Chapter 4 Flashcards
peptide bonds
C-N (bond carboxyl group with amino group through condensation rxn)
protein backbone sequence
N-C-C; hydrophilic (H-bonds with itself)
primary structure of proteins
amino acid sequence
secondary structure of amino acids
alpha helix and beta sheet folding caused by hydrogen bonding of the backbone
tertiary structure of proteins
specific folding caused by side chains, final shape
quaternary structure
2 or more polypeptide chains arrangement
alpha helix
secondary structure caused by hydrogen bonding between O-H of carboxyl and amino groups 4 amino acids away
can cross lipid bilayer if side chains (exterior) are nonpolar
beta sheet
held together by hydrogen bonds between adjacent strands in picket fence organization
parallel or antiparallel
three types of noncovalent bonds that contribute to protein shape/stability
ionic/electrostatic bonds
Van der Waals forces
hydrogen bonds
hydrophobic forces
nonpolar molecules repel water and force nonpolar side chains together
disulfide bonds
covalent bond between adjacent cysteine side chains by oxidation rxn
takes place in ER only (NOT form in cytosol)
important for secreted proteins to maintain function
protein domain
segment of polypeptide chain that fold independently into compact stable structure
protein motif
simple combinations of secondary structures, not stable by itself, can’t fold by itself
coiled-coil
protein motif
2 a-helices coiled around each other with hydrophobic in center and hydrophilic parts exposed
protein subunit
separate polypeptide chain of a protein that assembles with other polypeptide chains to form a protein complex
hemoglobin structure
made of 2 alpha globin and 2 beta globin subunits, becomes functional at quaternary stage
denatured: loses quaternary, tertiary, and secondary structures
myoglobin
made of 1 polypeptide chain, functional at tertiary structure
denatured: loses secondary and tertiary structures
globular proteins
one binding site, form dimers
filamentous proteins
multiple binding sites, form long helical filament
ring
formed when 2 binding sites of identical proteins are disposed appropriately to each other
actin filament
helical structure formed by many identical subunits
collagen
fibrous protein
triple helix formed by 3 polypeptide chains
bone, cartilage, skin
cross-linked in ECM to form collagen fibrils
elastin
fibrous proteins
cross-linked by covalent bonds to form elastic fibers, stretchy protein
important in stretchy tissues, lungs, bladder, some blood vessels
Fibrous protein molecules
keratin, elastin, collagen, actin(polymer)
Globular protein molecules
lysozyme, hemoglobin, actin(monomer)
serine proteases
family of protein-cleaving (proteolytic) enzymes that include digestive enzymes (chymotrypsin, trypsin, elastase) and proteases involved in blood clotting
chaperons
proteins that help other proteins fold, many are heat-shock proteins or isolation chambers
denaturation
unfolding due to changes in temp, pH, chemicals, usually reversible
protein aggregation
occurs with misfolded proteins in the nervous system, causes neurodegenerative diseases (Alzheimer’s, Huntington’s)
prion
pathogenic misfolded protein that can pass shape to other proteins, “mad cow” disease
ferritin
storage protein that stores iron in the liver
insulin
signal protein that controls blood glucose levels
receptors
proteins that detect signals and transmit to cell’s response machinery
hemoglobin/myoglobin
transport proteins that carry O2 and CO2 in blood and muscles, respectively
collagen/keratin
structural proteins that form cartilage, hair, and nails
actin/myosin
motor proteins that allow muscles to contract
immunoglobins(antibodies)
defense proteins that recognize foreign organisms and cancer cells
transcription factors
regulatory proteins that regulate gene expression
Green fluorescent proteins (GFP)
special-purpose protein from jellyfish that emits green light
Binding sites
allow proteins to bind to specific ligands, many covalent bonds
biochemical pathway
multiple chemical reactions that occur at the same area and the product of one enzyme becomes the substrate of the next (Enzymes work in sets)
statins
drug that blocks enzyme activity of HMG-CoA reductase
nuclease
breaks down nucleic acids by hydrolyzing bonds between nucleotides
protease
breaks down proteins by hydrolyzing peptide bonds between amino acids
kinase
catalyzes the addition of phosphate groups to molecules. protein kinases are an important group of kinases that attach phosphate groups to proteins
phosphatase
catalyzes the hydrolytic removal of a phosphate group from a molecule
structure of an antibody
2 identical heavy chains and 2 light
stabilized by S-S bonds
constant domain base, variable domain at the top
antigen binding site forms where VH and VL come together at “Y” tips
ways to homogenize (pop) cells/tissues
high frequency sound
force thru small hole/high pressure
mild detergent
shear cells in vessel with close fitting rotating plunger
centrifugation
separates pellet if denser and larger materials
differential centrifugation
progressively higher speeds of centrifugation separates based on size
SDS Page
added to break S-S linkages, gives proteins a negative charge and unfolds them so that they migrate through the gel at a rate that reflects their molecular weight
affinity chromatography
collect protein of interest by pouring sample through column with antibodies that attach to protein. Antigen can then be eluted from column to get pure sample.
Gel Exclusion (size exclusion) chromatography
smaller proteins retained in the column longer, longer retention time
ion exchange chromatography
charged column attracts proteins f opposite charge
binding strength depends on net charge of the protein
cation exchanger charge of resin
negative
anion exchanger charge of resin
positive
allosteric enzymes
have 2 or more binding sites that increase or decrease activity for the others
phosphorylation controls protein activity by causing a
conformational change
feedback inhibition
late product of the pathway inhibits enzyme early in pathway
can be positive
reversible
When GTP (guanosine triphosphate) is bound to proteins,, they are
active
GTP is hydrolyzed by
releasing Pi (inorganic phosphate), becomes GDP, inactive
reactivation involves dissociation of GDP and replacement by GTP
PTM
post translational modifications
covalent modifications that change protein properties
ubiquitination (PTM)
tags a protein for degradation
Phosphorylation
phosphorylation by protein kinases can increase or decrease activity
conformational change
reversible
ATP hydrolysis
used by motor proteins, separation of chromosomes during mitosis, movement within cells
ATP Binding (conformation A-B)
ATP hydrolysis (B-C)
release ADP and Pi (C-A)
Scaffolds
proteins that interact with other macromolecules and bring them together to facilitate function
unstructured and structured regions
Intracellular condensates
biochemical subcompartments in the cell formed by weak interactions between macromolecules (I.e. nucleolus)
can fuse and separate
