Protein Structure

Question 1

Primary Structure

Answer 1

In proteins, the linear arrangement (sequence) of amino acids within a polypeptide chain

Question 2

Secondary Structure

Answer 2

In proteins, local folding of a polypeptide chain into regular structures including the a helix, B sheet, and B turns; stable spatial arrangements held together by hydrogen bonds between backbone amide and carbonyl groups and often involving repeating structural patterns

Question 3

Alpha Helix

Answer 3

Common protein secondary structure in which the linear sequence of amino acids is folded into a right-handed spiral stabilized by hydrogen bonds between carboxyl and amide groups in the backbone

Question 4

Beta Sheet

Answer 4

A flat secondary structure in proteins that is created by hydrogen bonding between the backbone atoms in two different polypeptide chains or segments of a single folded chain

Question 5

Beta Turn

Answer 5

A short U-shaped secondary structure in proteins

Question 6

Structural Motif

Answer 6

A particular combination of two or more secondary structures that form a distinct three-dimensional structure that appears in multiple proteins and that often, but not always, is associated with a specific function

Question 7

Leucine Zipper

Answer 7

A type of coiled-coil structural motif composed of two a helices that form specific homo- or heterodimers; common motif in many eukaryotic transcription factors

Question 8

Helix-turn-helix

Answer 8

A structural motif in which two alpha helices are connected by a short stretch of connecting residues; can perform various functions, including binding calcium and binding DNA

Question 9

Zinc Finger

Answer 9

Several related DNA-binding structural motifs composed of secondary structures folded around a zinc ion

Question 10

Tertiary Structure

Answer 10

In proteins, overall three-dimensional form of a polypeptide chain, which is stabilized by multiple non covalent interactions between side chains

Question 11

Domains

Answer 11

A region of protein that has a distinct, and often independent, function or structure, or that has a distinct topology relative to the rest of the protein

Question 12

Functional Domain

Answer 12

A region of a protein that exhibits a particular activity characteristic of that protein, usually even when isolated from the rest of the protein

Question 13

Protease

Answer 13

Any enzyme that cleaves one or more peptide bonds in target proteins

Question 14

Topological Domain

Answer 14

Regions of proteins that are defined by their distinctive spatial relationships to the rest of the protein

Question 15

Structural Domain

Answer 15

A region about 40 or more amino acids in length, arranged in a single, stable, and distinct structure often comprising one or more secondary structures or structural motifs

Question 16

Homolog

Answer 16

A protein that shares a common ancestor, and therefore is similar in sequence and/or structure, with another protein

Question 17

Globular Protein

Answer 17

Water-soluble, compactly folded structure, often spheroidal, that comprise a mixture of secondary structures

Question 18

Fibrous Protein

Answer 18

Large, elongated, often stiff molecules; often made up of helical polypeptide chains or repeating globular subunits; usually play a structural role or participate in cellular movements

Question 19

Integral Membrane Protein

Answer 19

Imbedded within the phospholipid bilayer of the membranes that enclose cells and organelles

Question 20

Disordered Protein

Answer 20

Do not form thermodynamically stable structures; flexible in conformation, which is key to their functional activities

Question 21

Intrinsically Disordered Protein

Answer 21

Do not have well-ordered structures in their native, functional states due to an entirely disordered polypeptide chain; typically serve as signaling molecules, regulators of the activities of other molecules, or as scaffolds for multiple proteins, small molecules, and ions

Question 22

Quaternary Structure

Answer 22

The number and relative positions of the polypeptide chains in multimeric proteins

Question 23

Biomolecular Condensates

Answer 23

A specialized subunit of a cell, not bounded by a membrane. Often compared to a liquid droplet, it is chemically and physically distinct from its surroundings and is formed as a consequence of a liquid-liquid phase separation or aggregation of proteins and RNAs

Question 24

Liquid-Liquid Phase Seperation

Answer 24

Process in biomolecular condensates; multiple copies of one or more macromolecules separate from the bulk surrounding fluid

Question 25

Hydrophobic Amino Acid

Answer 25

Amino acid with non polar side chain; poorly soluble in water
Larger non polar side chain = more hydrophobic amino acid

Question 26

Aliphatic Amino Acid

Answer 26

Amino acid with linear or branched hydrocarbon that does not form a ring; nonpolar

Question 27

Hydrophilic Amino Acid

Answer 27

Amino acid with a polar side chain; most hydrophilic amino acids have side chains that are charged (ionized) at the pH typical of biological fluids both inside and outside the cell