Proteins Flashcards
What is the genome?
Total genetic material in a cell (complete set of DNA)
What is the proteome?
Entire set of proteins that can be expressed from a genome
What are non-coding RNA genes?
Genes that aren’t expressed as proteins in a particular cell type
Non-coding RNA genes are transcribed to produce…
tRNA
rRNA
RNA molecules that control the expression of other genes
The proteome is larger than… because…
The number of genes (particularly in eukaryotes) because more than one protein can be expressed from a single gene due to alternative RNA splicing
Factors that affect the set of proteins produced in a cell type…
Metabolic activity of cell
Cellular stress
Response to signalling molecules
Diseased vs healthy cells
Boundary around outside of eukaryotic cells?
Plasma membrane
Eukaryotic cells also have a… which..
System of internal membranes that increases the total area of the membrane available for vital metabolic processes
Endoplasmic Reticulum (ER)?
Forms network of membrane tubules continuous with the nuclear membrane
What are the 2 types of ER?
Rough (RER) - has ribosomes
Smooth (SER)- no ribosomes
What is the Golgi apparatus?
Series of flattened membrane discs
What are lysosomes?
Membrane-bound organelles containing a variety of hydrolases that digest proteins, carbohydrates and nucleic acids
What are hydrolases?
Enzymes that catalyse the cleavage of a covalent bond using water
Function of vesicles
Transport materials between membrane components
Membranes are made of…
Lipids and proteins synthesised in the ER
Where are lipids synthesised?
SER and inserted into its membrane by enzymes
Where are cytosolic proteins synthesised?
Cytosolic ribosomes and remain in the cytosol (liquid component of cytoplasm)
Examples of cytosolic proteins…
Enzymes for glycolysis
Enzymes that attach amino acids to tRNA at ribosomes during protein synthesis
Where are transmembrane proteins synthesised?
Begins at cytosolic proteins and completed inside ER
Transmembrane proteins carry a…
Signal sequence
What does a signal sequence do?
Halts translation and directs ribosome synthesising the protein to dock with the ER, forming RER
What is a signal sequence?
Short stretch of amino acids at one end of the polypeptide that determines the eventful location of a protein in a cell
Why does protein pore remove cytosol particle and signal sequence after docking?
To allow translation to continue
As translation continues after docking…
The protein is inserted into the membrane of the ER
What is post-translational modification?
When polypeptide chains have carbohydrates or phosphates added to them or are cleaved to form an active protein
What is the major modification?
Addition of carbohydrates
To form carbohydrates…
Enzymes catalyse the addition of various sugars in multiple steps
What are microtubules?
Structures that make the cell’s cytoskeleton and offer support and a means of transport
Where do vesicles that leave the Golgi apparatus take proteins?
Plasma membrane and lysosomes
Vesicles move along microtubules to…
Other membranes within cell and fuse with them
What are proteins transported by once they are in the ER?
Vesicles that bud off from the ER and fuse with the Golgi apparatus
How do molecules move through the Golgi discs?
In vesicles that bud off from one disc and fuse with the next in the stack
Due to their size, eukaryotes have a relatively small surface area to volume ratio so…
Plasma membrane is too small an area to carry out all the vital functions of the membrane
Examples of secreted proteins
Peptide hormones such as insulin and digestive enzymes such as trypsin
Many secreted proteins are synthesised as…
Inactivate precursors so require proteolytic cleavage to produce active proteins
What is proteolytic cleavage?
Type of post-translational modification where polypeptide is cut
What are amino acids?
Building blocks of proteins
Amino acid sequence determines…
Protein structure
What are proteins?
Polymers of amino acid monomers
Amino acids have the same… differing only in…
Basic structure, R group present
Amino acids are linked by… (occurs during translation at ribosomes)
Peptide bonds to form polypeptides
How is a peptide bond formed?
Enzyme causes condensation reaction between 2 adjacent amino acids (water is removed)
What kind of bond is a peptide bond?
Strong covalent bond
All amino acids contain an…
Amine (NH2) and acid group (COOH)
Name R groups
Acidic- hydrophilic, - , COOH
Basic- hydrophilic, + , NH2
Polar- hydrophilic, slightly charged, CO, OH, NH2
Hydrophobic- hydrophobic, no charge, CH3
R groups vary in…
Shape, size, charge, hydrogen bonding capacity and chemical reactivity
Diversity of R groups accounts for…
The wide range of functions carried out by proteins
What is primary structure?
Sequence in which amino acids are synthesised into polypeptide
What is secondary structure?
Result of hydrogen bonding along backbone of protein strand
What is tertiary structure?
Final folded shape of the polypeptide and stabilised by interactions between R groups of amino acids
What are the interactions between R groups?
Hydrophobic interactions
Ionic bonds
London dispersion forces
Hydrogen bonds
Disulphide bridges
What is quaternary structure?
Spatial arrangement of subunits, only exists in proteins with 2 or more polypeptide subunits
Subunits are linked by…
Bonds between r groups of polypeptide chains
What are London dispersion forces?
Very weak attractions between electron clouds of atoms
What are hydrogen bonds?
Strong attractions between hydrogen atom and an electronegative atom (O2 or N2)
What are disulphide bridges?
Covalent bonds between R groups containing sulphur
What are ionic bonds?
COOH and NH2 groups ionise to become COO- and NH3+ which are strongly charged and attracted to each other
What are hydrophobic interactions?
As a polypeptide folds into its functional shape, the hydrophobic R groups are repelled by water so usually end up on the inside of the protein away from the surface
What is a prosthetic group?
Non-protein subunit bound tightly to protein and necessary for its function
Ability of haemoglobin to bind oxygen is dependent upon…
non-protein haem group (prosthetic group)
Effect of increasing temperature on interactions between R groups
Disrupts interactions that hold the protein in shape so protein begins to unfold and eventually denatures
Effect of changing pH on interactions between R groups
As pH increases/decreases away from optimum, the normal ionic interactions between charged groups are lost which gradually changes the conformation of the protein until it denatures
What is a ligand
A substance that can bind to a protein
Binding sites on surface of protein will have…
Complementary shape and chemistry to ligand
Mechanism used to regulate protein activity
Conformational change
What is an allosteric enzyme?
Enzyme whose activity is regulated by altering its conformation, contain a second type of binding site (allosteric site)
Where does a substrate bind?
Active site
Where does a substance other than the substrate bind?
Allosteric site
What does a modulator do?
Regulate the activity of an enzyme by binding to the allosteric site, change conformation of enzyme which alter affinity of active site for substrate
A positive modulator…
Increases the enzyme’s affinity for the substrate, increasing activity
A negative modulator…
Decreases the enzymes affinity for the substrate, decreasing activity
Many allosteric proteins consist of…
Multiple subunits so have quaternary structure
What does allosteric mean?
‘other shape’ Refers to proteins that have interactions between spatially distinct sites (on same protein)
What happens when a ligand binds to a protein binding site?
Protein changes conformation so function changes
What is phosphorylation?
When a phosphate group is added or removed from the protein, common form of post-translational modification
A large subset of proteins is… when first synthesised so require…
Inactive, post-translational modification to become activated
What do protein kinases catalyse?
The transfer of a phosphate group from ATP to other proteins, the terminal phosphate of ATP is transferred to specific R groups
What do protein phosphatases catalyse?
The transfer of a phosphate group from protein to ADP to generate ATP (reverse reaction)
What allows binding of ligands?
R groups not involved in protein folding
What does phosphorylation do to a protein?
Conformational changes which can affect protein’s activity
Haemoglobin is made of…
4 polypeptide subunits (haem groups)
What is co-operativity?
When changes in binding at one subunit alter the affinity of the remaining subunits (shown by allosteric proteins)
What causes the activity of allosteric enzymes to vary greatly?
Small changes in substrate concentration
Binding of a substrate molecule to one active site of an allosteric enzyme…
Increases the affinity of the other active sites for binding of substrate molecules
Haemoglobin shows co-operativity in…
binding and release of oxygen
What happens when an oxygen molecule binds to one subunit of haemoglobin?
Conformation of the subunit changes
what happens when an oxygen molecule is release from haemoglobin?
Decrease in affinity of other subunits to maximise the release of oxygen where it is needed e.g. working tissues
When temperature is increased and pH reduced in actively respiring tissues
