Chapter 4 Flashcards
What are some of the different types of proteins?
- enzymes (DNA polymerase)
- structural proteins (keratin)
- transport (hemoglobin and ion channels
- storage proteins (ferratin- store iron)
- motor proteins (myosin)
- signaling (insulin)
- receptors (rhodopsin)
- gene regulatory protein
What is a polypeptide chain?
a long chain of amino acids which are held by peptide bonds which are covalent bonds; you CANNOT rotate around a peptide bond but the chains can have many different shapes because rotate around other chains
What is the typical structure of an amino acid? How do two amino acids join?
- Carbon, amino group NH2, H, R side chain, carbonyl group (C double bond O and OH)
- Join by removing OH from one carbonyl and 1 H from amine group on other to connect C of carbony to N of other amine grou
What is the peptide backbone? What is the N terminus? C terminus?
- backbone is everything minus the R groups
- N terminus is the left side of bond near amine
- the c terminus is the carbonyl group
What is the classification scheme for the 20 amino acids?
Done by R group
- acidic- aspartic acid, glutamic acid
- basic- argenine, lysine
- uncharged polar- serine, tyrosine
- non polar (hydrophobic)- glycine
What’s the deal with protein shape? What’s folding controlled by?
Determined by amino acid structure, which consists of polypeptide chain which will fold up in characteristic (single stable shape….with lowest energy) ways due to interactions between atoms in polypeptide chains.
-folding is controlled by weakb bonds (h bonds, ionic interactions, hydrophobic interactions)
How can we study the shape of proteins?
- well there are many variations (if protein chain=300 aa there is 20^300 possible sequences)
- proteins in cells will have the most stability
- can study by: purifying protein an watching it how it folds; denaturing it and then renaturing it since proteins fold up w/o help, chaperons in cells may help w/ folding sometimes
What is protein organization?
- primary structure- sequence of amino acids in polypeptide chain
- secondary structure- alpha helix and beta sheet
- tertiary structure- 3D structure of polypeptide chain
- Quaternary structure- proteins are formed by larger interactions between more than 1 polypeptide chain
What’s up with secondary structures?
form due to interactions between chains of repeating backbone of a polypeptide chain (not R groups) and fold in 2 ways: alpha and beta helix
What is an alpha helix?
- single polypeptide chain that folds around itself to form a rigid cylinder
- R groups stick out of cylinder since hydrophobic
- .54 nm and 3.6 aa from one turn of the helix
- this structure is very common in membrane proteins (r groups in hydrophobic area of membrane)
Coil-Coil alpha helices
2 alpha helices intertwine in aqueous environments to minimize exposure of hydrophobic amino acid side chains to aqueous environment ex Keratin
What is a beta sheet like?
- found in the core of many proteins
- 2 types: parallel- forms from chains running in same direction and antiparallel (forms from chains running in opposite directions
- rigid structure with h bond joining peptide bonds in neighboring chains (r groups not involved) but stick out from surface of sheet
What is a protein domain?
- another level of protein organization where any segment of a polypeptide chain that folds up independently into a compact stable structure
- defined by its function
- Ex CAP protein has 2 domains
- small domain binds to DNA
- large domain binds to nucleotides
Quaternary Structure
large protein structures will have more than one polypeptide chain
- each polypeptide chain is referred to as a subunit
- binding site: any region of protein surface that interacts with another molecules vias sets of non-covalent bonds (h bonds, ionic bonds)
Classification of proteins based on quarternary structure:
homodimer?
heterodimer?
heterotetramer?
- 2polypeptide chains are the same
- 2 polypeptide chains are different
- 4 polypeptide chains that are different
How can proteins be classified?
- similar aa sequences
- similar 3D shapes
- similar function
What is a disulfide bond?
a covalent bond that often stabilizes extracellular proteins (stronger than H bonds); only can form in oxidation conditions
- cytosol is reducing environment so these bonds cant form
ex: seen in er lumen, vesicles, antibodies (which are heterotetramer
How do proteins work?
- protein structure determines function since proteins are binding specific
- this means that each protein can usually bind to 1 or a few out of thousands of molecules it will encounter
What is a ligand?
any molecules that binds to a protein; binding is dependent of on weak non-covalent bonds between matching surface of a protein and a ligand
What is a binding site?
- a cavity in the surface of a protein
- shape changes allow the protein to do work with thing is in binding site
- binding between protein and ligand induces a change in the protein shape
- hand in a glove kind of deal
What are enzymes?
powerful highly selective catalysts and also are protein
- speed up reactions
- aren’t used up in reaction
- binds to ligands
- they work in teams and can speed up a reaction by a factor of 1 million
- names end in -ase
What is Lyzozyme?
an easily purifiable protein found in eggs which is easy to isolate
- performs hydrolosis= prevents bacteria from growing in egg
- adds H20 to break a bond between 2 adjacent sugars in a polysacarride
- reaction is - delta g, spontaneous,
- helps reaction occur more readily
How are proteins controlled by cells?
- can control how much is synthesized and when protein is made
- rate at which protein is degraded is its half life
- can control how much of a protein is active or inactive
What is negative regulation of a protein?
What is positive regulation of a protein?
activity of protein is inhibited
activity of protein is increased
One type of protein regulation is Feedback Inhibition, explain
regulates the flow of metabolites through metabolic pathway
- basically final product of pathway inhibits the 1st enzyme that is unique to its synthesis
What are allosteric enzymes?
enzymes that can interact with the substrate and the final product (Which is an additional ligand which would inhibit its activity)
-these enzymes are inactivated by binding to end product of pathway
Another type of protein regulation is protein phosphorylation, explain
- regulates protein activity via addition or removal of phosphate group to a protein
- phosphate from ATP is added to a protein by kinase which may turn protein on (if not naturally on or off if it is)
What is kinase?
What is phosphotate?
- enzymes that add phosphate group to protein
- enzymes that remove phosphate group to protein
