amphipathic

asymmetric carbon

carboxyl group

amino group

side chain

*the side chain can be hydrophobic, hydrophilic, charged, or neutral

a 50% double bond in peptide bonds indicates..

gastric, urine, saliva, blood, pancreas

compare primary, secondary, tertiary, and quaternary structures

primary: linear amino acid sequence

secondary: alpha-helix and parallel/antiparallel pleated sheets

tertiary: interaction of secondary structures within a protein - 3D structure

quaternary: interaction of multiple homo or hetero subunits - consists of noncovalent bonds

insulin

intrachain and interchain disulfide bonds are located at..

intrachain disulfide bond located at C6 and C11

interchain disulfide bond located at C7 and C7/C19 and C20 

a substitution of one amino acid for another that is of similar polarity

a substitution of one amino acid for another that is of dissimilar polarity or geometric configuration

1. peptide bond planes are (parallel/perpendicular) to the helix axis

2. side chains are on the (inside/outside) of the spiral structure

1. parallel

2. outside

describe globular proteins and their function

spheroidal shape

relatively high water solubility

functions include: catalysts, transporters, metabolic and pathway gene expression regulators

long cylindrical (rod like) shape

low water solubility

contain larger amount of secondary structure

have a structural role in the cell or organism

1. collagen is composed primarily of what?

2. what sequences are repeated in tandem several hundred times?

3. carbohydrates are attached to the hydroxyl group of hydroxylysine by what type of bond?

1. glycine

proline

4-hydroxyproline

5-hydroxylysine

2. Gly-Pro-Y and Gly-X-Hyp

3. covalent

# of mature polypeptide chains in collagen; # of types of collagen

3; 6 (I to VI)

extracellular enzyme in collagen converts _______ to an aldehyde form (allyl-lysine) that reacts with other lysine groups within a collagen molecule in a fibril

skin (74%)

cornea (64%)

cartilage (50%)

provides organs and tissues elastic support in terms of stretching without tearing, such as ligaments, lungs, walls of arteries, and skin

what are some unique properties of elastin

1. do NOT contain the Gly-Pro-Y and Gly-X-Hyp repeats and does not fold into a poly Pro helix

2. lacks secondary structure but contains unordered coiled structure

3. contains covalent crosslinks between lysine residues

1. where can glycoproteins be found?

2. what are the three main types of covalent linkages of carbohydrates to proteins?

1. on plasma membranes, secreted and structural proteins in the plasma (ex: blood clotting factors and thyroid stimulating factor TSF)

2. N-glycosyl linkage to asparagine (most common)

O-glycosyl linkage to serine

O-glycosyl linkage to 5-hydroxlysine (esp. seen in mammalian systems)

separates protein based on charge

affinity chromatography (more difficult; more information obtained)

denaturing - separates proteins on basis of MW

non-denaturing - separates proteins on basis of charge

separates proteins on basis of charge to mass ratio

in gel permeation chromatography (also called gel filtration), separation is based on the Stokes radius, the apparent diameter which is related to size and shape of a protein. what size molecules elute first, large or small?

in SDS-PAGE, what is the function of SDS (sodium dodecyl sulfate)?

technique where a protein is fragmented using proteolytic enzymes or chemical cleavage then separated by electrophoresis/chromatography; fragments can then be analyzed by mass spectrometry

protein fingerprinting

how can a protein be denatured?

4; sporadic most common (unknown)

(other types are familial - mutation, iatrogenic - accidental, and variant - food contamination)

antibodies are proteins produced by what cells?

light chain = 220 AA (25,000 MW)

heavy chain = 440 AA (50,000 MW)

compare constant and variable regions of an immunoglobulin

constant regions form the structure of the antibody; IgG constant regions bind complement proteins and are sites for crossing of immunoglobulins across placental membranes

variable regions form the binding sites for antigens and haptens

1. IgG consists of 2 light chains and 2 heavy chains; the constant domains are divided into 3 groups known as....

2. how many antigen binding sites per molecule?

CH1, CH2, CH3

2 - formed by VH and VL (heavy and light variable chains)

describe the various roles of the 5 classes of immunoglobulins; which is the most common and which has the heaviest MW?

IgG: most common; highest concentration in plasma; promotes phagocytosis

IgM: heaviest MW; found in the plasma; first Ab produced in response to foreign antigen; low levels in mucosa

IgA: found in mucosal secretions; initial defense against virus and bacteria

IgD: function unknown

IgE: plays major role in allergies, anaphylactic shock, hay fever and asthma

1. which immunoglobulin is always a pentamer?

2. which exists mostly as a monomer, but can have dimers, trimers, and even tetramers sometimes?

1. IgM

2. IgA

*polymeric forms of both contain a polypeptide known as the J chain that is linked by 2 disulfide bonds to the Fc region in 2 different monomers

1. ELISA (enzyme linked immunoglobulin substrate assay) - can be used to read immunoglobulin + antigen

2. Immunohistochemical Staining - staining of tissue sections with primary and secondary antibody for identification of specific proteins in tissue sections

3. FACS (fluoresence activated cell scanning) - a mixed T lymphocyte suspension is mixed with primary antibodies that bind to cell surface markers on T-helper and T-killer cells; these are then incubated with fluorescent labeled secondary antibodies

1. only 1 serine is catalytically active

2. histidine/aspartic acid are always associated with serine

3. eukaryotic ones exhibit high sequence and structural similarity

4. genes that encode serine proteases are organized similarly

5. synthesized in zymogen form to permit transport to site of action

6. regulated by specific inhibitors with non-cleavable bonds and high binding affinities