1.2 Flashcards
What is the proteome?
The proteome is the entire set of proteins expressed by a genome
Why is the proteome larger than the number of genes?
Because more than one protein can be produced from a single gene as a result of alternative RNA splicing
What is alternative RNA splicing?
When different proteins can be formed from the same primary RNA transcript. (Due to alternative segments of RNA being treated as exons and introns)
What are non coding RNA genes?
Genes that dont code for proteins (not expressed)
What are some examples of non coding RNA genes?
tRNA, rRNA and RNA molecules
What is a responsive gene expression?
When a set of proteins expressed by a given cell type vary over time and under different conditions
What 4 factors affect the set of proteins expressed by a given cell type?
Metabolic activity of the cell
Cellular stress
Response to signalling molecules
Diseased versus healthy cells
What is differential gene expression?
When Identical genomes can express very different proteins
Allows cell to become more specialised and support tissue and systems which they are apart of
What are two post translational modifications?
Adding additional molecules
Proteolytic cleavage
Are eukaryotes or prokaryotes smaller?
Prokaryotic cells are smaller - limited by number of metabolic reactions it can carry out on its plasma membrane
What does it mean when it is said that eukaryotes have a small surface area to volume ratio?
Their plasma membrane is too small to carry out vital functions carried out by membranes.
Only possible because of internal membranes - increase total area of membrane
What is an endoplasmic reticulum?
Forms a network or membrane tubules continuous with the nuclear membrane.
What is the ER involved in?
The synthesis of proteins and lipids
What are vesicles?
They transport materials between membrane compartments
What is the golgi apparatus?
Series of flattened membrane discs.
What is the golgi apparatus involved in
The transport and modification of proteins
What are lysosomes?
Membrane bound organelles containing a variety of hydrolases
What do hydrolases digest?
Proteins, lipids, nucleic acids and carbohydrates
What is the cytoplasm of eukaryotes made up of?
Cytosol (liquid component)
Ribosomes (and membrane bound organelles - ER, etc)
What is the definition of cytosolic proteins?
The synthesis of cytosolic proteins is completed there (cytosolic ribosomes) and these proteins remain in the cytosol
What are examples of cytosolic proteins?
Enzymes of glycolysis
Enzymes that attach amino acids in tRNA molecules for use in protein synthesis at the ribosome.
Why are cytosolic ribosomes so important?
They are where the synthesis of all proteins begins.
What are the two types of endoplasmic reticulum
Rough endoplasmic reticulum
Smooth endoplasmic reticulum
What is the rough endoplasmic reticulum?
Has ribosomes on its cytosolic face (surface if membrane)
What is the smooth endoplasmic reticulum?
Lacks ribosomes
What are some examples of post translational modifications?
Phosphorylation
Lipidation
Hydroxylation
Give examples of secreted proteins
Include peptide hormones e.g. insulin and digestive enzymes such as pepsin
What is the secretary pathway of proteins?
Secreted proteins are translated in ribosomes on the rough endoplasmic reticulum and enter its lumen these proteins then move through the Golgi apparatus and undergo post translation notifications and are packaged into secretary vehicles that move to infuse with the plasma membrane
Many secreted proteins are synthesised as an active precursors. What is required to produce an active protein?
Proteolytic cleavage.
Digestive enzymes are an example of secreted proteins that require this to become active.
What type of reaction does an enzyme cause?
Causes a condensation reaction between two adjacent amino acids resulting in a peptide bond between them
What is the R group?
A chemical group attached to the carbon of an amino acid they very incise shape charge hydrogen bonding capacity and chemical reactivity
In what four classes are amino acids classified?
Basic (positively charged)
Acidic (negatively charged)
Polar
Hydrophobic
How is it determined which class the amino acids classify into?
Depending on their R groups
Given an example of an acidic functional R group
Carboxylic acid group (COOH)
Given an example of a basic functional R group
Amine group (NH2)
Given an example of a polar functional R group
Carbonyl (CO)
Hydroxyl (OH)
Amine (NH)
Given an example of a hydrophobic functional R group
Hydrocarbon (CxHy)
What are the four levels of structure in proteins?
Primary
Secondary
Tertiary
Quaternary
What is the primary protein structure?
The sequence in which amino acids are synthesised into the poly peptide
This determines all higher levels of a polypeptide structure
What does the primary protein structure have at each end?
The primary sequence has an N-terminus at one end and a C-terminus at the other
What is the secondary protein structure?
Amino acids along the length of the polypeptide chain interact and hydrogen bonds (between atoms of the same chain). This stabilises the secondary structure.
Between what do these hydrogen bonds exist?
Different peptide bonds, for example, the hydrogen of the amine group (N-terminus = weak positive charge) and the oxygen of the carboxyl group (C-terminus = negatively charged)
What are the three types of secondary structure?
Alpha helix
Beta pleated sheets
Turn
What is the alpha helix secondary structure?
A spiral formed by twisting the polypeptide chain and stabilising with hydrogen bonds
(R group sticks outwards)
What is the beta pleated sheet secondary structure?
Parts of the polypeptide chain running along side each other forming a corrugated sheet with R groups sitting above and below
What is a parallel Beta pleated sheet?
When all the N termini of successive strands are oriented in the same direction
What is an anti-parallel beta pleated sheet?
When successive beta strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next
What can a polypeptide chain also form?
Turns where the chain folds back on itself
What is the tertiary protein structure?
The final folded shape of the polypeptide (due to stabilised interactions between R groups
What are the five possible interactions between R groups? (Secondary structure brings them close enough to interact)
Hydrophobic interactions
Ionic bonds
London dispersion forces
Hydrogen bond
Disulphide bridges
What are hydrophobic interactions?
Because hydrophobic R grips are repelled by water, they end up to the inside of the polypeptide away from water = hydrophobic interactions
What are ionic bonds?
Strongly charged and attracted to each other
COOH and NH2 groups ionised to COO- and NH 3+
What are London dispersion forces?
We attractions between the electron cloud of atoms
May result in attraction or repulsion
What are hydrogen bonds?
Weak electrostatic forces of attraction between hydrogen atom and electronegative atoms such as oxygen or nitrogen
What are disulphide bridges?
Covalent bonds between sulphur containing R groups
What is quaternary structure?
This term describes the spatial arrangement of two or more connected polypeptide sub units in a protein.
For example, haemoglobin is made of four sub units .
What is a prosthetic group?
Non-protein units tightly bound to a protein and necessary for its function
How does temperature affect protein?
Increasing temperature denatures the protein as it begins to unfold
How does pH affect a protein?
As pH increases or decreases the normal ionic interactions are lost gradually changing the confirmation of the protein, denaturing it
What is a ligand?
Substance that can bind to a protein
What happens as a ligand binds to a protein binding site?
The confirmation of the protein changes causing a functional changes as well
What are allosteric interactions?
Interactions between spatially distinct sites on the same protein
What are allosteric enzymes?
Any enzymes whose activity is regulated by altering its conformation
What is the second type of site on an allosteric enzyme called?
Allosteric site
What are modulators?
Can regulate the activity of the enzyme when they bind to the allosteric site changing the confirmation of the enzyme therefore changing the affinity of the active site for the enzyme substrate
What are the two types of modulators?
Positive and negative
What is a positive modulator?
Activators that increase the enzymes affinity for the substrate
What are negative modulators?
Inhibitors that reduce the enzymes affinity for the substrate
What is cooperativity?
When changes in binding at one sub unit, alter the affinity of the remaining subunits
What can cause reversible confirmational change in proteins?
The additional removal of a phosphate (common in post translational modification)
What is phosphorylation and dephosphorylation?
Phosphorylation-addition of phosphates
Dephosphorylation -removal of phosphate
What do protein kinases do?
Catalyse the transfer of the terminal phosphate of ATP to specific R groups of other proteins (KAPO)
What do protein phosphatases do?
Catalyse the reverse reaction or transfer a phosphate group from proteins onto ADP to regenerate ATP (PEPA)
What are the effects of phosphorylation?
Some proteins are activated whilst others are inhibited.
Ionic interactions in on phosphorated proteins can be disrupted and new ones created
