2. Biomolecules and Enzymes Flashcards
made of long
unbranched chain of
these amino acids
proteins
repeating sequence of
atoms along the core of
the polypeptide chains
polypeptide backbone
give amino acids its unique properties
side chains
bonds of protein foldings
hydrogen bonds,
electrostatic attractions, and van der Waals
assist in protein folding
molecular chaperones
generated when a single
polypeptide chain twists around
on itself to form a rigid cylinder
a helix
form from neighboring segments of the polypeptide backbone that run in the same orientation
parallel chains
hydrogen bonding of the peptide
backbone; helices and β sheet
secondary structure
from a polypeptide backbone that folds back and forth upon itself, with each section of the chain running in the direction opposite of that of its immediate neighbors
antiparallel chains
formed from two or
more have most of their nonpolar
side chains on one side
coiled-coil
amino acid sequence
primary structure
full 3D organization of a polypeptide chain
tertiary structure
readily recognized when the genome of any organism is sequence
protein families
protein molecule formed as a complex of more than one polypeptide chain
quaternary structure
human genome have how many coding genes
21,000 protein-coding genes
tests to be undergone for protein sequence viewing
x-ray crystallography and nuclear
magnetic resonance (NMR)
the basic units of proteins that can fold, function, and evolve
independently
protein domains
process of creating new combination of gene functional domains
domain shuffling
during vertebrate evolution has given rise to many novel
combinations of protein
domains
domain shuffling
the subset of protein domains, mobile during evolution
protein modules
recognition domain – only in
humans
Major Histocompatibility
Complex (MHC) antigen
any region of a protein’s
surface that can interact with another molecule
binding site
forming a symmetric complex of two protein subunits (dimer)
head to head arrangement
ropelike structures;
important component of the cytoskeleton
intermediate filaments
two identical α-globin
subunits and two identical β-globin subunits, symmetrically arranged
hemoglobin
why is a helix a common
structure in biology?
all subunits are identical, they
can only fit together in one
way – rarely straight line
resulting in a helix
intrinsically disordered regions of
proteins are frequent in nature,
WHY?
to form specific binding sies for
other protein molecules that
are of high specificity
abundant outside the cell; main component of the gel-like extracellular matrix
fibrous proteins
main component in long
lived structures
keratin filaments
a dimer of two identical subunits
a-keratin
elongated three-dimensional
structure
fibrous protein
___ can spontaneously assemble into the final structure under the appropriate condition
purified subunits
another abundant
protein in ecm; highly
disordered polypeptide
elastin
4 process of disoerdered polypeptide chain
binding
signaling
tethering
diffusion barrier
consists of three long
polypeptide chains, each containing that nonpolar
amino acid glycine at every 3rd position
collagen
2 examples of prion diseases
scrapie in sheep,
Creutzfeldt-Jakob disease (CJD) in
humans
Kuru in humans
bovine spongiform encephalopathy (BSE) in
cattle
guide construction but take no part in the final assembled structure
assembly factors
Can Form from
Many Proteins; self
propagating, stable β-sheet
aggregates
amyloid fibrils
example of capable of self
assembly from its component parts
tobacco mosaic virus (TMV)
consist of amyloid fibrils – acts like a vesicle containing peptide
and hormones
secretory granules
the substance that is bound by the protein
ligand
each protein molecule can usually bind just one or a few molecules out of many thousands
specificity
secretes proteins
that form long amyloid fibrils
projecting from the cell
exterior that help to bind
bacterial neighbors to biofilms
in bacteria, secretory granules
Proteins aggregates may be released from dead cells and accumulate as
amyloid
Which disease can produce amyloid
Prion diseases
The ability of a protein to bind selectively and with high affinity to a ligand depends on the formation of a set of _____
weak noncovalent bonds
4 weak noncovalent bonds
hydrogen bonds
electrostatic attractions
van der Waals attractions
favorable hydrophobic interactions
the region of protein that associates with a ligand
Binding site
the interaction of neighboring parts of the polypeptide chain may _____
restrict the access of water molecules to that protein’s ligand binding sites
the clustering of neighboring polar amino acid chains can _______
alter their reactivity
3 types of interface
- surface-string interaction
- helix-helix
- surface-surface
binds tightly to a particular target molecule (antigen), inactivating directly or making it for destruction
Antibody or immunoglobulins
complementary to a small portion of the surface of the antigen molecule
Y-shaped molecules with two identical binding sites
cause the chemical transformations that make and break covalent bonds in cells
Enzymes
Enzymes + substrates
Products
Speeds up reactions, act as catalysts
Enzymes
Enzymes that hydrolytic cleavage reaction
Hydrolases
Break down nucleic acids by hydrolyzing bonds
Nucleases
Breaks down protein
Proteases
Synthesize molecules
Synthases
Joins together two molecules
Ligases
Catalyze the rearrangement of bonds
Isomerases
Catalyze polymerization reactions
Polymerases
Adds phosphate group
Kinases
Catalyze the hydrolytic removal of phosphate group
Phosphatases
Oxidized and redox
Oxido-reductases
Hydrolyze ATP
ATPases
Hydrolyze GTP
GTPases
Formula of enzyme substrate complex
E + S → ES → EP → E + P
the maximum rate of reaction divided by the enzyme concentration
Turnover number
enzymes achieve ______ of chemical reactions
extremely high rates
enzymes greatly increase the local concentration of both these ____ at the _____
substrate molecule at the catalytic site
unstable intermediate state
Transition state
the free energy required to attain the transition state
Activation energy
adds a molecule of water to a single bod bet. two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break
Hydrolysis
catalyzes the cutting of polysaccharide chains in the cell walls of bacteria.
Lysozyme
assisting the hydrolysis reaction. In other enzymes, a small organic molecule serves a similar purpose. Such organic molecules are often referred to as
Coenzyme
a large protein assembly; allows the product of enzyme A to be passed directly to enzyme B, and so on
Multienzyme complex
controls how many molecules of each enzyme it makes by ____
regulating the expression of the gene that encodes that enzyme
controls enzymatic activities by confining sets of?
enzymes to particular compartments
a product produced late in a reaction pathways inhibits an enzyme that acts earlier in the pathway
Feedback inhibition
prevent an enzyme from acting
Negative regulation
regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down
Positive regulation
Greek words ___ meaning “other” and _____ meaning “solid or 3d”
Allos, stereo
Enzyme having two binding sites – active and regulatory site
Allosteric enzymes
Recognizes the substrates
Active site
Recognizes a regulatory molecule
Regulatory site
Interaction between separated sites on a protein
Conformational change
positive regulation caused by ____ between two separate binding sites
conformational coupling
if the shift of a protein to a conformation that binds glucose best also causes the binding site for X to fit X better, then the protein will bind glucose more tightly when X is present than when X is absent
Positive regulation caused by conformational coupling between two separate binding sites
if a shape change caused by glucose binding decreases the affinity of a protein for molecule X, the binding of X must also decrease the protein’s affinity for glucose
Negative regulation caused by conformational coupling between two separate binding sites
can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site
Cooperative allosteric transition
transfer of the terminal phosphate group of an ATP molecule to the hydroxyl group
Protein phosphorylation
Phosphorylates
Protein kinase
phosphate removal, dephosphorylate
Protein phosphatase
phosphate is part of guanine nucleotide GTP; addition and removal of phosphate
GTP-binding proteins (GTPases)
What happens when a tightly bound GTP is hydrolyzed by the GTP-binding protein to GDP,
Conformational change then inactivated
They generate forces responsible for muscle contraction and the crawling and swimming of cells; a series of conformational changes
Motor proteins
they help to move chromosomes to opposite ends of the cell during mitosis
Motor proteins
coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein
unidirectional conformation changes
Membrane bound transporters with function to export hydrophobic molecules from the cytoplasm
ABC Transporters (ATP-binding cassette)
proteins binding sites for multiple other proteins
Scaffold proteins
they serve both to link together specific sets of interacting proteins and to position them at specific locations inside a cell
Scaffold proteins
