Notes

genome - complete set of genes or genetic material
the proteome is the entire set of proteins expressed by a genome
proteome is larger then the number of genes
true in eukaryotes
this is because more than one protein can be produced by a gene cause of RNA splicing
the set of proteins expressed can change over time due to
factors affecting what proteins are expressed are - cellular stress, metabolic activity, response to signalling molecule ,diseased vs healthy cells
genes that don't code for proteins are called non-coding rna regions - they make tRNA, rRNA, RNA that control expression of other genes

proteomics is study of proteins - structure and functions
proteins are main physiological part of metabolic pathway

intracellular membranes
organelle - tiny cellular structure that performs specific functions in a cell -embedded in cytoplasm
eukaryote - any cell that has a clearly defined nucleus
these cells have a nuclear membrane surrounding it
eukaryotic cells have a relatively small surface area to volume ratio due to their small size.
therefore the plasma membrane of eukaryotic cells has too small surface area to carry out all the vital functions carried out by membranes
so they have a system of internal membranes ,which increase surface area so functions can be carried out
the endoplasmic recticulum forms a network of membrane tubules continuous with the nuclear membrane
rough ER and smooth ER
rough ER has ribosomes on its cystolic face - important in synthesis and packaging of proteins
cystolic face - surface directing towards the cytoplasm
smooth ER lacks ribosomes - storage organelle . important in creation and storage of lipids and steroids

golgi apparatus - in cytoplasm
complex of vesicles and folded membranes
involved in secretion and intracellular transport - process and packages proteins for secretion
transport of lipids and creation of lysosomes
folds are called cisternae
series of flattened membrane discs . discs are connected allowing molecules to move within it. it Is adjacent to the ER.

lysosomes - cytoplasm
membrane bound organelles containing a variety of hydrolases that digest lipids ,carbohydrates and nucleic acids. interior of lysosome is acidic so enzyme works to its optimum.

vesicles - transport materials between membrane compartment. consist of an aqueous solution enclosed by a lipid bilayer
move molecules , secrete substances, digest materials



synthesis of membrane components
lipids and proteinase synthesised In the ER
lipids are synthesised in the smooth ER and inserted into its membrane
lipids are organic compounds that are fatty acids or their derivatives - insoluble in water soluble in other organic solvents
ser not used in protein synthesis

synthesis of all proteins starts in cystolic ribosomes -RER
ribosomes are the sight of translation
translation translates mRNA into polypeptide chain.

the synthesis of cytosolic proteins is completed there and these proteins remain in the cytosol
proteins in cytosol play important role in signal transduction and glycolysis
cytosol made of mainly water , small molecules, dissolved ions , large water soluable molecules

a transmembrane protein, integral membrane protein spans whole of cell membrane and permenantly attached
transmembrane proteins carry a signal sequence, which halts translation and directs ribosome synthesising the protein to dock with ER forming RER.

this signal sequence is a short stretch of amino acids at one end of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.
translation continues after docking, and the protein is inserted into the membrane of the ER.

movement of proteins between membranes
once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.
as proteins move through the Golgi they undergo post-translational modification.
post-translational modification is the covalent modifications made to the protein after translation.
the polypeptide chain undergoes PTM to form the mature product
PTM- important in cell signalling

molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack
as they move the PTM takes place

addition of carbohydrates is the major ptm , enzymes catalyse the addition of various sugars in multiple steps to from carbohydrates.


vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.
vesicles going to the plasma membrane leave the Golgi network in steady stream
the membrane proteins and lipids provide new components for the cells plasma membrane
soluble proteins in vesicles are secreted to extracellular space

vesicles move along microtubules to other membranes and fuse with them within the cell

secretory pathway
secreted proteins are translated in ribosomes on the RER and enter its lumen.
peptide hormones like insulin and digestive enzymes like trypsin are examples of secreted proteins
the proteins move through the Golgi and are packaged into secretory vesicles
these vesicles move to and fuse with the plasma membrane releasing the proteins out of the cell

this is possible due to the fluid nature of plasma membrane
both vesicle and plasma membrane are phospholipid bilayers
this allows vesicle to fuse with membrane

many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins.
proteolysis is the breakdown of proteins into smaller polypeptides or amino acids
typically catalysed by cellular enzymes called proteases but may also occur by intramolecular digestion
another type of PTM
digestive enzymes are example of secreted proteins that require proteolytic cleavage to become active


amino acids are the building blocks of proteins
held together by peptide bonds
polypeptide goes through Golgi to undergo ptm to be protein
amino acid sequence determines protein structure.

monomer - a molecule that might bind chemically to form a polymer
polymer- long chain of monomers
proteins are polymers of amino acid monomers
amino acids are linked by peptide bonds to form polypeptides

peptide bond is a chemical bond - strong covalent
formed between two molecules when the carboxyl group of one molecule reacts with amino group of another and releases water

all amino acids have a central carbon with 4 groups attached
- amine group NH2
- carboxyl group - COOH
- side chain - r group
- a hydrogen H

the r group differs in each amino acid , all aminos have same basic structure differing only in the R group
r groups vary in
-size
-shape
-charge
-chemical reactivity
-hydrogen bonding capacity

amino acids are classified according to their r groups
- basic (+ charge)
hydrophilic and key component of their R group is NH2
-acidic (- charge)
acidic are hydrophilic and key component of their R group is COOH
-polar
hydrophilic and the key component of their R group is ,C=O,OH,NH.
-hydrophobic
non polar key component to their R group is hydrocarbon group

the wide range of functions carried out by proteins result from the diversity of R groups

protein structure
1- primary …..
primary structure is the sequence in which the amino acids are synthesised into the polypeptide
even slight change in primary structure can affect its shape and ability to function
main type of bonds In this structure are peptide

2- secondary
some amino acids form hydrogen bonds resulting in a secondary protein
caused by hydrogen bonds between amino and carboxyl groups
can contribute to how the polypeptide chain folds and coils
h bonds can be weak
the secondary structure is stabilised by h bonds between atoms of same chain

secondary structures include
-alpha helices
-parallel beta plated sheets or opposite antiparralel

alpha helices -spiral with r group sticking outwards
beta sheets has parts of chain running alongside eachother forming a sheet , r group sits above or below sheet

the polypeptide folds into a tertiary structure