Cell and Molec Ch 4: Protein Structure and Function

central dogma of biology

the flow of genetic material from DNA transcripted into RNA and translated into protein

structural protein function

provides the cell with shape and structure

enzyme protein function

catalyzes the breakage or formation of covalent bonds

transport protein function

carries molecules and ions

motor protein function

generates movements in the cells and tissues

storage protein function

storing small molecules or ions

signal protein function

carrying signals from cell to cell or within a cell

receptor protein function

detects signals and sends them to the response machinery

gene regulation protein function

binding to DNA to switch genes on or off

peptide bonds

link amino acids together

polypeptide chain

amino acids linked together that makes up a protein

n-terminus

beginning of the chain on the left

c-terminus

end of the chain on the right

side chains

extensions off the polypeptide backbone that consist of specific amino acid sequences

hydrogen bonds

interactions between H+ and H- atoms that help proteins fold, backbone to backbone, backbone to side chain, and side chain to side chain

ionic bonds and van Der Waals attractions

help proteins fold through hydrophobic interactions causing the backbone to bend away from water

hydrophobic forces

nonpolar side chains get packed into a hydrophobic core while polar side chains hydrogen bond to water and keep protein folded

denatured protein

a protein that has lost its natural shape due to heat, exposure to other materials, pH change, they can sometimes refold

prior disease

when a rare protein misfolds and it becomes infectious

chaperone proteins

guide the folding of new polypeptide chains to make sure it’s correct

primary protein structure

the amino acid sequence of the 20 possible amino acids arranged along the backbone and held by peptide bonds

secondary protein structure

alpha helices which are the coiled up polypeptide chain that’s twisted and held by hydrogen bonds and beta sheets that are polypeptide chains held together parallel or antiparallel by hydrogen bonds

tertiary protein structure

the side chains on the backbone use hydrophobic forces to fold the protein up into a compact formation with nonpolar hydrophobic chains on the inside and polar side chains on the outside binding to water

quaternary protein structure

the creation of protein functional domains consisting of multiple polypeptide chains in one complex, it can be all alpha helices, alpha helices and beta sheets, or all beta sheets

complex structures

proteins can form into dimers, helices, and rings when binding to each other or into filaments, tubes, and spherical shells

actin filament

identical protein subunits that came together to provide the cell with shape and structure

collagen

a triple helix protein where three protein chains wrap around each other

disulfide bonds

stabilize a favor protein conformation

scaffold proteins

bring together interacting proteins in large complexes to concentrate them to a certain place

ligand

anything that bonds to a protein through noncovalent bonds

cavity

a divot created by a folding of a polypeptide chain where ligands can bind to

binding sites

areas on the protein where specific ligands can interact

antigen

the ligand that specifically binds to an antibody on two identical binding sites

substrate

the ligand that specifically binds to enzymes to promote catalysis and increase the rate of a chemical reaction

hydrolase

enzymes that catalyze a hydrolytic cleavage reaction

nuclease

breaks down nucleic acids

protease

breaks down proteins

ligase

joins two molecules together

isomerase

rearranges bonds in a single molecule

polymerase

polymerizes reactions like the synthesis of DNA and RNA

kinase

adds phosphate groups to molecules like proteins

phosphatase

removes phosphate groups from molecules

oxido reductase

catalyzes reactions where one molecule is oxidized and the other is reduced like oxidases, reductases, and dehydrogenases

ATPase

hydrolyzes ATP to release energy

feedback inhibition

regulates protein activity like gene expression, protein location, and feedback loops

feedback inhibitor

when an end product prevents an event from occurring by inhibiting the pathway

conformational change

triggered by feedback inhibition and causes a change in shape

protein phosphorlyation

regulates protein activity by adding or removing phosphate groups to start or stop a process

protein modification

controls protein behavior by producing regulatory code at multiple sites

p53

tumor supressor protein