Proteins Flashcards
Proteins
- made of amino acids
- Amino acids attached together by peptide bonds
- -a chain of a.a attached by peptide bonds make up a protein
Hsp 70
Example of a protein CHAPERON
Has a nucleotide binding domain and substrate binding domain.
- requires ATP
-The nucleotide binding domain binds ATP & the substrate binding domain bind the newly formed piece of protein.
-need help from DnaJ & Hsp40)
- also needs help from others protein to stick in another phosphate group so that the substrate domain release the polypeptide chain
What are the not functional groups of a protein?
Non-functional groups are:
The amino group
The carboxyl group
What is the functional group of a protein?
The R group= the side chain
Dictate how proteins folds and how proteins folds dictate the protein’s function.
What are the non-polar R-groups
Hydrophobic don’t want to interact with water.
-all R-groups are a carbon chain that increase in length.
What are the polar amino acids
Side chain with polar covalent groups . ( Except for glycine )
- want to interact with water
Charge amino acids?
Acids and basic side changes
- acidic negative charge and like to five up a proton
- basic are positive charge and like to accepts a proton
Amino acids
There are 20 amino acids
- basic structure of each Amino acid is : an amino group, carboxyl group and a a R-chain attached to alpha Carbon
- the side chain is what change between each amino acid.
Levels of protein structure?
Primar y , secondary, tertiary and quaternary
Primary structure: linear change of a.a constructed by the ribosome
- non-specifics structures dictated by mRNA
- has directionality (N terminus & C-terminus)
N-terminus
The amino group has N-group Sticking out
C-terminus
Carboxyl end has a carboxyl group
Peptide bond formation
Forms from a dehydration = condensation reaction.
- lost of a water molecule joints two amino acids together.
Secondary structure
–Due to hydrogen bonds between the polypeptide backbone (non-functional groups )
Alpha helix/ Bleated sheet / Beta turns
Alpha helix
Secondary structure
Formed by hydrogen bonds between the remnant of amino group hydrogen bonding with the remnant of the carboxyl group further up in the chain.
Only good at certain area of proteins.requires a specific angles for the hydrogen bonds to form.
- prolines because of the amino group in the side chain, do not form alpha helixes,(aka alpha helix breakers) and disrupt the hydrogen bonds
Beta pleated sheet
-usually forms the face(side) of a proteins.
Hydrogen bonds between amino and carboxyl groups
-
Beta turns
Involves primarily 2 a.a= proline&glycine
Proline makes a tight turn and glycine helps because of its small R- group
Tertiary structure
Formed by interactions between the R-groups
- Hydrogen bonds b/w polar a.a
- disulfide bridges b/w 2 cystine
- Van der waals = hydrophobic
- ionic interaction
Quaternary structure ( not always present)
Formed when two or more proteins interact with each other.
Each individual protein involved is refer as a subunit
-
Motifs ( repeated patterns)
- tertiary structures found often in proteins and they are given name.
- coiled & coiled
- helix loop helix
- zinc fingers
Coiled & coiled ( structural motifs)
Formed by hydrophobic forces
Formed by multiple alpha helixes
Structure hold by hydrophobic interactions, in the center of coiled & coiled are the hydrophobic a.a and in the outside is the hydrophilic
- the coiled &coiled structure is hold by van der waals forces .
Helix loop helix ( structural motifs)
Loop usually towards the surface of the protein.
-Inside the loop is usually located an ion that helps regulate the function of the protein.
Zinc fingers ( structural motifs)
Composed of an alpha helix and 2 beta sheets and Zinc. Held together by zinc
Zinc: helps to coordinate
One of the structure that allow protein latch onto the DNA.
Domains ( protein structure )
Ways of describing the function of an area of a protein.
Domains: involves tertiary structure
- functional domain: area of the protein that comfort the protein ‘s function.
- structural domain: provide the protein with its structure.has nothing to do with the protein ‘s function
- topological domain: determine where inside the cell that protein is going to be founded or direct it to.( at the cell wall or ER)
Protein folding:
Self folding but with limitations because the Peptide bond act as a double bond
- gets help from chaperones & chaperonins
What are the forces driving self - folding?
- what is the limitation of self folding?
During self folding hydrophobic a.a go to the inside and hydrophilic go to the outside.
- self folding is driven by
- –hydrophobic / hydrophilic
- -hydrogen bonding
- -steric hindrance
- The limitation comes because the peptide bond has the characteristics of a double bond
What assist newly formed proteins folded inside the cell?
Molecular chaperones & chaperonis.
Molecular chaperones
- Are proteins as well
- Example HS70
- Help proteins fold up in the correct tertiary structure.
- stabilize short sequences( sticky part) to prevent aggregation ***
What does DnaJ/Hsp40 do?
They cause Hsp70 ATP to loose a phosphate group ( ATP-> ADP ), causing the substrate binding domain to change shape and act as clamp, and grab the polypeptide , shielding the polypeptide chain from this sticky area.
What are chaperonins?
Act like a barrel
- chambers that hid parts of proteins allowing time to fold properly
- examples of chaperonins: GroEl &GroES
- requires ATP
Name a eukaryotic chaperonins
Hsp60
GroEl & GroES ( en E. Coli)
Prokaryotic chaperonins
-requires ATP
GroEL: act as barrel
GroES: cap the other side.
-Either correct folding or initiate folding.
- barrel creates a microenvironment allows the protein to unfold and refold property or allow the proper folding.
What happens when folding goes wrong ???
Nose
PRIONS?
Misfolded proteins.
- proteins that replicate on its own
Example: mad cow disease
PrP SC?
A prion that causes mad cow diseases
- causes human PrP c to turn into a bad protein by 2alpha helixes into two beta sheets .
Types of proteins?
- Structural proteins : hold everything together inside your cell.
- functional proteins: do work ( enzymes)
What are scaffold proteins ?
Put multiple function proteins in one location
What are some functional proteins ?
Scaffold
- transport: across membrane
- Regulatory: help turn on/off genes
- motor: move protis & bacteria (cilia)
Proteins usually work together ?
Yes , proteins interact with each other
What is a ligan?
A molecule ( ion, hormone, drugs) that binds to a protein
How we describe how ligans bind to a protein?
Specificity & affinity
What is protein Specificity ?
The ability of a protein to bind to a ligan.
- high specificity -> only binds to one ligan.
– low specificity the protein binds to multiples ligans
What is protein affinity?
Tightness or strength of binding between ligan and protein.
-express as Kd. High Kd value-> low affinity.
Bases on molecular complement arty
Why would a protein have low specificity ?
Because some proteins would like to bind to multiple ligans to integrate multiple signals inside the cell.
Antibodies
2 light chain + 2 heavy chain
Have very high specificity and look for very specific ligan
- have high affinity to hold long enough to the antigen to allow opzimization.
What are enzymes?
Are proteins
act as catalyst
lower the activation energy ( speed up the reaction)
- get reactants together and orient them in the proper direction
- usually have high specificity
Lock & key vs. induced fit
- Lock ( enzyme) , key (ligan). Enzymes is static
- induced fit: the enzyme is always moving***
Part of the enzyme?
- Active site: where substrate binds to enzyme. Only a free a.a fits.
- catalytic site: area where the action is performed ( can be separate from active site or not)
E+S E-S —> E+P
Kd= [E] [S]/[E-S]
K1: how fast enzyme & substrate combine
K-1: enzymes & substrate falling apart
If Kd is low is because [E-S] is a big number meaning the combine very fast.
-but if Kd is high there is a low affinity meaning the numerator [E]or [S] value is high. Therefore there are more enzymes and substrate hanging around than forming a complex.
How enzymes work metabolic pathway ?
Each one of the reaction is catalyzed by a different enzyme.
Optimality in enzymatic reactions
Range values over which enzymes can work–> @ optimal point you obtain the optimum catalyst
- optimum pH
- optimum temperature
What happen If you lower or raise the optimum temperature of an enzyme?
If lower you reduce the kinetic energy and reaction slows down
- if you raised above you start denaturing the enzyme and the breaking the hydrogens bonds holding together the proteins in your proteins so the enzyme not longer work.
What happen if you change the pH to other than optimum of your emzymes?
One of the thing hold tertiary structures is charges in the e chain. By hanging the ph amino acids start changing charges and you change the 3D structures.
How serine protease works?
The binding site control specificity because asp a.a is negative charges therefore only + charged would go in
- serine in the catalytic site will break the peptide bond thus cutting the polypeptide chain (protein ) in half
3 steps of protein purification ?
- tagging
- purification
- SDS PAGE electrophoresis
Tags used to identify ( purify ) proteins?
-6x HIS tag ( string of 6 a.a)
Will attach to Ni
-FLAG tag ( DYKDDDDK)
Will attach to an antibody
What is western blot?
Use antibodies to see if protein is been purify.
Steps in western blot?
-SDS PAGE GEL
Separate things based on its size
What is western blot?
Relays in 2 antibodies and tells I if you purify your protein
- primary antibody specific to your protein or tag
- secondary antibody is specific for the primary antibody
Secondary often has a molecule you can see
What technique would used to determine protein sequences ?
Mass spectroscopy determines the sequence of protein based on its mass.
Works on crude or purified proteins.
How does yeast to hybrid works?
Attach half of transcription factor gal4.
If the half come together transcription factor activates and thus the proteins interacted together
How is Gal4 used in yeast to hybrid?
TF gal4 function as a signal.
Has an activating binding domain and DNA binding domain.
- attach Activating binding domain to the bait
- attach the DBD to the pray
– if the two proteins interacts the 2 domains will come close together and the gene will be transcribed .
How BifC ?
Works as yeas two hybrid but uses half of a fluorescent proteins attach to a bait and pne half to apray if the bait and the brait come together the two half of the fluorescent protein come together and a light is visible.
What technique would use to determine if two proteins interact in Vivo?
- Yeast two hybrid
- BifC ( bifluorescent complement action)
