Biology 302- Chapter 4: Protein Structure and Function

Lecture notes put into quiz form to prep for a BIOL302 (Molecular Biology) exam.

What is a structure protein? What are some examples?

It is a protein that provides the cell with shape and structure.

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Ex: tubulin and actin

What are enzymes? What is an example?

Enzymes catalyze covalent bond breakage or formation. They are biological molecules that allow for catalytic reactions to take place.

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Ex: pepsin

What are transport proteins? What is an example?

Transport proteins carry other molecules or ions. They allow for movement within cells.

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Ex: hemoglobin carrying oxygen in the bloodstream

What are motor proteins? What is an example?

Motor proteins generate movement in cells and tissues. They function slightly differently than transport proteins.

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Ex: Myosin

What are storage proteins? What are some examples?

Sotrage proteins store small molecules or ions.

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Ex: ferritin stores iron in the liver

What are signal proteins? What is an example?

Signal proteins carry signals from cell to cell. They signal events to take place.

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Ex: insulin signals certain glucose levels within the body

What are receptor proteins? What are some examples?

Receptor proteins detect signals and transmits them to the cell’s response machinery.

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Example: receptors for signal proteins; insulin receptors

What are gene regulatory proteins? What are some examples?

Gene regulatory proteins bind to DNA to switch genes on or off.

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Ex: transcriptional factors - lactose repressor

What are amino acids?

They are the monomers (building blocks) that form proteins.

R-group and Residue are other names for a protein’s _____.

side-chain

Polymers are:

constructed of multiple amino acids

What do amino acids consist of?

Amino acids contain a central α (alpha) carbon, the n-terminus, the side chain, and the c-terminus.

The following is an example of a ______ reaction.

condensation

Identify the carboxyl group (C-terminus) of this protein.

Identify the amino group (N-terminus) of this protein.

Polypeptides are:

constructed of multiple covalent bonds.

What is the terminus?

It is the end of the amino acid.

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Examples: amino group, carboxyl group

What is the peptide bond?

It is the bond between the carboxyl group from one molecule and the amino group from another molecule.

Whether or not an amino acid is polar or non-polar is dependent upon their:

side chain structure.

What are the three-letter and one-letter abbreviations for **Aspartic Acid**?

Asp; D

What are the three-letter and one-letter abbreviations for **Glutamic Acid**?

Glu; E

What are the three-letter and one-letter abbreviations for **Arginine**?

Arg; R

What are the three-letter and one-letter abbreviations for **Lysine**?

Lys; K

What are the three-letter and one-letter abbreviations for **Histidine**?

His; H

What are the three-letter and one-letter abbreviations for **Asparagine**?

Asn; N

What are the three-letter and one-letter abbreviations for **Glutamine**?

Gln; Q

What are the three-letter and one-letter abbreviations for **Serine**?

Ser; S

What are the three-letter and one-letter abbreviations for **Threonine**?

Thr; T

What are the three-letter and one-letter abbreviations for **Tyrosine**?

Tyr; Y

What are the three-letter and one-letter abbreviations for **Alanine**?

Ala; A

What are the three-letter and one-letter abbreviations for **Glycine**?

Gly; G

What are the three-letter and one-letter abbreviations for **Valine**?

Val; V

What are the three-letter and one-letter abbreviations for **Leucine**?

Leu; L

What are the three-letter and one-letter abbreviations for **Isoleucine**?

Ile; I

What are the three-letter and one-letter abbreviations for **Proline**?

Pro; P

What are the three-letter and one-letter abbreviations for **Phenylalanine**?

Phe; F

What are the three-letter and one-letter abbreviations for **Methinonine**?

Met; M

What are the three-letter and one-letter abbreviations for **Tryptophan**?

Trp; W

What are the three-letter and one-letter abbreviations for **Cysteine**?

Cys; C

What does conformation mean?

any of the spatial arrangements which the atoms in a molecule may adopt and freely convert between, especially by rotation about individual single bonds.

What are the three types of covalent bonds (as well as an interaction)?

• Hydrogen bonds

• Electrostatic attractions

• vaan der Waal’s attractions

• Hydrophobic interactions

Even though hydrogen bonding is a fairly weak bond, multiple hydrogen bonds can add to the _____ ______ of the molecule.

structural integrity

Prion diseases are caused by:

rare proteins whose mis-folding is infectious.

What is a heterodimer?

Two different proteins interacting.

What is a homodimer?

Two of the same proteins interacting.

___________ can guide the folding of a newly synthesized polypeptide chain.

Chaperone proteins

What are the levels of protein organization?

• Primary

• Secondary

• Tertiary

• Quaternary

What does the primary structure of a protein refer to?

The linear amino acid shape/structure/sequence of the protein

What does the secondary structure of a protein refer to?

An organization that forms within certain segments of the polypeptide chain; Specific folding patterns (motifs)

What does the tertiary structure of a protein refer to?

The full, three dimensional conformation of the entire polypeptide; The fully folded form of protein

What does the quaternary structure of a protein refer to?

a complex of more than one polypeptide joined together

What is the polypeptide backbone?

The polypeptide backbone is the key contributor to protein secondary structure, which involves backbone-to-backbone hydrogen bonding

What is this an image of?

The alpha helix folding pattern is demonstrated in a linear sequence of amino acids that folds in a helical manner that is stabilized internally through hydrogen bonds between the polypeptide backbone.

What is this an image of?

When alpha helices interact and intertwine with each other. When they do this, it is referred to as a “coiled-coil” interaction. The helices do this coiled-coil arrangement in order to minimize the exposure of their hydrophobic residues to their surrounding aqueous environment.

What is this an image of?

The β-sheet folding pattern. It involves neighboring regions of the polypeptide chain that are associated side-by-side through hydrogen bonding and give it a flat/rigid structure.

What is this an image of?

A β-sheet variety called parallel. It is where neighboring polypeptide chains run in the same orientation

What is this an image of?

A β-sheet variety called anti-parallel. It is where neighboring polypeptide chains run in opposite direction.

What is a functional domain?

Domains are distinct functional and/or structural units in a protein. Usually they are responsible for a particular function or interaction, contributing to the overall role of a protein.

Proteins can assemble into:

filaments, sheets, or spheres.

The orientation in which a protein forms is affected by:

the number of binding sites each protein contains.

If a protein has only one binding site, it can form a _____ with another identical protein.

dimer

Identical proteins with 2 binding sites will often form a long _____ *___*__.

helical filament

If the two identical proteins with two binding sites are oriented properly, the proteins can also form a ______.

sphere/ring

Single protein subunits can pack to form a:

filament, tube, or spherical shell.

______ _______ help stabilize a favored protein conformation.

Disulfide bonds

Proteins often form large complexes that function as machines. Many interacting proteins are brought together by:

scaffold proteins

What is a ligand?

Any molecule that can bind to another protein

If the binding of the protein and the ligand is unfavored or has poorly matching surfaces, the two molecules will:

dissociate (pull apart).

What is feedback inhibition?

When an enzyme that acts early in a pathway is inhibited by a late product of the pathway. Feedback inhibition regulates the flow through biosynthetic pathways. In some occasions, it can trigger a conformational change in the protein.

What are the nucleoside triphosphates?

ATP (Adenosine Tri-Phosphate)

CTP (Cytidine Tri-Phosphate)

TTP (Thymidine Tri-Phosphate)

GTP (Guanosine Tri-Phosphate)

The binding of a regulatory ligand can change the _______ between two protein conformations.

equilibrium

Protein ______ is a very common means of regulating protein activity.

phosphorylation

The enzyme involved in the removal of a phosphate group is called:

phosphatase

GTP-binding proteins form:

molecular switches.

The modification of a protein at multiple sites produce a regulatory code that controls the:

protein behavior.

K! 1) How many different amino acids are used in making proteins?

20

K! 2) The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The enzyme that catalyzes the addition of a phosphate group onto a protein is called a:

kinase

K! 3) Which of the following is *not* a feature commonly observed in β sheets?

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a. anti-parallel regions

b. coiled-coil structure

c. parallel regions

d. extended polypeptide backbone

coiled-coil structure

K! 4) In a folded protein, most of the nonpolar amino acids are buried inside the protein fold, whereas the polar and charged side chains are exposed to the components in the cytosol. This fold is more stable because of the expulsion of non-polar atoms from contact with water, favoring the interaction of non-polar atoms with each other. What is this type of non-covalent interaction called?

hydrophobic interaction

K! 5) The correct folding of proteins is necessary to maintain healthy cells and tissues. Abnormally folded proteins can be responsible for such neurodegenerative disorders as Alzheimer’s, Huntington’s, and Creutzfeld–Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, abnormally folded proteins?

Incorrectly folded proteins can develop into protein aggregates with an amyloid structure and damage cells or tissues.

K! 6) Why are α helices and β sheets common folding patterns in polypeptides?

Because the bonds involved are hydrogen bonds, not the side-chain.

K! 7) What does the primary structure of a protein refer to?

The amino acid sequence of the protein.

K! 8) What are protein families?

Evolutionarily related proteins that are similar in amino acid sequence and 3D shape.

K! 9) Protein molecules that have a quaternary structure have:

two or more polypeptide chains.