Chapter 4: protein structures and function

What are enzymes?

Molecules that catalyze chemical reactions and speed up reactions

What are structural protein?

proteins that are able to 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 transcription regulators?

Regulators that can dictate specific cell types and regulate proteins and genes that are being expressed

What are specific purpose proteins?

Proteins that are highly variable with each one having 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 between the carboxyl and amino group

• Van deer Waals attraction

How can a peptide chain fold?

The can fold 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 an overall protein determined?

By the 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?

they are little parts of proteins that are independently folded that are either a-helixes or beta sheets or both

What is the backbone model?

A model that shows the central carbon of every amino acid

What is the ribbon model?

a model that highlights the different parts and characteristic of each structure in the protein

What is the wire model?

A model that shows the little details labeled and proportional to each thing found in the protein

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 which determines the helical structure

Where are alpha helixes found?

they are found everywhere such as 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?

A structure that is formed when beta sheets are stacked on top of one another, forming the insoluble protein aggregate

What is the prion disease?

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

How does prion infected proteins affect neighboring proteins?

The interact with normal folded proteins and convert them into abnormal beta sheets that are aggregated into amyloid fibrils

How many amino acids does a protein consist of on average?

It consists of 300 amino acids on average with every position consisting of 20 different possibilities

What can occur to some sequences of amino acids?

Some can aggregate and form problematic species that are not functional

How are similarities between proteins identified?

By looking at the sequence of amino acids or by looking at the structure and domain of the protein

What is the quaternary structure?

A protein structure that contains multiple peptide chains that are folded independently into its 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 actin proteins responsible for?

They are responsible for movement, muscle contraction, and cell migration to different locations

What are viral capsids?

They are spherical proteins that hold a viruses gene via DNA or RNA

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 for the cell in the extracellular space and is the most abundant expressed protein

what are disulfide bonds?

Covalent bonds that are formed between existing amino acid that have a free SH group and a cysteine, which forms elastic structures