1.2 proteins Flashcards
what is the proteome?
the entire set of proteins expressed by a genome
why is the proteome larger than the genome?
due to alternative splicing and post-transational modification (more than one protein being produced by a single gene)
what is the name for genes that do not code for a protein?
non-coding RNA genes
which genes are included in non-coding RNA genes?
those that are needed to transcribe tRNA, rRNA, and other RNA molecules that directly control the expression of other genes
the set of proteins expressed by a given cell
type can vary over time and under different
conditions. what are some factors that affect this?
metabolic activity
cellular stress
response to signalling molecules
diseased vs healthy cells
eukaryotes have a relatively small surface area : volume ratio. what does this mean?
the plasma membranes of these cells are too small to carry out the vital functions required
what is present in eukaryotic cells to account for the small plasma membrane?
a system of internal membranes to increase the total surface area
what are the endoplasmic reticula? (ER)
a network of membrane tubules that are continuous with the nuclear membrane
what are the golgi apparatus?
a series of flattened membrane discs
what are lysosomes?
membrane-bound organelles that contain a variety of hydrolases that digest
proteins, lipids, nucleic acids and
carbohydrates
what is the role of vesicles?
transport materials between membrane compartments
where are lipids made before being inserted into the membrane?
in the SER
in which type of ribosome are all proteins made?
in the cytosolic ribosomes
what happens once cytosolic proteins are synthesised?
they remain in the cytosol (liquid part of the cytoplasm)
what is the purpose of the signal sequence carried by transmembrane proteins?
to halt translation and direct the ribosome synthesising the protein to dock
with the ER, forming RER
what is a signal sequence?
a short stretch of amino
acids at one end of the polypeptide that
determines the eventual location of a protein
in a cell
what happens after docking?
translation continues and the protein is inserted into membrane of the ER
what happens once proteins have been synthesised at the ER?
they are transported to the Golgi apparatus by vesicles that bud off of the ER
how do molecules move through the Golgi?
in vesicles that come from one disc and fuse to another
what happens at the Golgi apparatus?
post-translational modification
what is classed as major protein modification?
the addition of sugars in steps to form carbohydrates (catalysed by enzymes)
what happens once post-translational modification is completed?
vesicles take the modified proteins to the plasma membrane and lysosomes, which bind to the membrane and allow the proteins to be released
how to vesicles move from one structure to another?
along microtubules, fusing to other membranes within the cell
what are examples of secreted proteins?
peptide hormones and digestive enzymes
what are the steps of the secretory pathway?
1) translation in RER, proteins enter lumen
2) proteins move through Golgi and packaged into vesicles
3) vesicles fuse to pm and proteins are released
many proteins are synthesised as inactive precursors. what is required to produce active proteins from them?
proteolytic cleavage
what is proteolytic cleavage?
another type of post-translational modification
what is an example of secreted proteins that require proteolytic cleavage?
digestive enzymes
what are factors that are different between R groups?
size, shape, charge, H bonding capacity, chemical reactivity
are peptide bonds strong?
oui oui
how are amino acids classified?
according to their R group
what are the 4 amino acid classifications?
basic
acidic
polar
hydrophobic
what are the characteristics of acidic R groups?
donates a H+ ion
negatively charged
what are the characteristics of basic R groups?
accepts H+ ions
positively charged
what are the characteristics of polar R groups?
include oxygen and nitrogen in the side chain
what are the characteristics of hydrophobic R groups?
do not include oxygen and nitrogen in the side chain
what is the primary protein structure?
the order in which the amino acids and synthesised into a peptide
what is the secondary protein structure?
where hydrogen bonding in the backbone of the protein forms alpha helices, beta pleated sheets and turns
what is tertiary protein structure?
refers to the overall folding of the peptide and its final shape, stabilised by many different interactions between the R groups
describe hydrogen bonds
weak, between hydrogen and electronegative atom (NOF)
describe ionic bonds
strong, between positive and negative ions
describe LDFs
very weak
describe hydrophobic interactions
strong, reversion to avoid water
describe disulfide bridge
strong, between two R groups containing sulfur
what is the purpose of prosthetic groups?
to give the protein added function
in which type of protein structure are prosthetic groups found?
in the tertiary structure
what is an example of a prosthetic group?
haem group on haemoglobin is essential for oxygen binding
describe quaternary structure
exists in proteins with several connected polypeptide subunits. it is a description of the spatial arrangement of the subunits
how do increasing temperatures affect proteins?
it disrupts the interactions that hold the protein in shape, causing the protein to unfold, eventually becoming denatured.
how does pH affect proteins?
it affects the charges of acidic and basic R groups
as pH strays from its optimum, the normal ionic interactions between charged groups are lost, which changes the conformation of the protein until it becomes denatured
what is a ligand?
a substance that can bind to a protein
what happens when a ligand binds to a protein binding site?
conformational change
what happens in allosteric enzymes?
modulators bind at secondary binding sites which are separate from the active site
what occurs during cooperativity?
binding of one subunit changes the affinity of the remaining subunits
what is an example of cooperativity?
the binding and release of oxygen to haemoglobin - binding of one increases affinity for the others
what happens when temperature in haemoglobin increases or pH decreases?
the affinity is lowered and oxygen binding is reduced
what happens in actively respiring tissue?
affinity for oxygen decreases, releasing it into the tissue
what does the binding of an activator to an active/allosteric site do?
increases the affinity of the other active site for binding
what happens when a modulator binds to an allosteric site?
they change the conformation and alter the affinity of the active site for the substrance
how can the addition or removal of phosphates affect proteins?
can cause reversible conformational changes in proteins, affecting protein activity
what is phosphorylation of proteins a form of?
post-translational modification
what is kinase?
an enzyme that catalyses phosphorylation
what is phosphatase?
an enzyme that catalyses dephosphorylation
are proteins activated or inhibited by phosphorylation?
either
how does adding a phosphate group alter a protein?
it adds negative charges
interrupts original ionic interactions and creates new ones
