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Biochem Exam 1
UFCOP
115
Medical
Graduate
09/11/2008

Additional Medical Flashcards

 


 

Cards

Term
angle between 2 hydrogen atoms of water
Definition
104.5
Term
where a drug remains in the body depends on..
Definition
where it is ionized
Term
conjugate acid
conjugate base
Definition
proton donor
proton acceptor
Term
constituents of blood plasma and cell fluid
Definition
Na+ and Cl- more abundant in the plasma
K+, proteins, and phosphates more abundant in the cell
Term
reactions catalyzed by catalase
Definition
1) 2H2O2 --> 2H2O + O2
2) RH2 + H2O2 --> R + H2O
Term
buffer
Definition
ability of a solution to resist change in pH when acid or base are added
Term
2 common types of buffers found in the blood and intracellular fluid
Definition
HPO4(2-) and HCO3-
Term
prokaryotes vs eukaryotes
Definition
prokaryotes: inner and outer membrane/no internal organelles/simple DNA/unicellular
eukaryotes: single plasma membrane/intracellular organelles with a nucleus/complex DNA/multicellular
Term

amphipathic

Definition
also known as amphiphilic. possessing both hydrophilic and hydrophobic properties (i.e. plasma membranes and water)
Term
amino acid structure
Definition

asymmetric carbon

carboxyl group

amino group

side chain

 

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

Term
Glycine
Definition
Gly-G
Term
Alanine
Definition
Ala-A
Term
Valine
Definition
Val-V
Term
Leucine
Definition
Leu-L
Term
Isoleucine
Definition
Ile-I
Term
Proline
Definition
Pro-P
Term
Phenylalanine
Definition
Phe-F
Term
Tyrosine
Definition
Tyr-Y
Term
Tryptophan
Definition
Trp-W
Term
Methionine
Definition
Met-M
Term
Serine
Definition
Ser-S
Term
Threonine
Definition
Thr-T
Term
Cysteine
Definition
Cys-C
Term
Asparagine
Definition
Asn-N
Term
Glutamine
Definition
Gln-Q
Term
Aspartate
Definition
Asp-D
Term
Glutamate
Definition
Glu-E
Term
Lysine
Definition
Lys-K
Term
Arginine
Definition
Arg-R
Term
Histadine
Definition
His-H
Term

a 50% double bond in peptide bonds indicates..

Definition
the bond is fixed and there is no rotation. this occurs between the carbonyl carbon and the nitrogen which makes the peptide unit planar and rigid. rotation is restricted to the bonds involving the alpha carbon.
Term
a general name for a long peptide
Definition
oligopeptide or polypeptide
Term
each torsion angle in the extended TRANS conformation in a polypeptide
Definition
180
Term
which amino acid is most water soluble
Definition
proline
Term
list the order of pH found throughout the body from most acidic to basic
Definition

gastric, urine, saliva, blood, pancreas

Term
what kind of bond is shown between 2 cystine residues
Definition
disulfide bond
Term
what is the effect of disulfide bond formation
Definition
allows for folding within a polypeptide
Term
which conformation (cis or trans) is energetically favorable with an amino acid with the exception of proline
Definition
trans
Term
provides a precise 3D structure of the protein at near atomic resolution; requires that the protein be crystallized
Definition
x-ray crystallography
Term
most abundant protein
Definition
collagen
Term

compare primary, secondary, tertiary, and quaternary structures

Definition

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

Term

insulin

intrachain and interchain disulfide bonds are located at..

Definition

intrachain disulfide bond located at C6 and C11

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

Term
two sequences that are highly alignable
Definition
homologous
Term

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

Definition
conservative substitution
Term

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

Definition
non-conservative substitution
Term
# of hydrogen bonds each peptide bond forms
Definition
2
Term

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

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

Definition

1. parallel

2. outside

Term
# of amino acids per 360 degree turn
Definition
3.6 (collagen has 3)
Term
what type of bond occurs between polypeptides in alpha and beta sheets?
Definition
hydrogen bond
Term
protein domain classification based on predominant type of secondary structure (i.e. mainly alpha, mainly beta, or equal)
Definition
class
Term
protein domain classification based on arrangements of secondary structures within the domain
Definition
fold
Term
protein domain classification based on sequence identity between proteins
Definition
family
Term
what is the purpose of protein domain classification?
Definition
to characterize limited mutations in the amino acid sequence of a protein
Term

describe globular proteins and their function

Definition

spheroidal shape

relatively high water solubility

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

Term
describe fibrous proteins and their function
Definition

long cylindrical (rod like) shape

low water solubility

contain larger amount of secondary structure

have a structural role in the cell or organism

Term

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?

Definition

1. glycine

proline

4-hydroxyproline

5-hydroxylysine

 

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

 

3. covalent

Term

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

Definition

3; 6 (I to VI)

Term
in collagen the plane of the peptide bond is (parallel/perpendicular) to the helix to form strong hydrogen bonds with other polyproline helical polypeptides
Definition
perpendicular
Term
polypeptide chains are held together in collagen by what type of interaction?
Definition
hydrophobic with glycines on apolar edge of each of the polypeptide chains; covalent crosslinks between lysine residues
Term

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

Definition
ε-lysine
Term
where is collagen the most abundant in the body?
Definition

skin (74%)

cornea (64%)

cartilage (50%)

Term

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

Definition
elastin
Term

what are some unique properties of elastin

Definition

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

Term
carbohydrate added to a protein
Definition
glycoprotein
Term

1. where can glycoproteins be found?

 

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

Definition

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)

Term

separates protein based on charge

Definition
ion exchange chromatography (separates based on surface charge)
Term
separates protein based on MW
Definition
gel permeation chromatography
Term
separates protein based on binding affinity for a specific ligand
Definition

affinity chromatography (more difficult; more information obtained)

Term
technique to obtain protein conformations in solution
Definition
NMR; 2D NMR can solve up to 150 AA while multidimensional NMR can solve up to 250 AA
Term
polyacrylamide gel electrophoresis
Definition

denaturing - separates proteins on basis of MW

non-denaturing - separates proteins on basis of charge

Term

separates proteins on basis of charge to mass ratio

Definition
capillary electrophoresis
Term
separates proteins based on isoelectric point (the point at which the protein is neutral)
Definition
isoelectric focusing
Term
combines separation of protein based on MW and isoelectric point; can be used to examine changes in protein levels between different cell types or different cell states
Definition
2-dimensional electrophoresis
Term
identifies proteins on basis of MW (mass:charge ratio); is used in combination with 2D gel to identify proteins either as whole protein or from proteolysis
Definition
mass spectroscopy
Term
column chromatography
Definition
used to separate macromolecules; contains a stationary phase (column matrix) and a soluble phase (buffer solution); standard (low pressure) and high performance systems (high pressure); separate based on composition of stationary phase
Term

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?

 

Definition
large
Term
what are 2 disadvantages of affinity chromatography?
Definition
recovery can be difficult if protein affinity is high; has to be tailored to each protein
Term

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

Definition
denatures and coats proteins; because SDS is negatively charged, all proteins have a constant charge to mass ratio and migrate based on mass
Term

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

Definition

protein fingerprinting

Term
Edman Degradation
Definition
sequencing of proteins from the N-terminus
Term

how can a protein be denatured?

Definition
change in pH, increase in temperature, or addition of denaturant (i.e. urea, guanidine hydrochloride, and sodium dodecyl sulfate)
Term
how many forms of Creutz-Jakob disease are there and which is the most common?
Definition

4; sporadic most common (unknown)

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

Term
protein that acts as an infectious agent in the absence of RNA and DNA
Definition
prion
Term
coil of several fibrils, arranged in a helical beta sheet of strands perpendicular to a cylindrical axis
Definition
amyloid fibril
Term

antibodies are proteins produced by what cells?

Definition
B cells
Term
what is the MW of a light chain and a heavy chain in an immunoglobulin
Definition

light chain = 220 AA (25,000 MW)

heavy chain = 440 AA (50,000 MW)

Term
polypeptide chains of immunoglobulins are held together by what type of bond
Definition
disulfide bonds; also know that chains are parallel and have ionizable groups (COOH, NH2)
Term
portion of a protein that binds to the antibody; what is the minimal amino acid sequence number?
Definition
antigen; 6-7 amino acids
Term
small molecule to which an antibody can bind and can only elicit antibody production if bound to a larger molecule (form strong covalent bonds)
Definition
hapten
Term

compare constant and variable regions of an immunoglobulin

Definition

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

Term

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?

Definition

CH1, CH2, CH3

 

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

Term

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

Definition

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

Term

1. which immunoglobulin is always a pentamer?

 

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

Definition

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

Term
heavy and light polypeptide chains within an immunoglobulin have an amino acid repeat containing how many amino acids?
Definition
110 AA (there are 2 in the light chain and 4 in the heavy chain)
Term
an immunizing vaccine may contain what?
Definition
killed bacterial cells/virus, nonvirulent form of live bacterium/virus, denatured bacterial toxin or viral protein, or recombinant protein
Term
name and describe the 3 various analytical tests for antibodies
Definition

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

Term
describe the difference between an endoprotease and exoprotease
Definition
endoprotease: cleaves peptide bonds within polypeptide chain

exoprotease: cleaves peptide bond at either C-terminus or N-terminus
Term
procoagulation can occur by what 2 different pathways? both lead to activation of what?
Definition
intrinsic and extrinsic; intrinsic use factors VIIa,IXa,XIa (7,9,11); both lead to activation of factor X
Term
the conversion of plasminogen to plasmin degrades fibrin. what is the plasminogen activator?
Definition
tissue plasminogen activator (t-PA) or recombinant t-PA (rt-PA), which can increase recovery after myocardial infarction
Term
what two conversions are required by serine proteases in the formation of a blood clot?
Definition
prothrombin --> thrombin
fibrinogen --> fibrin
Term
which serine enzyme activates plasminogen, but also increases metastasis of cancer cells
Definition
urokinase
Term
what does the serine protease active site triad consist of?
Definition
aspartic acid, histidine, and serine

*serine exerts nucleophilic attack on substrate peptide bond
Term
what are 6 common structural serine protease features?
Definition

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

Term
what type of protease is HIV-1 protease?
Definition
aspartic acid protease
Term
hemoglobin can bind to what 3 things?
Definition
oxygen, carbon dioxide, nitrous oxide (vasodilator)
Term
what is the binding site for O2 and CO2 in heme?
Definition
the Fe2+ ferrous ion coordinated in a tetrapyrrole ring
Term
what is the valence of Fe2+ and what are the bonds formed in the heme group?
Definition
6; 4 bonds are formed with the pyrrole rings, the 5th with a proximal histidine, the 6th with O2
Term
through what association does heme interact with protein subunits?
Definition
hydrophobic
Term
compare hemoglobin to myoglobin
Definition
hemoglobin contains 4 polypeptides/4 O2 binding sites; myoglobin contains 1 polypeptide/1 O2 binding site
Term
what type of saturation curves do hemoglobin and myoglobin make?
Definition
hemoglobin: sigmoidal due to cooperative binding of O2

myoglobin: hyperbolic due to simple protein-ligand interaction
Term
increasing pO2 (increases/decreases) the degree of O2 saturation
Definition
increases
Term
oxygen binding in hemoglobin induces a conformational angle change of what?
Definition
15 degrees - goes from tense to relaxed state
Term
compare the symmetrical and sequential models for O2-HB cooperative binding
Definition
symmetrical: high and low affinity states are in equilibrium - binding of O2 locks Hb into a high affinity state facilitating binding of additional O2

sequential: as each O2 molecule binds, the next subunit is converted from a low affinity to a high affinity state
Term
a decrease in pH causes a (increase/decrease) in O2-Hb binding affinity
Definition
decrease (O2 is released quicker to tissues - known as the Bohr effect)
Term
what intermediate modulates Hb-O2 binding affinity and how does it work?
Definition
2.3-Bisphosphoglycerate; has an affinity for the deoxy conformation Hb (T) and stabilizes it's conformation; dissociates as O2 binds
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