proteins and nucleic acids

Proteins

Proteins are made up of carbon, hydrogen, oxygen and nitrogen, and some proteins may contain sulfur as well.

Roughly 60% of the molecules in cells are proteins, excluding water.

Proteins are the basic materials for cell growth, cell repair and replacement of materials.

Basic builiding block of a protein- an amino acid

Amino acids all have the same structure: an amino group (-NH2) at one end of the molecule and a carboxyl group (-COOH), also called an organic acid group, at the other end.

These two groups are attached centrally with a carbon atom that carries a hydrogen atom on one side and an R group on the other.

It is the R group that is different in each of the 20 amino acids that make up proteins.

Once amino acids are joined together by peptide bonds, they are referred to as amino acid residues.

All polar R groups are hydrophilic groups, creating a hydrophilic end to the molecule.

Non-polar amino acids are hydrophobic.

Forming peptide bonds- condensation and hydrolysis

Proteins are large molecules; they are called polymers because they are made up of many similar subunits or molecules, the amino acids.

Two amino acids are joined by a condensation reaction, with one molecule of water lost.

The resulting covalent bond is called a peptide bond, and the molecule formed is a dipeptide.

This bond can be broken by a hydrolysis reaction using one molecule of water.

polypeptides

When a chain of amino acids is formed, each new amino acid is joined by a peptide bond.

The resulting chain is called a peptide, and longer chains are called polypeptides.

Primary structure

The primary structure of a protein is the sequence, type, and number of amino acids in the amino acid chain as well as the position of the disulfide bonds if present.

Each protein is made up of many amino acids, each joined to the chain by a condensation reaction forming a peptide bond.

The structure and amino acids present determine the protein’s function.

secondary structure

Once the primary structure is formed, the chain takes a particular shape by folding or coiling as a result of the bonds that form between certain amino acids in the chain.

Two main forms of secondary folding: alpha helix and beta-pleated sheet.

The alpha helix is held permanently in place by hydrogen bonds between amino acids in one part of the chain and those a little further along the chain.

The beta-pleated sheet has hydrogen bonds connecting to the adjacent pleated sheet.

Tertiary structure

The tertiary structure is the 3D shape of the protein molecule that occurs when the secondary structure becomes further coiled or twisted into a complex shape.

Two main types are globular and fibrous.

When the protein folds and coils to form a 3D shape, it is called a globular protein.

The 3D shape makes globular proteins important in metabolic processes- all enzymes are globular proteins.

The globular shape allows enzymes to have a specifically shaped active site which is complementary to a specific substrate that the enzyme catalyses.

Globular proteins are usually soluble.

If the protein twists into a long fibrous structure, the protein is called a fibrous protein.

These fibrous proteins are important in structural roles such as keratin in hair and nails and collagen in skin and bones. Fibrin, the blood clotting protein, is a fibrous protein.

In both globular and fibrous proteins, several different types of bonds stabilise the molecule and hold it in place.

Some of these are weak bonds such as hydrogen bond ehich individually can be broken very easily but being present in large numbers helps to stabilise molecules.

Ionic bonds and hydrophobic interactions also form between the different R groups.

Other bonds are covalent bonds- strong bonds that aren’t easily broken- such as disulfide bonds.

Quaternary structure

Some proteins are made up of more than one polypeptide chain.

Two or more chains function as a whole.

The protein will not function unless all subunits are together.

In some cases, an inorganic molecule or ion is also required for the protein to function.

Globular proteins- haemoglobin

Haemoglobin is an example of a globular protein with a quaternary structure, a haem group containing an inorganic ion (metal iron- gives the typical red colour).

Adult haemoglobin has 4 polypeptide chains- two alpha and two beta chains- each associated with a haem group.

The four chains are held together by different bonds to make a stable globular molecule with a specific shape to carry out the molecule’s function of transporting oxygen.

The haem part of the molecule is the prosthetic group, which makes haemoglobin a conjugated protein.

Globular proteins- enzymes

Globular protein molecules include enzymes, for example amylase and catalase, which rely on their 3D shape to carry out their function of catalysing chemical reactions

Fibrous protein- collagen

Collagen is an example of a fibrous protein with a quaternary structure.

It has 3 polypeptide chains twisted around each other like a plait.

Each chain is made up of three repeating amino acids.

Strength is provided by many hydrogen and covalent bonds between the chains.

The chains in turn form a collagen fibril that links with others to form a collagen fibre.

Collagen provides support and strength in many structures in the body such as the heart and arteries.

Keratin and elastin are also examples of fibrous proteins.

Elastin can stretch and return to its usual shape- found in connective tissue, tendons, skin and bone.

Fibrous is insoluble.

Fibrous has no prosthetic group.

inorganic ions

Biological processes involve enzymes and their substrates, and also several important inorganic ions.

Inorganic ions in plants and animals are essential for vital cellular activity.

They contribute to the osmotic pressures of body fluids, may act as cofactors and may provide other important functions.

Calcium ions - cofactor in blood clotting, part of bone and enamel structure, involved in nerve transmission across a synapse, and in muscle contraction

Sodium ions- an electrolyte, essential function in nerve transmission, essential in water reabsorption

Potassium ions- an electrolyte, essential in nerve transmission, essential in water reabsorption, used in plant guard cells as a part of stomatal opening mechanism

Hydrogen ions- in hydrogen bonds, involved in ATP formation, involved in the control of blood pH and in the transport of carbon dioxide.

Ammonium ions- an intermediate ion in the deamination of proteins

Nitrate- nitrogen source for green plants to manufacture proteins

Hydrogen Carbonate- involved in carbon dioxide transport in the blood

Chloride- the shift of chloride ions in and out of red blood cells, maintaining a pH balance during carbon dioxide transport

Phosphate- phosphates form part of cell membranes as phospholipids.

Hydroxide- one of the important ions in bonding between biochemical molecules.

biosensors

Chromatography and biosensors offer methods for obtaining quantitative results.

A biosensor is a very precise and accurate analytical device.

It converts a biological response into an electrical signal using a catalyst, usually a highly specific and stable enzyme.

A common example is a blood glucose biosensor- this uses the enzyme glucose oxidase to break down blood glucose.

The enzyme, which includes FAD, oxidises the glucose and then uses two electrons to reduce the FAD to FADH2.

This is oxidised by the transducer (electrode in the device), which creates a current.

The current is a measure of glucose concentration.

A drop of blood is obtained from the patient using a sterile lancet, which is squeezed onto a test strip and inserted into the biosensor meter, which displays a blood glucose reading as a digital figure.

Structure of ADP and ATP

Adenosine triphosphate is a compound which transfers energy within cells; it is the universal energy currency.

It is composed of the nitrogenous base adenine covalently bonded to the pentose sugar ribose (forming adenosine) and three phosphate groups forming a short chain.

During transfer, the final phosphate group is removed by hydrolysis to release energy and phosphate, leaving the compound ADP (adenosine diphosphate).

Nucleic acids

There are two types of nucleic acid: deoxyribonucleic acid and ribonucleic acid.

Nucleic acids are vital molecules because they carry the genetic code in all living things and are important in controlling cellular activity and protein synthesis.

Nucleic acids are made up of carbon, hydrogen, oxygen, nitrogen and phosphate.

DNA is a double-stranded polynucleotide, which means it’s made up of many nucleotide molecules joined to each other with covalent bonds formed by condensation reactions.

strucutre of a nucleotide as a monomer

Each nucleotide is a monomer and is the basic building block of the nucleic acid molecules.

Unlike the monomers of other biological molecules, nucleotides are made up of three biological molecules that are bonded together with a covalent bond formed by a condensation reaction.

The subunits are:

A pentose sugar molecule- either ribose or deoxyribose-both of which contain 5 carbon atoms.

An organic nitrogenous base: adenine, cytosine, thymine, guanine or uracil.

A phosphate group

Uracil replaces thymine in RNA.

organic bases

Organic nitrogenous bases are of two types: purines or pyrimidines.

Purines consist of two carbon-nitrogen rings. (adenine and guanine)

Pyrimidines consist of a single nitrogen ring. (thymine, cytosine, and uracil)

structure of DNA- a polynucleotide

Nucleotides are joined together by a condensation reaction to form a polypeptide chain.

The phosphate group of one nucleotide is joined to the sugar molecule of the next nucleotide.

This forms one of the two sugar-phosphate backbones of the DNA molecule.

At this stage, the chain is a single chain with organic bases attached and projecting from this chain.

Only nucleotides with the same pentose sugar are attached to each other to form the chain.

DNA - the nucleic acid

The nucleic acid forms when two polypeptide chains join together by hydrogen bonds between the nitrogenous bases to form a double-stranded molecule

When nucleic acid contains the sugar deoxyribose and the base thymine, the molecule is known as DNA.

A pyrimidine always joins with a purine because only this pairing allows hydrogen bonds to form between the bases.

This specific pairing is called complementary base pairing.

In DNA, adenine always pairs with thymine and cytosine always pairs with guanine.

The double strand of DNA is formed when the two parallel polypeptide strands are joined together by hydrogen bonds between the nitrogenous bases that project out from the sugar phosphate backbone.

The strands are described as antiparallel as they run in opposite directions to each other.

Once formed, the DNA molecule is twisted into a helical shape with other backbones twisting, and so it is called the double helix.

DNA semi conservative replication

The DNA replication must be an exact copy to form two sister chromatids, and so the process must be accurate.

To replicate, DNA helicase unwinds the strands at the centre by breaking the hydrogen bonds between the nitrogenous bases, leaving two separate strands.

The two separate strands act as templates for new double DNA molecules to be formed.

New DNA nucleotides are attached to the exposed bases.

Exact copies are made because of complementary base pairing.

Hydrogen bonds form between the base pairs, and the enzyme DNA polymerase catalyses the condensation reaction to covalently bond each nucleotide to adjacent ones along sugar phosphate back one.

Two exact copies of the DNA have now been made, with one original strand and one strand of new nucleotides.

The gene- the genetic code

The code for DNA is a triplet code in which three bases code for an amino acid.

There are 20 different types of amino acids and 64 combinations of triplet codes; therefore, some triplets code for the same amino acids.

There may be up to 6 different codes for an amino acid; however, they only differ by one base.

The advantage of having different codes for the same amino acid is that if a mutation causes a base change, the triplet may still code for the same amino acid and therefore not change the protein produced.

Some amino acids only have one triplet code.

Three codes act as full stops signalling the end of a message.

Genes are a sequence of bases that code for the amino acids making up a single protein.

Length of a gene varies; some may be 50-100 nucleotides, but most are thousands of nucleotides long.

Transcription

Within each gene, one of the DNA strands is known as the “coding strand”, and the other is known as the “template” strand.

When the cell needs to produce a protein from this gene, the enzyme RNA polymerase binds to the DNA and unzips the two strands.

The RNA polymerase then moves along the template strand in the 3’ to 5’ direction

As it moves along, it pairs free RNA nucleotides with complementary nucleotides on the DNA template strand.

These RNA nucleotides are then covalently linked with phosphodiester bonds to create a polypeptide chain, growing in the 5’ to 3’ direction known as mRNA.

mRNA will have the same sequence of nucleotides as the DNA coding strand because it was formed by complementary pairing with the DNA template strand.

translation

The mRNA, once formed, leaves the nucleus via the nuclear pore for the ribosomes, where it acts as a template for the proteins to be synthesised.

Each triplet is called a codon.

There are different short transfer RNA (tRNA) molecules for each amino acid, and so they pick the correct amino acid and carry it to the correct position on the mRNA template.

At the opposite end of the tRNA is an anticodon, which is a triplet complementary to the mRNA codon. This ensures that the amino acids are correctly sequenced along the mRNA.

The ribosomes read the code three bases at a time, one codon at a time. Each amino acid is in turn attached by a condensation reaction to form a peptide bond with the next amino acid.

The ribosomes move along the chain and hold the tRNA and amino acid in place by temporary hydrogen bonds that break once a peptide bond is formed, leaving the tRNA to move off to collect another amino acid, and the ribosome moves along the chain.

This process continues until the chain of amino acids is complete and primary protein structure is formed.

RNA- a polynucleotide

RNA is a single-stranded polynucleotide, which means it’s made up of several RNA nucleotide molecules joined to each other with covalent bonds that form by condensation reactions.

Messenger RNA

When the DNA has unzipped, mRNA is made by attaching bases to the short section of exposed DNA.

RNA nucleotides attach to the exposed DNA bases with hydrogen bonds, building a new mRNA molecule; complementary base pairing means that the correct bases are always attached.

Transfer RNA

tRNA molecules are short chains of RNA that fold onto themselves.

These tRNA molecules carry amino acids to the mRNA and the ribosomes, where an enzyme forms peptide bonds between each pair of amino acids to form a polynucleotide chain.

Ribosomal RNA

rRNA molecules are short chains which, when attached to the ribosomal protein molecules, form ribosomes. These are the sites of protein synthesis.

DNA precipitation

The cells are first disrupted by breaking the cell and nuclear membranes using a concentrated detergent solution.

Filtering the resulting suspension removes cell debris and membrane fragments, leaving soluble proteins and DNA.

A protease enzyme is then used to remove the protein, leaving only the DNA, which can be precipitated using ice-cold ethanol.

The resulting white precipitate can then be used for analysis or in other investigations.