CHEM 53.10 - Levels of Protein Structure 02

Tertiary structure

Describes the global arrangement of all the atoms in a protein

True

T or F: In a tertiary structure, amino acids that are distance in the sequence can be brought close together

Secondary structure

Describes the spatial arrangement of residues relatively close together

Tertiary structure

The way secondary structures pack close together to form a three-dimensional structure of a protein

False

T or F: Proteins can only fall into one major class of a tertiary structure

Globular proteins

(Major class of tertiary structure) Compactly folded polypeptides that gives a roughly spheroidal shape

Globular proteins

(Major class of tertiary structure) A mixture of secondary structures can compose this

False

T or F: The compact folding of globular proteins is due to intermolecular forces

True

T or F: Most globular proteins are water-soluble

Hydrophobic, hydrophilic

Interior of globular proteins is ____. The exterior is ____

Fibrous proteins

(Major class of tertiary structure) Large, elongated molecules

Fibrous proteins

(Major class of tertiary structure) Long polypeptide chains that consists of long strands or sheets that are organized approximately parallel along a single axis

True

T or F: Fibrous proteins can aggregate to form thicker structures

Fibrous proteins

(Major class of tertiary structure) These are mechanically strong and play a structural role in cells

False

T or F: Fibrous proteins are relatively insoluble in water

Globular

Some fibrous proteins are composed of repeating ___ units

Protein tandem repeats

Repeating short sequences of amino acids in fibrous proteins that form multi-protein fibers that are coiled coils

Membrane proteins

(Major class of tertiary structure) Associated with lipid bilayer of cells

Hydrophobic

The lipid-embedded surface of membrane proteins is ____

Peripheral proteins

Type of membrane proteins that are more loosely attached to the membrane

Integral proteins

Type of membrane proteins that span the bilayer

Transmembrane

Another name for integral proteins

Lipid-anchored proteins

Type of membrane proteins that are bound covalently to lipid molecules

False

T or F: Membrane proteins are categorized according to degree of hydrophilicity

True

T or F: Membrane proteins can also have globular units soluble in water

Exterior

In membrane proteins, the hydrophobic residues are typically on the ___ of the protein and is in contact with the hydrophobic environment

Intrinsically disordered proteins

IDP stands for ____

IDP

(Major class of tertiary structure) Has no stable three-dimensional structure

False

T or F: IDPs can spontaneously fold into a random structure

True

T or F: IDPs fluctuate through a range of conformations

True

T or F: IDPs have greater flexibility

Charged, hydrophilic

IDPs are biased towards ___ and ___ amino acids

False

T or F: Only a portion of IDPs are intrinsically disordered and never the whole chain

True

T or F: IDPs can interact with multiple partners

True

T or F: IDPs can fold into well-defined conformations after binding to a partner

IDPs

(Major class of tertiary structure) Involved in apoptosis

False

T or F: There is one proposed mechanism of the generation of well-ordered proteins

True

T or F: Tertiary structures are held together by a mix of covalent and noncovalent interactions

Side chains

Interactions that lead to the tertiary structure are primarily between the atoms of the ___ and their surroundings

Charge-charge

All forces between molecules are ultimately ____ interactions

Salt bridges

Interactions between fully charged groups that are relatively strong, non-covalent interactions

True

T or F: Buried charges are relatively stronger than those found in the surfaces of proteins

Zinc fingers

Common example of metal ions that mediate ion pairing and help with stability

Van der Waals

Weak non-covalent interactions that hold the tertiary structure

Hydrogen bonds

Strong non-covalent interactions that hold the tertiary structure

Crosslinking via covalent bonds

Strongest of the interactions that hold a protein’s shape

Motifs

Recurring patterns of secondary structures found in a protein’s tertiary structure

Motifs

Considered to be supersecondary structures

True

T or F: Motifs are more stable during evolution than amino acid sequences

True

T or F: Similar motifs may appear in different proteins even if the sequences of the motifs are dissimilar

Alpha-alpha motif

Motif composed of 2 alpha-helices connected by loops

Helix hairpin

Two antiparallel alpha helices connected by a loop or two or more residues

Four helix bundle

Motif composed of two helix hairpins

Helix-loop-helix motif

Motif with two helices connected by a loop

Helix-loop-helix motif

Also a functional motif that binds ligands

B-meander

Consecutive antiparallel B-strands linked by hairpins

Greek key

Motif that has a B-hairpin folded to form 4 anti-parallel B-strands

Beta-alpha-beta

Most common form of supersecondary structure

Molecular chaperones

Proteins that aid in protein folding