Biology - Chapter 3: Proteins | Quizlet

protein

an organic compound that is made of one or more chains of amino acids linked together with a peptide bond

peptide bond

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

polypeptide backbone

repeating sequence of atoms along the core of the polypeptide chain

side chains give proteins

unique properties

noncovalent bonds between side chains determine

folding of the protein

polarity of side chains (hydrophobic repulsion)

folds the protein so that the nonpolar side chains are not in contact with water/polar side chains are in contact with water

denaturation of a protein

unfolding of the protein's tertiary and secondary structure

proteins will fold into conformation of ______ energy

lowest

molecular chaperones

special proteins that assist in the protein folding

protein domains

structural units that fold more or less independently of each other

primary structure of protein

amino acid sequence

secondary structure of protein

Stretches of polypeptide chain that form α helices and β sheets

α helix

forms when a single polypeptide chain twists around on itself to form a rigid cylinder

β sheet

forms either from neighboring segments of the polypeptide backbone that run in the same orientation (parallel chains) or from a polypeptide backbone that folds back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbors (antiparallel chains)

coiled-coil structure

a secondary structure where a pair of alpha helices that are coiled around each other; hydrophobic strip in the center

tertiary structure of protein

full three-dimensional structure

quaternary structure of a protein

if a particular protein molecule is formed as a complex of more than one polypeptide chain

protein family

a group of proteins that are structurally and functionally related

protein module

structural or functional units that are common to many different proteins

binding site

any region of proteins surface that can interact with other molecule through sets of noncovalent bonds

protein subunit

polypeptide chain in a multi-protein complex

globular proteins

spherical, water-soluble proteins

globular proteins can form

long helical proteins

fibrous proteins

long, insoluble, structural proteins

disordered proteins

rubberlike, elastic meshwork (elastin in EM)

covalent cross-linkages

stabilize extracellular proteins (disulfide bonds)

reasons why large structures are formed by subunits (proteins)

1. small genetic information is needed

2. easy assembly and disassembly

3. errors in synthesis can be more easily avoided

assembly factors

proteins that are required for formation of a macromolecular structure but are not themselves part of that structure

amyloid fibrils

Self-propagating, stable β-sheet aggregates (Alzheimer's, Parkinson's and prion diseases)

ligands

any molecule that binds specifically to a receptor site of another molecule

three ways of two proteins binding

1) surface-string

2) helix-helix (coiled coil)

3) surface-surface

hydrolase

hydrolytic cleavage

nuclease

breaking down nucleic acid by hydrolysis

protease

breaking down proteins by hydrolysis

synthase

synthesizing two molecules in anabolic reactions by condensation

ligase

joining two molecules in energy-dependent process

isomerase

rearrangement of bonds

polymerase

catalyzing polymerization reactions

kinase

catalyzing addition of phosphate groups

phosphatase

hydrolytic removal of phosphate groups

oxido-reductase

catalyzing redox reactions

ATPase

hydrolyzing ATP to ADP

GTPase

hydrolyzing GTP to GDP

phosphorylation

the addition of a phosphate group to a molecule

regulation by phosphorylation

-two negative charges on a phosphate group can greatly change proteins conformation

-phosphate group can be recognized by other proteins' binding sites

-can disrupt protein-protein interactions

Src family of protein kinases

controlling signal-processing proteins by adding phosphates and removing them

Ras protein

monomeric GTPase that drives the growth, proliferation, and migration of cells

GTP-binding proteins

proteins which are 'on' (actively signaling) when GTP is bound, and 'off' when GDP is bound

GAP

GTPase activating protein binds to Ras and induces hydrolysis of GTP

GEF

guanine nucleotide exchange factor binds to GAP-Ras causing the release of GDP

ubiquitination

targets a protein for degradation by a proteasome

ubiquitination process

1. E1 (ubiquitin-activating enzyme) uses ATP hydrolysis to bind ubiquitin to itself

2. E1 passes ubiquitin to E2 (ubiquitin conjugating enzyme) that works in conjunction with E3 (ubiquitin ligase)

3. E3 binds to degradation signals (degrons) in protein substrates

motor proteins

specialized proteins that use energy to change shape and move cells or structures within cells

How is unidirectional movement of motor proteins achieved?

By coupling one of the conformational changes to ATP hydrolysis.

transport proteins

a transmembrane protein that helps a certain substance or class of closely related substances to cross the membrane

ABC transporters (ATP-binding cassette)

carrier proteins that use energy from ATP to transport solutes (mostly hydrophobic molecules out of the cell)

rotary pumps

membrane-bound pump

-couple ATP hydrolysis to the H+ transport

-acidify the interior of lysosomes

-can function in reverse to catalyze the phosphorylation of ADP

scaffold proteins

proteins with binding sites for multiple other proteins (link and position the proteins)