exam 1exam chapter 3 and 4 Flashcards
non polar, aliphatic R groups
glycine
alanine
proline
valine
leucine
isoleucine
methionine
R group ishydrogen, found in flexible
parts of proteins, not chiral, can be modified
by addition of a fatty acid (myristate – 14
Carbon)
glycine
R group is CH3 (methyl group)
alanine
Extended aliphatic chains and can be branched
Valine (V, Val)
Leucine (L, Leu)
Isoleucine (I, Ile)
Only imino acid, affects protein folding, often found at bends in protein 3-D structures. Hydroxylation of___ important for the structure of collagen
proline pro p
Contains sulfur, can interact and bind
with metal ions, often found in
metalloproteins
methionine Met M
aromatic R group
phenylalanine
tyrosine
tryptophan
Can be phosphorylated on hydroxyl groups
Tyrosine, Serine, and Threonine
polar, uncharged R groups
Serine
Threonine
Cysteine
Asparagine
Glutamine
Classified as amides
* Neither acidic or basic
* Forms H-bonds
* Asn can be modified with sugars to
form glycoproteins
Asparagine (N, Asn) and Glutamine (Q,
Gln)
Sulfhydryl side chain (-SH) (gives the polarity)
* Can oxidize to form disulfide bonds that strengthen protein structure
* Disulfide bonds are covalent but reversible upon reduction
Cysteine (C, Cys)
positive charged R group
Lysine
Arginine
Histidine
UV absorbing at 250-300 nm – can be useful to
identify proteins in a mixture
phenylalanine
tyrosine
tryptophan
Side chains gain a proton at
physiological pH (Positively
charged)
Lysine
Arginine
Histidine
negatively charged R group
Aspartate
Glutamate
is ionizable at physiological pH; therefore can act as a proton donor or acceptor depending on the pH surrounding.
histidine
Found in collagen, the principle component of
connective tissue.
Hydroxyproline and hydroxylysine
modified after incorporation ,Modifications essential for maintaining normal
connective tissues in tendons, cartilage,
bones, teeth, skin
Proline and lysine
The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy
Hydrophobic effect
Interaction of N−H and C=O of the peptide bond leads to local regularstructures such as
alpha helices and beta sheets
Hydrogen bonds
Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein
London dispersion
long-range strong interactions between permanently charged groups
* Salt bridges, especially those buried in the hydrophobic environment, strongly stabilize the protein
Electrostatic interactions
a resonance hybrid of two canonical structures
peptide bond
spherical proteins that are folded into a three-dimensional structure
globular protein
covalent chemical bond that forms between the carboxyl group (COOH) of one amino acid and the amino group (NH2) of another amino acid, resulting in the formation of a dipeptide.
peptide bond
is formed by the assembly of individual polypeptides into a larger functional cluster.
quaternary structure
Loss of structural integrity with accompanying loss of activity is called
denaturation
are composed of different motifs
folded together.
Globular proteins
is the main protein in silk from moths and
spiders
Fibroin
superstructures are formed by
cross-linking of collagen triple-helices to
form collagen fibrils.
collagen
are covalent bonds between
Lys or HyLys, or His amino acid residues.
crosslink
occur frequently whenever strands in beta sheets change the direction
beta turns
__ in position 2 or__ in position 3 are
common in beta turns
Proline
glycine
beta turn is stabilized by ____from a carbonyl oxygen to amide proton three residues down the sequence
hydrogen bond
In ___ beta sheets, the H-bonded strands run in
opposite directions
antiparallel
In beta sheets, the H-bonded strands run in the
same direction
parallel
The ____ is a planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure
Beta sheet
acts as a helix breaker because the rotation around the N-Ca (φ-angle) bond is impossible
proline
acts as a helix breaker because the tiny R group
supports other conformations
Glycine
Small hydrophobic residues such as Ala and Leu are
strong helix formers
Helical backbone is held together by
hydrogen bonds between the backbone amides of an n and n + 4 amino acids
alpha helix
stabilized by hydrogen bonds between nearby residues
alpha helix
stabilized by hydrogen bonds between adjacent
segments that may not be nearby
beta sheets
secondary structure
α-helix
β-sheet
β-turns
role of hydrogen bonding
Tertiary structure
α-keratine
collagen
silk fibroin
the process by which a protein molecule assumes its three-dimensional structure or conformation, typically referred to as its native state
protein folding
are proteins or segments of proteins that lack a stable three-dimensional structure under physiological conditions
Intrinsically disordered proteins
a natural protein fiber produced by certain insects, primarily silkworms, and spiders.
silk fibroin
a fibrous structural protein found in the skin, hair, nails, feathers, and horns of vertebrates, including mammals, birds, reptiles, and amphibians
α-keratine
the most abundant protein in the human body and is found in connective tissues such as tendons, ligaments, skin, cartilage, bones, and blood vessels
collagen
are secondary structural elements found in proteins. They are characterized by a tight turn in the polypeptide chain that reverses the overall direction of the backbone.
beta turns
is a common secondary structure motif found in proteins.
beta sheet
a common secondary structure motif found in proteins. It is characterized by a right-handed coil or helix in which the backbone of the polypeptide chain forms hydrogen bonds between the carbonyl oxygen of one amino acid residue and the amide hydrogen of an amino acid residue four positions down the chain.
α-helix
a chemical method used to determine the amino acid sequence of a peptide or protein
Edman degradation
a monomer refers to a single unit of a protein chain, which is typically an individual amino acid
Monomer
refers to a molecule composed of a few (usually a small number) of monomer units linked together.
Oligomer
