperature rather than solid, and they are therefore described as oils rather than fats.

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Saturated fats leading to health problems

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Plants contain unsaturated triglycerides, which normally occur as oils, and tend to be more healthy in the human diet than saturated triglycerides, or (solid) fats. There has been some evidence that in excess, saturated fats can lead to coronary heart disease, however the evidence remains inconclusive. An excess of any type of fat can lead to obesity, which also puts a strain on the heart.

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Properties of triglycerides

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good energy storage (long fatty acid tails contain lots of chemical energy), insoluble in water (doesn’t affect water potential, the fatty acids are hydrophobic so repel water (shield themselves from water by bundling together in droplets

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Phospholipids

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Phospholipids are modified triglycerides and contain the element phosphorus along with carbon, hydrogen, and oxygen. Inorganic phosphate ions (PO,) are found in the cytoplasm of every cell. The phosphate ions have extra electrons and so are negatively charged, making them soluble in water. One of the fatty acid chains in a triglyceride molecule is replaced with a phosphate group to make a phospholipid.

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Hydrophobic and hydrophilic triglycerides

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Phospholipids are unusual because, due to their length, they have a non-polar end or tail (the fatty acid chains) and a charged end or head (the phosphate group). The non-polar tails are repelled by water (but mix readily with fat). They are hydrophobic. The charged heads (often incorrectly called polar ends) will interact with, and are attracted to, water. They are hydrophilic.

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What happens when triglycerides interact with water

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As a result of their dual hydrophobic/hydrophilic structure, phospholipids behave in an interesting way when they interact with water. They will form a layer on the surface of the water with the phosphate heads in the water and the fatty acid tails sticking out of the water. Because of this they are called surface active agents or surfactants for short.

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Triglyceride bilayers

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They can also form structures based on a two-layered sheet formation (a bilayer) with all of their hydrophobic tails pointing toward the centre of the sheet, protected from the water by the hydrophilic heads. It is as a result of this bilayer arrangement that phospholipids play a key role in forming cell membranes. They are able to separate an aqueous environment in which cells usually exist from the aqueous cytosol within cells. It is thought that this is how the first cells were formed and, later on, membrane-bound organelles within cells.

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Sterols

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Sterols, also known as steroid alcohols, are another type of lipid found in cells. They are not fats or oils and have little in common with them structurally. They are complex alcohol molecules, based on a four-carbon ring structure with a hydroxyl (OH) group at one end. Like phospholipids, however, they have dual hydrophilic/hydrophobic characteristics. The hydroxyl group is polar and therefore hydrophilic, and the rest of the molecule is hydrophobic.

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Cholesterol as a sterol

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Cholesterol is a sterol. The body manufactures cholesterol primarily in the liver and intestines. It has an important role in the formation of cell membranes, becoming positioned between the phospholipids with the hydroxyl group at the periphery of the membrane. This adds stability to cell membranes and regulates their fluidity by keeping membranes fluid at low temperatures and stopping them becoming too fluid at high temperatures. Vitamin D, steroid hormones, and bile are all manufactured using cholesterol.

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Roles of lipids

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Due to their non-polar nature, lipids have many biological roles: membrane formation and the creation of hydrophobic barriers hormone production electrical insulation necessary for impulse transmission waterproofing, for example in birds' feathers and on plant leaves. Lipids, triglycerides in particular, also have an important role in long-term energy storage. They are stored under the skin and around vital organs.

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Storage around vital organs also provides

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thermal insulation to reduce heat loss for example, in penguins cushioning to protect vital organs such as the heart and kidneys- buoyancy for aquatic animals like whales.

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Identification of lipids

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Lipids can be identified in the laboratory by a simple test known as the emulsion test. First, the sample is mixed with ethanol. The resulting solution is mixed with water and shaken. If a white emulsion forms as a layer on top of the solution this indicates the presence of a lipid. If the solution remains clear the text is negative.

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Changing health advice

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It can be confusing because health advice constantly changes. The way that new advice is issued in the media from new findings is partly responsible. The validity of the research has not usually been evaluated, the science is often not easy to explain, and as the majority of the general public do not have scientific background they are not aware of the fluid nature of scientific understanding. Scientific knowledge is also constantly changing as technology develops and so our understanding of biological processes increases.

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Food synergy

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It is often difficult to isolate the effect of just one nutrient and, in fact, it is now generally believed that nutrients do not work in isolation but as part of the combined effect of a whole range of nutrients. This is called food synergy. For example, whole grains are believed to have a greater beneficial effect than any of their individual components and it is the combined effect of fish, fruit and vegetables that help prevent certain types of heart disease.

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Flaws in data reports related to diet

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The data used in reports is often flawed, particularly where diet is concerned, as the subjects involved in studies often do not provide accurate information. People tend to underestimate what they eat, they forget what they have eaten and don't often know the exact ingredients of meals, particularly if they are eating out. People are also different due to their genetic makeup and therefore respond differently to different nutrients. The studies that catch the headlines often involve small numbers of subjects and these inherent differences distort the findings. The resulting headlines can be eye-catching, but not very accurate, and are often contradicted by the next study.

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Fats in our diet

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The presence of a double bond in a fatty acid leads to a kink in the chain causing the lipid to be more liquid in nature and, as you will discover in later sections, a more healthy component of the diet than saturated fats. Plants contain unsaturated triglycerides, which normally occur as oils. Animals (but generally not fish] contain saturated triglycerides, or (solid) fats. As mentioned, the evidence that saturated fats cause heart diseases is inconclusive. Previously it was thought that saturated fats did cause heart disease, but more recent evidence has contradicted this.

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Margarine versus butter

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Butter is an animal fat made from cows' milk and is therefore high in saturated lipids. Various alternatives to butter have been developed over the last 200 years with the focus initially being to find cheaper or longer-lasting substitutes. More recently the aim has been to produce more 'healthy' substitute for butter.

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Main problem of using vegetable oils to produce substitute butters

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The main problem faced initially by food scientists was that the vegetable oils used to produce the 'substitute butters' are more liquid than the animal fats in milk.

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How the problem of using vegetable oils, which are more liquid than fats in milk, to produce butters was overcome

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This was overcome by using hydrogen to saturate, or removing the double bonds from, the unsaturated fatty acids in the vegetable oils. Solid hydrogenated fat was produced, and the oil was said to have been hardened. The fat was then coloured and sometimes mixed with butter to improve the taste. Different degrees of hardening. colouring and mixing with butter gave the many different margarines on the market. An unwanted by-product of the hardening process was the production of trans fats. These are unsaturated lipids in which the kinks that the double bonds naturally form in the fatty acid chains have been reversed. Trans fats, which actually increase the shelf life of baked products, have more recently been linked with the development of coronary heart disease and are now usually removed from foods.

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What is happening now there is more focus on producing healthy alternatives to butter

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With more focus on producing healthy alternatives to butter, and improvements in the manufacturing process, many spreads now contain less, if any, hydrogenated fats. Mono- and polyunsaturated plant oils are used instead, and these have been shown to reduce high cholesterol levels, which are a factor in the development of coronary heart disease.

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Reduced fat spreads

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Lipids release the same quantity of energy gram for gram when respired whether saturated or unsaturated, so butter and margarine have always had the same calorific value. More recently the focus has been to reduce the overall fat content in such spreads.

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Carbohydrates

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Carbohydrates are also known as saccharides or sugars. A single sugar unit is known as a monosaccharide, examples include glucose, fructose, and ribose. When two monosaccharides link together they form a disaccharide, for example lactose and sucrose. When two or more (usually many more) monosaccharides are linked they form a polymer called a polysaccharide. Glycogen, cellulose, and starch are examples of polysaccharides.

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Glucose structure

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The basic building blocks, or monomers, of some biologically important large carbohydrates are glucose molecules, which have the chemical formula C,H,0, Glucose is a monosaccharide composed of six carbons and therefore is a hexose monosaccharide (hexose sugar). In molecular structure diagrams, the carbons are numbered clockwise, beginning with the carbon to the right (clockwise) of the oxygen atom within the ring. There are two structural variations of the glucose molecule, alpha (a) and beta (6) glucose, in which the OH (hydroxyl) group on carbon I is in opposite positions.

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Why are glucose molecules polar?l

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Glucose molecules are polar and soluble in water. This is due to the hydrogen bonds that form between the hydroxyl groups and water molecules. This solubility in water is important, because it means glucose is dissolved in the cytosol of the cell. Reduction is a reaction involving the gain of electrons. All monosaccharides and some disaccharides are reducing sugars. This means they can donate electrons or reduce another molecule or chemical.

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Properties of glucose

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Glucose is the major energy store for most cells, highly soluble and is the main form in which carbs are transported around the body.

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Condensation reactions

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When two alpha glucose molecules are side by side, two hydroxyl groups interact (react). When this happens, bonds are broken, and new bonds reformed in different places producing new molecules. Two hydrogen atoms and an oxygen atom are removed from the glucose monomers and join to form a water molecule. A bond forms between carbons I and 4 on the glucose molecules and the molecules are now joined. A covalent bond called a glycosidic bond is formed between two glucose molecules. The reaction is called a condensation reaction because a water molecule is formed as one of the products of the reaction. Because in this reaction carbon I of one glucose molecule is joined to carbon 4 of the other glucose molecule, the bond is known as a 1,4 glycosidic bond. In this reaction the new molecule is called maltose. This is an example of a disaccharide.

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Glucose function

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Glucose is stored as starch by plants or glycogen by animals and fungi, until it is needed for respiration - the process in which biochemical energy in these stored nutrients is converted into a useable energy source for the cell.

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Glucose hydrolysis reaction

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To release glucose for respiration, starch or glycogen undergo hydrolysis reactions, requiring the addition of water molecules. The reactions are catalysed by enzymes. These are the reverse of the condensation reactions that form the glycosidic bonds.

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Monosaccharide examples

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glucose, fructose, and ribose.

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Alpha glucose

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a form of glucose where a hydrogen atom attached to carbon 1 is ‘up’ when the pyranose ring is closed. This leaves OH ‘down’ on carbon 4 of the second molecule. This is highly significant as when other alpha glucose molecules appear, the OH which is ‘down’ on carbon 4 of the second molecule can form 1,4 glycosidic bond via a condensation reaction (a water molecule is removed)

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Beta glucose

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a form of glucose where a hydrogen atom attached to C1 is ‘down’ when the pyranose ring is closed. This means that in order to form a 1,4 glycosidic bond, every other unit of beta glucose needs to ‘flip’ through 180* in order to bring two OH groups closer together to form the bond and create a molecule of water (condensation reaction).

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How maltose molecules are created

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when two alpha molecules are side by side, two hydroxyl groups interact. When this happens, bonds are broken, and new bonds reformed in different places producing new molecules. As the two H are so close, they react, forming a covalent bond called a glycosidic bond. A glycosidic bond is a condensation reaction between two alpha glucose molecules. This happens between sugars between the C1 on the first molecules and C4 on the second. This bond is known as an alpha 1,4 glycosidic bond. This creates a maltose molecules.

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Fructose and galactose

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are hexose monosaccharides. Fructose naturally occurs in fruit, often in combination with glucose forming the disaccharide sucrose, commonly known as cane sugar or just sugar. Lactose is commonly found in milk and milk products. Fructose is sweeter than glucose, and glucose is sweeter than galactose.

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Pentose monosaccharides

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contain five carbon atoms and form a ring. Hexose monosaccharides have six carbon atoms. Ribose and deoxyribose are important constitutes of RNA and DNA.

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Examples of disaccharides

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lactose, sucrose and malto(a)se. lactose = glucose + galactose

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Sucrose

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(table sugar) is formed from glucose and fructose joined by an alpha 1-4 glycosidic bond.

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Lactose

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(milk sugar) is formed from galactose and glucose joined by a beta 1-4 glycosidic bond.

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Maltose

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(malt sugar) is formed from two glucose molecules joined by an alpha 1-4 glycosidic bond.

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Examples of polysaccharides

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glycogen, collagen, and starch.

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Properties of starch

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Many alpha glucose molecules can be joined by glycosidic bonds to form two slightly different polysaccharides known collectively as starch. Glucose made by photosynthesis in plant cells is stored as starch. It is a chemical energy store. used by plants as an energy store (can be hydrolysed when needed and used for respiration); compact (a lot can be stored in a small space); large (does not diffuse out of cells); insoluble (doesn’t affect water potential so water is not drawn in by osmosis); branched (greater area for enzymes to act on so hydrolysis can happen rapidly).

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Amylose

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formed by alpha glucose molecules joined together only by 1-4 glycosidic bonds. The angle of the bond means that this long chain of glucose twists to form a helix which is further stabilised by hydrogen bonding with the molecule. This makes the polysaccharide more compact, and much less soluble than the glucose molecules used to make it. One of the polysaccharides in starch is amylose.

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Amylopectin

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formed when glycosidic bonds form in condensation reactions between C1 and C6 on two glucose molecules, this means that amylopectin has a branched structure with the 1-6 branching points occurring around once every 25 glucose subunits. Amylopectin is also made by 1-4 glycosidic bonds between alpha glucose molecules, but (unlike amylose) in amylopectin there are also some glycosidic bonds formed by condensation reactions.

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Properties of glycogen

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used by animals and fungi as an energy store (can be hydrolysed when needed and used for respiration), compact (a lot can be stored in a small space); large (doesn’t diffuse out of cells); insoluble (doesn’t affect water potential so water is not drawn in by osmosis); highly branched (greater area for enzymes to act on so hydrolysis can happen rapidly).

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Glycogen

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The functionally equivalent energy storage molecule to starch in animals and fungi is called glycogen. Glycogen forms more branches than amylopectin, which means it is more compact and less space is needed for it to be stored. This is important as animals are mobile, unlike plants. The coiling or branching of these polysaccharides makes them very compact, which is ideal for storage. The branching also means there are many free ends where glucose molecules can be added or removed. This speeds up the processes of storing or releasing glucose molecules required by the cell.

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Properties of cellulose

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a major component of plant cell walls, insoluble, provides strength to the cell and prevents it from bursting.

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Structure of cellulose

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Long, unbranched chains of beta glucose joined by glycosidic bonds. Beta glucose molecules are unable to join together in the same way that alpha glucose molecules can. The hydroxyl groups on C1 and C4 of the two glucose molecules are too far from each other to react. The only way that beta molecules can join together and form a polymer is if alternate beta glucose molecules are turned upside down. It is unable to coil or form branches. Chains are linked by H bonds, chains are grouped to form microfibrils, microfibrils grouped to form fibres. When a polysaccharide is formed from glucose in this way it is unable to coil or form branches. A straight chain molecule is formed called cellulose.

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Hydrolysis of carbohydrates

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used to break polysaccharides and disaccharides into monosaccharides. Hydrolysis reactions are opposite to condensation reactions.

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Benedict's test for reducing sugars

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In chemistry reduction is a reaction involving the gain of electrons. All monosaccharides and some disaccharides (for example maltose and lactose) are reducing sugars. This means that they can donate electrons or reduce another molecule or chemical. In the chemical test for a reducing sugar, this chemical is Benedict's reagent, an alkaline solution of copper(l1) sulfate.

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Benedict’s test for reducing sugars step-by-step

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Place the sample to be tested in a boiling tube. If it is not in liquid form, grind it up or blend it in water. Add an equal volume of Benedict's reagent. Heat the mixture gently in a boiling water bath for five minutes.

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How to read the results of Benedict’s test for reducing sugars

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Reducing sugars will react with the copper ions in Benedict's reagent. This results in the addition of electrons to the blue Cu²* ions, reducing them to brick red Cu' ions. When a reducing sugar is mixed with Benedict's reagent and warmed, a brick-red precipitate is formed indicating a positive result. The more reducing sugar present, the more precipitate formed and the less blue Cu²* ions are left in solution, so the actual colour seen will be a mixture of brick-red (precipitate) and blue (unchanged copper ions) and will depend on the concentration of the reducing sugar present. This makes the test qualitative.

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Using Benedict's test for non-reducing sugars

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non-reducing sugars do not react with Benedict's solution and the solution will remain blue after warming, indicating a negative result. However, sucrose is the most common non-reducing sugar. If sucrose is first boiled with dilute hydrochloric acid it will then give a positive result when warmed with Benedict’s solution. This is because the sucrose has been hydrolysed by the acid to glucose and fructose, both reducing sugars.

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iodine test for starch

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The iodine test is used to detect the presence of starch. To carry out the test, a few drops of iodine dissolved in potassium iodide solution are mixed with a sample. If the solution changes colour from yellow/ brown to purple/black starch is present in the sample. If the iodine solution remains yellow/brown it is a negative result and starch is not present.

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Reagent strips

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Manufactured reagent test strips can be used to test for the presence of reducing sugars, most commonly glucose. The advantage is that, with the use of a colour-coded chart, the concentration of the sugar can be determined.

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Colorimetry

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In a Benedict's test, the colour produced is dependent on the concentration of reducing sugar present in the sample. A colorimeter is a piece of equipment used to quantitatively measure the absorbance, or transmission, of light by a coloured solution. The more concentrated a solution is the more light it will absorb and the less light it will transmit. This can be used to calculate the concentration of reducing sugar present.

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Procedure to determine the concentration of a solution of glucose

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A filter was placed in the colorimeter. The colorimeter was calibrated using distilled water. Benedict’s test was performed on a range of known concentrations of glucose. The resulting solutions were filtered to remove the precipitate. The % transmission of each of the solutions of glucose was measured using the colorimeter. Using this information, a calibration curve was plotted. Steps 3-6 were repeated using the solution with the unknown concentration of glucose.

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Biosensors

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Biosensors use biological components to determine the presence and concentration of molecules such as glucose. The analyte is the compound under investigation.

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Molecular recognition

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a protein (enzyme or antibody) or single strand of DNA (ssDNA) is immobilised to a surface, for example a glucose test strip. This will interact with, or bind to, the specific molecule under investigation.

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Transduction

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this interaction will cause a change in a transducer. A transducer detects changes, for example in pH, and produces a response such as the release of an immobilised dye on a test strip or an electric current in a glucose-testing machine.

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Display

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this then produces a visible, qualitative, or quantitative signal such as a particular colour on a test strip or reading on a test machine.

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Elements

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Different types of atoms are called elements. Elements are distinguished by the number of protons in their atomic nuclei. There are over a hundred known elements in the universe but only a small percentage of these are present in the living world.

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Which elements are most dominant in living things

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All living things are made primarily from four key elements - carbon (C), hydrogen (H), Oxygen (o) and nitrogen (N). In addition, phosphorus (P) and sulfur (S) also have important roles in the biochemistry of cells. These six elements are by far the most abundant elements present in biological molecules. Other elements, including sodium (Na), potassium (K), calcium (Ca), and iron (Fe), also have important roles in biochemistry.

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Bonding

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Atoms connect with each other by forming bonds. Atoms can bond to other atoms of the same element, or atoms of different elements. provided this follows the 'bonding rules'. When two or more atoms bond together the complex is called a molecule. A covalent bond occurs when two atoms share a pair of electrons. The electrons used to form bonds are unpaired and present in the outer orbitals of the atoms.

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Bonding rules

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Bonding follows some simple rules, determined by the number of unpaired electrons present in the outer orbitals of different elements: Carbon atoms can form four bonds with other atoms. Nitrogen atoms can form three bonds with other atoms. Oxygen atoms can form two bonds with other atoms. Hydrogen atoms can only form one bond with another atom.The number of bonds formed by these elements can be no more or less than stated. There are, however, exceptions to this rule. Life on this planet is often referred to as being 'carbon-based' because carbon, which can form four bonds, forms the backbone of most biological molecules.

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Ions

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An atom or molecule in which the total number of electrons is not equal to the total number of protons is called an ion. If an atom or molecule loses one or more electrons it has a net positive charge and is known as a cation. If an atom or molecule gains electrons, it has a net negative charge and is known as an anion. In ionic bonds, one atom in the pair donates an electron and the other receives it. This forms positive and negative ions that are held together by the attraction of the opposite charges.

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What are ions in solution called?

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electrolytes

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Which elements are in carbohydrates

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carbon, hydrogen, and oxygen

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Which elements are in Lipids

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carbon, hydrogen, and oxygen.

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Which elements are in Proteins

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carbon, hydrogen, oxygen, nitrogen, and sulfur.

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Which elements are in Nucleic acids

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carbon, hydrogen, oxygen, nitrogen, and phosphorus.

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Polymers

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Biological molecules are often polymers. Polymers are long-chain molecules made up by the linking of multiple individual molecules (called monomers) in a repeating pattern. In carbohydrates the monomers are sugars (saccharides) and in proteins the monomers are amino acids.

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Cations – calcium ions (Ca2+)

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nerve impulse transmission and muscle contraction

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Cations – sodium ions (Na+)

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nerve impulse transmission and kidney function

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Cations – potassium ions (K+)

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nerve impulse transmission and stomatal opening

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Cations – hydrogen ions (H+)

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catalysis of reactions and pH determination

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Cations – ammonium ions (HN4+)

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production of nitrate ions by bacteria

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Properties of water – density

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caused by hydrogen bonds. below 4 degrees Celsius hydrogen bonds fix the positions of the polar molecules slightly further apart than in liquid state. less dense in solid-state. ice floats forming an insulating layer - when the temperature of atmosphere falls below 0 degrees Celsius, the water at the surface gradually freezes to ice, but the water under the ice layer remains at 4 degrees C. this means fish can swim, provides a more stable environment, and makes a good body temperature for enzymes.

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Properties of water – liquid

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less dense in solid-state. when water is liquid at room temperature water can allow photosynthesis to occur; provide habitats for living things in rivers; lakes and seas; allows transport of molecules; forms a major component of the tissues in living organisms; provides a reaction medium for chemical reactions; provides a transport medium e.g., blood.

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Properties of water – cohesion and adhesion

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stuck to each other and stuck to other molecules. water molecules are attracted to substances other than water. this is what allows water to move upwards through plant against gravity (water clings to the sides of the plant's veins - capillary action). it's allows atoms to bond together more easily. good for transpiration, surface tension and transport in the body. It moves as one mass because the molecules are attracted to each other (cohesion). It is in this way that plants are able to draw water up their roots and how you are able to drink water through a straw. Water also has adhesive properties - this is where water molecules are attracted to other materials. For example, when you wash your hands your hands become wet, the water doesn't run straight off.

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Properties of water – high latent heat of vaporisation

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takes a lot of energy (heat) to break the hydrogen bonds between water molecules, so it requires a lot of energy to turn water into a gas. this is useful for living organisms because it means water is good at cooling things e.g., sweating. Properties of water – high specific heat capacity - a large amount of energy must be transferred away from water to make it freeze, which is important for organisms with high body water content (it makes sure the temperature is not too high or not too low) and for those living in water to provide a stable environment.

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Properties of water – metabolic

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allows chemical reactions to occur e.g., hydrolysis, condensation, and photosynthesis.

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Properties of water – solvent

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can be used to transport substances through active transport to keep cells alive e.g., minerals in the Xylem, active transport and solvents also dilute toxic substances.

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Why there are regions of positivity and negativity in water

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oxygen and hydrogen don't share electrons. In an O-H bond, oxygen always has a much greater share. This means O-H (hydroxyl) groups are slightly polar. polar molecules interact with each other as the positive and negative regions attract each other and form hydrogen bonds. these are weak interactions which constantly break and reform between moving water molecules, these reactions occur in high numbers, even though they are weak.

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Slightly negative and slightly positive

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in water molecules, positive sodium ions attract the negative oxygen atoms and the negative chloride ions attract the positive hydrogen atoms. Slightly negative - delta negative, slightly positive, delta positive. negative electrons are not always shared equally by the atoms of different elements. molecules in which this happens are said to be polar - they have regions of positivity and regions of negativity.

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Universal solvent – many solutes in living organisms can be dissolved in water

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H

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Universal solvent

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many solutes in living organisms can be dissolved in water

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Anions – nitrate ions (NO3-)

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nitrogen supply to plants for amino acid and protein formation

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Anions – hydrogen carbonate ions (HCO3-)

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maintenance of blood pH

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Anions – chloride ions (Cl-)

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balance positive charge of sodium and potassium ions in cells

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Anions – phosphate ions (PO43-)

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cell membrane formation, nucleic acid and ATP formation and bone formation

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Anions – hydroxide ions (OH-)

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catalysis of reactions and pH determination