BIOL115: Chapter 3: Protein Structure and Function

Active site

the location in an enzyme molecule where substrates (reactant molecules) bind and react

Quaternary structure

the overall three-dimensional shape formed from two or more polypeptide chains (subunits); determined by the number, relative positions, and interactions of the subunits

Tertiary structure

the overall three-dimensional shape of a single polypeptide chain, resulting from multiple interactions among the amino acid side chains and peptide backbone

Polymerization

the process of linking monomers together

Primary structure

the sequence of amino acid residues in a peptide or protein

Because each contact between R-groups causes the peptide-bnded backbone to bend and fold, each contributes to the distinctive _________________ of a polypeptide.

three-dimensional shape

While all amino acids share the same ______________, each of the 20 R-groups is unique. The _____________ of amino acids vary because their R-groups vary.

core structure; properties

Hydrophobic

does not react with water; non polar side chains

Substrate

(1) a reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reactions; (2) a surface on which a cell or organism sits

Four varieties/shapes of proteins:

1. TATA box-binding protein (saddle-shaped; binds DNA) 2. Porin (doughnut-shaped; forms a pore) 3. Trypsin (globular; binds substrates) 4. Collagen (fibrous; provides structural support)

Amino acid chains distinguish the different amino acids and can be grouped into four general types:

1. Acidic 2. Basic 3. Uncharged polar 4. Nonpolar

Proteins are crucial to most tasks required for cells to exist:

1. Catalysis (most important) 2. Movement 3. Signaling 4. Structure 5. Transport

If given a structural formula for an amino acid, you can determine which type of amino acid it is by asking three questions:

1. Does the side chain have a negative charge? If so, it has lost a proton, so it must be acidic. 2. Does the side chain have a positive charge? If so, it has taken on a proton, so it must be basic. 3. If the side chain is uncharged, does it have an oxygen atom? If so, the highly electronegative oxygen will result in a polar covalent bond and thus is uncharged polar.

All 20 amino acids have a common core structure-with a central carbon atom bonded to the four different atoms or groups of atoms:

1. H-a hydrogen atom 2. NH₂-an amino functional group 3. COOH-a carboxyl functional group 4. a distinctive "R-group" (often referred to as a "side chain")

5 types of interactions involving side chains:

1. Hydrogen bonding- forms between polar R-groups and opposite partial charges either in peptide backbone or other R-groups 2. Hydrophobic interactions- water forces hydrophobic nonpolar side chains to coalesce into globular masses; when these non-polar R-groups come together, surrounding water molecules form more hydrogen bonds with each other, increasing the stability of their own interactions 3. *van der Waals interactions*- occurs once hydrophobic side chains are close to one another; their association is further stabilized by electrical attractions 4. Covalent bonding- forms between side chains of two cysteine through reaction between the sulfhydryl groups; these are called *disulfide ("two-sulfur") bonds* and are referred to as bridges 5. Ionic bonding- forms between groups that have full and opposing charges

Four basic levels of organization:

1. Primary 2. Secondary 3. Tertiary 4. Quaternary

4 Main Biological Macromolecules:

1. Proteins 2. Nucleic Acids 3. Carbohydrates 4. Lipids

There are three key points to note about the peptide bonded backbone:

1. R-group orientation- side chains extend out from backbone, allowing interaction with each other and water 2. Directionality- amino acid sequences always written from the N-terminus to the C-terminus because N-terminus is start of chain when proteins are synthesized 3. Flexibility- single bonds on either side of peptide bond can rotate, making the structure flexible

Two reasons for why the charges on the functional groups of an amino acid are important:

1. They help amino acids stay in solution, where they can interact with one another and with other solutes. 2. They effect the amino acid's chemical reactivity.

In most proteins, these polar groups are aligned and form hydrogen bonds with one another when the backbone bends to form one of two possible structures:

1. an *α-helix* (alpha-helix), in which the polypeptide's backbone is coiled; or 2. a *β-pleated sheet* (beta-pleated sheet), in which segments of a peptide chain bend 180° and then fold in the same plane

Hydrogen bonding between sections of the same backbone is possible only when a polypeptide bends in a way that puts ______ and ______ groups close together.

C=O; N-H

Molecular chaperones

proteins that help other proteins in folding

________ are polymers made up of ____________.

Proteins; amino acids

Changes in primary structure affect protein ___________________.

function

Oligopeptide, or Peptide

a chain composed of fewer than 50 amino acids linked together by peptide bonds

Polypeptide

a chain of 50 or more amino acids linked together by peptide bonds

Protein

a macromolecule consisting of one or more polypeptide chains composed of 50 or more amino acids linked together; each protein has a unique sequence of amino acids and generally possess a characteristic three-dimensional shape

Most molecules are composed of just 20 different building blocks, called __________.

amino acids

Primary structure is the sequence of ___________ in a polypeptide. It is stabilized by ______________.

amino acids; peptide bonds

Macromolecule

any very large organic molecule, usually made up of smaller molecules (monomers) joined together into a polymer

Amino acids polymerize when a bond forms between the ___________ group of one amino acid and the ______________ group of another.

carboxyl; amino acid

No other class of macromolecule can match proteins for their _______________. The variety of reactive functional groups present in amino acids is much better suited for this activity than those found in nucleotides or sugars.

catalytic potential

Monomers polymerize through ________________________, also known as ________________________.

condensation reactions; dehydration reactions

No matter how large or complex a protein may be, its underlying structure can be broken down into just _______ basic levels of organization.

four

Proteins have up to ______ levels of structure.

four

Macromolecular machine

groups of multiple proteins that assemble to carry out particular function

The key thing to note is that protein structure is ______________. Quaternary structure is also based on tertiary structure, which is based in part on secondary structure. All three of the higher-level structure are based on _______________.

hierarchical; primary structure

Primary structure is also fundamental to the ______________ of protein structure: secondary, tertiary, and quaternary.

higher levels

Hydrophilic

interacts readily with water; polar or charged side chains

With 20 types of amino acids available and length ranging from two amino acid residues to tens of thousands, the number of primary structures that are possible is practically ___________.

limitless

Secondary structure

localized folding of a polypeptide chain into regular structures (i.e. alpha-helix and beta-pleated sheet) stabilized by hydrogen bonding between atoms of the peptide back bone

In general, a molecular subunit such as an amino acid, a nucleotide, or a sugar is called a _____________. When a large number of monomers are bonded together, the resulting structure is called a _____________.

monomer ("one-part"); polymer ("many-parts")

Condensation reaction

monomer in, water out

Hydrolysis

monomer out, water in

Tertiary structure is the ______________________ of a polypeptide. It is stabilized by bonds and other interactions between R-groups, OR between _________ and the ____________________.

overall-three dimensional shape; R-groups; peptide-bonded backbone

Quaternary structure is the shape produced by combinations of polypeptides. It is stabilized by bonds and other interactions between R-groups, AND between _________________________________.

peptide backbones of different polypeptides

When the carboxyl group of one amino acid reacts with the amino group of another amino acid, a strong covalent bond called a ___________ bond forms. Small chains are called _______________; large chains are called _______________, or ______________.

peptide bond; oligopeptides; polypeptides; proteins

In most cases, secondary structure consists of α-helices and β-pleated sheets. When one forms, if either, depends on the molecule's _______________-specifically, the __________ and __________ of the amino acids in the sequence.

primary structure; geometry; properties

Prions

protein that can fold in multiple, structurally distinctive ways

Some proteins contain multiple polypeptides that interact to form a ________________.

single structure

Proteins can serve diverse functions in cells because they are diverse in _____ and ______ as well as in the ______________ of their amino acid residues.

size; shape; chemical properties

Enzymes _________ chemical reactions by binding _________ at their _________, where catalysis takes place.

speed up; substrates; active site

Peptide bond

the covalent bond formed by a condensation reaction between two amino acids; links the residues in peptides and proteins

Denatured

unfolded

Each amino acid has distinctive chemical properties because each has a _______________.

unique R-group

Proteins are the most _________________ in cells, and each function is directly connected to _________.

versatile large molecules; structure

Fold

when a protein assumes its functional shape

Secondary structure is the formation of ______________ and ____________ in a polypeptide. It is stabilized by ___________________ between groups along the peptide-bonded ______________.

α-helicases; β-pleated sheet; hydrogen bonding; backbone