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408 Cards in this Set

  • Front
  • Back
Energy is extracted from carbon-containing compounds via __________________.
oxidation (i.e. reacting them with oxygen to produce carbon dioxide)
What occurs when organisms oxidize food molecules?
they are coupling the oxidation reaction (energy release) to energy requiring reactions
What is always assumed regarding acid/base chemistry/the dissociation of a hydrogen ion from an acid?
that the reaction is at equilibrium -does not require an enzyme
Biological catalysts are made from ___________ and called _____________.
proteins; enzymes

*or RNA ...called ribozymes!
What are the polar amino acid side-chains?
COO-, NH3+, OH, SH
In the most simplistic way, how do enzymes work?
by stabilizing the transition state between substrate/product by virtue of favorable side chain interactions
In a test tube reaction you would expect to get an equal mixture of stereoisomers, while in a living cell you would expect to find what?
only one stereoiosmer present
The similarity between metabolic pathways of all organisms is believed to be a result of what?
evolution from common ancestral life
The process of accumulating sequence differences while retaining similar function is called "______________ _______________."
divergent evolution
What is divergent evolution?
The process of accumulating sequence differences while retaining similar function.
What are "homologous enzymes?"
Enzymes which arise via divergent evolution are are expected to carry out similar functions in different organisms/species.
When two or more versions of a gene remain in the same genome they are called a ________ ___________.
gene family
What is one pertinent example of a gene family?
the genes that code for collagen
What are genes made of?
deoxyribonucleic acid; a polymer of a phosphorylated sugar to which one of four bases is attached
A single phosphorylated sugar with its base (AGCT) is called a _______________.
What is the central dogma of molecular biology?
replication of DNA --> transcription of DNA to RNA --> translation of RNA into protein
What is the significance of DNA and RNA acting as a template during the transfer of genetic information?
It facilitates an increase in the number of copies of certain genetic information without violating the law of conservation of mass.
Proteins have an _________ group at one end and a ____________ group at the other.
amino; carboxyl
What are the two types of centrifugation?
1. rate (velocity) sedimentation
2. buoyant density centrifugation
rate (velocity) sedimentation separates cellular components based on what?
mass and shape
rate (velocity) sedimentation centrifugation is used to isolate which cellular components based on mass and shape?
-microsomes (fragments of ER)
-virus particles
-large individual macromolecules
buoyant density centrifugation is used to isolate which cellular components?
Enamel, dentin and cementum can be isolated from each other using a form of which type of centrifugation?
buoyant density centrifugation
What does a typical biochemical assay detect?
The presence of an enzyme by measuring the reaction catalyzed by the enzyme
What density of bromoform-acetone could be used to separate cementum from dentine using the buoyant density centrifuge technique?
2.70 gm/ml
How was it determined that lactobacilli are not capable of initiating caries?
germ-free rats were infected with lactobacilli are were not capable of initiating caries
what is the major causative agent of caries?
s. mutans (streptococcus mutans)
What are the two biochemical properties that contribute to the caries-causing capability of S. mutans?
1. the synthesis of dextrans from sucrose
2. the production of acid
what are dextrans?
dextrans are branched polymers of glucose with a-1,6 linked glucose chains joined primarily at a-1,3 branches but also at a-1,4 branches.

dextrans are produced by S. mutans and constitute a majority of the glycocalyx synthesized by S. mutans.
the glycocalyx (extracellular polysaccharide layer) produce by S. mutans is composed mainly of what?
dextrans (branched polymers of glucose)
the higher the percentage of _________ linkages in a dextran molecule, the lower the solubility in water.
Why/how do a-1,3 linked dextrans contribute to caries?
they are the primary component of the glycocalyx produced by S. mutans and are insoluble in water and are therefore "sticky," adhering first to the surface of teeth and then adhering acidophilic bacteria to the tooth.

a-1,3 linked dextrans are the "glue" between the tooth and the bacteria
___________________ and other bacteria that survive well in an acidic environment are more prevalent in plaque, but ______________ is the primary microbiological causative agent because it makes the plaque (through the production of a-1,3 linked dextrans in the glycocalyx that act as the glue between the tooth surface and bacteria)
Lactobacilli; acid; S. mutans
Why does plaque cause caries?
(1) creates a barrier and prevents the diffusion of acid away from the tooth and

(2) is capable of defeating the buffering action of bicarbonate in the saliva
What does the typical progression of a carious lesion consist of?
years of repeated bouts of acid attack interspersed with periods of neutral pH and remineralization
Where is S. salivarius found?
in the saliva; not in the plaque
What does S. salivarius do?
found in saliva; causes dextrans to "release" their adhesion between tooth surface and bacteria

(makes dextrans less "sticky" and consequently helps to prevent the development of a carious lesion)
what enzyme synthesizes the dextrans of s. mutans?
dextransucrase (AKA glucosyltransferase)
Sucrose is composed of ______ and _________
glucose and fructose
The unusual _______ link in sucrose is a higher energy bond than the linkages in the glucans, therefore the synthesis requires no other source of energy.
What role does sucrose play in caries?
when the unusual ab-1,2 linkage between glucose and fructose is split by the dextransucrase enzyme, energy is released which is then used in the polymerization of the insoluble (a-1,3 linked) dextran responsible for causing caries (by adhering bacteria to the surface of the tooth)
What is the alternative fate of sucrose, if it's not converted to dextran?
sucrose can be split by the levansucrase enzyme to create a polymer of fructose called "levans"
What is a levan?
a polymer of fructose formed by the splitting of sucrose by the enzyme levansucrase
What is xerostomia?
"no saliva" ; condition caused by radiation treatment of head and neck cancers and which results in prevalent caries (especially at base of tooth near gingiva)
How does acid contribute to dental caries?
as plaque accumulates it acts as a barrier preventing diffusion of oxygen, generating an anaerobic environment at the tooth surface. Bacteria have to grow by anaerobic respiration and produce (lactic) acid as a byproduct which penetrates the enamel and alters the solubility of the calcium phosphate resulting is dissolution of the enamel
Which type of bacteria tends to predominate in deep carious lesions and why?
Lactobacilli because as carious lesions progress they become more acidic and only bacteria that thrive in highly acidic environments can survive beneath the plaque
What is the formula for hydroxyapatite?
(Ca)10 (PO3-4)6 (OH)2
What is the highly insoluble salt of calcium and phosphate (the mineral phase of enamel)?
hydroxyapatite Ca10PO43-OH2
How does saliva help to prevent caries?
1. contains s. salivarius which helps to make dextrans less "sticky"

2. introduces Calcium and Phosphate into environment; supports mineralization of teeth

3. contains a pH buffer (bicarbonate) which neutralizes acids in the mouth
The concentration of the OH- and PO4-3 species is very _______ at reduced pH, and _________ with decreasing pH, ultimately resulting in the dissolution of the enamel.
low; decreases
What is the pH at which the components of hydroxyapatite (phosphate and OH-) are present in the saliva at such low concentrations the enamel will start to dissolve?
pH _____ is the point (given the concentrations of phosphate and calcium in saliva) below which ________________ will start to dissolve. Most of the time the pH is above that and hydroxyapatite is actually deposited to reinforce the surface of the enamel. That’s also why plaque calcifies to form tartar.
5.5; hydroxyapatite
Fluoride ions are incorporated into the ______________________ during _________________ phases.
hydroxyapatite; remineralization
Although both _______________ and ________________ contribute to pH buffering in the saliva, _________________ is considered the major pH buffer because there is more of it.
bicarbonate and phosphate; bicarbonate
How does fluoride protect hydroxyapatite?
1. reducing its acid solubility
2. accelerating remineralization
3. reducing carbonate substitution
What must happen in order for fluoride to be effective?
it must be ingested and recirculated in crevicular fluid
What form must fluoride be in in order to pass through membranes?
HF form
What is the pK of fluoride? What is the consequence of this regard uptake?
3.18; acidic environment of the stomach is required for uptake
Ultimately, what is the reason for the anticariogenic effect of fluoride?
it is concentrated in plaque to about 100x the salivary concentrations by the action of bacteria
Fluroide inhibits bacterial glycolysis by inhibiting ___________.
enolase (glycolytic enzyme)
Does fluoride inhibit dextran production?
How does fluoride protect against dental caries?
1. supports remineralization

2. inhibits the production of the glycolytic enzyme enolase which impedes the production of acid by bacteria; at a high enough fluoride concentration, bacteria can actually make the pH go up instead of down.

("halt or reverse" effect that bacteria has on pH)
When the fluoride concentrations are high enough, bacteria can actually make the pH go up instead of down. Why is this so?
Because as the fluoride is taken up by bacteria and inhibiting glycolysis (by inhibiting enolase) it impedes acid production and forces the bacteria to metabolize amino acids instead resulting in the release of basic ammonium ions
What becomes concentrated within plaque?
What are the three major fibrous proteins found in humans?
1. collagen
2. alpha keratin
3. elastin
What make fibrous proteins suitable for forming the structural framework within cells?
Because fibrous proteins are elongated, highly cross-linked (and therefore insoluble) molecules
What is the major fibrous protein of non-connective tissues (i.e. epithelial tissue)?
alpha keratin
What are the major fibrous proteins of the connective tissue?
1. collagen
2. elastin
What is the fundamental building block of a keratin fiber?
A coiled dimer of type I and type II keratin polypeptide
Which amino acids are uncommon in the alpha-helical structure of alpha keratin?
proline and glycine
The presence of which amino acid in alpha keratin is directly correlated with brittleness/hardness of the keratin? Why?
cystine due to the presence of cystine-disfulfide bridges
The fundamental peptide chain of alpha keratin is a ________-_________ _________ ________ which is stabilized by _____________ bonds.
a right-handed alpha helix; hydrogen bonds
What effect does steam-treating have on alpha keratin?
angstrom unit stretched from 5.5 to 7; hydrogen bonds break and alpha helix converts to parallel beta structure because hydrogen bonds are required to stabilize alpha helix
What is the cellular location of collagen?
extracellular matrix
What is the structure of collagen?
triple helix (tropocollagen)
What is the function of alpha keratin?
provides insoluble structural protein for body surfaces; intracellular
What is the function of collagen?
provides tensile strength to soft connective tissue
Does the PDL contain elastin?
The characteristics of connective tissue depend on the relative proportions of what?
1. collagen
2. elastin
3. ground substance
Which has more collagen, a ligament or a tendon?
tendon has more collagen, ligament has more elastin
a 1 mm fiber of collagen can support up to ______ kilograms
Approximately 1/3 of amino acid residues in collagen are _______.
More than 10% of the residues in collagen are ________.
proline (an imino acid)
What are the majority of AA residues in collagen?
Why can't collagen polypeptides exist has alpha-helicies?
because of the high proline and hydroxyproline content
Is the triple stranded tropocollagen molecule stabilized with H bonds?
yes! (it's the single polypeptide chain that is not due to high proline content(
What is the basic structural unit of collagen?
which AA residue points inward in toropocollagen molecule and why?
glycine because it has no side side chain and can fit into the crowded center of the triple helix
tropocollagen molecules assemble into microfibrils through the association of what?
regions with polar side chains (particularly on N and C terminus) on parallel molecules
In type I collagen, tropocollagen units assemble to give rise to what?
a quarter-staggered array with a gap of 300 angstroms between adjacent molecules of tropocollagen (which gives rise to pattern of bands within collagen fibers)
How many different types of collagen are there?
Genetic defects in type VII collagen cause _____________ ____________ _________, which features blistering of the skin and mucosa.
Dystrophic Epidermolysis Bullosa
Type IV collagen forms __________ _________ and makes ___________ ______________.
planar arrays; basement membranes
Type III collagen is AKA ...
elastic collagen or extensible collagen
What is the composition of type I collagen?
two alpha1 (I) polypeptides + one alpha2 (I) polypeptide
What is the composition of type II collagen?
3 identical alpha1 (II) polypeptides
What is the composition of type III collagen?
3 identical alpha1 (III) polypeptides
What is the composition of type IV collagen?
selection of six chains
Type I collagen is found where?
skin, tendon, bone, dentine
Type II collagen is found where?
Type III collagen is found where?
extensible connective tissues
Type IV collagen is found where?
basement membrane
What disease result due to defects in type I collagen?
1. Osteogenesis Imperfecta
2. Dentinogenesis imperfecta
How many different collagen genes exist?
What is the mutagenic basis of the type I collagen defect that results in osteogenesis imperfecta and dentinogenesis imperfecta?
single base subsitution (glycine replaced by cystine)
What is Ehlers-Danlos Syndrome?
defect in type III collagen resulting in hyper-elasticity of the skin (often associated with TMJ problems)
Where does hydroxylation of proline and lysine occur?
RER and finishes in golgi
What are the enzymes required for the hydroxylation of proline and lysine? What do both of these enzymes require?
procollagen prolyl hydroxylase and lysyl hydroxylase

both require:
1. ascorbic acid (vit. c)
2. alpha-ketogluterate and
3. iron
What function does vitamin c play in hydroxylation of proline and lysine?
required as a reducing agent by the procollagen hydroxylase enzymes
How does the cross-linking in collagen differ from that in alpha keratin?
collagen cross-linking involves covalent lysine cross bridges while alpha keratin involves cystine disulfide bridges.
In collagen, cross-links involving __________ are more stable than those involving _____________.
hydroxylysine are more stable than those involving lysine!
How is the structure of elastin similar to collagen? different?
both contain 1/3 glycine residues and are rich in proline.

In elastin, glycine does NOT occur every 3rd residue.

elastin contains very little hydroxyproline, NO hydroxylysine and few polar amino acids, being rich instead in nonpolar amino acids (very hydrophobic)
What is a desmosine?
unique cross-link found in elastin derived from four lysine side chains
How is elastin synthesized?
elastin producing cells synthesize precursor callled proelastin which is secreted in extracellular space and cleaved to yeild tropoelastin which is assembled with microfibrils (containing fibrillin) and cross-linked (via desosines/lysine) to form mature elastic fibers
What is the structure of elastin?
beta spiral
What is fibrillin?
the glycoprotein that forms the outer envelope of elastin microfibrils
What are two compositional qualities of glycosaminoglycans?
1. strongly negative (due to carboxyl and sulfate groups)

2. large numbers of hydrophillic hydoxyl groups (bind water)
What are the different core proteins used to make large aggregating proteoglycans?
1. aggrecan
2. versican
3. neurocan
One component of innate immunity involves the ability of virally infected cells to sense their infection and secrete ____ and _____ _____________. What effect does this have on neighboring cells?
alpha and beta interferon -induces antiviral state in neighboring cells
What is innate immunity?
the ability to resist infection prior to the activation of the T and B cell response
Why are macrophages an important component of innate immunity?
because of their ability to directly recognize bacteria via receptors for bacterial cell wall components, become active, phagocytose the invader and send inflammatory signals.
Activated macrophages present their ingested antigens to _______ cells
CD4 receptor bearing (helper T cells)
What is the reticuloendothelial system?
a network of supporting reticular (endothelial) cells within tissues
extracellular fluid filters through the ________________ _____________ into specialized structures called ______ _________.
reticuloendothelial system; lymph nodes
Antigen is presented in the lymph nodes to by specialized phagocytic cells called ____________ cells.
What are the nongranular leukocytes? What are the granulocytes?
nongranular leukocytes: lymphocytes and monocytes

granular leukocytes: neutrophils, basophils, eosinophils
What is the difference between TH1 and TH2 helper T cells?
TH1 -drive classic inflammatory response

TH2 -drive allergy-like response wherein they activate eosinophils and initiate IgE production
Where do T and B cells spend most of their time? By which process do they migrate?
in lymph nodes and tissue; migrate through blood stream in process called homing
What is homing?
process wherein B and T cells (neutrophils and monocytes also) enter the blood stream to migrate to a specific site:

Cell-surface adhesion protein recognizes tissue-specific ligand on inside on blood vessel -when cell passes by it's target tissue, its receptor is activated and it leaves the vessel - homing receptors are changed often throughout the life of a T or B cell!
_____________ are circulating macrophage precursors.
_________________ are incapable of further differentiation of mitotic division. They carry granules filled with _____________ substances and mediators of the inflammatory response which they discharge when activated.
granulocytes (neutrophils, eosinophils, basophils); cytotoxic
Which type of blood cell contains histamine and is activated through surface bound IgE?
True or false: Basophils and neutrophils are normally found in circulation, while eosinophils are not.
True; eosinophils are only found in circulation briefly as they hone to the vicinity of external body surfaces
How are eosinophils activated? How are basophils activated?
eosinophils are activated by mast cell products while basophils are activated by surface-bound IgE.
Circulating neutrophils containing phagocytic granules and which are ready to respond immediately to injury are called what?
PMN: neutrophilic polymorphonuclear leukocytes (neutrophils)
How does the body increase the number of circulating neutrophils during an infection?
There is a large reserve of neutrophils in the bone marrow
What are the two phases of an inflammatory response?
1. destruction
2. resolution
What are the key players in the destruction phase of inflammation?
1. neutrophils
2. macrophages
inflammation is signaled by which four things?
calor, dolor, rubor, tumor (heat, pain, redness and swelling)
What are the three predominant ways macrophages are activated?
1. toll like receptors (TLR 1-10)
2. T-cell signaling
3. opsonization
Tissue injury causes inflammatory mediators such as _________ , __________, and __________ to be released.
histamine, kinins, and serotonin
Are erythrocytes typically found in inflamed area?
What are the predominant WBC's involved in the inflammatory response?
PMN neutrophils and monocytes are attracted to site of injury by chemotactic factors
What are the first WBC's to arrive on the scene of an injury and how do they gain access to the site?
neutrophils; margination (adhere to capillary wall in response to the released mediators/chemotactic factors)
After the initial stages of inflammation, which type of WBC predominates? Why?
Macrophage, because site usually becomes acidic and neutrophils do not survive the acidic conditions whereas macrophages can
How do neutrophils and macrophages destroy inflamed connective tissue?
secretion of collagenase and elastase and activation of matrix metalloproteases (MMPs)
Neutrophils are the "first-responders" during inflammation. What do activated neutrophils secrete?
1. oxygen radicals
2. antimicrobial peptides
3. lysosomal granules
4. signals to attract monocytes -->macrophages
Why do fibroblasts produce the destructive enzyme collagenase?
for remodeling purposes of newly synthesized connective tissue
What is purulent exudate?
pus; necrotic tissue and dead neutrophils and macrophages
An inflamed area in which pus gathers is called an _______.
What is the difference between acute and chronic inflammation with regard to kinin receptors?
acute inflammation: B2 receptor (rapidly desensitized kinin receptor)

chronic inflammation: B1 receptor (chronic, destructive stimulation by kinin)
What is periodontitis characterized by?
chronic inflammation and infiltration of lymphocytes and macrophages
What are the four mechanisms of hemostasis?
1. vascular spasm
2. platelet plug
3. blood coagulation

(4. growth of connective tissue into the blood clot to close the severed vessel permanently)
What is vascular spasm?
a mechanism of hemostasis involving nerve and myogenic contraction of the severed vessel
What triggers platelet aggregation?
when circulating platelets come into contact with (adhesion molecules become engaged) the exposed collagen of the damaged subendothelial tissue
What happens during platelet aggregation? What additional adhesion molecules are exhibited by the platelet? What do the activated platelets secrete?
platelets swell and asume an irregular form exhibiting additional adhesion molecules for fibrinogen and Willebrand's factor and secrete ADP and thromboxane which activates more platelets
What are fibrinogen and Willebrand's factor?
two fibrous proteins in the blood stream recruited by activated platelets
How does asprin inhibit platelet aggregation?
inhibits the formation of thromboxane by the platelets

(platelets can't make thromboxane)
How does aspirin permanently (until new platelets are formed) damage/reduce the quality of platelets?
by acetylating the enzyme cyclooxygenase (COX); the platelets can't synthesize new enzyme.
What signals vascular spasm?
1. thromboxane A2
2. thombin
What effect does Plavix have on platelet plugging?
irreversibly inhibits the platelet ADP receptor (preventing platelets from being activated in cascade)
What is thrombocytopenia?
condition characterized by having low levels of circulating platelets
Both coagulation pathways are dependent on what?
vitamin k
Both coagulation pathways are inhibited by what?
coumarin -inhibit conversion of vitamin K to its active form
What are coumarin drugs used for?
anticoagulants -their effect can be reversed by the administering vitamin K
What are the substances that regulate coagulation in the body?
1. heparin within mast cells
2. heparin sulfate on surface of endothelial cells
3. thrombomodulin
4. prostaglandin I2
What proteolytic enzyme converts fibrinogen to fibrin?
How does thrombin convert fibrinogen into fibrin?
cleaving N. ter. propeptides
What are the two different types of hemophilia?
A: missing coagulation factor #8

B: missing coagulation factor #9
How is hemophilia genetically transmitted?
both types of hemophilia are X-linked
What is von Willebrand's disease?
an autosomal dominant disorder involving a defective gene for the VW factor characterized by abnormal platelet function
Symptoms of VWD are similar to those of which type of hemophilia ?
VWD symptoms are similar to those of mild type A hemophilia (factor 8 deficiency)
What drug can be administered prior to performing dental surgery on a patient with VWD?
administration of desmopressin ( causes release of additional VW factor)
How is the fibrin clot stabilized?
the formation of covalent PEPTIDE cross-links between glutamine and lysine side chains by factor 8a in a transamidation reaction
Through which type of reaction are the peptide cross-linkages between glutamine and lysine side chains in a fibrin molecule formed?
The peptide cross-linkage (covalent) in a fibrin clot is between the side chains of which two molecules?
glutamine and lysine
How is fibrin cross-linked?
transamidation of glutamine and lysine side chains in the fibrin fiber
How is fibrinogen converted into fibrin?
propeptides are removed (by thrombin!)
glycosaminoglycans are polymers that include ...
hyaluronic acid, which has CARBOXYL groups on at least half of its monomers
glycosaminoglycans polymers have both sulfate and carboxyl groups on their monomers, but which one do they contain more of (on at least half of its monomers)?
What is the relationship between B-lymphocyte function and class II (MHC or HLA) presentation molecules?
B-cells use class II molecules to present their recognized antigen to helper-T cells
The molecule activated in the coagulation cascade and which functions to alter permeability in surrounding vasculature and to attract neutrophils is _____.
Which cells undergo homing?
lymphocytes, neutrophils and monocytes
The key coagulation factor that makes the INR sensitive to vitamin K status is _________
VII (7)
Which coagulation factor does von Willebrand factor complex with?
VIII (8)
What are conjugate acid-base pairs?
two compounds related to one another by the gain or loss of a hydrogen ion (H+)
The lower the pH, the _______ the [H+] concentration.
In pure water, [H+] is __________
1 x 10^-7 M
pH + pOH =
_______________ ______________________ are polyhydroxylated hydrocarbons of up to seven carbon atoms that have carbonyl groups.

______________ _______________ are those which can be broken into __________ _______________ by hydrolysis with 1M HCl.
simple carbohydrates; complex carbs; simple carbs
What is the smallest of the simple carbohydrates?
what are the two isomers of glyceraldehyde?
D- and L-
What is an isomer?
compounds that have the same number and kinds of atoms and have the same molecular weight
What are structural isomers?
isomers in which atoms are attached to each other differently (ex. isobutane and butane)
What are sterioisomers?
isomers that have the same atomic composition and bonding structure but have one or more asymmetric (chiral) centers.
sugars with oxidizable groups are called _________ _________.
reducing sugars
What are optical isomers?
isomers which rotate polarized light in different directions
what do you call an equal mixture of optical isomers?
racemic mixture ; no optical activity
which carbon in glyceraldehyde is chiral?
are D- and L-glyceraldehyde optical isomers?
What arrises from the oxidation of the aldehydic group of glyceraldehyde?
glyceric acid and lactic acid
Does the direction that a sugar rotates polarized light predict whether a sugar is D- or L-?
How was asymmetric carbons are in erythrose? How many isomers?
2 asymmetric carbons; 4 isomers
What are the names of the 4 erythose isomers?
D-erythrose, L-erythrose, D-threose and L-threose
The inversion of one chiral compound creates a _________ ___________, while inversion of both creates an _________________ (the mirror image compound).
new compound; enantiomer
what is the general formula for deciphering the number of sterioisomers of a sugar with 'n' asymmetric carbons?
2^n ; of these, only half are new compounds (the rest are enantiomers)
What is the result of the oxygen bridge forming between carbon 1 and 5 in glucose?
-alpha and beta -glucopyranose are formed
-additional asymmetric carbon is formed
-2 anomers of glucose (a and b) are created
What is the normal amount of glucose in blood?
70 - 120 mg/ 100 ml
Which sugars are sterioisomers of glucose?
mannose and galactose
The cyclic version of fructose is called what?
furanose ring (related to compound called furan) similar to how
What determines whether or not a sugar is reducing?
the presence or absence of a free anomeric hydroxyl group in a cyclized carbohydrate*
What is Fehling's solution?
an alkaline solution of cupric ions used to test for a reducing sugar
a-D-gulopyranose (gulose) is the C3 epimer of ___________.
why does glucose form a pyran-derived cyclic structure while fructose forms a furan-derived cyclic structure when they both have 6 carbons?
because glucose is an aldohexose and fructose is an ketohexose (2 R groups)
how are simple carbohydrates joined?
glycosidic bonds
glycosidic bonds are classified as being alpha or beta depending on what?
the configuration of the anomeric hydroxyl involved in the formation of the linkage
What is the glycosidic linkage of maltose?
2 glucose molecules joined via a-1,4 linkages
What is the glycosidic linkage of lactose?
D-galactose and D-glucose joined via b-1,4 linkages
Which disaccharides are non-reducing?
sucrose; non free anomeric hydroxyl
What are starches?
a-linked polymers of glucose containing more than 200 glucose residues
What is Amylose? Amylopectin?
both forms of starch:

amylose -linear polymer of a-1,4-linked D-gluocse
amylopectin - same but with a-1,6-branches
What is the most abundant carbohydrate in mammalian cells?
What is the difference between amylose and cellulose?
amylose: a-1,4 linked D-glucose

cellulose: b-1,4 linked D-glucose
How is glycogen different than amylopectin?
both a-1,4 linked glucose with a-1,6 branches but glycogen has much higher frequency of branching (more compact thus more soluble)
Glycosaminoglycans are alternating copolymers of a ___________ __________ and an _______ ___________ ______________.
a uronic acid and an amino sugar derivative
_________________ _______ is an alternating copolymer of N-acetylglucosamine and glucuronic acid via alternating b-1,3 and b-1,4 linkages.
hyaluronic acid
chondroitin sulfate is made up of what?
glucuronic acid and N. acetylgalactosamine (joined via alternated b-1,4 and 1,3 linkages)
hyaluronic acid is made up of what?
glucuronic acid and N. acetylglucosamine (joined via alternating b-1,4 and 1,3 linkages)
What is alginate?
-linear block copolymer of b-1,4 linked D-mannuronate and a-1,4 linked L-guluronate

-cross-linked by divalent cations

-dental impression material
How does penicillin work?
by binding to and inactivating enzymes (glycopeptide transpeptidase) that cross-link the peptidoglycan strands of bacterial cell walls.
What is the peptidoglycan repeating unit composed of?
N-acteyl glucosamine and N-acetyl muramic acid
What is the space in bacteria between the cell membrane and cell wall where there is considerable enzymatic activity?
What is the digestive compartment of bacteria?
The action of glycopeptide transpeptidase requires what?
extra D alanine since there is no energy source in the periplasm
Mechanism of glycopeptide transpeptidase involves a _____________ intermediate between the enzyme and the D-Ala moiety.
What does the term beta lactam refer to?
a drug with a four membered ring
How does penicillin inhibit glycopeptide transpeptidase? What is penicillin considered because of this?
Penicillin has a reactive peptide bond as a part of its beta-lactam ring which mimics the one found in D-alanine.

glycopeptide transpeptidase forms a acyl intermediate with penicillin as it normally would with D-alanine, however the penicillin moiety can not be displaced by the pentaglycine bridge!

Penicillin is a "suicide inhibitor"
What is beta-lactamase?
a varient of glycopeptide transpeptidase that imparts penicillin resistance on the bacteria that produce it by avoiding D-Ala-D-Ala and reacting with penicillin instead and allowing water to hydrolyze the intermediate.
Is vancomycin a beta lactam?
No, it's a complex cyclic peptide ring that is locked into a rigid structure and has an attached disaccharide
What are the two features of vancomycin that impart antibiotic action?
1. complex rigid cyclic peptide ring (inhibits transpeptidase)
2. attached disaccharide (inhibits transglycosylase, which is what builds the NAM-NAG chain)
How does tetracylcin work?
inhibits bacterial translation at the ribosome (aminoiacyl-tRNA binding step)
What are 'R factors' ?
plasmids that tend to accumulate resistance determinants (genes) through a process called transposition
How are R factors passed from one bacterial species to another?
What is P. glycoprotein (mdra gene)?
functions to pump toxins out of cell; amplified in cancer cells rendering them drug-resistant
how does Acycloguanosine (acyclovir) work?
it is a guanosine analogue and when incorporated into the DNA (by herpes-specific thymidine kinase) causes a break in the backbone
What are the names of two anti-herpes viral agents?
acyclovir and denavir
The ability of both myoglobin and hemoglobin to bind oxygen is dependent upon what?
a prosthetic heme group
What is myoglobin?
the oxygen storage protein found in human muscle (especially the heart)
What does a heme prosthetic group consist of?
a protoporphyrin (4 pyrrole groups) surrounding a central Fe iron either in a +2 or +3 oxidation state
The four pyrrole groups in the heme prosthetic group are linked by _____________ __________ to form a tetrapyrrole ring which has four methyl, two vinyl, and two propionate side chains attached.
methene bridges
The tetrapyrrole structure of a heme prosthetic group is synthesized from what?
glycine and succinyl-CoA
How many bonds can the iron in heme form?
6 (four within the plane of the heme and the other 2 projecting out either side)
The exterior of the myoglobin molecule is composed of mostly _________ amino acid residues, while the interior is composed of only __________ AA residues with the exception of 2 histidines which are required for interaction with heme.
polar; nonpolar
What is the position of the iron atom in Heme of deoxyhemoglobin?
Fe+2 slightly outside the plane of the porphyrin ring
Oxygen binding to causes which structural changes to the iron atom in heme?
it moves into the plane of the ring and the proximal histidine is pulled along with the iron.
Bound oxygen is stabilized by ___________ ______________ to the side chain of a second histidine at the top of the heme.
hydrogen binding
The tilt of the O2 _________ the O2 binding affinity, but ___________ the binding affinity for CO even more, explaining why the tilt evolved.
lowers; lowers
The major effect of the tilt when oxygen is bound to hemoglobin is ...?
decreased binding of CO that improves selection for binding of O2
Two sugar diastereomers are related by what?
changing of the configuration of at least one chiral C of at least two that exist
How do myoglobin and hemoglobin differ in structure?
in their quaternary structures; almost identical in primary and tertiary
What does hemoglobin consist of?
four polypeptide chains held together by noncovalent bonds
What is the principle hemoglobin in adults?
hemoglobin A; two alpha chain and 2 beta chains each containing one heme group (4 binding sites for oxygen)
Do hemoglobin and myoglobin both bind oxygen cooperatively?
NO, only hemoglobin binds oxygen cooperatively
What is the shape of the oxygen binding curve for hemoglobin?
sigmoidal (cooperatively)
What is the shape of the oxygen binding curve for myoglobin?
hyperbolic (non-cooperative)
What two things result in the release of O2 from hemoglobin
1. decrease pH
2. increase partial pressure of CO2
At any given O2 pressure, _____________ has a higher affinity for oxygen than _________________.
myoglobin; hemoglobin (in an environment containing both, O2 will be transferred to myoglobin)
The strong effect of pH on the oxygen-hemoglobin equilibrium is called the ___________ _____________.
Bohr Effect
What are the two most important factors regulating the function of hemoglobin in the transport of oxygen?
1. partial pressure of oxygen
2. pH
In what form is most CO2 carried in the blood?
as bicarbonate
How does your body adjust to high altitude hypoxia?
by increasing red cell BPG concentration
How does BPG reduce the affinity for oxygen?
by prefernetially binding the deoxy form (promotes O2 release)
How does BPG bind to hemoglobin?
through electrostatic interactions b/w its negatively-charged groups and six positively charged groups on the two beta subunits
enhanced oxygen affinity of fetal hemoglobin is a result of what?
diminished interactions with BPG
Why does fetal hemoglobin have a decreased affinity for BPG?
because it has gamma chain instead of b-chains which do not bind well to BPG; result is an increased binding affinity for O2, causing O2 to flow from maternal oxyhemoglobin to fetal deoxyhemoglobin.
Binding of what 3 allosteric effectors results in the decrease of oxygen binding by hemoglobin?
1. BPG
2. H+ (decrease pH)
3. CO2
What is the molecular defect of sickle cell anemia (hemoglobin s)
alpha subunits are the same; defect is that a hydrophillic glutamate residue is replaced with hydrophobic valine reside at position six of the beta-chains

hydrophobic interactions cause polymerization and crescent shape RBCS
In an amino acid what is the pKa of the carboxyl group? the amino group?
carboxyl: 2.1
amino: 9.5
What is the one imino acid?
proline (NH instead of NH2) contains secondary amino group instead of a primary amino group
What is a zwitterion?
a molecule with a single positive and single negative charge
What is the average net charge on an amino acid at pH 7?
Amino acids have at least one __________ _________, except for glycine.
chiral center
Which is the only amino acid that lacks at least one chiral center?
glycine; because its 'R' group is another H
Amino acids are _____ _______ with at least ______ dissociable hydrogen ions (protons).
weak acids; 2
Which is the only form of amino acids that exists naturally?
Which are the two acidic AAs?
asparate and glutamate
At high pH, _______ group on an AA is ____________.
neither; protonated
At low pH, ________ groups on an AA are ___________.
both; protonated
What are the two aliphatic hydroxyl AAs?
serine and threonine
What are the two aliphatic amide AAs?
asparagine and glutamine
What are the sulfur containing AAs?
cysteine and methionine
y-carboxyglutamic acid is found in proteins that form blood clots, namely _____________.
probthrombin (vit. k dependent)
phophoserine is associated with ...?
hormones can induce the phosphorylation of serine residues on target enzymes, leading to their activation
What are the hydrophobic AA categories?
-alipathic (hydrophobic)
-imino acid
What are the hydrophilic AA categories?
-aliphatic (hydoxyl)
-aliphatic ( amine)
aspartic acid and glutamic acid are negatively charged above pH ___.
What are the two ways to determine 3D structure of a protein?
NMR spectroscopy and X-ray crystallography
Which method of determining 3D protein structure can be used on proteins up to 50 kDa?
Which method of determining 3D protein structure can be used of proteins of all sizes?
X-ray crystallography
Are enzymes always proteins?
No, they can be proteins or RNA (ribozymes) or a combination of both
What is true if deltaG is negative?
products are favored
The amount of energy required to overcome the barrier created by the chemical bonds which must be broken in order for a reaction to proceed is known as the ____________ ____________.
activation energy
The structure of the reactants at the at the top of the barrier (activation energy) is called the ________________ _________.
transition state
The rate of rxn can be increased in what 2 ways?
1. increase temp
2. decrease activation energy (energy required to reach transition state)
Do catalysts change the equilibrium constant of a reaction?
No, because they increase rates of both the forward and reverse reactions
What is the active site of an enzyme?
a small region of the enzyme where the reaction occurs; generated by tertiary structure of the enzyme
What level of protein structure is responsible for the active site on an enzyme?
tertiary structure
What are cofactors?
additional substances required by enzymes for catalysis (metal ions, or coenzymes (organic compounds)
T/F: coenzymes are cofactors
T/F: cofactors are coenzymes
false; coenzymes are cofactors
What is a prosthetic group?
a very tightly bound cofactor (heme, for example)
enzymes are catalysts that affect the _______ of a reaction.
What is Vmax? What is it a function of?
maximum velocity; function of [enzyme]
What is V0?
initial velocity
What is S?
substrate concentration
What is Km?
The Michaelis constant; Km = S when V0=1/2Vmax
When is Km equal to the substrate concentration?
at half Vmax
Why was the Lineweaver-Burk equation formulated?
because Km and Vmax are not easily nor accurately interpreted by hyperbolic substrate saturation plot given by the michaelis-menton equation (Vmax vs. S)
The slope on the Lineweaver-Burk Plot represents what?
Reversible inhibition of enzymes is characterized by an ___________________ between the enzyme and the inhibitor.
What are the three types of reversible enzyme inhibition?
1. competitive
2. uncompetitive
3. noncompetitive ("mixed")
Which type of enzyme inhibition is characterized by parallel lines?
Which type of enzyme inhibition is characterized by an unchanged Vmax and y-intercept and an increase in slope?
Which type of enzyme inhibition is characterized by a change to y-int but NOT to slope, and a lowered vmax?
Which type of enzyme inhibition is characterized by an increase in both slope and y-int and a seemingly lower Vmax?
Enzymes that exhibit a characteristic kinetic response to changes in the concentration of substrates, activators, and inhibitors are called ___________ ___________.
allosteric enzymes
What reactions are often characterized by allosteric enzymes?
the rate-limiting reactions in different metabolic pathways
Allosteric enzymes exhibit either __________ or __________ cooperativity with respect to the substrate.
positive; negative
Most allosteric (regulatory) enzymes exhibit what type of kinetics?
What are isozymes?
different forms of an enzyme that catalyze the same reaction (different forms encoded by different genes) generally have different Km and Vmax values
Do allosteric enzymes usually consist of multiple subunits?
Yes, may be identical or different
An expressed sequence tag (EST) library is used to do what?
locate exons in genomic sequence and diagnose splicing patterns
In an experiment to break the genetic code a synthetic ribotrinucleotide was added to a cell extract. The trinucleotide was playing the role of ____.
BRCA1 is a human gene for which women inheriting a defective copy are at a higher than normal risk of breast cancer. This kind of gene is called a(n) _________.
tumor suppressor
Which one of the following is a capability of the polymerase chain reaction (PCR)?
PCR can quickly recover the DNA for a particular gene from a large number of patients.
A difference between the PT (or INR) and the PTT laboratory tests is that ______.
PT is done with a trigger of the extrinsic coagulation pathway, whereas PTT is done with a trigger of the intrinsic coagulation pathway
In the ABSENCE of foreign antigens, which one of the following may act to signal an inflammation?
kinin activated in association with the intrinsic coagulation pathway
An_______________ is an enzyme without its coenzyme.
Hemoglobin first saturates with oxygen at oxygen pressures _______ the partial pressure of oxygen in the atmosphere and, therefore, can be made to increase release of oxygen to tissues by binding of H+ and CO2; the response to H+ and CO2 is called the ________.
less than, Bohr effect
O2 bound to hemoglobin contacts ________ .
a histidine and an iron atom
A vitamin C deficiency causes a defect in a modification made to an amino acid. A result is ....?
reduced hydroxylation of proline
Which two of the amino acids are known as α and β secondary structure breakers?
Glycine, Proline
Titration of hydrogen ion from local anesthetics (lignocaine and procaine, for example) promotes ________.
more permeation of cells
Bicarbonate is an effective physiological buffer because ________.
it converts to carbonic acid which decomposes
What is a zymogen?
an inactive enzyme precursor that requires proteolytic cleavage of a peptide bond in the primary sequence to become active
Is activation of a zymogen reversible?
no, irreversible
Digestive enzymes are an example of _________.
Although some hormones require proteolytic cleavage, they are not called _____________, because they do not have enzymatic activity.
What is the purpose of zymogen formation?
prevents enzymic catalysis in inappropriate tissues and cells; activation (proteolytic cleavage) does not occur until the zymogen is in its target tissue
What are the two type of covalent modifications that can be made to enzymes?
1. proteolytic cleavage (zymogen activation)
2. new covalent bond to an AA (phosphorylation)
What is an example of phosphorylation (covalent modification to an enzyme)?
glycogen metabolism in skeletal muscle
What is an example of a zymogen?
digestive enzymes, complement components, clotting factors
What is a holoenzyme?
apoenzyme + cofactor
What is an apoenzyme?
enzyme without it's cofactor
Which laboratory test measures the effectiveness of the extrinsic pathway?
PT (prothrombin time) Called INR when normalized into ratio indicated by VII, X, II, V, and I (three of which are clotting factors: VII, II and X)
Which laboratory test measures the intrinsic pathway?
Partial thromboplastin time (PTT)
The bond between the deoxyribose and the base is called a ____________ linkage and is in the __ configuration.
glycosidic; beta
What are the four bases that appear in RNA?
What are the four bases that appear in DNA?
Which of the bases are pyrimidines?
Which of the bases are purines?
What revealed the helical structure of the DNA molecule?
X-ray diffraction
What is Chargaff's rule?
The amount A=T and G=C in naturally occurring DNA
a nucleotide with the phosphate group removed is called a ___________.
How many hydrogen bonds are between an AT basepair?
How many hydrogen bonds are between a CG basepair?
By convention, DNA sequence is always written __ to __ prime.
5' to 3'
What is the name of the enzymes that catalyze the replication of DNA?
DNA polymerases
How do DNA polymerases work?
by adding 5'-nucleoside triphosphates to the 3' OH end of a growing DNA chain according to the template
In what direction do all DNA polymerases work? As a result of this, ________________ replication is required
5' to 3' ;discontinuous replication
_____ _________________ requires a primer, while _____ ________________ does not.
DNA polymerase; RNA polymerase
What are steps required to start DNA synthesis?
1. RNA polymerase synthesizes short stretch of RNA
2. DNA polymerase using RNA as primer for DNA synthesis
3. The RNA primer is degraded
4. The 'nick' between the 5' phosphate and 3' OH of abutted (but unjoined) newly synthesized DNA is ligated by DNA ligase which synthesizes missing phosphodiester bond (Okazaki fragments)
What are Okazaki fragments?
The fragments of newly synthesized DNA that are transiently present prior to ligation by DNA ligase
In addition to the single circular chromosomes containing about 3 X 10^6 basepairs, bacteria also contain small circles of DNA within bacteria are called __________ or _________ .
episomes or plasmids
A huge, single, linear molecule of double-helical DNA is called a _________________.
How is structural condensation of DNA achieved?
DNA is wrapped around proteins called Histones
What is chromatin?
DNA with its associated proteins
What enzyme is particularly useful for in vitro copying of mRNA into DNA (called cDNA) which can be used in molecular cloning experiments?
What are restriction enzymes?
Enzymes that put staggered breaks in DNA at specific nucleotide sequences
What is recombinant DNA technology? (AKA molecular cloning)
Replication of human (or other) genes in high volume within bacteria chemical analysis
What does molecular cloning/ recombinant DNA technology permit?
1. Large-scale production of mammalian protein in E. Coli
2. Sequence determination of gene from which we can sometimes predict function
3. Derive hybridization probes for screening in genetic disease
Which genetic technology rapidly detects, amplifies, and purifies a DNA fragment and is useful in the detection of minute quantities of a gene?
What does transgenic technology permit?
1. transfer of an inheritable gene into genome (a transgene)
2. knockout mutants
3. RNA silencing
There are a number of mammalian genes that cause cancer if mutated. The mutated genes are called __________ and their precursors are called ______________.
oncogenes; protooncogenes
Genes that protect against rouge replication are called ___________ _____________, and are often mutated in cancer cells.
tumor suppressors
The formation of ___________ ____________ in DNA is induced by UV exposure.
thymine dimers
What is Xeroderma pigmentosum?
genetic disease in which afflicted individuals lack the enzyme system responsible for excising the thymine dimers formed by UV exposure; high incidence of skin cancer
The conversion of a protooncogene into an oncogene is an example of a _______-of-_____________ mutation.
Local anesthetics are all ___________ ________
weak acids
The midpoint of a titration is always the point at which buffering capacity is greatest where ______ = ______ .
pKa of acid being titrated = pH
Why is bicarbonate the primary buffering system in the body despite the fact that its pKa is is so far from the pH of serum?
Because it is converted to carbonic acid by carbonic anhydrase which is volatile and is excreted effectively through the lungs during respiration
MHC proteins are encoded by an array of highly __________________ genes
polymorphic ( many different alleles) lots of diversity
The component of blood minus cells and clotting factors is called what?
How are the two identical heavy chains held together in an IgG? Heavy and light chains?
noncovalent forces and disulfide bonds
The ____________ regions of both heavy and light chains combine to form the antigen binding site on an IgG molecule.
Where is the hinge-region on an IgG molecule?
between CH1 and CH2
What are the functions of the IgG class?
1. complement activation
2. cross the placenta
3. cell attachment
4. rate of clearance from bloodstream
papain digestion of IgG yields what?
Fc and 2 Fab
A single Ab can only have one type of light chain, either 2 _____________ or 2 _____________.
kappa, lambda (differ in constant region)
Which class of antibody is surface bound on naive B lymphocytes?
Which class of antibody is the first Ab detected in blood following antigenic challenge?
Which class(es) of Ab is/are dependent on J-chain?
IgM and IgA
Which class of Ab is particularly good at agglutination?
IgM and IgA
Which is the Ab in secretions?
Which class of Ab can occur as a monomer, dimer or tetramer?
Does IgA activate complement?
Which Ab class is found on the surface of B-cells and signals maturation ?
What are the viatmin K dependent factors?