exam 1b Flashcards
(28 cards)
amino acids are grouped into
polar and non polar groups. within polar there are subgroups based on their charge
amino acids are linked together by
covalent peptide chains
peptide bonds are found
between N and C
types of non covalent bonds used to build the 3D structure of a polypeptide chain
hydrogen bonds, ionic bonds, and van der waals
how the hydrophobic force helps determine protein shapes
In a folded protein, polar amino acid side chains tend to be displayed on the surface, where they can interact with water; nonpolar amino acid side chains are buried on the inside to form a tightly packed hydrophobic core of atoms that are hidden from water
Chaperone proteins …
guide the folding of a newly synthesized polypeptide chain. Act as isolation chambers that help a polypeptide fold without aggregating with other polypeptides in the cytoplasm
Different ways to represent protein conformations
backbone, ribbon, wire, space-filling
Importance of hydrogen bonds in the formation of alpha helix and beta sheet
in an alpha helix, the N-H of every peptide bond is hydrogen bonded to the C=O of the neighboring peptide bond located 4 amino acids away in the same chain.
In a β sheet, several segments (strands) of an individual polypeptide chain are held together by hydrogen-bonding
structure of alpha helix and beta sheet
alpha helix- ribbon, beta- zig zag
coiled structure is formed
2 or 3 alpha helices wrap around one another
prions and how they cause infectious neurodegenerative diseases
misfolded proteins. (A) A protein undergoes a rare conformational change to produce an abnormally folded prion form. (B) The abnormal form causes the conversion of normal proteins in the host’s brain into the misfolded prion form. (C) The prions aggregate into amyloid fibrils, which can disrupt brain-cell function, causing a neurodegenerative disorder
Difference between tertiary and quaternary structures
T- associate in a specific manner to form the structure, which describes the final folding of the polypeptide. Q- association of 2 or more polypeptides as they interact to form a functional multimeric protein
How to form and break a disulfide bond
linking two -SH groups together from cysteine side chains that are adjacent in the folded protein
immunoglobulin proteins aka antibodies …
are produced by the immune system in response to foreign molecules
Km and relationship to Km value and enzyme substrate binding
To determine how tightly an enzyme interacts with its substrate, a value KM (Michaelis constant) is used. KM is the concentration of substrate at which an enzyme works at half of its maximum speed. If a large amount of substrate is needed to achieve Vmax (large KM), this is an indication of weak bindingc
The reaction lysozyme catalyzes and how it acts as a natural antibiotic
acts as a natural ab in egg whites, saliva, tears, and other secretions. They sever the polysaccharide chain that forms the cell walls of bacteria and causes cell wall to rupture and therefore bursting of bacteria . Adds molecule of water to single bond between two adjacent sugar groups in the polysaccharide chain, causing the bond to break
How feedback inhibition works
an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway. Thus whenever large quantities of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its catalytic action
allosteric enzymes and Aspartate transcarbamoylase
Aspartate transcarbamoylase from E. coli catalyzes an important reaction to synthesize the pyrimidine ring of C, U, and T nucleotides. One of the final products of this pathway, cytidine triphosphate (CTP) binds to the enzyme to trigger a conformational change, which turn it off whenever CTP is plentiful.
phosphorylation can control
protein activities and the functions of kinase and phosphatase in the phosphorylation process
How the activity of GTP- binding protein is controlled
the phosphate is not enzymatically transferred from ATP to the protein. Instead, the phosphate is part of the guanosine triphosphate (GTP) that binds tightly various types of GTP-binding proteins
Different types of chromatography
ion exchange- association between a protein and matrix depends on the pH and ionic strength of solution, gel-filtration- size of proteins, affinity- contain a matrix covalently coupled to a molecule that interacts specifically with protein of interest. Can be released by a pH change or concentrated salt solutions
protein native conformation
folded shape of a protein
protein domains
is a conserved part of a given protein sequence and tertiary structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded.
protein families
is a group of proteins that share a common evolutionary origin, reflected by their related functions and similarities in sequence or structure.
