2.4 Proteins
Essential idea: Proteins have a very wide range of functions in living organisms.
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2.4.U.1 Amino acids are linked together by condensation to form polypeptides.
2.4.U.1 Amino acids are linked together by condensation to form polypeptides.
Be able to:
Describe polypeptide chain formation in terms of the formation of peptide bonds and condensation reactions.
Determine the number of peptide bonds given the number of amino acids in a polypeptide.
Define dipeptide, oligopeptides and polypeptide.
Polypeptides are chains of amino acids that are made by linking together amino acids by condensation reactions- this happens on ribosomes by a process called translation. Amino acids are the main component of proteins and in many proteins they are the only component
Polypeptides can contain one protein some contain more.
The condensation reaction involves the amine group (-NH2) of one amino acid and the carboxyl group (-COOH) of another. Water is removed as in all condensation reactions, and a new bond is formed between the two amino acids, called a peptide bond
2.4.U.2 There are 20 different amino acids in polypeptides synthesized on ribosomes.
2.4.U.2 There are 20 different amino acids in polypeptides synthesized on ribosomes.
Be able to:
State the number of amino acids used by living organisms to make polypeptides.
Given an image of an amino acid, classify the amino acid chemical properties based on R group properties.
Outline the role vitamin C plays in the conversion of proline to hydroxyproline.
2.4.U.3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.
2.4.U.3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.
Be able to:
Calculate the possible number of amino acid sequences given n number of amino acids.
Polypeptides are molecule consisting of many amino acids linked by peptide bonds. The polypeptides can contain any number of amino acids through chains of fewer than 20 amino acids are usually referred to as oligopeptides rather than polypeptide
insulin – small protein that contains two polypeptides, one with 21 amino acids and the other with 30
Ribosomes link amino acids together one at a time until a polypeptide is fully formed. Ribosomes make peptide bonds between any pair of amino acids so any sequence of amino acids is possible.
The amount of amino acid sequences can be calculated starting with dipeptides. Amino acids in a dipeptide can be any of the 20 so there are 20 times 20 possible sequences – there are 20 x 20 x 20 possible tripeptide sequences for a polypeptide of n amino acids there are 20 n possible sequences # of amino acids in a Polypeptide can be from 200 to 1000s example, 400 amino acids there are 20^400 possible amino acid sequences
2.4.U.4 The amino acid sequence of polypeptides is coded for by genes.
2.4.U.4 The amino acid sequence of polypeptides is coded for by genes.
Be able to:
Outline the relationship between genes and polypeptides.
The number of amino acids sequences that could be produced is immense but living organisms only actually produce a small fraction of these. A typical cell produces polypeptides with thousands of different sequences and must store the information needed to do this- the amino acid of sequence of each polypeptide is stored in a coded form in the base sequence of a gene.
Some genes have other roles but most genes in a cell store the amino acid sequences of a polypeptide- using a genetic code to do this. Three bases of the gene code are needed to code for each amino acid in the polypeptide. The base sequence that actually codes for a polypeptide is known to molecular biologists as the open reading frame- one puzzle is that open reading frames only occupy a small proportion of the total DNA of a species.
2.4.U.5 A protein may consist of a single polypeptide or more than one polypeptide linked together.
2.4.U.5 A protein may consist of a single polypeptide or more than one polypeptide linked together.
Be able to:
Outline the structure and function of three example proteins composed of two or more polypeptides linked together.
Some proteins are single polypeptides but other are composed of two or more Polypeptides linked together.
a dipeptide is a molecule consisting of two amino acids linked by a peptide bond
amino acids that are linked together by ribosomes to make polypeptides all have some identical structural features – a carbon atom in the centre of the molecule is bonded to an amine group, a carboxyl group and a hydrogen atom
carbon atom is also bonded to an R group = different in each amino acids
amine groups and the carboxyl groups are used up in forming the peptide bond – R group of the amino acids that give a polypeptide its character
repertoire of R groups allows living organisms to make and use an amazingly wide range of proteins
certain proteins possess a fourth level of structural organisation called a quaternary structure
quaternary structures are found in proteins that consist of more than one polypeptide chain linked together
alternatively, proteins may have a quaternary structure if they include inorganic prosthetic groups as part of their structure
not all proteins will have a quaternary structure – many proteins consist of a single polypeptide chain
2.4.U.6 The amino acid sequence determines the three-dimensional conformation of a protein.
2.4.U.6 The amino acid sequence determines the three-dimensional conformation of a protein.
Be able to:
Contrast the structure of globular proteins with the structure of fibrous proteins.
Describe the structure of membrane bound globular proteins.
Where no secondary structure exists, the polypeptide chain will form a random coil conformation of a protein is its three dimensional structure.
The overall three-dimensional configuration of the protein is referred to as the tertiary structure of the protein The tertiary structure of a polypeptide chain will be determined by the interactions between the variable side chains
These interactions may include hydrogen bonds, disulphide bridges, ionic interactions, polar associations, etc.
determined by the amino acid sequence of a protein and its constituent polypeptides
fibrous proteins such a collagen are elongated usually with a repeating structure
many proteins are globular with an intricate shape that often includes parts that are helical or sheet like
amino acids are added one by one to form a polypeptide
they are always added in the same sequence to make a particular polypeptide
in globular proteins the polypeptides gradually fold up as they are made to develop the final conformation= this is stabilized by bonds between the R groups of the amino acids that have been brought together by the folding
globular proteins that are soluble in water- there are hydrophilic R groups on the outside of the molecules and there are usually hydrophobic groups on the inside
in globular membrane proteins there are regions with hydrophobic R groups on the outside of the molecules which are attracted to the hydrophobic centre of the membrane
in fibrous proteins the amino acid sequence prevents folding up and ensures that the chain of amino acids remains in an elongated form.
2.4.U.7 Living organisms synthesize many different proteins with a wide range of functions.
2.4.U.7 Living organisms synthesize many different proteins with a wide range of functions.
Be able to:
Contrast the generalized function of globular proteins with generalized function of fibrous proteins.
List ten functions of proteins in a cell or organism.
Describe the function of enzyme proteins.
Describe the function of hormone proteins.
Describe the function of immunoglobulin proteins.
Describe the function of pigment proteins.
Describe the function of structural proteins
2.4.U.8 Every individual has a unique proteome.
2.4.U.8 Every individual has a unique proteome.
Be able to:
Define proteome.
Contrast proteome with genome.
The proteome is the totality of proteins expressed within a cell, tissue or organism at a certain time. The proteome of any given individual will be unique, as protein expression patterns are determined by an individual’s genes
all of the proteins produced by a cell, a tissue or an organism .
compared to the genome is all of the genes of a cell, a tissue or an organism
to find out how many different proteins are being produced mixtures of proteins are extracted from a sample and are then separated by gel electrophoresis
this is to indentify whether or not a particular protein is present, antibodies to the protein that have been linked to a fluorescent marker can be used – if the cell fluoresces the protein is present
BUT the genome of an organism is fixed,the proteome is variable because different cells in an organism make different proteins
even in a single cell the proteins that are made vary over time depending on the cells activities – the proteome therefore reveals what is actually happening in an organism, not what potentially could happen
within a species there are strong similarities in the proteome of all individuals, but also differences
proteome of each individual is unique partly because of differences of activity but also because of differences in the amino acid sequence of proteins- with the possible exception of identical twins, none of us have identical proteins, so each of us has a unique proteome, even the proteome of identical twins can become different with age.
2.4.A.1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.
2.4.A.1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.
Use the link above to research more information about each of the six proteins listed here.
2.4.A.2 Denaturation of proteins by heat or by deviation of pH from the optimum.
2.4.A.2 Denaturation of proteins by heat or by deviation of pH from the optimum.
Be able to:
Define denaturation.
Outline the effect of heat and pH on protein structure.
Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Denaturation disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape
Denaturation of proteins can usually be caused by two key conditions – temperature and pH
Temperature
Temperature
High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)
pH
pH
Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
All proteins have an optimal pH which is dependent on the environment in which it functions (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)
2.4.S.1 Drawing molecular diagrams to show the formation of a peptide bond.
2.4.S.1 Drawing molecular diagrams to show the formation of a peptide bond.
Be able to:
Draw peptide bond formation in a condensation reactions.
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