Biology IB HL - 2.4 Amino Acids

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

Amino acids all share a common basic structure, with a central carbon atom bound to:

An amine group (NH2)

A carboxylic acid group (COOH)

A hydrogen atom (H)

A variable side chain (R)

There are 20 different amino acids which are universal to all living organisms

Amino acids are joined together on the ribosome to form long chains called polypeptides, which make up proteins

Each type of amino acid differs in the composition of the variable side chain

These side chains will have distinct chemical properties (e.g. charged, non-polar, etc.) and hence cause the protein to fold and function differently according to its specific position within the polypeptide chain

Amino acids can be covalently joined together in a condensation reaction to form a dipeptide and water

The covalent bond between the amino acids is called a peptide bond

long chains of covalently bonded amino acids are called polypeptides

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

Peptide bonds are formed between the amine and carboxylic acid groups of adjacent amino acids

The amine group loses a hydrogen atom (H) and the carboxylic acid loses a hydroxyl (OH) – this forms water (H2O)

The order of the amino acid sequence is called the primary structure and determines the way the chain will fold

NO

Different amino acid sequences will fold into different configurations due to the chemical properties of the variable side chains

Alpha helices

Beta-pleated sheets

Alpha helices occur when the amino acid sequence folds into a coil/spiral arrangement

Beta-pleated sheets occur when the amino acid sequence adopts a directionally-oriented staggered strand conformation

Both α-helices and β-pleated sheets result from hydrogen bonds forming between non-adjacent amine and carboxyl groups

Where no secondary structure exists, the polypeptide chain will form a random coil

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.

The affinity or repulsion of side chains will affect the overall shape of the polypeptide chain and are determined by the position of specific amino acids within a sequence

Hence, the order of the amino acid sequence (primary structure) determines all subsequent levels of protein folding

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

NO

| Not all proteins will have a quaternary structure – many proteins consist of a single polypeptide chain

An example of a protein with a quaternary structure is haemoglobin (O2 carrying molecule in red blood cells)

Haemoglobin is composed of four polypeptide chains (two alpha chains and two beta chains)

It is also composed of iron-containing haeme groups (prosthetic groups responsible for binding oxygen)

Denaturation is 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 or abrogation of the tertiary structure will alter its activity

temperature and pH

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)

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)

A gene is a sequence of DNA which encodes a polypeptide sequence

transcription and translation

making an mRNA transcript based on a DNA template (occurs within the nucleus)

using the instructions of the mRNA transcript to link amino acids together (occurs at the ribosome)

one gene will code for one polypeptide

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

The proteome is the totality of proteins expressed within a cell, tissue or organism at a certain time

YES

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

The proteome is always significantly 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 (e.g. glycosylated, phosphorylated, etc.) following translation to promote further variations

Structure – e.g. collagen, spider silk

Hormones – e.g. insulin, glucagon

Immunity – e.g. immunoglobulins

Transport – e.g. haemoglobin

Sensation – e.g. rhodopsin

Movement – e.g. actin, myosin

Enzymes – e.g. Rubisco, catalase

Collagen: A component of the connective tissue of animals (most abundant protein in mammals)

Spider silk: A fiber spun by spiders and used to make webs (by weight, is stronger than kevlar and steel)

Insulin: Protein produced by the pancreas and triggers a reduction in blood glucose levels

Glucagon: Protein produced by the pancreas that triggers an increase in blood glucose levels

Immunoglobulins: Antibodies produced by plasma cells that are capable of targeting specific antigens

Haemoglobin: A protein found in red blood cells that is responsible for the transport of oxygen

Cytochrome: A group of proteins located in the mitochondria and involved in the electron transport chain

Rhodopsin: A pigment in the photoreceptor cells of the retina that is responsible for the detection of light

Actin: Thin filaments involved in the contraction of muscle fibres

Myosin: Thick filaments involved in the contraction of muscle fibres

Rubisco: An enzyme involved in the light-independent stage of photosynthesis