Unit 1 KA2 Flashcards
What is the proteome?
It is all the proteins made from all the genome
In eukaryotic cells, what size is the proteome compared to the genome. (2 points) Why? (3 points)
- Larger
- Because alternative RNA splicing allows for more than one protein to be expressed
Not all genes are expressed as…
Proteins in a particular cell type
What can happen to the set of proteins expressed over time?
They can vary because of certain conditions
Name the factors that can affect types of proteins expressed
- Metabolic activity
- Cellular stress
- Response to signalling molecules
- Disease
Give an example of metabolic activity
Age
Dormancy state
Give an example of cellular stress
Extremes of:
- temperature
- pH
-exposure of toxins
Give an example of a response to signalling molecules
Hormones
What can RNA genes be transcribed to produce?
tRNA, rRNA, mRNA, RNA molecules that
1. Control gene expression of other genes
2. Protection of telomeres
Alternative RNA Splicing
definition
Removal of non-coding introns from a primary mRNA transcript to leave only the coding exons; several different mature transcripts can be produced from a single primary transcript
ER
what does it stand for and what is the definition?
- endplasmic reticulum
- a network of membrane tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane
exon
definition
a section of RNA that is usually retained in splicing
Glycoprotein
definition
a protein with a carbohydrate added by post-translational-modification
Golgi Apparatus
how is it identifiable? definition.
- it is a series of membrane discs
- it packages proteins into membrane bound vesicles inside the cell before the vesicles are sent to their destination
looks like pancakes, acts as the amazon of the cell
Hydrolases
a class of enzymes that use water the break chemical bonds
intron
a section of RNA that is usually removed during splicing
Lysosome
definition
a modified golgi vesicle containing hyrolytic enzymes
Non-coding RNA gene
A gene that codes for RNAs other than mRNA so do not code for a protein
phospholipid
definition
component of cell membranes
post-translational modification
definition
addition of different chemical groups to, or modification of, a protein to allow a particular function
Proteolytic cleavage
definition
A major form of post-translational modification
digestive enzymes require this
activate protein
Proteolytic cleavage
process in brief and the purpose of this
occurs when a protein cleaves one or more bonds in a target protein to activate, inhibit or destroy the protein’s activity
cleaves- cuts out
RER
definition
- Rough endoplasmic reticulum
- organelle made up of membranes with ribosomes attached
Signal sequence
a short stretch of amino acids at one end of the polypeptide that determines its eventual location in the cell
SER
what it stands for and definition
- Smooth endoplasmic reticulum
- an organelle found in most eukaryotic cells
what does SER produce compared to RER
SER- lipids, steroid hormones
RER- proteins
vesicles
definition
small membrane bound compartments filled with liquid
microtubules
definition
a network of tubes where vesicles move across the cell
cytosolic proteins
definition
finish translation in cytosol and stay there to synthesise proteins
carry a signal sequence that directs them to the correct location inthe cell
cytosolic proteins
examples
enzymes of glycolisis
enzymes that attach amino acids to tRNA molecules for use in protein synthesis
where does ALL protein synthesis start?
cytosol
transmembrane protein production
steps
- begins in cytosolic ribosomes
- signal sequence causes CR to dock with ER forming RER
- translation is halted
- transmembrane protein is synthesised
- once translation is completed ribosome is released back into cytosol
- proteins that are in the ER are transported by vesicles and fuse with thegolgi apparatus
what happens to the vesicles after transmembrane protein production
they go through the golgi apparatus where they undergo post translational modification
after the vesicles leave the golgi what happens
how is this done?
they take they proteins to the plasma membrane and lysosomes
they move along microtubules
sectretory pathway
steps
- secreted proteins are translated in ribosomes on the RER and enter its lumen
- proteins move through the golgi and then are packaged into sectretory vesicles
- these vesicles move to and fuse with the plasma membrane
- this releases the proteins out of the cell
proteolytic cleavage
steps
inactive protein has its masking sequece cleaved to produce an active enzyme
4 types of amino acid groups
- basic (+ve)
- acidic (-ve)
- polar
- hydrophobic
what does the R group do to the amino acid
it gives unique chemical propities and specific shape
basic amino acid
how many and how are they uniquely identifiable?
- 3
- have NH2 on the R GROUP
they are strongly hydrophilic
acidic amino acid
how many are there and how are they made uniquely identifiable?
- 2
- they have a carboxylic group on the R group
they are strongly hydrophobic
polar amino acids
how are they identifiable?
they either have N, O, S on their side chain
also may include hydorxyl, carbonyl and amine group
hydrophobic (non-polar) amino acid
how are they identifiable?
they have long R chains with H on them
nothing special about them and have no charge
What is the primary structure of proteins?
SQA definition
sequence in which the amino acids are synthesised into the polypeptide
What is the secondary structure of proteins?
SQA definition
hydrogen bonding along the backbone of the protein strand results in regions of secondary structure
What are the 3 types of secondary structure in proteins?
- Alpha-helices
- parallel/antiparallel beta-pleated sheets
- turns
How can secondary protein structures be identified?
their features
- Alpha-helices = spirals
- Beta-pleated sheets = zigzags or corregated material
- Turns = a point in which the polypeptides reverses or changes direction
What types of interactions hold the R groups in the tirtery structure together?
- Hydrophobic interations
- ionic bonds
- hydrogen bonds
- LDFs
- Van der Waals interactions
- Disulfide bridges
What is the quaternary protein structure?
It exists in proteins with several connected polypeptide subunits held together by the interations seen in the tirtary groups
What is a prosthetic group?
Give an example
- they are a non-protein structure that are necessary for its function
- example of haem on haemoglobin
What are the two factors that affect protein structure?
- pH
- temperature
When changing the factors that affect protein structure, what specifically happens to bonding and interactions?
include both factors in your answer
- An increase in temperature will disrupt weaker bonds and possibly melt covalent ones
- A change in pH will result in the normal ionic interations between R groups being lost.
What is the name given to the ends of the secondary structure?
c terminus and n terminus
What is a ligand?
a substance that can bind to a protein
What allows binding to ligands?
R groups
What does protein folding produce?
ligand binding sites on the surface of the protein
what is a nucleosome?
combination of DNA being wrapped around histone protein
What is a ligand?
a substance that can bind to a protein
What does protein folding produce?
ligand binding sites that will have complementary shape to the ligand
Nucleosome
DNA is wrapped around histones to form this
What changes when the ligand binds to a protein binding site?
conformation of protein which therefore changes function of protein
What does the binding of one molecule do to one active site of an allosteric enzyme?
it increases the affinity of the other active sites for binding of subsequent substrate molecules
In binding what do many allosteric enzymes show?
co-operativity
What is co-operativity?
changes in binding at one subunit alter the affinity of the remaining subunits
What are allosteric enzymes?
enzymes that contain an allosteric site (non-substrate binding site)
What are modulators?
they are examples of ligands
What do modulators do?
regulate the activity of the enzyme when they bind to the allosteric site
What happens after the binding of a modulator to the allosteric site?
the conformation od the enzyme changes which alters the affinity of the active site for the substrate
What do + and - modulators do?
+ increase the affinity of the enzyme to the substrate +
- decrease the affinity of the enzyme to the substrate -
Give an example of cooperativity
release of oxygen in haemaglobin- changes the binding of oxygen at one subunit alters the affinity of the remaining subunits for oxygen
What affect the binding of oxygen to haemaglobin
- pH
- temperature
how do the factors lower the affinity of haemaglobin for oxygen?
a decrease of pH (from the production of carbonic acid)
an increase in temperature
this means when your body is hot oxygen can be released into your blood
how do factors increase the affinity of haemaglobin for oxygen?
increase in pH
decrease in temperature
reduces oxygen delivery to tissue
What can cause reversible conformational change in proteins?
The addition or removal of phosphate
what is phosphorilation?
a common form of post transational modification
what do protein kinases do?
catalyse the transfer of a phosphate group to other proteins
add to
What do protein phosphatases do?
catalyse the removal of phosphate from a protein
take away
Phosphorylation
- can activate or inhibit proteins
- brings about conformational change that can affect te proteins activity
- adding a phosphate group creates a negative charge
- activity of cellular proteins can be regulated by phosphorylation
