lecture 8 Flashcards
protein structure II: fibrous and globular proteins
what type of protein is an immunoglobulin?
large globular proteins
what type of protein is insulin?
a small globular protein
describe what immunoglobulins do?
1) antibodies that provide a defense against invasion of the body by foreign organism
2) mark foreign invaders for destruction by phagocytic cells
3) bind to antigens on the invading organism
4) the epitope is the actual site of attachment for the antibody on the antigen
5) lots of diversity
what is the actual site of attachment for the antibody on the antigen?
the epitope
what immunoglobulins also known as?
antibodies
describe the structure of the immunoglobulin?
its a globular protein, base structure is a tetramer, chains forms a flexible Y-shaped molecule, L is linked by disulfide bonds and the two H chains are linked by disulfide bonds
what is the base structure of the immunoglobulin?describe it?
tetramer; pairs of heavy (H) and light (L) chains, H2L2
what shape is the immunoglobulin?
Y-shaped
for the immunoglobulin, how is the tetramer linked, describe how the L and H chains are linked?
L is linked by disulfide bonds, the two H chains are linked by disulfide bonds
what type of protein structure do immunoglobulins contain? is there anything that makes it special?
both alpha and beta secondary structure; Yes, they have domains that impart special function, including the antigen binding site and constant region
on the antibody structure, what contains the antigen binding site?
the arms of the Y contain the antigen binding site, one per arm
in the antibody structure, what are the H and L composed of?
variable (V) and constant (C) domains
in the antibody structure, how many H domains and name them?
four H domains, V sub H, C sub H 1-3
in the antibody structure, how many L domains and name them?
two L domains, V sub L and C sub L
what is responsible for antibody specificity?
the variable domain
what forms the bulk of the antibody?
constant domain
what are the main secondary structures of the antibody comprised of? does it contain carbohydrates, Y/N? explain
strands of Beta sheet; Yes, these are bound to the C sub H domains
how many classes of antibodies are there? name them
5 classes of immunoglobulins/antibodies
α H chain: IgA γ H chain: IgG μ H chain: IgM δ H chain: IgD ε H chain: IgE
how is antibody class determined?
Heavy Chain Constant region (C regions of H chains) and specificity for antigen determined by
Variable region on the Heavy and Light Chains
what is IgA?
main antibody of external secretions (e.g., tears, saliva) thus serving as the first line of defense
what is IgG?
main circulating Ab in blood. Only IgG’s can cross placental barrier to confer protection on fetus
what is IgM?
first antibody to appear in blood in an immune response, some external secretions
what is IgD?
works with β cells, function not well known
what is IgE?
mediates allergic reactions
why do proinsulin and insulin fold differently?
the extra protein in proinsulin, the connecting peptide, causes the protein to fold differently influenced by the weak electrostatic interactions. If proinsulin got out in the blood it would be unrecognizable by RBC’s, so when pancreas sends signal for beta insulin to be released, the c-peptide is released and insulin refolds into final form
how is insulin released?How is it related to C-peptide?
after proinsulin is clipped, c-peptide also comes along and is released into the blood with insulin which is eventually picked up and eliminated. Insulin is degraded faster than C-peptide, which indicates the status of insulin; if no, than issue is focus on insulin production
what kind of protein is collagen?
a fibrous protein
what kind of protein is keratin?
a fibrous protein
why does insulin have a globular look?
because the globular protein has a lot of beta pleated sheets and alpha helices contributing to fluffy look; insulin has a helical look
what is a fibrous protein?
a dense network of thin strands that provide strength and stability when grouped together, bone is a good example
what are some unique characteristics of collagen?
dark (collagen) and light spots (gaps) indicating the tropocollagen molecules lined in an overlapped staggered formation with breaks. You would notice little dotted lines also called covalent cross links, covalent bonds between different tropocollagen molecules folded together;
since we are studying collagen we know the little strands supporting collagen are called tropocollagen? how are these arranged and their significance?
the tropocollagen molecule has an intertwining weaving of three individual collagen molecules and by weaving together they make a really strong rod like structure cross linked this makes the fiber strong and gaps allow for flexibility
what is collagen to mammals?
extracellular structural protein
what is collagen used to make in the human body and also mammals?
connective tissue, like tendons, ligaments, cartilage and bone
which collagens form fibrils?what else do they do?
I,II,III,V,XI; form networks, associate with with fibrils and some cross membranes
what is the helical structure of collagen?
a left handed helix
what do 3 collagen proteins interact to form?
a right handed coiled coil or a tropocollagen and this is a very tightly packed structure with every third residue being close contact with other helices.
what is the repeating sequence of collagen
Glycerol-X-Y
in the repeating sequence of collagen, what is residue X?residue Y?
proline; 4-hydroxyproline, a posttranslationally modified AA formed in an ascorbic acid dependent reaction
what are some other residues collagen contains?
lysine residues, some modified to allysine, an oxidized form of lysine or 4 hydroxyl lysine (post translational modification)
what is the collagen triple helix (tropocollagen) stabilized by?
INTERCHAIN H-bonds between amide NH of a glycine and of one collagen molecule with an amide carbonyl of residue X of another collagen molecule within the triple helix.
with respect to the collagen triple helix, what kind of bonds form between the individual collagen helices and what effect does this have?
H bonds; this very tight association makes the tropocollagen molecule very strong and rigid.
Keep in mind weak electrostatic interactions is what also facilitates the tight association (bone, hair, teeth and skin)
with respect to the collagen triple helix, what amino acid will you primarily find in the center?what does it do?outside?
glycine; facilitates packing of helices; all the other side chains. If glycine were replaced the interaction among the individual collagen molecules would be blocked, H-bonds unavailable and the triple helix useless. An example of this is osteogenesis imperfecta
what kind of protein structure is collagen?
tertiary structure
what is the protein interaction for a tropocollagen?
interquaternary protein interactions with lysine and proline
what do ordered arrays of tropocollagen form?what are the shorter fibers called? what can these fibers form?
collagen fibers; fibrils; longer fibers
how are tropocollagen stabilized?how?
covalent bonding between individual tropocollagens; allysine residues and 4-hyroxylysine residues are involved in covalent bonds that join the tropocollagen
what benefit does the overlapping packing of collagen fibers provide?
flexibility however the individual tropocollagens are rigid but the fiber is flexible
what amino acids can be used in cross linking the collagen triple helices together?
proline and lysine can undergo strong oxidizing reactions, introducing an OH on both causing covalent bonding because of the chemical modification of these amino acids
why is vitamin C deficiency harmful?
vitamins serve as cofactors for enzyme that allow for modifications of side chains for the amino acids like lysine and proline to facilitate the covalent bonding/crosslinking of the tropocollagen
how many types of collagen have been identified and studied?
29
what percent of collagen in the human body is type 1
90% with the remainder being types II, III, IV
how are the different types of collagen differentiated?
they are based on different genes with slight or not so slightly differences in primary structure and final assembly and tissue location
what is collagen I
skin, tendon, vascular, ligature, organs, bone (main component of bone)
what is collagen II
cartilage (main component of cartilage)
what is collagen III
main component of reticular fibers, commonly found alongside type I.
what is collagen IV
forms bases of cell basement membrane
what is collagen V
cells surfaces, hair and placenta
how do collagen related diseases arise? name an example?
genetic defects, nutritional deficiencies affecting biosynthesis, assembly, posttranslational modification, secretion, and other processes involved in normal collagen production; scleroderma due to excessive deposition of collagen fibers in skin
what do collagen abnormalities cause?
center of aging and a number of disease states
why is the cross linking of of collagen a time dependent process?
because when we age for example, increased cross links decreases the flexibility and pliability of collagen leading to wrinkles in the skin
what is the formation of cross links between fibrils dependent on?
vitamin C
since we know vitamin C is an important cofactor in in the formation of the collagen cross links, why, if there was suddenly to be a deficiency in this vitamin, is it important to note?example?
it results in a decrease in cross links, decreasing the strength of the fibrils and loss of connective tissue integrity. Loss of teeth
what are some examples of collagen disorders?
lupus erythematosis, osteogenesis imperfecta, Ehlers-Danlos Syndrome; also specific bacteria and virus virulence factors attack healthy collagen
what is Lupus erythematosis?
autoimmune disease that attacks healthy collagen
what is osteogenesis imperfecta?
genetic mutation where Gly is replaced with other aa
what is ehlers-danlos syndrome?
genetic, deficiency in synthesis of mature collagen (I and III)
You are treating a patient who has osteogenesis imperfecta. A mutation in which of the following proteins is most likely the cause for this disorder?
Actin Collagen Elastin Hemoglobin Myosin
collagen
what other fibrous protein is similar to collagen? How?
keratin; long fibrous structures formed by alpha-helices that are coiled, then form a protofilament, that assembles into larger filaments.
what does alpha keratin play a major roll in the production of?
hair and nails, however B-keratin is more rigid and provides stronger structural support in the production of nails
in keratin, why are disulfide bonds important?
they lock the structure together and increase rigidity
what type of bonds would you find in keratin that provides it with increased rigidity?
disulfide bonds
what is an example of complex structures? use?
Ca2+ transporting ATPase; muscle relaxation
how does the Ca2+ pump of the muscle work?
Uses the energy of ATP to transport Ca2+ ions across a membrane
since we know that the Ca2+ pump is a complex structure, describe the complex structure, make-up and function?
three globular domains, one transmembrane (M) domain, the Ca2+ binding to M stimulates structure change affect the N, P, and A domains which causes a structure change in M affecting movement of calcium ions across the membrane
what are the three binding domains of the Ca2+ structure?
nucleotide domain: binds ATP; phosphorylation domain: binds phosphate; actuator domain: coordination of movements needed to bring N and P domains together
what is the transmembrane (M) domain of the Ca2+ ATPase pump made of?
made up of ten alpha helices and contains Ca2+ binding sites
*how does the structure as mentioned in the M domain affect the Ca2+ ATPase?
for Ca2+ ATPase, the conformational change leads to Ca2+ ions moving across the membrane
what is a variation in protein structure called?
isoform
what is an isoform?name an example
the same protein but with slight changes in primary sequence; collagen I,II, III
how do protein structures vary?
they vary slightly, yet have the same folded form and function; keep in mind important parts of the protein are not changed and if there is, then loss of function occurs
name examples of protein variation?
protein structure polymorphisms, protein families and superfamilies, tissue and developmental variations, species variations
what are protein structure polymorphisms since they are examples of protein variations?
Protein Structure Polymorphisms: arise from mutations in DNA that result in changes in protein structure; most are harmless though many are critical and we see this in mitochondrial metabolism
what are protein families and superfamilies since they are examples of protein variations?
groups of proteins that have similar structures and related functions and examples include hemoglobin and myoglobin, G-proteins, ATP dependent transporters
what are tissue and developmental variations since they are examples of protein variations?
Slight changes in protein structure between prenatal and adult forms of protein, giving different function (Hemoglobin F and A).
Proteins in different tissues will have slightly different structures to give slightly different function, matched to the needs of the tissue. Example is lactate dehydrogenase…different forms in different tissues = functional differences.
what are species variations since they are examples of protein variations?
different species of organisms may have the same protein carrying out the same function, but the structures of the proteins may vary.
what is significant about lactate dehydrogenase?
Catalyzes the reversible conversion of lactate to pyruvate
Tissue-dependent production and utilization of lactate as fuel source
Isozyme composition in various tissues changes activity in that tissue
LDH is also described in terms of isozymes found in the heart (LDH-1, four subunits specific for heart, H4) versus those found in liver and skeletal muscle (LDH-5, four subunits M4). LDH-2 is the predominant form found in serum. So if LDH-1 shows up in the blood, it is an indicator of a problem with heart muscle cells, i.e., infarction.
how many isoforms of lactate dehydrogenase are there? where can they be found
5; liver, muscle, white cells, brain, red cells, kidney and heart
Fibrous proteins are strong, but they are still flexible, name an example?
this important for structure, an example would be the collagen found in bone and skin
Most globular proteins are compact, but they exhibit remarkable, and specific, flexibility, name an example?
conformational changes are key to function and an example is hexokinase; Enzymes change their shape in response to substrate binding. These structural changes drive the function of the protein and are possible because the protein is flexible and can change its shape (conformation).
name an example in which it is extremely important for proteins to be flexible?
hemoglobin; it changes its shape in response to oxygen binding;
