terms Flashcards
This amino acid has an aromatic ring and is neutral at pH 7 however when it pH 5 it becomes active
His (histidine)
This little guy is non-polar and is very flexible because it has no side chain
Gly (glycine)
This amino acid is charged and has a carboxylate group on it
Asp (aspartate)
this amino acid 3 carbons in its side chained followed by nitrogen
Lys (lysine)
This amino acid is able to form disulfide bonds
Cys (cysteine)
This amino acid has an aromatic ring with a hydroxyl group on the end
Tyr (tyrosine)
This amino has a small side chain, polar and a hydroxyl group on the end
Ser (serine)
this amino acid has a cyclic side chain and is very rigid
Pro (proline)
The sequence of amino acid side chains is determined by DNA sequence of gene
primary structure
This is the hydrogen bonding of the peptide backbone and not directly dependent on sidecahins
secondary structure
this is the 3-dimensional packing of a whole protein chain
tertiary structure
this is the interaction between global domains such as actin & myosin, collagen, hemoglobin (association between multiple protein molecules)
quaternary structure
this is a protein that is more or less spherical in shape and has less surface area to volume ratio
globular domain
This is a protein that is very elongated and usually has some structural function
fibrous protein
connects i, i+4 amide groups and is has self-contained hydrogen bonding. binds carbon (i) and another carbon 4 away (i+4`)
alpha helix
this are things that allows the amino acid to rotate is two different places and they are known as.
phi/psi angles
this is important in understanding protein structure and lead to steric hinderance
torsion angles
if molecules are brought to close together and want to repel this is known as
steric hindrance
_______ can either lead to the polypeptide being in parallel form or antiparraller
beta sheet
without the _____ the enzyme may be unable to function like thiamine is a _____ for pyruvate dehydrogenase
cofactor
_____ aka iron
heme
this protein is composed of two alpha-helices wrapped around each other and they can be help together by disulfide linkages to become long stiff fibers
keratin
A _____ ______l is a structural motif in proteins in which 2-7 alpha-helices are coiled together like the strands of a rope
coiled coil
this is essentially a triple helix made from gly-pro-(anything else) and results in a very stiff, strong and is non-strecthy. Therefore it is good for bones and tendons
collagen
______ is composed of three polypeptides that are interwound such as DNA
triple helix
This occurs when molecules are afraid of water and wanter to be in the middle of the protein away from the water
hydrophobic effect
When a protein becomes unfolded this is referred to as
denaturation
this is a chaperone that helps unfold misfolded proteins
GroEL/GroES
sigmoid curve is the hallmark and when one thing binds more things want to bind. For example when people realize alex is taken all of the sudden they want to join
positive cooperativity
the binding sites become weaker after the initial thing binds and makes response to changes in substrate concentration more gradual, allowing for a broader dynamic range
negative cooperativity
this is an allosteric effector that binds to hemoglobin lower the binding affinity for oxygens and going towards the T state
2,3-BPG
This molecule is a competitive inhibitor with oxygen and can be removed from hemoglobin if p___ drops again
carbon monoxide
____=CO
something that fights with the correct molecule to bind in the active site is known as???
competitive inhibitor
Something that binds away from the active site and cause the molecule to become less active
allosteric inhibitor
Something that binds away from the active site and cause the molecule to become more active
allosteric activator
multiple forms of proteins-
multiple form os enzymes
isoform Ex Hb and HbF
isozyme
Helix rest in major groove of DNA and protein fold up around the ZN++ ion. Pretty much the smallest protein
zinc finger protein
reconition helix nestles into major groove and contacts bases (reads sequence). Stabilization helix sits behind it, and contacts the DNA backbone.
helix-turn-helix proteins
????
examples
very similar to chymotrypsin, essentially they are divergent
trypsin
this is the precursor to trypsin
trypsinogen
_____ has ser, asp and his in the active site and responsible for catalysis
chymotrypsin
this is the precursor to chymotrypsin
chymotrypsinogen
________ is an enzyme whose zymogen (pepsinogen) is released by the chief cells in the stomach and that degrades food proteins into peptides.
pepsin
________ is a non-specific protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis
subtilisin
_________ is an enzyme produced by cells of the duodenum and involved in human and animal digestion
enteropeptidase
The _____ ______ are a family of enzymes that ydrolyzecertain peptide bonds in other proteins.
serine protease
A _____ ______ is a group of three amino acids that are found in the active sites of some proteases involved in catalysis
catalytic triad
An _____ _____ is a pocket in the structure of an enzyme which stabilizes a deprotonated oxygen or alkoxide, often by placing it close to positively charged residues. In our case it stables the tertiary structure of the serine protease mechanism
oxyanion hole
