AH Biology 1.2 Proteins

Proteome

The entire set of proteins expressed by a genome

• Larger than the genome as multiple proteins can be produced from a single gene as a result of alternative RNA splicing and PTM

Non-coding RNA genes

Genes that are transcribed to produce tRNA, rRNA and other RNA molecules that control the expression of other genes

(genes that are not expressed as proteins)

The set of proteins expressed by a given cell type is affected by

• Cellular stress

• Healthy vs diseased cells

• Response to signaling molecules

• Metabolic activity of the cell - cell function

Eukaryotic cells have a system of internal membranes, which increases the total area of membrane

Endoplasmic reticulum

Forms a network of membrane tubules continuous with the nuclear membrane

• rough ER has ribosomes

• smooth ER synthesizes lipids

Cells that synthesize and release lots of proteins have a large amount of ER as they need larger surface area of internal membrane (e.g. liver/pancreas cells)

Gogli apparatus

A series of flattened membrane discs

Lysosomes

Membrane-bound organelles containing a variety of hydrolases that digest:

• proteins

• lipids

• nucleic acid

• carbohydrates

This membrane bilayer prevents hydrolases inside the lysosomes from destroy the cell

Vesicles

Transport materials between membrane compartments

(small spheres of membrane)

Membrane is made out of two main components

• Lipids

• Proteins

Lipids are synthesized in the smooth ER and inserted into its membrane

The components for lipids are floating in the cytosol

Cytosolic proteins

• Proteins for nucleus, mitochondria, chloroplast etc

• Synthesis start and end in the cytosol

• Remain in the cytosol

Transmembrane proteins

• Carry a signal sequence [short strand of amino acids at one end of the polypeptide that determines the eventual location of the protein]

• Signal sequence halts translation and direct the ribosome to dock with the ER forming rough ER, before resuming translation

• Membrane protein is inserted into the membrane of the ER

• Secreted protein enter the lumen of the ER

Post-Translational Modification

• Addition of chemical groups in the Golgi apparatus

• Proteolytic cleavage after the protein leaves the cell

Addition of chemical groups in the Golgi apparatus

1. Proteins in the ER are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus

2. Molecules move through the golgi discs in vesicles that bud off from the last disc and fuse with the next one

3. They undergo PTM catalysed by enzymes while moving through the discs (e.g. addition of a carbohydrate - adding various sugars in multiple steps to form a carbohydrate)

4. Vesicles leaving the apparatus may…

   • carry proteins to the plasma membrane and lysosomes

   • move along microtubes to fuse with other membranes

Proteolytic cleavage (for secreted proteins)

• Secreted proteins are packaged into secretory vessels which fuse with the plasma membrane, releasing proteins out of cell

• Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to become acive proteins (e.g. digestive enzymes) [usually involves removing parts of the proteins]

R groups of amino acids vary in

• Size

• Shape

• Charge

• Chemical reactivity

• Hydrogen bonding capacity

Amino acids are classified according to their R groups

• hydrophobic

• polar*

• acidic* (-)

• basic* (+)

*hydrophilic

Levels of proteins structure

• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

Primary structure

The sequence in which amino acids are synthesised into the polypeptide

Secondary structure

Arise from hydrogen bonding along the backbone of the polypeptide

• Alpha helices

• Beta-pleated sheet [parallel/anti-parallel]

• Turns

Tertiary structure

Further folding of the polypeptide stabilised by interactions between R groups:

• Hydrophobic interactions

• Hydrogen bonds

• Ionic bonds

• London Dispersion Forces

• Disulfide bridge (covalent bond between R groups containing sulfur)

Quaternary structure

Exists in proteins with multiple connected polypeptide subunits (e.g. haemoglobin)

Prosthetic groups

Non-protein unit tightly bound to a protein

• necessary for its function

Factors affecting R groups interaction in proteins

• pH →

  • ionic interaction between charged R groups are lost when pH increase/decrease from the optimum

• temperature →

  • disrupt interactions between R groups causing unfolding of protein [denature]

Ligand

A substance that can bind to a protein

R groups not involved in protein folding form binding sites that have complementary shape and chemistry to the ligand

Ligand bind → conformation change → function change

Allosteric enzymes

Enzymes whose activity is regulated by changing its conformation

• active site → substrate

• allosteric site → ligand [modulators]

Modulator bind → conformation change → affinity change

Positive modulators increase the active site’s affinity for substrates

Negative modulators reduce the enzyme’s affinity for substrates

Co-operativity

= changes in binding at one subunit alter the affinity of the remaining subunits

Most allosteric proteins have quaternary structure & show cooperativity in binding. (e.g. haemoglobin)

When an oxygen bind to a haem group

Affinity of other haem groups for oxygen increase

→ easier to gain oxygen

When an oxygen is released by a haem group

Affinity of the other haem groups for oxygen decrease

→ easier to lose oxygen

Haemoglobin hold more oxygen in a high oxygen environment (lungs) and hole less oxygen in a low oxygen environment (tissues)

Exercise increase body temp and produce CO2, acidifying the blood

→ high temp + low pH

→ haemoglobin’s affinity for oxygen decrease

→ release more oxygen into tissues

The addition/removal of phosphate (a form of PTM) can cause reversible conformational changes in proteins which affect their activity.

• Adding a phosphate group adds -ve charges which affect ionic interactions in proteins

The activity of many cellular proteins [enzymes/receptors] are regulated by activating/inhibiting them using phosphorylation

Protein kinase → phosphorylate

Catalyse the transfer of the terminal phosphate of ATP to (specific R groups in) other proteins

Phosphatase → dephosphorylate

Catalyse the removal of a phosphate group from proteins