Exam 1 Cell Structure and Function- Proteins

Macromolecules

A very large organic molecule composed of many smaller molecules

Enzymes

biological catalysts that increase the rates of chemical reactions

Structural Proteins

physical support and shape

motility proteins

contraction and movement

regulatory proteins

control and coordinate cell function

Transport Proteins

move substances in and out of cells

signaling proteins

communication between cells

receptor proteins

enable cells to respond to chemical stimuli from the environment

defensive proteins

protect against disease

storage proteins

store amino acids

How many kinds of amino acids are used in protein synthesis?

20

How many possibilities of proteins are there?

practically infinite

True or False: Two different proteins can have the same amino acid sequence

False

True or false: every amino acid has the same basic structure

true

Carboxyl group

COOH

Amino group

NH2

R group

defines a particular amino acid

alpha carbon

Central carbon atom in amino acids.

Each amino acid consists of

central carbon atom, hydrogen atom, amino group (-NH2), carboxyl group (-COOH), R group

All amino acids in the human body are

L- amino acids

L- amino acid

amino group on the left

D-amino acid

amino group on the right

Polar, charged (Acidic) Amino Acids

R-group side chain has a negative charge

Polar, charged (Basic) Amino Acids

R-group side chain has a positive charge

Polar, uncharged (Hydrophilic) Amino Acids

R-group has no charge, but has Oxygen (O), Nitrogen (N), or Sulfur (S) atoms

Nonpolar (Hydrophobic) amino acid

R-group made almost entirely of Carbon (C) and Hydrogen (H) atoms with no charges and no (-OH) groups.

What nonpolar amino acid is the only amino acid to not have separate L and D isomers?

Glycine

dehydration (condensation) reaction

A chemical reaction in which molecules combine by removing water

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

Which two functional groups must react with each other to link two amino acids together

carboxyl group of the first amino acid and the amino group of the second amino acid.

two distinct ends of any growing polypeptide chain

The N-terminus (free amino group at the start) and the C-terminus (free carboxyl group at the end).

Product of dehydration

Water

Monomeric proteins

consist of a single polypeptide

multimeric proteins

consist of two or more polypeptides

Dimers

proteins with two polypeptide subunits

Trimers

proteins consisting of three polypeptides

Hemoglobin structure

two alpha subunits and two beta subunits

Distinction between polypeptide and protein

Proteins may be made up of multiple polypeptides

Protein conformation

proper three-dimensional shape of a protein.

True or False: Proteins rely only on noncovalent interactions to fold properly and maintain stability.

False

Which three parts of an amino acid residue can actively participate in the bonds and interactions that stabilize a protein?

The carboxyl group, the amino group, and the R group (side chain)

Amino acid residues

amino acids which have been incorporated into the peptide chain

disulfide bond

the covalent bond formed between the sulfur atoms of two cysteines in a protein; typically causes the protein to fold by bringing otherwise distant parts of the protein close together

Cysteine Residues

Amino acids forming disulfide bonds in proteins.

Covalent bonds in protein folding and stability

peptide bonds, disulfide bonds

Non-covalent bonds in protein folding and stability

hydrogen bonds, ionic bonds, van der waals and hydrophobic interactions

type of weak forces make up the absolute majority of interactions responsible for holding a folded protein together

Van der Waals and hydrophobic interactions.

disulfide bonds are most commonly found stabilizing what specific category of proteins?

extracellular proteins

True of False: Hydrogen bonds are less polar than ionic bonds

true

ionic bond

charged interaction between fully positive and fully negative functional groups

primary structure of a protein

amino acid sequence

Which type of chemical bond holds the primary structure together?

Covalent peptide bonds.

True or False: R-group side chains are actively involved in stabilizing secondary protein structures.

False

secondary structure of protein

Local structure of a protein structure formed by folding and twisting of amino acid chain into alpha helices or beta pleated sheets

Which specific groups form the hydrogen bonds that stabilize secondary structure?

The amino (NH) and carboxyl (CO) groups of the peptide bonds in the backbone.

protein conformation

the specific, proper way a protein is folded based on both covalent bonds, and noncovalent interactions

tertiary structure of protein

3D folding of. single polypeptide chain via interactions of disulfide bonds, hydrogen bonds, van der waals forces, and hydrophobic interactions

Amino Acid sequences are written

N-terminus to C-terminus

Direction in which polypeptides are synthesized

N to C terminus

First protein to have its amino acid sequence determined

hormone insulin

Insulin is made up of what?

2 polypeptide chains linked by disulfide bond(1 alpha and 1 beta subunit)

Importance of primary structure

affects the secondary, tertiary, and quaternary structure and overall shape and function of the protein

Alpha Helix

Secondary structure- Spiral shape, peptide backbone, R groups facing outwards from spiral, H-bond forms between CO group of one a.a and NH group of another a.a

Beta Sheet

Secondary Structure- Extended Sheet-like conformation, atoms of polypeptide chains located at peaks and troughs, R groups on alternating sides of sheet

In a standard beta-sheet secondary structure, how are the side chains (R groups) of adjacent amino acids along a single beta-strand spatially oriented relative to the plane of the sheet?

side chains project outward in opposite directions

Why is a beta sheet structurally referred to as a beta -pleated sheet?

Because its successive backbone atoms are located at alternating "peaks" and "troughs", giving it a folded, accordion-like conformation.

Where are the amino acid R groups (side chains) located relative to the \(\beta \) sheet plane?

They jut out on alternating sides of the sheet (one pointing up from a peak, the next pointing down from a trough)

What is the general shape of an alpha helix

spiral

In alpha helix, where are the R groups (side chains) located?

R groups jut outward away from the spiral backbone.

How many turns away is the matching NH group from its corresponding CO partner in the helix?

1

What is the specific hydrogen bonding pattern that stabilizes an alpha helix?

A hydrogen bond forms between the CO group of amino acid \(n\) and the NH group of amino acid n+4

what structural component forms the inner spiral core of the alpha helix?

Peptide backbone

While some beta sheets form between completely separate, different polypeptide chains, they can also frequently form between different regions within a

single polypeptide chain

parallel beta sheet configuration

The interacting strands run with the same polarity relative to their N- and C-termini.

Antiparallel beta sheet configuration

The interacting strands run with opposite polarity relative to their N- and C-termini.

What type of bonding saturation characterizes a finished beta sheet secondary structure?

maximum of hydrogen bonding between the involved strands.

What is a motif (or supersecondary structure) in protein anatomy?

A supersecondary structure composed of a few secondary structure elements.

hairpin loop motif

Two adjacent, antiparallel beta strands connected by a loop

Proline is referred to as the "helix breaker" because

It lacks the hydrogen atom needed for hydrogen bonding.

What specific part of the amino acid sequence determines a protein's tertiary structure?

The interactions of the R groups (side chains).

What physical behavior do hydrophobic residues exhibit that helps drive tertiary folding?

fold inward to avoid interacting with water.

Fibrous proteins have a highly ordered, repetitive structure because they contain extensive regions of ____________ structure.

secondary

Fibroin produces silk and is made predominantly of \(\beta \) sheets, whereas keratin is the primary component of hair and is composed of many ____________.

alpha helices

Globular proteins

Compact, ball-shaped proteins that include most enzymes.

Protein domains

Individual, functional units within a protein that each do a specific job.

Proteins with multiple

functions usually have

a separate domain for

each function

AlphaFold

An AI system used to predict the 3D shapes of proteins.

Quaternary structure

multiple separate subunits interact and assemble

True or False: Secondary, tertiary, and quaternary structures are maintained solely by non-covalent bonds.

False, while they mostly use non-covalent interactions, tertiary and quaternary structures can also contain strong, covalent disulfide bonds.

What type of strong covalent bond can be found stabilizing both tertiary and quaternary protein structures?

Disulfide bonds

Which of the following is a classic example of a multimeric protein because it contains two or more different types of interacting polypeptide chains?

Hemoglobin