ch 3: protein structure and function Flashcards
structure of amino acids
a central carbon that bonds to four different atoms
what are the 4 groups that the carbon bonds to?
- hydrogen atom
- amino functional group (NH2)
- carboxyl function group (COOH)
- R group (side chain)
what does the functional group do for the amino acids?
the charges help them stay in solution, where they interact with each other
what happens if amino group acts as a base?
it attracts protons to form NH3+ and the carboxyl group would then act as an acids and it loses a proton to form COO-
what affects reactivity of amino acids?
functional groups
what affects solubility of amino acids?
polarity and charge of R-groups
do polar and electrically charged R-groups interact with water or not?
yes, they are hydrophilic
why do nonpolar charges not form H-bonds?
they lack charge which then makes them hydrophobic
- they combine in aqueous solutions, instead of dissolving
what 3 groups are R-groups divided into?
charged, uncharged polar, and nonpolar
charged R-groups
includes acidic and basic
- negative charge: acidic and lost proton
- positive charge: basic and gained proton
uncharged polar
contains oxygen and forms polar covalent bond
nonpolar
no negative charge, positive charge or oxygen atom
how do amino acids polymerize?
when a bond forms between carboxyl group of one amino acid and amino group of another
peptide bonds and how does it form?
C-N covalent bond that results from condensation reaction
are peptide bonds stable?
no, because N donates its unshared valence electrons to the carbon in C-N bond, to form C=N which causes electrons from C=O to go to O and make it C-O-
what is the orientation of the R-group in a peptide-bonded backbone?
extends out of the backbone, making it possible for them to interact with each other and with water
what is directionality of the peptide-bonded backbone?
N-terminus to C-terminus = NH3+ on one end to COO- on the other
flexibility of peptide-bonded backbone
single bonds on either side can rotate but the bond itself cannot because of its double bonded nature
oligopeptide
fewer than 50 amino acids linked together
polypeptide
more than 50 amino acids linked together
protein
consists of one or more polypeptide chains
primary structure
order of amino acids in a chain
what are primary structures stabilized by?
peptide bonds
secondary structure
first step of 3-D folding created and stabilized by weak hydrogen bonds between carboxyl and amino groups of amino acids on the backbone
a-helix
polypeptide’s backbone is coiled from hydrogen bonds
b-pleated sheet
two or more polypeptide chains are aligned after 1 big turn, hydrogen bonds from between the chains
- linear
why are alpha helix and beta pleated sheets stable?
due to the large number of hydrogen bonds on both of these
tertiary strucutre
2nd step of 3-D folding stabilized by disulfide bridges, van der Waals, ionic bonds, and hydrogen bonds between R-side chains of amino acids
what are the 5 possible interactions of tertiary structures?
hydrogen bonding, hydrophobic interactions, van der waals, covalent bonding, and ionic bonding
quaternary structure
stabilized by tertiary structures bonded together and final function form of protein
folding of a protein
hydrophobic interactions drive proteins to fold and their nonpolar R-groups come together in the interior, that increase entropy of surrounding water
is a folded or unfolded molecule more stable?
folded because it has less potential energy
denatured
treatment with compounds that break hydrogen bonds and disulfide bonds and causes protein to lose function
what is the function of protein dependent on?
its shape
how are proteins denatured?
heat, pH, salt, and solvents
what are 6 things are proteins crucial for?
catalysis, structure, movement, signaling, transport and defense
catalysis
speed up chemical reactions
what functions as a catalyst?
enzymes: proteins
substrates
a reactant that interacts with a catalyst in a chemical reaction
active site
location in an enzyme molecule where substrates bind and react
structure
structural proteins make up body compartments such as hair and fingernails
movement
motor proteins are responsible for moving the cell itself, or large molecules
signaling
proteins carry and receive signals from cell to cell inside the body
transport
proteins allow certain molecules to enter and exit cells or carry them throughout the body
defense
antibodies attack and destroy viruses and bacteria that cause disease
