Chapter 4: protein structures and function

What are enzymes?

Molecules that catalyze chemical reactions and speed up reactions

What are structural protein?

proteins that provide mechanical support inter-cellularly or extracellularly

What are transport proteins?

Proteins that binds molecules to itself for transport to another location, dissociating from it once arrived

What are motor proteins?

Proteins that utilizes ATP to transport molecules around

What are storage proteins?

Proteins that store energy and act as a source of energy

What are signal proteins?

Proteins that can be modified or modify other molecules and allow for coordinated communication between cells

What are receptor proteins?

Proteins that communication with external signals and involves the binding of the ligand

What are specific purpose proteins?

Proteins that have specialized properties that can be activated by the organism

What does the first and last amino acid of a protein contain?

A free amino group labeled the N-terminus and a free carboxyl group labeled the C-terminus

What do amino acids linked by peptide bonds form?

they form a polypeptide backbone

What are the largest class of amino acids?

They are non-polar amino acids that are hydrophobic

what are the 3 types of noncovalent bonds that help proteins fold?

• ionic bonds

• H-bonds

• Van deer Waals attraction

How is a peptide chain folded?

They are folded into distinct shape with the nonpolar chains being buried in the middle of the chain and the polar/charged chains being present in the outside of the chain

How is the shape of a protein determined?

By its amino acid sequences

How are protein structures studied?

By purifying them from the cell using urea, denaturing them in order to be unfolded, once the study is finished the urea is removed which allows for the protein to fold back to its original conformation

Why is urea used to study protein structures?

Due to its chemical structure being able to form strong h-bonds with all the sidechains and disrupt the h-bonds that are holding the structure

Why must proteins be folded?

In order to be folded into its lowest energy level and most stable form as an unfolded protein can cause problems

What protein helps in the folding of proteins?

Chaperone proteins

How do chaperone proteins help in the folding of proteins?

They bind to the target protein in order to ensure they are folded properly

What is another way that chaperone proteins help in the folding of protein ?

They form chambers that allows for unfolded proteins to fold, increasing the chances of the protein to fold into its correct structure

• and remain in the chamber until the protein is mature or folded

What are protein domains?

Proteins that are independently folded into either an a-helix, beta sheet, or combination of both

What does the primary structure dictate?

it dictates the order in which the amino acids are lined up as

how are alpha helixes formed?

through h-bonds between amino and carboxyl group, determining the helical structure

Where are alpha helixes found?

Between phospholipids in the lipid bilayer

How are complex helixes formed?

When 2 helixes twist around each other with their side chains controlling the folding to form the complex, with the hydrophobic parts being buried in the middle

How are beta sheets formed?

Through h-bonds between distant amino acids that are going in an antiparallel direction in a plain formation

• can be found in fluorescence proteins

What are amyloid structures?

An insoluble protein aggregate that forms when beta sheets are stacked on top of one another

What is the prion disease?

A disease that is caused when a protein adopts a folded prion form

How does prion infected proteins affect neighboring proteins?

The interact with a protein and convert them into abnormal beta sheets that aggregate into amyloid fibrils

What can occur to some sequences of amino acids?

Some can aggregate and form problematic species that are not functional

What is the quaternary structure?

A protein structure that contains multiple peptide chains that are folded independently into their own 3D space and come together to form a large complex

how do peptide chains come together in the quaternary structure?

through H-bonds or ionic bonds

What are actin proteins?

Proteins that can self fold and interact with one another to form long chains that are tightly regulated

What are elastic fibers?

Fiber found in the skin that can be stretched due to the proteins being able to form complex structures that can extend or shrink into different forms

What are collagen fibrils?

A protein that provides a stable environment in the extracellular space of a cell and is the most abundant expressed protein

what are disulfide bonds?

Covalent bonds that are formed between a free SH group on an amino acid and a cysteine, forming an elastic structure

What form does a protein have to be in for an event to take place?

It has to be properly folded in order to be able to interact with other molecules containing various resides

What is the Antigen-binding site in an antibody?

A site at the end of an antibody that determines specificity and recognizes antigens

What are B cells?

Lymphocytes similar to antibodies that contain B-cell receptors that are anchored on its plasma membrane

What occurs if an antigen binds to a b-cell receptor?

It will trigger a signal pathway to the nucleus and trigger either the amplification of the B cell or the production of actual antibodies

What occurs once an antibody binds to a protein, virus, or bacteria?

The antibody can be recognized by the immune system and either:

• Trigger engulfment through phagocytosis and break them down into harmless molecules

• trigger production of proteins that can form complexes to kill the antigen

What are lysozymes?

they are a type of protein that can hydrolyze oligosaccharides found in the cell wall of bacterias, causing degradation and exposing its membrane, allowing for the bacteria to be killed

What are the 3 ways that enzymes can encourage a reaction to occur?

• By binding 2 substrates from 2 separate reactions into a small region for a reaction to occur between the 2

• changing the shape of a substrate to cause it to be vulnerable for the next step of a reaction

• By binding to a substrate and facilitating the exchange of electrons, temporarily becoming charged and more reactive with other molecules

Why do enzymes sometimes have to bind to small molecules?

In order for the function of certain proteins to occur

What occurs as the concentration of a substrate and the rate of an enzyme reaction increases?

it will constantly increase until the maximum rate of an enzyme reaction is reached

What if an enzyme has a high affinity to a substrate?

The Kn value will be very low

What are competitive inhibitors?

Drugs that mimics a substrate in order to prevent the enzyme from associating with its substrate

What do competitive inhibitors impact?

They impact KN by increasing the value and VMAX by decreasing the value

What is feedback inhibition?

they are drugs that can regulate the production of a product by binding to an enzyme and changing its conformation, preventing it from associating with its substrate

What is phosphorylation?

A covalent modification that allows for a phosphate group to modify molecules inside of the cell

What does phosphorylation change?

It changes the biochemical properties of a proteins structure

What occurs to protein when modified by phosphorylation?

The side-chain of a specific amino acid is bonded to another molecule, causing it to be unrecognizable due to the lose of its function

Leading to rapid degradation or an increase in stability of the protein

What is GTP?

A molecule frequently found in the trafficking pathway that can bind to small molecules and be used in RNA synthesis

What occurs when GTP binds to a specific protein?

It causes the protein to remain active until it is hydrolyzed into GDP in which the protein will become inactive and release GDP

How do motor proteins make proteins “walk”?

By hydrolyzing ATP into ADP, providing energy for the proteins to switch around their conformation and allow for the protein to move in a single direction

What is a protein machine?

groups of proteins that come together to perform various complex jobs together

What are protein scaffolds?

They are large proteins that supports nerve cell activites by allowing cells to communicate effectively

How do scaffold proteins interact with other proteins?

By folding in a specific way to place interaction proteins in the right position to perform their jobs

Why can some scaffold proteins facilitate the interactions of protein?

Because they can concentrate proteins in the cell