IB biology: topic 2: proteins

what are proteins made up of?

proteins are comprised of long chains of recurring monomers called amino acids

what is the structure of an amino acid?

• An amine group (NH₂)

• A carboxylic acid group (COOH)

• A hydrogen atom (H)

• A variable side chain (R)

how many amino acids are there that are universal to all living organisms?

20

how are amino acids distinguished from each other?

different side chains will have different chemical properties cause the protein to fold and function differently.

how are amino acids joined together?

• amino acids covalently joined together in a condensation reaction

• forms a dipeptide and water.

• bonded by peptide bonds.

how are proteins/polypeptide chains broken down?

Polypeptide chains can be broken down via hydrolysis reactions, which requires water to reverse the condensation process.

what is the primary structure of proteins?

• the order of the amino acid sequence.

• determines the way the chain will fold.

• different amino acids have different variable side chains with different properties.

what is the secondary structure of proteins?

• alpha helices vs beta-pleated sheets.

• alpha helices = folds into a coil.

• beta-pleated sheets = staggered strand conformation.

• hydrogen bonds forming between non-adjacent amine and carboxyl groups.

what bonds form in the secondary structure of proteins?

hydrogen bonds form between non-adjacent amine and carboxyl groups

what is the third structure of proteins?

• tertiary structure - 3D configuration.

• determined by the interactions between the variable side chains.

• interactions may include hydrogen bonds, disulphide bridges, ionic interactions, polar associations.

what are examples of the interactions between cvariable side chains in the tertiary structure of proteins?

hydrogen bonds, disulphide bridges, ionic interactions, polar associations…

what is the 4th process of structural organisation in proteins?

• quaternary structure.

• found in proteins that consist of more than one polypeptide chain linked together / include inorganic groups.

how is the primary structure linked to the tertiary structure of a protein?

• affinity/repulsion of side chains affects overall shape of the polypeptide chain.

• determined by the position of specific amino acids within a sequence.

what is denaturation?

a structural change in a protein that results in the loss (usually permanent) of its biological properties.

• because the way a protein folds determines its function, any change to tertiary structure will alter its activity.

how does temperature change give rise to denaturation?

• high temp. disrupt hydrogen bonds that hold the protein together.

• the protein will begin to unfold and lose its capacity to function as intended.

• most human proteins function optimally at body temperature (~37ºC).

how does pH change give rise to denaturation?

• amino acids have both negatively (COO–) and positively (NH3+) charged regions.

• changing pH will alter the charge of the protein, which alters solubility and overall shape.

All proteins have an optimal pH which is dependent on the environment in which it functions.

what is a gene?

a sequence of DNA which encodes a polypeptide sequence

what steps convert a gene sequences to a polypeptide chain?

• transcription – making an mRNA transcript based on a DNA template.

• translation – using the instructions of the mRNA transcript to link amino acids together.

how may a single gene code for multiple polypeptides?

genes may be alternatively spliced to generate multiple polypeptide variants:

• genes encoding tRNA sequences are transcribed but never translated.

• genes may be mutated (their base sequence is changed) and consequently produce an alternative polypeptide sequence.

how many polypeptides does one gene code for TYPICALLY?

one gene codes for one polypeptide

what are exceptions to “one gene codes for one protein”?

Genes may be alternatively spliced to generate multiple polypeptide variants.

Genes encoding tRNA sequences are transcribed but never translated.

Genes may be mutated (their base sequence is changed) and consequently produce an alternative polypeptide sequence.

what is the proteome?

• the totality of proteins expressed within a cell, tissue or organism at a certain time.

• proteome of any given individual will be unique, as protein expression patterns are determined by an individual’s genes.

why is the proteome always larger than the number of genes in an individual?

Gene sequences may be alternatively spliced following transcription to generate multiple protein variants from a single gene.

Proteins may be modified following translation to promote further variations.

what are the different roles of proteins?

Structure - collagen

Hormones - insulin

Immunity - immunoglobulins

Transport - haemoglobins

Membranes - pump proteins

Enzymes - catalyse