Topic 1 & 2 - Proteomics and protein structure, binding and conformational change Flashcards
What is a genome ?
Entire hereditary information encoded in the DNA. It’s made of genes and other DNA sequences that don’t code for proteins
Eg: introns and Exons
What is a proteome
Entire set of proteins expressed by a genome.
It’s larger than the genome due to RNA Splicing and post- transitional modifications
What is a transcriptome
Full range of messenger RNA, or mRNA oR messenger mRNA and molecules expressed by an organism
What is micro- array analysis
Technique used to study transcriptome.
Step 1 of micro - array analysis
Makes copies of all the genes in the genome
Step 2
Separates all strands into single strands
Step 3
Places copies at each separate gene onto a specific point on a neatly ordered slide suspends on a droplet
Step 4
Take the cell type being studied and apply to microarray
Step 5
Scan microarray for attached cDNA
Step 6
Use logged locations to determine which genes at active in the studied cells
_____________ __________ can drive the function and often altering the structure back
Conformational change
_________ causes a conformational change in the protein, which may result in an altered function, may be reversible
Binding
Proteins are polymers of _________
Amino acids
Amino acids link _________ to form ________ ________
Peptide
Polypeptides
What is the primary sequence
It’s the order in which the amino acids are synthesised into the polypeptide
Secondary structure
Result from hydrogen bonding along the back bone of the protein strand
3 types of secondary structure formed
Alpha helices
Parallel or anti parallel beta
Turns
4 types of R Groups
Negatively charged/ acidic
Positively charged/ basic
Non-polar/ hydrophobic amino acids
Acidic amino acids have a _______ on the R Group
COOH
Are they positively or negatively charged
Negatively
Hydrophobic or hydrophilic
Hydrophilic
They ____ a proton to another atom
Donate
Two types of amino acid in this group
Aspartame and glutamate
Basic amino acids have ____ on the R group
NH2
They _____ a proton
Accept
Positively or negatively charged
Positively
Hydrophilic or hydrophobic
Hydrophilic
Name 3 basic amino acids
Lysine, arginine and histidine
3 things o the R side chain on polar amino acids
Oxygen nitrogen or sulfur
Hydrophilic or hydrophobic
Hydrophilic
They form ____ hydrogen bonds
Weak
Six polar acids name 2
Define and cysteine
Do they or do they not have OH,COOH,NH2 or SH
Don’t have
Negatively or positively charged
Neither
Hydrophilic or hydrophobic
Hydrophobic
They have ___________ and a lot of carbon atoms
Benzene rings
2 types
Glycine and phenylalanine
When polypeptide folds they become ________
Tertiary structure
Effects include _
Interactions of R groups in hydrophobic Regions Ionic bonds Hydrogen bonds Van der waals interactions Disulphides bridges
______________ groups give proteins added functions
Prosthetic
An example of a prosthetic group
Haem in haemagloblin
Quaternary structure is ____________
Several connected polypeptide subunits
2 things that influence interactions of R groups
Temperature and pH
Name for protein that has lost its shape
Denatured
Increasing temperature effect
Melt weak bonds and then stronger bonds
pH effect
Shift acidic base characters of the R group on particulate amino acids
This results in ___________
Change in ionic interactions of amino acids
Hydrophilic are __________
Water loving
These R groups predominate on ________
Surface of a soluble protein in the cytoplasm
Hydrophobic are ___________
Water hating
There R groups ________
Cluster in the centre to form a globular structure
Fluid mosaic model
Phospholipid bilayer Hydrophilic hydrophobic hydrophilic Contains proteins [ intergral/transmembrane channels/ peripheral/ transmembrane]
What is a ligand
Substance that bonds to a protein
Ligand effects the _____ of a protein
Activity
Eg enzymes, the specific shape give the _______ _____ for the substance to bind
Active site
In cell signalling why is ligand binding essential
Activate receptors or channels
Is a histone positively or negatively charged
Positive
What’s the next step
Bonds to sugar phosphate back bone
Is that positively or negatively charged
Negatively
What is a nucleosome
DNA weapped around a histone
Other protein binding sites either stimulate or inhibit _______
Transcription
Ligand binding changes ______
The confirmation of a protein
What does this cause
The functional change in a protein
Eg enzymes what two things relate to induced fit
Specified between active site and substrate
What happens when the substrate binds
Temporary change in the active site occurs
This then _______ binding and integration with the substrate
Increases
What produces lower activation energy
Chemical environment
Once _________ takes place, the original enzyme is resumed and products are ________ from active site
Catalysis
Released
What is an allosteric enzyme
Enzyme that can have its activity alerted by a ligand
What’s this type of ligand called
Modulator
These modulators bind to _________ binding sites
Secondary
The _____________ changes and alter the _______ of the active site
Confirmation
Affinity
What is the role of negative modulators
Reduce enzyme affinity for the substrate
Deoxyhaemoglobin has a ____ ________ for oxygen
Low affinity
When one molecule of oxygen binds to one of four haem groups it _______ the affinity of the remaining three haem goups
Increases
Oxyhemoglobin ______ it’s ability to ______ oxygen
Increase
Lose
This creates what ?
Oxygen dissociation curve
Low ph =
Low affinity
High temp =
Low affinity
Exersice increases body ___ and produces ___________ the body
Temp
Co2 acidifying
What is a phosphate
Highly charged group
If added or removed what does it create
A reversible conformational change in proteins
What does this charge do
Alter the r group interactions within a protein
Types of protein involved in phosphate movement
Kinease
phosphatase
ATPase
What is kinase
Group of enzymes that move things (kinetic)
Adds phosphate
Phosphorylates other proteins though ATP
What is phosphatase
Enzyme that dephosphoryaltes groups
What’s is ATPase
Enzymes use phosphate for ATP
Eg: glucose symport and muscle contractions
___________ hydrophilic signaling molecules are involved in the ________ of extracelluar _______ proteins
Extracellular
Activation
Receptor
What do they interact with ?
Intercellular proteinsthrough a series of kinases and phosphatases
The cascade of ________ and __________ activates ___________ events
Phosphorylation and dephosphoralation
Intracellular
What’s controlled this way
Insulin and blood sugar level
What happens when muscle contracts
Actin and myosin slide past each other
Step 1
Myosin heads act as cross bridges as they bind to actin at specific binding sites allowing muscle to contract
Step 2
When actin binds to myosin , the head detaches from actin singing forward and reminds. The rebounding releases the ADP and a phosphate and drags the myosin along the actin filament
