Term
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Definition
| The basic macromolecular compartments of living things |
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Term
| Hydrogen bond is MOST stable |
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Definition
| When the H atoms and the 2 electronegative atoms are aligned or nearly in line. Hydrogen bonds are highly directional |
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Term
| Nonpolar solutes molecules are driven together in water NOT because they have a high affinity for each other BUT |
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Definition
| Water bonds strongly to itself. Water has a high affinity for each other. |
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Term
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Definition
| Molecules that are both hydrophilic and hydrophobic. Contain a polar group with a hydrophobic tail |
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Term
| Name the four noncovalent bonds from strongest to weakest |
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Definition
| Charge-charge > Hydrogen bonding > Hydrophobic interactions > Van de waals |
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Term
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Definition
| Atom to which H is more tightly associated. O-H, N-H |
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Term
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Definition
| Atom to which H is less tightly associated. O or N. The acceptor has partial negative charge that attracts H atom |
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Term
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Definition
| MAJOR driving force for folding of macromolecules, binding of substrates to enzymes & formation of membranes |
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Term
| Equilibrium constant for water |
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Definition
Keq= [H+][OH-]
__________
H2O |
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Term
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Definition
Kw = [H+][OH-]
Kw= 1.0X10^-14 M^2 |
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Term
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Definition
The negative logarithm of the concentration of H+
pH= -log[H+] |
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Term
| Henderson-Hasselbalch Equation |
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Definition
pH = pKa + log[A-]/[HA]
Used to determine the final pH of a weak acid solution once the dissociation reaction reaches equilibrium |
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Term
| Human blood pH is regulated by |
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Definition
| CO2-carbonic acid-bicarbonate buffer system |
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Term
| Examples of Protein Function |
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Definition
1. Enzymatic catalysts
2. Transport & storage
3. Coordinated motors |
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Term
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Definition
Carboxylate group
Amino group
Hydrogen atom
Side chain (R group) |
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Term
| All amino acids EXCEPT ____ can exist as enantiomers. Enantiomers of amino acids are called D (righted hand) or L (left handed) |
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Definition
| Glycine because its R group is a H atom. Therefore, the molecule is not chiral. |
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Term
| Properties of the side chains GREATLY affect |
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Definition
| The overall 3-dimensional shape (conformation) of a protein |
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Term
| Four aliphatic amino acid |
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Definition
Glycine
Alanine
Valine
Leucine
Isoleucine |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| The only cyclic amino acid |
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Term
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Definition
Phenylanine (Phe, F)
Tyrosine (Tyr, Y)
Tryptophan (Trp, W) |
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Term
| What type of R groups absorb UV light? |
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Definition
| Characteristics of aromatic R groups |
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Term
| What type of R group is almost always the 1t amino acid in a polypeptide chain |
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Definition
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Term
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Definition
| Stabilize the three dimensional structures of proteins by covalently cross linking cysteine residues in peptide chains |
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Term
| Sulfur-containing R groups |
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Definition
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Term
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Definition
Serine (Ser, S)
Threonine (Thr, T) |
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Term
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Definition
Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)
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Term
| Acidic R groups and Amide Derivatives |
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Definition
Aspartate (Asp, D)
Glutamate (Glu, E)
Asparagine (Asn, N)
Glutamine (Gln, Q)
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Term
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Definition
| Acidic R groups that are dicarboxylic acids and are negatively charged at pH 7 |
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Term
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Definition
| Amide Derivatives that are uncharged but highly polar. Found on the surface of proteins where they interact with H2O molecules. |
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Term
| For a solution BELOW the pKa |
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Definition
| The PROTONATED form dominates (AH) |
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Term
| For a solution pH ABOVE the pKa |
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Definition
| The UNPROTONATED form predominates (B) |
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Term
| Formation of a peptide bond |
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Definition
| Eliminates the ionizable alpha-carboxyl and alpha-amino groups of the free amino acids EXCEPT for those at the amino & carboxyl termini |
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Term
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Definition
| Fibrous and globular proteins |
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Term
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Definition
| Structural proteins that provide mechanical support to cells or organisms |
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Term
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Definition
| Most of these proteins are enzymes. |
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Term
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Definition
| The linear sequence of amino acid residues in a protein |
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Term
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Definition
| Structure maintained by hydrogen bonds between amide hydrogens and carbonyl oxygens of the peptide backbone. Major structures include the alpha-helix and beta-strands |
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Term
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Definition
| The three-dimensional conformation of a protein |
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Term
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Definition
| Structures that involves the association of two or more polypeptide chains into a multisubunit |
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Term
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Definition
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Term
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Definition
| Spatial arrangement of groups that are free to assume different positions in space without breaking any bonds |
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Term
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Definition
| spatial arrangement of atoms that CANNOT be changed without breaking covalent bonds |
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Term
| The primary structure is made of |
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Definition
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Term
| Carbony C and N is ___ than C-N single bonds but ____ than C=N double bonds |
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Definition
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Term
| Cis conformation is less favorable due to |
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Definition
| steric inteference of alpha-carbon SIDE CHAINS |
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Term
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Definition
| is restricted due to the double bond nature of the resonance hybrid form |
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Term
| Peptide bonds have a repeating |
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Definition
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Term
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Definition
| Used to determine the three-dimensional conformation of proteins via crystals |
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Term
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Definition
| Determine the three-dimensional conformation of proteins in solution without the use of crystals |
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Term
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Definition
| Proposed alpha-helix and beta-sheets as types of structures in proteins |
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Term
| Alpha-helix can be either ___ or ___ but almost always ___ |
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Definition
left handed or right handed
right handed |
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Term
| Side chains of alpha helix |
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Definition
| All side chains point outward from cylinder of helix |
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Term
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Definition
May be parallel or anti-parallel
Side chains point alternatively above and below plane of strand |
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Term
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Definition
| Allow a peptide chain to FOLD BACK ON ITSELF to make a compact structure |
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Term
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Definition
| Often contain hydrophilic residues and are found on protein surfaces |
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Term
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Definition
| Loops containing 5 residues or less |
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Term
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Definition
rise= 0.15 nm
pitch = 0.54
3.6 residue per turn |
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Term
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Definition
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Term
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Definition
| Independently folded, compact, distinct structural units in proteins. |
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Term
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Definition
| recurring protein structures |
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Term
| Secondary structure is stabilized by |
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Definition
| Hydrogen bonding between amide hydrogen and carbonyl oxygen of the polypeptide backbone |
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Term
| Tertiary structure is stabilized by |
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Definition
| Noncovalent interaction between the side chains of amino acid residues |
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Term
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Definition
| Formation of one structure leads to formation of remaining structure |
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Term
| Hydrogen bonding and Van de waals |
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Definition
| Stabilizes globular protein folding |
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Term
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Definition
Proteins that bind newly synthesized polypeptides & assist in proper folding
Increases rate of correct folding and prevents incorrect folding
Binds unassembled protein subunits, prevents incorrect aggregation |
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Term
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Definition
| heat-shocked proteins such as HSP70 |
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Term
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Definition
| A monomeric protein that facilitates the diffusion of oxygen in vertebrates |
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Term
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Definition
| A tetrameric protein that carries oxygen in blood |
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Term
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Definition
| Formed by three alpha-helices and two loops. Found in the heme prosthetic group of myoglobin |
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Term
| Characteristics of Enzymes |
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Definition
10^3 - 10^20 times faster
Speeds up the attainment of equlibrium
Temporarily changed, but remains unchanged in the overall process
Do NOT change the position of the equi. only the E by lowering it.
Speeds up BOTH forward & reverse rxns. |
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Term
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Definition
| Catalyze oxidation=reduction reactions. |
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Term
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Definition
| Catalyze group-transfer reactions and many require the presence of COENZYMES |
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Term
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Definition
| Catalyse hydrolysis. Water serves as the acceptor of the group transfer |
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Term
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Definition
| Catalyze lysis of substrate, generating a DOUBLE BOND |
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Term
| A lysase that catalyzes an addition reaction in cells |
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Definition
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Term
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Definition
| Catalyze structural change within a single molecule (isomerization reactions) |
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Term
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Definition
| Catalyze ligation or JOINING of two substrates. Requires ATP. Usually refers as synthetases |
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Term
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Definition
| The major protein component of the connective tissue of vertebrates; it constitutes about 25-35% of the total protein in mammals. |
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Term
| What does collagen structure consist of? |
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Definition
| 3 left-handed helical chains coiled around each other to form a right handed supercoil. Each left handed helix in collagen has 3.0 amino acid residues per turn and a pitch of 0.94 nm, giving a rise of 0.31 nm per residue. |
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Term
| What causes the red color in myoglobin and hemoglobin? |
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Definition
| The heme prosthetic group. Heme consists of a tetrapyrrole ring symste called protoporphyrin IX complexed with iron. |
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Term
| The four pyrrole rings of heme are linked by ___? |
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Definition
| Methene (-CH=) bridges, so that unsaturated porphyrin is highly conjugated and planar. The bound iron is the ferrous (Fe II), oxidation state. |
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