Molec Cell Test 1

ATP

Adenosine Triphosphate, source of energy for most of the cells actions

ADP

Adenosine Diphosphate the used form of ATP and must add another phosphate for it to be used again (can be hydrolyzed to AMP for more energy but uncommon)

Enzymes

Protein Catalysts

Heredity

transfer of genetically determined characteristics from one generation to the next

Ribozymes

RNA molecules that catalyze reactions

Transcription Factors

Switches that activate or repress transcription of particular genes

Hydrophilic

Water liking

Hydrophobic

Water fearing

Amphipathic

Hydrophilic and Hydrophobic section on one molecule

Van Der Waals interaction

temporary dipole- temporary dipole attractive forces

Hydrophobic effect

nonpolar molecules aggregating in water caused by repulsion of an unstable state

Molecular Complementarity

Lock and key fit between shaps, charges, or other properties of two molecules

Greater affinity of 2 molecules means

Better fit of those 2 molecules

Binding dissociation Constant K_d

measure of affinity between 2 molecules

Induced Fit

Binding of a molecule changes the shape to its binding partner

What stereoisomer of Amino Acid Groups are found in proteins?

The L stereoisomer

Purines

Adenine, Guanine; bases with a pair of fused rings

Pyrimidines

Cytosine, Thymine, Uracil; Bases that contain a single ring

Nucleosides

Combination of a base and a sugar without a phosphate group

Glycosaminoglycans

major polysaccharide component of the extracellular matrix

Mitogen

Inducer of cell division

Microscopic reversibility

the ability of a reaction to go backwards

Chemical Equilibrium

The rate of forward RXN = The rate of the backward RXN; the constant is K_eq

Catalyst

Increases the reaction rate but not the K_eq

Steady State

System of linked Reactions for producing and consuming that substance

K_d- Dissociation constant

the inverse of the equilibrium constant; the lower the K_d The higher the affinity

allostery

Change in shape from binding a molecule

Pronucleus

2 nuclei from both parents

Differentiation

Signals from environment and nucleus cause this to happen to cells in multicellular organisms;

Depends on which proteins are expressed, amount of protein produced, localization of the protein, modification of the protein, and associated partners

Peptidyle-proline Isomerases (PPIases)

catalyze the cis/trans isomerizations so that prolien in the folding protein quickly forms the proper isomer

Denaturation

disruption of a proteins structure; caused by heat, pH, denaturantes, and reducting agents

Chaperones

facilitate proper protein folding by preventing aggregation by binding to the polypeptide, also can disassemble toxic protein aggregates that form from misfolding

HSP 70

Heat Shock Protein with 70kDa MW; Inhibits innapropriate protein folding while bound tightly (costs ATP)

Zwitterion

has both a plus and minus charge

Peptide Bonds

Bonds that form polypeptides and proteins, which are amide linkages

Protein control mechanisms

allosteric effector-binding covalent phosphorylation, ubiquitinylation

Protein uses

Signaling, transport, movement, structure, molecular transformation

Oligopeptide

20-30 amino acids long

polypeptide

200-500 amino acid residues long

Protein

A single or multiple polypeptides with a 3D structure

Secondary Structure

Alpha helix, beta sheet, and beta turn

Structural motiff/ supersecondary structure

combination of 2+ secondary structures forming a distinct 3D structure

Domains

distinct regions of a protein structure with a particular activity characteristic even when isolated

Proteases

enzymes that cleave peptide bonds in proteins

Globular proteins

Water soluble, spherical, and compact protein type

Fibrous protein

Long, elongated, and stiff protein type

Integral membrane protein

protein imbedded in the phospholipid bilayer

Intrinsically disordered proteins

entire chain of this protein is disordered, typically a signaling molecule, regulator of other molecules, or a scaffold

Intrinsically disordered region

disordered segments of well-structured proteins

Supramolecular complexes

Highest level in protein structure, biopolymers containing 10-100 polypeptide chains

Biomolecular condensates

membraneless compartments in cells that are chemically and physically distinct from their surroundings formed from multivalent macromolecules

What drives protein folding

Free energy, caused by hydrophobicity, flexibility, and chemical interactions and bonds

Order of protein folding

Primary (chain)—> Secondary (close residues) —> Tertiary (far away residues)—> quaternary (multiple polypeptides)

What bonds are in secondary structure

Hydrogen bonding across the backbone of the proteins

Ligand

the molecule to which a protein binds to can cause a conformational change

Specificity

The ability of a protein to bind one molecule or a small group of molecules in preference to all other molecules

Antibodies

Proteins circulating in the blood made to combat antigens in infections agents; Y shaped molecules forming complexes causing a cascade of protective reactions from the immune system

Metabolic coupling

polypeptides with different catalytic activities cluster closely together as subunits of a multimeric enzyme or assemble on a scaffold to hold them together;

Causing the products of the reaction to be channeled directly to the next enzyme

Regulating protein function

regulation is needed to not waste resources and energy, take in certain resources, control timing, and prevent cancer

3 ways to regulate protein activity

1. Cells can increase or decrease the steady state level of the protein by altering the rate of synthesis, its rate of degradation or both

2. Cells can change the intrinsic activity as distinct from the amount of the protein (ex: noncovalent and covalent interactions)

   1. Change in the location or concentration withihn the cell, for the substrate or the cofactor

Roles of protein degradation

Removes potentially toxic proteins, improperly folded or assembled or damaged

Proteostasis

controlled production and destruction of otherwise normal proteins

Proteasome

Very large, multisubunit, protein-degrading molecular machine

Steps of degradation

1. Protein is tagged to target it for degradation'

2. the proteasome binds to the targeted protein via the tag and unfolds the protein as it is transferred into an internal chamber

   1. protein-cutting subunits of the proteome degrades the target protein into small peptides, which are released into the cytosol for further processing

Ubiquitin (Ub)

The 76 residue polypeptide that binds covalently (multiple times) to a deffective protein to mark it for degradation

Ubiquitinylation process

1. Activation of ubiquitin-activating enzyme (E1) by the addition of a Ubiquitin molecule using ATP

2. Transfer of Ubiquitin molecule to a cystein residue in a ubiquitin-conjugating enzyme (E2)

3. Formation of a covalent bond between the carboxyl of the C-terminal glycine76 of the Ub bound to E2 and the lysine side group in the target protein, catalyzed by ubiquitin-protein ligase (E3)

Proteome releases UB from the protein so it can tag more cells for degradation

Allostery

Any change in a proteins tertiary or quaternary structure

Feedback inhibition

Final product reduces the activity of an enzyme that catalyzes an early rate controlling step in that pathway

Cooperativity

positive or negative influence of a bound ligand has at one site on the binding of another molecule at the same type of site for the same ligand on a different binding site.