Flashcards in Chapter 4 Proteins Deck (108):
What percent of a cell are proteins?
What determines the shape of a protein?
the amino acid sequence (polar, nonpolar, positively charged, negatively charged). Proteins fold into the shape that requires the least energy.
Is the peptide bond flexible and what does this mean?
Yes, they are flexible. Their flexibility allows r-groups to orient in all sort of directions.
What holds proteins in their functional shape?
Weak, non-covalent interactions (electrostatic attractions, hydrogen bonds, van der Waals interactions) hold proteins in their functional shapes. Even though these forces are weak, when there are many of them they additive and when many are collected together they become strong.
What is unique about protein structure in aqueous solutions?
Side chains affect conformation in aqueous solutions. This is because all of the non-polar (hydrophobic) side chains will bring themselves to the core and hydrogen bonds will form between the polar side chains and the water.
What is the difference between monomeric and multimeric proteins?
Multimeric proteins are made of multiple polypeptide chains, each of which is called a subunit. Monomeric proteins are made of a single polypeptide chain.
The polypeptide backbone is a repeating sequence of what?
What are the two ends of a polypeptide chain?
N-terminus with an amino group NH3 at one end and a C-terminus with a carboxyl group COOH at the other end.
What is the native state of a protein?
The specific, conformation that a protein will fold into without any interaction. There are thousands of possibilities, but only one native shape. The native shape is almost always the one that takes the least energy to form.
What are Van der Waals attractions?
A weak electrostatic attraction that are collectively very strong.
Name three ways hydrogen bonds affect protein confirmation?
1.) Backbone to backbone bonds
2.) Backbone to side chain bonds
3.) Side chain to side chain
Name the bonds that effect a protein confirmation.
All non-covalent. ionic bonds, van der Waals interactions, hydrogen bonds, hydrophobic interactions
Name a covalent bond that affects protein confirmation
disulfide bonds. These bonds are stabilizing and typically form between sulfur atoms on cysteine amino acids.
What happens when proteins can't fold on their own?
What are the two groups of chaperone proteins?
What do molecular chaperones do?
By binding to proteins, they prevent the aggregation of unfolded or misfiled proteins, allowing unfolded proteins to have a little more time.
What do chaperonins do?
They create small chambers to sequester unfolded proteins. This allows proteins to fold w/o interference of water or other molecules in the cytosol. The chaperonins contain a cylindrical folding core. Entrance to the chaperonin proteins are controlled by lids.
Name an example of molecular chaperones.
Name an example of chaperonin proteins.
Name two disease that result from incorrect protein folding.
Parkinson's and alzheimers
What is the primary structure of protein?
The linear sequence of amino acid in a polypeptide chain
What holds the amino acids of the polypeptide chain together?
Covalent peptide bonds.
What is the secondary structure of protein?
The close/local/nearby formed by the polypeptide backbone. Amino groups are not involved in forming these structures. It is just the structure created by hydrogen bonds between the carboxyl groups to the amino acids.
Said another way, "Secondary structure is the hydrogen bonds between the backbone of the polypeptide chain"
What are alpha helixes?
Part of the secondary structure of proteins. They are hydrogen bonds made between every fourth amino acid linking one C=O to the an N-H. They can coil to the left of right.
Name the two structures of the secondary protein structure?
alpha helixes and beta pleated sheets.
Where are alpha helixes particularly abundant?
In hair and skin cells and in cell membranes. Coiled coils are very common in skin and hair.
What gives rise to beta pleated sheets and alpha helixes?
Hydrogen bonds between the amino groups (N-H) and the carboxyl groups (C=O).
How does the hydrophilic amino acid backbone of beta pleated sheet relate to the hydrophobic cell membrane when it is embedded?
Nonpolar r groups are on the outside.
What are coiled-coils?
Very stable structures made of two or three alpha helixes wrapped around one another.
What are beta-pleated sheets?
They are segments of polypeptides chains running parallel (or anti-parallel) to one another. They are bonded by hydrogen bonds between the amino and the carboxyl groups. Beta-pleated sheets can run between segments of a single chain of between different chain. In the latter case they are a part of the quaternary structure of protein.
Beta-pleated sheet are what gives silk its extraordinary tensile strength.
What causes alzheimer's?
When abnormally folded proteins are stabilized by beta-pleated sheets.
What is the tertiary structure of protein?
The non-covalent interaction between the r-goups within the protein.
What it he 3-D structure of protein called?
The tertiary structure
What are protein domains?
A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.
What percent of the mass of the cell is protein?
How many proteins are there in the human genomes?
Name some functions of proteins.
Structural Protein (colagen)
transcription factors (regulate genes)
What gives rise to the function?
What are the models of proteins?
space filling model
How long is insulin?
51 amino acid
How long tightin (a muscle protein)?
10,000 amino acids
How are peptide bond formed?
condensation (C-N) (C=O)
Hydrophoic amino acids?
How to denture a protein?
Heat, changes in pH, chemical compounds such as urea can take the hydrogen bonds that folded the protein. In a sense it outcompetes the hydrogen within the protein.
How strong are hydrogen bonds?
What are heat shock proteins?
They are chaperones that help proteins refold after being overheated.
Why is insulin so stable?
How did proteins evolve?
By bringing these fundamental units (domains). In a sense it conserved these valuable units across evolution. Highly conserved functional units.
What are disordered regions of protein?
Regions of proteins that lack stable secondary structures. They are highly flexible and can assume a stable structure after interacting with another protein.
What is a ligand?
the molecule that binds to a protein
What is a binding site?
the part of a protein to which ligands bind
What determines binding affinity?
How rare the thing to which the protein wants to bind is. If it is very rare then binding affinity tends to be quite high. If it is not rare binding tend to be less tight.
What level of structure contains domains?
The tertiary structure
What are the two main types of proteins that tertiary structures form?
Fibrous and globular
Fibrous: proteins with an elongated shape
Globular: Protein with an elongated shape
What is a dimer?
Two structurally similar monomer joined together
What types of bond create the quaternary structure of proteins?
Non-covalent bonds and disulfide bonds
What is the purpose of disordered regions?
Provide flexibility to protein structure and folding. To scaffold protein together.
What bond is responsible for stabilizing large protein complexes?
Disulfide bonds. Other than disulfide, almost all structures that hold protein complexes together are non-covalent. Disulfide bonds form between 2 cysteine amino acids.
How specific is protein binding?
Very specific. Most proteins only bind to one or at most a few ligands
what is affinity?
it measure the strength of the bond between the protein and the ligand
How does the ligand bind to the binding site?
What are the weak non-covalent interactions between ligands and proteins that lead to high affinity?
hydrogen bonds, electrostatic attractions, van der Waals attractions and hydrophobic forces is what binds a ligand to its binding site. As each bond is weak, many bonds must be formed simultaneously in order for the ligand to bind. This is only possible if the contours of the ligand match the binding site like a hand in a glove.
This specificity is how unwanted interactions are avoided.
What are antibodies?
They are Y-shaped immunoglobulin proteins produced by the immune system in response to foreign molecules. There is a small variable region at the tip of the branched part of the Y that changes depending on the antigen. The best of the Y is constant no matter what it is responding to.
They can be created to suit almost any molecule.
What is the target of an antibody called?
What is an epitope?
The region of the antigen to which antibodies bind
How precise are antibodies?
Very precise. Even if there is one amino acid off in the antigen, it won't bind.
What are substates?
Ligands that bind to enzymes and are converted by the enzyme into some sort of chemically modified product
How are enzymes grouped?
based on the functional reactions they catalyze.
What is kinase?
It catalyzes the addition of phosphate groups to molecules.
What is protein kinase?
It catalyzes the addition of a phosphate group to a protein.
What does the binding of an antibody to an antigen do?
The tight binding between the two either inactivates it or marks it for destruction
How do antibody recognize antigens?
small amino acid loops at the tips of the branched portion.
What is an active site?
The site where ligands bind to enzymes and chemical reaction take place
What is protein phosphorylation?
The reversible addition of a phosphate group to an r group.
Phosphate groups have a charge of negative 2. This negative charge changes the conformation of the protein and thus its activity.
This is a very common method for protein regulation.
What regulates protein phosphorylation?
Protein kinase adds phosphate groups
Protein phosphatase peels phosphate groups off
What are kinases and phosphatases?
Kinases add phosphate groups and phosphatase take them away.
What are GTP binding proteins?
Some proteins are regulated by the binding to GTP instead of ATP. When GTP binds to the protein, it becomes active, then one of the phosphate groups is hydrolyzed off and GDP left and the protein is inactive. A new GTP is added and the protein is active again.
What is protein purification?
The isolation of a single protein
This is done by growing protein in an isolated bacterial culture. Fractionalization then separates the proteins into individual factions based on properties such as size and charge. Proteins can also be tagged to make them easier to purify.
How do motor proteins work?
By the hydrolysis of ATP, this also prevents the protein from wandering around as the ATP can't be rehydrolizes
What is chromatography?
Allows for the separation of proteins based bases on certain properties
What is gel electrophoresis?
Separates proteins based on a charge to mass ratio
How do enzyme inhibition drugs work?
They bind on the substrate binding site and prevent catalysis
When is antibody and antigen equilibrium reached?
When the number of antigens bound to antibodies is equal to the number of unbound antigens.
How are antibodies uses in research?
make an antibody that attacks the process you want to study, add a florescent protein and then inject it into a cell.
How is binding strength studied?
By asking the question, at what concentration are half the antigens bound? The lower the number, the higher the affinity. This method can also be used to study affinity between ligand and receptor.
Said another way, at what concentration will equilibrium be reached?
What is special about the binding of rare molecules?
They have high affinity. Meaning that even at a very low concentration many will be bound.
How does positive feedback regulation work?
A regulatory molecule stimulates the activity of the enzyme, usually between two pathways. For example increased ADP in one pathway causes the glycolysis pathway to activate so that more ATP can be made
How does allosteric regulation work?
Binding of a downstream product to the allosteric site causes confirmational changes to the active site such that protein/enzyme turns on or off.
How many protein kinases do we have
What are the residues to which protein kinase is attached?
Serine, threonine and tyrosine
At any given time, what percent of proteins in a cell are phosphorylated?
How does protein phosphorylation work?
The negative PO4 allows of the attraction of a positively charged side chain. Changes electrostatic interactions, which changes the folding of the protein and the folding of the backbone.
This three-dimensional change can make a protein more or less active.
It is reversible.
Beyond turning a cell on or off, what other changes can protein phosphorylation cause?
Protein-protien interactions. It can also mark proteins for degradation
What else is notable about protein kinases and phosphatase?
Many of the genes that cause cancer encode for protein kinases. Mis-regulation of the of protein kinases will lead to phosphorylation of the wrong things which leads to cancer. For example SRC can lead to muscle cancer.
Protein kinases can lead to misregulation proteins and have very broad impacts as can phosphatase
What is like a protein on/off switch?
What happens is hydrolysis is prevent when GTP is bound to a protein?
It cannot turn off.
How does ATP regulate the movement of motor proteins?
It acts allosterically to prevent the proteins from moving backward
what is post translation modification?
Phosphorylation is one type, there is also the attachment of acetyl or ubiquitin, proteolytic cleavage, methylation, fatty acid acylation, prenylation, sulfation. These are all covalent modifications
What is ubiquitin?
It is a post translational modification
What do covalent modifications do?
They are post translational modification that affect protein activity.
What is glycosylation?
It is the reversible addition of carbohydrates. they attached to a nitrogen or an oxygen depending on which end of the amino acid they are being attached to.
How are post translational modification added to cells?
Through covalent bonds.
What are glycolipids?
They are lipids linked to sugars added to proteins
What is ubiquitination?
it is the addition of ubiquitin proteins, which target mark proteins for degradation.
What do post-translation modifications control?
cellular interaction, protein activity, cellular location
What is GFP used for?
highlight sub cellular compartments, follow the cellular distribution of proteins fused to it, kinetics of protein movement in a cell, detect protein protein interactions, gene reporter, marker for transgenic animals,
Describe the process of studying cells
1.) purify protein by disrupting tissues (break cells with high frequency, force cells through small hole with high pressure, use a morter and pestle style plunger, use a detergent,) This soup will contain many small molecules.
2.) Separate cell components (centerfuige, differential centrifuge (stages), velocity sedimentation (what goes to the bottom faster), equilibrium sedimentation (based on bouancy) or chromatography