Week 4 Flashcards
The ____ ____ of amino acids in a protein determine the shape and function of the protein.
exact order
Describe the structure of an amino acid.
It consists of a central carbon atom, called the 𝛼 (alpha) carbon, connected by covalent bonds to four different chemical groups: an amino group (–NH2, a carboxyl group (–COOH), a hydrogen atom (–H), and a variable side chain or R group.
define alpha carbon
The central carbon atom of each amino acid.
define amino group
NH2; a nitrogen atom bonded to two hydrogen atoms, covalently linked to the central carbon atom of an amino acid.
define carboxyl group
COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group.
define side chain or R group
A chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid.
What generally makes amino acids hydrophobic?
They are hydrophobic when their R group is a non polar hydrocarbon chain or ring
What causes the aggregation of hydrophobic amino acids?
The tendency of water to hydrogen bonds with itself and because of weak van der waals forces (temporary dipole interactions)
Why are hydrophobic amino acids usually burried deep in the interior of folded proteins?
to keep them away from water
Why are hydrophilic amino acids usually located on the outside surface of folded proteins?
Because the R groups may gain or lose an electron due to the pH of the cell causing them to interact with water and therefore want to be near the surface
Do charged R groups on the surface of proteins bond?
yes they bond with one another and with other charged molecules which is why that can associate with one another or other macromolecules such as DNA
The R groups of the basic and acidic amino acids are ____ _____
strongly polar
Basic R groups ____ a proton to become ____ charged in the pH of the cell
gain
positively
Acidic R groups ____ a proton to become ____ charged in the pH of the cell
lose
negatively
What make glycine different from other amino acids?
It has H as an R group so it is symmetric, non polar, and smaller than other amino acids. The H as an R group allows for free rotation around the C-N bond because H group is not big enough to interact enough with the other hydrogen on the N
How is proline different from other amino acids?
Its R group is bonded back to the amino group causing a kink or bend in peptide chains which puts restraints on protein folding
How is cytosine different from other amino acids?
the sulfur in the R group allows it to make disulfide bonds which are stronger than the ionic interactions of other pairs of amino acids
Define peptide bond
A covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid.
What is released when a peptide bind is formed?
water
what is the name of a C double bonded to and O?
carbonyl
what is the name of an H bonded to an N
amide group
Polypeptides have an ____ end that is ____ charged and a _____ end that is _____ charged
amino, positively
carboxyl, negatively
Define amino end
The end of a polypeptide chain that has a free amino group.
Define Carboxyl end
The end of a polypeptide chain that has a free carboxyl group.
Define residues
In the context of protein synthesis, any of the amino acids that is incorporated into a protein.
What are amino acids which are Incorporated in the protein called?
residues
Define primary structure
The sequence of amino acids in a protein.
The sequence of amino acids in a polypeptide is the proteins ____ _____
primary structure
Define secondary structure
The structure formed by interactions between stretches of amino acids in a protein.
What is the secondary structure of a protein a result of?
interactions between stretches of amino acids
What is the tertiary structure of a protein a result of?
long-range itneractions between the secondary structures
Define tertiary structure
The overall three-dimensional shape of a protein, formed by interactions between secondary structures.
Define quartenary structure
The structure that results from the interactions of several polypeptide chains.
The function of a protein is dependent on….?
the 3D shape of the protein
What are the two types of secondary structures found in found in different proteins?
alpha helix and beta sheet
Secondary structures are a result of ____ bonding between…?
hydrogen
the carbonyl group of one amino acid and the amide group of another amino acid
B sheets are typically denoted by…?
Broad arrows, where the direction of the arrow goes from the amino end to the carboxyl end
Tertiary structure is determined by the spatial distribution of?
Hydrophilic and hydrophobic R groups along the molecule and the various attractions between R groups
Define denaturation
The unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strands of nucleid acid.
When a protein is denatured what happens to the R group?
It loses its functional activity
Quarternary structures are made up of…?
Two or more proteins that are complete and fully functional in their tertiary structure
Define chaperone (in terms of protein folding)
A protein that helps shield a slow-folding protein until it can attain its proper three-dimensional structure.
