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In saturated fatty acids, the carbons are linked exclusively by single bonds.
Monosaturated fatty acids have ONE carbon-carbon double bond, and polyunsaturated fatty acids have MORE than one.
a) the first statement is true, 2nd is false
b) the 1st statement is false, 2nd is true
c) Both statements are true
d) Both statements are false
c) Both statements are true
Fats can be classified by the number of double bonds
between carbon atoms in their fatty acid molecules.
- Saturated fat = no double bonds
- Monounsaturated fat = one double bond
- Polyunsaturated fat = multiple double bonds
All FAs are building blocks of phospholipids and glycolipids and therefore needed for the synthesis of membranes. Essential FAs cannot be synthesized because of humans lack of omega-3 and omega-6 enzymes.
- *Cells derive energy from FAs through beta-oxidation
- *Some of the polyunsaturated FAs linoleic acid and linolenic acid are essential.
Dietary triglycerides are digested and broken down to free Fatty Acids and 2-monoacylglycerol by pancreatic lipase, and these breakdown products are absorbed with the help of:
d) Bile salts
- Bile salts
- Acts as an emulsifier, serving to solubilize the otherwise insoluble fat. The Micelles (tiny microdroplets emulsified by the bile salts) travel to the intestinal epithelial cells, which absorb the FAs.
- The bile salts are re-absorbed in the distal ileum via the Na+/bile acid cotrasporters, recycles by the liver and resecreted into the gut.
- Bile salts perform 2 important actions; 1. most important, help absorbed FAs by emulsifying FAs, monoglycerides, cholesterol, sat-soluble vitamins and lipids into Micelles. 2. Detergent action on the fat particles, decreases surface tension of food and allows agitation.
- Bile salts are usually cojugated with glycine or taurine, the cholic acid conjugates with glycine creating glycocholate and taurocholate.
- Fat malabsorption results in pancreatic failure, lack of bile salts or extensive intestinal diseases, condition is called Steatorrhea.
The only membrane phospholipid NOT derived from glycerol is:
- Sphingomyelin, most membrane phospholipids contain glycerol (lecithin, cerebroside and cardiolipin) EXCEPT Sphingomyelin which is based on sphingosine.
- 3 major types of body phospholipids
- 1. Lecithins, water soluble emulsifiers and membrane constituents.
- 2. Cephalins, phospholipids with hemostatic properties, found in brain and spinal cord tissue.
- 3. Sphingomyelins, found especially in nerve tissue and yield sphingosine, choline a FA and phosphoric acid upon hydrolysis. Membrane constituents, Niemann-Pick disease is associated with sphingomyelin accumulated in CNS tissue.
Which of the following sequences places the lipoproteins in the order of the most dense to the least dense?
a) HDL / VLDL / chylomicrons / LDL
b) LDL / chylomicrons / HDL / VLDL
c) HDL / LDL / VLDL / chylomicrons
d) VLDL / chylomicrons / LDL / HDL
e) chylomicrons / HDL / LDL / VLDL
- HDL / LDL / VLDL / chylomicrons
- Lipids (triglycerides and cholesterol) are NOT able to move in body fluids because of hydrophobic nature so they are packaged in lipoproteins (apolipoprotein is the protein alone). INVERSELY PROPORTIONED.
- Chylomicrons: lease dense lipoprotein, most triglyceride and least protein content (muscle and adipose tissue).
- VLDLs: (very low density lipoprotein) more dense than chylomicrons, high content of triglycerides (muscle and adipose tissue)
- LDLs: (low density lipoprotein) less tryglyceride and more protein content, highest cholesterol content. Primary carriers of cholesterol in plasma, especially to the liver.
- HDLs: most dense lipoprotein, lowest triglycerides and highest protein content. Delivery to the liver.
All of the following statements about plasma lipoproteins are false EXCEPT one. Which is the exception?
a) Chylomicrons are synthesized in the intestinal mucosal cells and transport triacyglycerol to the peripheral tissues.
b) HDL particles are produced from LDL particles in the circulation by the action of the lipoprotein lipase.
c) HDL competes with LDL for binding to receptors on the surface of cells in extrahepatic tissues.
d) LDL Particles have the least percentage concentration of cholesterol.
- Chylomicrons are synthesized in the intestinal mucosal cells and transport triacyglycerol to the peripheral tissues. They carry FA obtained in the diet to peripheral tissues where they are consumed or stored as fuel, remnants travel to the liver where they are recycled
- VLDLs = high concentration of triglycerides
- LDLs= very rich in cholesterol, "Lovastatin" lowers cholesterol by inhibiting HMG CoA redutactase (key enzyme in cholesterol synthesis)
- HDLs = protein rich, produced de novo in liver
Ketone bodies are formed only in:
- Liver diverts excess acetyl-CoA into ketone bodies. There are 3 types of ketone bodies; Acetoacetate, ß-hydroxybutyrate and acetone. Produced during conditions of starvation or diabetes mellitus (low glucose availability), and they are important sources of energy for peripheral tissues (except acetone) during this state.
- Ketone bodies are used exclusively by extrahepatic tissues and unlike FAs can be oxidized by the brain.
- Extrahepatic tissues convert ketone bodies back to acetyl-CoA vis succinyl-CoA.
All of the following are sources of acetyl-CoA for fatty acid synthesis EXCEPT one. Which is the exception?
- Glucose is the major source of acetyl-CoA for FA synthesis. In a high carb diet, FA synthesis occurs primarily in the cytoplasm of the liver and lactating mammary gland, adipose tissue and kidneys. It is FIRST degraded to pyruvate by glycolysis in the cytoplasm. Second, in the mitochondria pyruvate is made to acetyl-CoA where it serves as a substrate for citrate synthesis. THIRD, citrate goes to the cytoplasm via citrate-malate-pyruvate shuttle where fatty acids are synthesized.
- *Malonyl-CoA participates in biosynthesis of FA but NOT in their breakdown.
Which of the following is involved in both fatty acid catabolism and synthesis?
b) Coenzyme A
d) Alcohol dehydrogenase
- Coenzynme A (pantothenic acid-containing coenzyme)
- Carnitine = catabolism
- Malonyl-CoA = synthesis
- Alcohol dehydrogenase = neither
- FA catabolism: Carnitine is the carrier substance to take FAs to the liver where they are turned to acetyl CoA (via beta oxidation) which are then used in Krebs cycle to create NADH and FADH2 to be converted to ATP in ETC.
- FA Biosynthesis: occurs in the cytosol, malonyl-CoA is a key intermediate that is formed from acetyl-CoA, bicarbonate and ATP, irreversible reaction.
- *During FA synthesis Krebs cycle, glycolysis and enzyme pyruvate dehydrogenase are expected to be active.
A patient of yours has uncontrolled diabetes mellitus. This causes ketosis, or high levels of ketone bodies in the body tissues and fluids. Which of the following is NOT a symptom of this condition?
a) Fruity breath
b) Lowered pH of the blood
c) Decreased potassium in the urine
d) Ketone bodies in the urine
- Decreased potassium in the urine
- Ketosis is a condition characterized by abnormally elevated concentrations of ketone bodies in the body tissues and fluids. Occurs when FAs are not completely metabolized (acetone) due to starvation, fasting, alcoholism, Characterized by ketonuria, ketonemia, fruity odor in breath.
- Complete absence of insulin in diabetes type 1 causes diabetes ketoacidosis. Large amounts of glucose and ketone bodies are lost in urine, if untreated is fatal. Glucose is effective in reserving ketosis in non-diabetic patient.
- *In healthy diet Acetyl-CoA is processed through the TCA/Krebs. During fasting this is disrupted and TCA is reduced and some of the Acetyl-CoA produced from fats will be converted to ketone bodies.
All of the following statements concerning fatty acid synthesis are true EXCEPT one. Which is the exception?
a) FA synthesis involves two carbon additions primarily from acetyl-CoA
b) The important step in fatty acid synthesis is the first one in which acetyle-CoA, ATP, and biocarbonate form malonyl-CoA
c) FA synthesis is not a simple reversal of ß-oxidation used for the catabolism of FAs.
d) FA synthesis takes place in the mitochondria while FA breakdown (catabolism) occurs in the cytosol (cytoplasm).
- FA synthesis takes place in the mitochondria while FA breakdown (catabolism) occurs in the cytosol (cytoplasm). It is the opposite, synthesis takes place in the cytosol and catabolism in the mitochondria (where citrate is made).
- FAs are oxidized by pathway of ß-oxidation, active in the mitochondria. this produces Acetyl-CoA for TCA cycle
- The tail of a FA is a long hydrocarbon chain making it hydrophobic while the "head" molecule is a carboxyl group hydrophilic. This is the main component in soap (washes away dirt)
- Lipids: organic compounds that do not dissolve in water but in alcohol and other organic solvents. Major lipids are triacylglycerols (most common), phospholipids and steroids (colesterol is the most common steroid)
This molecule picture plays a major role:
a) As an energy source
b) As a membrane component
c) As a signal mechanism
d) Two of the above
d) all of the above
- a) As an energy sourceIt is a triglyceride a naturally occurring ester of 3-fatty acids and glycerol that is the chief constituent of fats and oils. Provides more than half the energy requirement of liver, heart and skeletal muscle, they are NOT membrane constituents. They contain twice as much energy as Carbs and the hormone glucagon signals the breakdown of triglycerides by hormone sensitive lipase to release FAs.
- High levels of triglycerides are linked to atherosclerosis, heart disease and stroke.
- Triglycerides are only used as storage for metabolic energy, other lipids have more specialized functions.
Choline is required for synthesis and release of acetylcholine.
Choline is also a precursor for synthesis of phospholipids phosphatidylcholine (lecithin) and sphiongomyelin.
a) 1st statement is true; 2nd is false
b) 1st statement is false, 2nd is true
c) both statements are true
d) both statements are false
c) both statements are true
-Although choline and carnitine can be synthesized de novo, but are essential.
- -Choline is important in synthesizing molecules for memory storage, muscle control and other functions like membrane function. intracellular signaling, hepatic export of VLDLs.
- - Rare choline deficiency can cause metabolic abnormalities like hepatic cirrhosis and fatty liver disease.
- Carnitine is required for FA transport across mitochondrial membrane. Can be synthesized de novo.
The binding of glucagon to its receptor:
a) deactivates adenylate cyclase
b) activates adenylate cyclase
c) Causes the breakdown of cyclic AMP to ATP
d) Causes the production of ATL from cAMP
e) Deactivates protein kinase
- b) activates adenylate cyclase
- Secretion of glucagon (from pancreatic alpha cells) is increased 3 fold by hypoglycemia and reduced to half of the basal release by hyperglycemia, through Cyclic AMP, it up-regulates glucose when dietary carbs are in short supply. Its actions are the opposite of insulin (produced by beta cells in pancreas) because it acts exclusively on the liver.
- *Hormones Glucagon and Epinephrine activate adenylate cyclase in the adipocyte plasma membrane (when metabolic energy is needed from triglycerides stored in adipose tissue) intracellular concentration of cAMP raises with a cAMP-dependent protein kinase, whichactivates hormone-sensitive triaglycerol lipase, which initializes the hydrolysis of the ester linkages of triglycerides, forming the free fatty acids and glycerol which will travel by albumin to tissues for fuel.
- *insulin causes activation of a phosphorylase that dephosphoylates the hormones sensitive lipase and diminishes lipolysis.
The nonessential amino acids are synthesized either from common metabolic intermediates or from other amino acids.
Only three amino acids, leucine lysine and histidine are exclusively ketogenic.
a) the 1st statement is true, 2nd is false
b) the 1st statement is false, 2nd is true
c) both statements are true
d) both statements are false
The 1st statement is true, 2nd is false
- - 11 of the 20 amino acids can be synthesized in the human body, those 9 that cannot are called "essential". The nonessential AA are synthesized from common metabolic intermediates or from other AAs.
- - AA are used for 3 major purposes
- 1. substrates for generation of metobolic energy
- 2. substrates for protein synthesis
- 3. substrates for other products, purines, pyrimidines, coenzymes, heme, melanin...
- - Can be ketogenic, glucogenic or both depending on the nature of their end products. Ketogenic can get degraded to ketone bodies and glucogenic can be converted to glucose and glycogen. Only leucine and lysine are purely ketogenic.
- *The nitrogen of the AA is incorporated in urea, a soluble non-toxic product excreted in the urine.
In eukaryotes, DNA does not exist free; it is complexed within an approximately equal mass of basic proteins called histones. These histones contain a large portion of.
a) Cysteine and lysine
b) Arginine and lysine
c) lysine and glutamine
d) Glutamine and arginine
- Arginine and lysine
- DNA of the nucleus has chromatin proteins, which consist of 5 types of histones (H1, H2A, H2B, H3 and H4) basic proteins charged positively with arginine and lysine, these bind to the negatively charged phosphate groups of DNA and keep DNA stabilized and compact.
- Histones package DNA into units called nucleosomes, which are repeating subunits of chromatin, consisting of DNA chain coiled around a core of histones.
- Chromatin contains small variety of nonhistone proteins, most are transcription factors. Phosphorylation of serine and threonine residues in histones for replication and acetylation of lysine in histones for transcriptional activation.
Which of the following statements about protein structure is the correct?
a) Proteins consisting of polypeptide can have quaternary structure
b) The formation of a disulfide bond in a protein requires that the two participating cysteine residues be adjacent to each other in the primary sequence of the protein
c) The stability of the quaternary structure in proteins is mainly due to covalent bonds among the subunits.
d) The information required for the correct folding of a protein is contained in the specific sequence of amino acids along the polypeptide chain.
The information required for the correct folding of a protein is contained in the specific sequence of amino acids along the polypeptide chain.
The correct folding of a protein is guided by specific interactions among the side chains of the AA residues of a polypeptide chain. Protein (polymer of AA joined by peptide bonds) folds in different ways and to different extents. Generally AA have an alpha carbon
attached to a hydrogen atom (H)
, a carboxyl group (COOH)
, an amino group (NH2)
and a 4th group that differs
one AA from another represented by the letter R
. (20 AA are found in the body possessing different R groups)
- *A protein is formed when an alpha amino group of one AA bonds to the alpha carboxyl group of another, this is called a peptide bond, and it forms a Dipeptide (2 AA joined). 10 or more AA joined are a polypeptide (chain). 100 or more AA in a polypeptide form a protein.
- *Many proteins are composed of 2 or more polypeptide chains, that along with noncovalent interactions and disulfide bonds form a protein quaternary structure (in which their function is related to)
Most plasma cells are derived from the:
c) plasma cells
- LiverOnly the Immunoglobulins are not produced by the liver, they are produced by the plasma cells. Liver produces 25g of plasma proteins daily (50% of total liver protein synthesis).
- Most plasma proteins EXCEPT albumin are glycoproteins and they also stabilize pH
- Albumin is 60% of total plasma protein, but provides 80% of colloid osmotic pressure (hydrophilic), its pressure is necessary to prevent edema (below 2.0g/dL)
- Globulins (35% of plasma protein), transport, ions, hormones and immune function.
- Fibrinogen (4% of plasma protein) blood clotting.
- Other plasma proteins: Lipoproteins (LDL, HDL, VLDL, chylomicrons) transport of lipids to liver and organs. Transferrin (iron transport). Prothrombin (Blood-clotting protein)
A peptide bond forms between the _____ group of one amino acid and the _____ group of the adjacent amino acid.
a) Amino; amino
b) Carboxyl; carboxyl
c) Carboxyl; amino
*When a peptide bond is formed (amino group of one AA and carboxyl group of another AA) a water molecule is released, this is a condensation reaction
. The resulting CO-NH is a peptide bond, molecule is an amine.
- *Peptide bonds are not cleaved by organic solvents or urea, but susceptible to strong acids (they are extremely stable). Uncharged but POLAR, bonds of alpha carbon rotate freely.
- *Another covalent bond that occurs with proteins is a disulphide bond, formed by a sulfhydrl (-SH) of each of 2 cysteine residues, to produce a cystine residue, these strong bonds stabilize the structure of the protein and prevent them from being denatured in the extracellular environment (insulin and immunoglobulins).
- *residue is a single AA within a polypeptide chain. Cystine is an AA found in many proteins. Hydroxyproline is a constituent of collagen rarely found in any other protein, provides stability to collagen. Glycine is the only non-chiral AA.
Both hemoglobin in RBCs and myoglobin in the muscles employ heme as a prosthetic group.
Myoglobin consists of a single polypeptide with a non-covalently bound heme group, while hemoglobin has 4 polypeptides, each other with its own heme.
a) 1st statement is true; 2nd is false
b) 1st statement is false, 2nd is true
c) both statements are true
d) both statements are false
- both statements are true
- Myoglobin consists of a polypeptide with with non-covalently bound heme group, while Hemoglobin consists of 4 polypeptides, each with its own heme, that can associate with 4 O2 molecules.
- -Myoglobin has a higher oxygen-binding affinity than do the hemoglobins although is is a monomeric heme protein (containing only one heme unit) this makes it a great for storing O2 within muscle cells
- -HbF has a higher affinity than HbA, HbA adult Hemoglobin, HbF fetal hemoglobin.
- -Carbon monoxide binds to heme ion stronger than oxygen, this is responsible for CO2 poisoning.
All amino acids found in proteins are of the:
- A stereoisomer are compounds with the same composition and order of anatomic connections, but with different atomic connections. In all AA (except glycine) the alpha carbon is asymmetric (called the chiral center).
- The naming of these different stereoisomers is based on the absolute configuration of the 4 constituents of the asymmetric carbon, the reference compound is the smallest sugar to have an asymmetric carbon glyceraldehide (established by x-ray diffraction analysis.
- Stereoisomers having configuration related to L-glyceraldehyde are designated L (same goes for D-glyceraldehyde) D-configuration AA are found in some antibiotics and some bacterial cell walls.
In contrast to hemoglobin and myoglobin where the iron is always in the ferrous state (Fe2+), the heme iron of the cytochromes.
a) is always in the Fe3+ state
b) is always in the Fe4+ state
c) is always in the Fe5+ state
d) switches back and forth between the Fe2+ and Fe3+
- -switches back and forth between the Fe2+ and Fe3+-Cytochromes is a membrane bound hemoprotein that contain heme groups and carry out electron transport. Their heme ion switches back and forth between Fe2+ and Fe3+and they receive electrons from the reduced form of coenzyme Q (ubiquinone).
- -Cytochromes a3 and a are the terminal members of the electron transport chain.
All amino acids have a carboxyl group and an amino group, both bound to the came carbon. This carbon is called the...
- alpha carbon
- In all amino acids except for Glycine, in which the R group is a hydrogen atom.
- When an AA loses its amino group and gets an oxygen atom in place, it becomes alpha-keto acid and can enter the Krebs cycle by way of pyruvic acid, this happens when proteins are used for energy.
Glutamate can be synthesized by the addition of ammonia to alpha-ketoglutarate. All of the following amino acids can be derived from glutamate EXCEPT one. Which is the exception?
- Synthesis of amino acids
- - alpha-ketglutarine gives rise to glutamate (precursor of glutamine, proline and arginine)
- - 3-phosphoglycerate gives right to serine (precursor of glycine and cysteine)
- - Oxaloacetate gives rise to aspartate (precursor of asparagine, methionine, threonine [precursor of isoleucine] and lysine)
- - Ribose-5-phosphate gives rise to histidine- Pyruvate gives rise to alanine, valine, leucine and isoleucine
*Humans can only synthesize 11 of the 20 common AA: P
eucine and L
ysine or PVT TIM H
Elastin has an aberrant amino acid composition, with high proportions of:
a) Valine, Phenylalanine and lysine
b) Tryptophan, histidine and methionine
c) Glycine, alanine and proline
d) Threonine, cysteine and glutamate
- - Elastic fibers of the Extracellular matrix have 2 components; inner core of elastin (which is composed of Glycine, Alanine and Proline) and microfibrils surrounding the elastin.
- - Similar to collagen elastin contains covalent crosslinks derived from allysine, therefore lysyl oxidase (copper requiring enzyme) is required for the synthesis of both. Covalent crosslinks differ in that desmosine is present in elastin but not collagen.
- - Collagen fibers are tough with high tensile strength, but elastin can be stretched, its subunit polypeptide is tropoelastin. Crosslinks of lysine and allysine covalentley linked in a demosine crosslink.
- - Amorphous elastin is surrounded by microfibrils, most important protein of which called fibrillin-1 is defective in Marfan's syndrome.
The TWO smallest proteins are:
Glycine and Alanine
- hydrophobic AA are non-polar (interior of proteins), hydrophilic and polar (found of exterior surfaces and reactive centers of enzymes)
- - small amino acids - Glycine and alanine
- - branched chain AA - valine, leucine, isoleucine
- - hydroxyl AA - serine and threonine
- - sulfur AA - cysteine and methionine
- - aromatic AA - phenylalanine, tyrosine and tryptophan
- - acidic AA - glutamate and aspartate
- - basic AA - lysine, arginine and histidine
- - Proline is a freak with nitrogen tied into a ring structure as a secondary amino group.
Unlike myoglobin, hemoglobin has:
a) a primary structure
b) a secondary structure
c) terciary structure
d) quaternary structure
- Myoglobin is monomeric, while hemoglobin has 4 subunits (the quaternary structure is how these subunits are arranged in space)
- - Proteins differ because of their distinctive number and sequence of AA residues (r-group)
- - primary structure consists of a sequence of AA linked together by covalent peptide bonds
- - secondary structure is the spatial arrangement of those polypeptides (alpha-helix, beta pleated sheets (zig-zag), beta-hairpin turns.
- - terciary structure the irregular folding of a polypeptide chain, the overall 3-D conformation (globular, fibrous, pleated sheet)
- - quaternary structure the spatial arrangements of the subunits that consist of more than one PP chain (hemoglobin and antibody molecules)
- - 3-D structure is determined with x-ray diffraction.
Patients with vitamin C deficiency (scurvy) form a collagen with insufficient:
- Hydroxylation of protyl and lysyl side chains in procollagen requires ascorbic acid (vit C). Pts with vit C deficiency form collagen with insufficient hydroxyproline that denatures at room temp. Vit C influences the formation of collagen which is the organic matrix found in dentin and cementum.
- Collagen is 25% of body protein in adults (15-20) in children (type 1 is the most abundant) it also has the most unusual AA composition 33% glycine and 10% proline
- Collagen and reticular fibers make up the stroma of all lymphoid tissues except the thymus.
Which of the following serves as a principal source of carbon for non essential amino acids?
- 10 of the nonessential AA contain carbon skeletons that can be derived from glucose (tyrosine, the 10th nonessential is synthesized by hydroxylation of the essential AA phenylalanine.
- Test the essential AAs
- Nonessential AA can be synthesized from the corresponding alpha-keto acids, an alpha-amino acid, specific transaminase enzyme and pyridoxal phosphate (these are alanine, aspartate and glutamate. Other nonessential AA are synthesized by amidation.
- AA are degraded to CO2, water and urea, first the amino nitrogen is separated from the AA (ammonia is toxis so it is converted in the urea cycle, a pathway ONLY found in the liver)
- Carbon skeletons of AA are channeled either into gluconeogenesis or into ketogenesis.
A patient suffers from phenylketouria (PKU), but cannot drink soda because (pick both that apply)
a) contains tyrosine, unable to metabolize
b) contains phenylalanine, unable to metabolize
c) needs to supplement phenylalanine levels
d) needs to supplement tyrosine levels
- contains phenylalanine, unable to metabolize
- needs to supplement tyrosine levels
- Tyrosine is formed from phenylalanine, which is an essential AA needed for growth in infants and nitrogen balance (caused by lack of dietary AA) in adults.
- Melanin, norepinephrine and epinephrine are synthesized from tyrosine.
- Albinism is caused by lack of tyrosinase (an enzyme that synthesized melanin.
All G proteins exist in 2 forms
A) an inactive GTP-bound form that acts on the effector and an active GDP form that does not
b) An active GTP-bound form that acts on the effector and an inactive GDP-bound form that does not
c) An active ATP-bound form that acts on the effector and an inactive ADP-bound form that does not
d) An inactive ATP-bound form that acts on the effector an an active ADP-bound form that does not.
All G proteins have An active GTP-bound form that acts on the effector and an inactive GDP-bound form that does not
The activity level of which enzyme controls the rate of glycolysis?
b) Phosphoglucose isomerase
d) Triose phosphate isomerase
- (PFK) is a glycolyctic enzyme that catalyzes the irreversible transfer of a phosphate from ATP to fructose-6-phosphate.
- Aldolase converts fructose-1,6-biphosphate into 3 carbon metabolites. called the "aldolytic reaction of glycolysis". Aldolase is plentiful in skeletal and heart muscle tissues.
- Fluoride inhibits enolase, decreasing pyruvate synthesis and in turn decreases bacterial acid production.
- Lactate dehydrogenase converts pyruvate to lactate (lactic acid) under anaerobic conditions.
All of the following are the most useful enzymes for the diagnosis of acute myocardial infarction EXCEPT one. Which is the exception?
a) creatine kinase (CK)
b) Lactate dehydrogenase (LDH)
c) Alanine transaminase (ALT)
d) Aspartate transaminase (AST)
- Alanine transaminase (ALT)
- Creatine kinase is the first heart enzyme to appear in the blood after heart attack, followed by AST and LDH.Some enzymes show activity in only some tissues, therefore their presence in blood plasma indicates damage to that tissue.
- Liver: Alanine transaminase (ALT) and Asparate transaminase (AST)
- Heart: Creatine kinase (CK), Lactate dehydrogenase (LDH), Aspartate Transaminase AST)
- Pancreas: Lipase and Amylase (differential diagnosis between acute pancreatitis and severe abdominal pain)
All of the following statements concerning transamination reactions are true EXCEPT one. Which is the one exception?
a) These reactions involve the transfer of amino group from one amino acid to an alpha-keto acid.
b) the enzymes that catalyze these reactions are known as transaminases or aminotransferases.
c) Glutamate and alpha-ketoglutarate are often involved in these reactions, serving as one of the AA/alpha keto acid pairs.
d) Pyridoxial phosphate (PLP), which is derived from vitamin B6, serves as the cofactor for these reactions.
e) All AA participate in these reactions at some point in their catabolism
- All AA participate in these reactions at some point in their catabolism
- This is false because serine and threonine are NOT transaminated, they are oxidatively deaminated by a dehydratase enzyme to form pyruvate and propionyl coA respectively.
- The first thing that occurs to an AA catabolized is the removal of the alpha amino group, that nitrogen is then incorporated to other compounds by transamination reactions.All transaminases require the coenzyme pyridoxial phosphate.Enzymes involved in deamination are glutamate dehydrogenase (for glutamate), histidase (for histidine) and serine hydratase (for serine and threonine)
All of the following are true of oxidative deamination reactions EXCEPT one. Which one is the EXCEPTION?
a) provide alpha-ketoacids for energy
b) provide ammonia for urea synthesis
c) occur mainly in liver and kidney
d) provide detoxification mechanism
- provide detoxification mechanism
- Deamination is an oxidative reaction that occurs under aerobic conditions in all tissues but especially in liver and kidneys. Oxidative deamination occurs primarily on glutamic acid.
- Serine and Threonine are deaminated by serine dehydratase.Glutamate dehydrogenase is an enzyme of the oxidoreductase class that catalyzes the oxidative deamination of glutamate.
Carbonic anhydrases are _____- containing enzymes that catalyze the reversible reaction between carbon dioxide hydration and bicarbonate dehydration.
- Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible reaction between carbon dioxide hydration and bicarbonate dehydration. As they both exist in equilibrium.
- Carbonic anhydrase is one of the fastest known enzymes and is found in great concentration in RBC, it enables them to transport carbon dioxide from tissues to lungs.
Which of the following components of the electron transport chain accepts only electrons?
a) FMN (flavin mononucleotide)
b) Coenzyme Q (ubiquinone)
c) Cytochrome b
- Cytochrome b
- The cytochromes accept only electrons. The other components accept hydrogen and electrons.
- The electron transport chain is (inner mitochondrial membrane) where electrons are transported to meet with oxygen from respiration. Along with oxidative phosphorylation are 2 pathways that occur continuously in all cells of the body with mitochondria.
- FMN: receives electrons from NADF and transfers them through Fe-S centers to coenzyme Q (ubiquinone). It is derived from riboflavin and NAD is derived from Niacin.
- Coenzyme Q: receives its electrons from FMN and also through Fe-S centers from FADH2, the body can synthesize it.
Which of the following is NOT an enzyme classification?
- Oxygenase is an enzyme but not a classification (it belongs to the oxidoreductase anzyme class)
- Enzymes are usually large proteins that are catalysts which bind to reactants to form a re reaction pathway that reduces the energy needed and speeds up the reaction. They are substrate specific and will only work when their active site can bind with the proper substrate.
- Oxidoreductases = redox reactions
- Transferases = transfer a functional group
- Hydrolases = cause hydrolysis
- Lyases = break C-O, C-C and C-N bonds
- Isomerases = rearrange functional groups
- Ligases = Join 2 molecules
- Inactive precursor of enzyme is a proenzyme, while the removal of the cofactor and inactivation of a protein is an apoenzyme.
Which of the following enzymes is responsible for dissolving bloodclots?
- Plasmin, which is normally found in blood as plasminogen gets activated to be converted into Plasmin which cleaves the peptide bonds in fibrin (which dissolves clots)
- Fibrinogen is a soluble protein found in plasma essential to the clotting process, it is converted to fibrin by the enzyme Thrombin.
- Prothrombin is the inactive precursor to Thrombin formed in the liver.
A zymogen is converted to the active enzyme form through which of the following ways?
a) removal of a peptide fragment
b) addition of a peptide fragment
c) addition of an amino group
d) removal of an amino group
- Removal of a peptide fragment
- Zygomens are enzymatically inactive precursors of proteolytic enzymes (enzymes that hydrolyze proteins), they are produced by the stomach and pancreas as zygomens (so they don't destroy cellular proteins) and are converted to their active form by the removal of a peptide fragment. Their secretion is mediated by the parasymp, secretin and cholecsytokinin.
- Acute pancreatitis is an example of when zymogens become active inside the cells. elastase, phospholipase A2 and trypsin produce auto-digestion of the pancreas.
- Zymogen-Active enzyme
- Pepsinogen-Pepsin (stomach)
- trypsinogen-trypsin (pancreas)
- proelastase-elastase (pancreas)
- procarboxypeptidase A and B-carboxypeptidase A and B (pancreas)
Starch molecules re broken down by enzymes known as:
- Amylases (aka Ptyalin) are Glycoside hydrolase enzymes that break down starch into glucose. They all act on alpha-1,4 glycosidic bonds.
- alpha-Amylase: major digestive enzyme in animals, both salivary and pancreatic amylases are ALPHA. They act randomly upon the starch chain yielding maltotriose, maltose, glucose and "limit dextrin" from amylopectin.
- beta-Amylase: work from non-reducing end , cleaves off 2 glucose units (maltose) at a time, catalyses the hydrolysis of the second alpha-1,4 glycosidic bond
- gamma-amylases: cleave the last alpha-1,4 glycosidic linkage , yields glucose and cleaves alpha 1,6-glycosidic bonds.
- Limit dextrins are various branched polysaccharide fragments that remain following the hydrolysis of starch
- Dissacharides are hydrolyzed at the intestinal brush border (lactase, sucrase, maltase and alpha-dextrinase). ONLY monosaccharides are absorbed in the small intestine.
Your patients medical history says that she has von Gierke's disease. She is missing the enzyme _______, which converts _______.
a) Glucose-6-phosphatase, glucose-6-phosphatase to glucose
b) Glucose-6-phosphatase, Glucose-6-phosphatase to fructose-6-phosphatase
c) Pyruvate carboxylase, pyruvate to phosphoenolpyruvate
d) pyruvate carboxylase, pyruvate to 2-phosphoglycerate
- Glucose-6-phosphatase, glucose-6-phosphatase to glucose is the liver enzyme that is vital for release of glucose into the bloodstream from glycogen breakdown (glycogenolysis)
- G6P occurs in kidney and liver (like pyruvate carboxylase) but NOT in muscle. Glucose in muscle will be oxidized by glycolytic pathway. In the liver G6P allows Glycogenolysis to generate free glucose for maintaining glucose levels in blood.
- Gluconeogenesis is a biochemical process where glucose is made from AA but NOT FATTY ACIDS. This occurs in the liver when sources of glucose are exhausted. It typically involved conversion of lactic acid or amino acids into pyruvate or phosphoenolpyruvate, which is then converted to glucose.
- In glycolysis glucose is converted to pyruvate, in gluconeogenesis pyruvate is converted to glucose.
All of the following statements concerning allosteric enzymes are true EXCEPT one. Which one is the exception?
a) They frequently catalyze a committed step early in a metabolic pathway
b) they often have two or more subunits, each with substrate binding sites that exhibit cooperativity
c) allosteric activators cause the enzyme to bind substrate more readily
d) allosteric inhibitors cause the enzyme to bind substrate less readily
e) they follow the Michaelis-Menton kinetics
- They follow the Michaelis-Menton kinetics, this is false because allosteric enzymes usually show a complex relationship between the velocity and the substrate concentration.
- The regulation of metabolic processes is achieved through 2 mechanisms acting directly on enzymes: allosteric regulation and covalent modification.
- Allosteric regulation: allosteric enzyme has both an active site for substrate and allosteric site for effector (non-active site) (negative and positive effectors decrease and increase catalytic activity respectively). Effectors cause conformational changes.
- Covalent modification: (the reversible covalent modification of an enzyme), enzyme phosphorylation is the most common form of covalent modification.
What is the substrate for glycogen synthesis?
- UDP-Glucose is the substrate for glycogen synthesis with glycogen synthase (makes 1,4 linkages in glycogen) as the main enzyme. When glucose enters the cell it is phosphorylated to glucose-6-Phosphate by hexokinase (like in glycolysis) or by glucokinase in the liver then it is reversibly converted to glucose-1-phosphate by phosphoglucomutase, which is then converted to UDP-Glucose by pyrophosphorylase.Glycogen synthase occurs in both phosphorylated and dephosphorylated forms; type A is dephosphorylated and is activated by insulin, while type B is the phosphorylated form and is activated by epinephrine in muscle and liver and glucagon in liver.
- Glycogen phosphorylase, which breaks down glycogen has 2 forms (A and B). It is activated by glucagon and epinephrine and inactivated by insulin.
Which of the following best describes and "uncompetitive inhibitor"?
a) Essentially a noncompetitive inhibitor that can bind only when the substrate is attached
b) Essentially a competitive inhibitor that can bind only when the substrate is attached
c) A noncompetitive inhibitor that can be overcome by increasing substrate concentration
d) An irreversible inhibitor (the two are synonyms
- Essentially a competitive inhibitor that can bind only when the substrate is attached
- Competitive inhibition: resembles the substrate and binds to the active site of the enzyme, the substrate is then prevented from binding. The hallmark is that the competitive inhibition can be overcome by increasing substrate concentration.
- Noncompetitive inhibition: the inhibitor and substrate can bind simultaneously (binding sites do NOT overlap). Since they do NOT compete. noncompetitive inhibitors cannot be overcome by increasing substrate concentration, they are allosteric inhibitors.
- Uncompetitive inhibition: like noncompetitive, the substrate and inhibitor will NOT overlap and have different binding sites, however the uncompetitive inhibitor will only bind to an enzyme that has a substrate already attached (ES complex).
- Mixed inhibition: inhibitor binds to a site other than the active site, but has a different affinity for the lone enzyme (E) versus the enzyme-substrate (ES) complex.
- Irreversible inhibition: Those that combine with or destroy a functional group on the enzyme essential for its activity. Classic example is COX (Cyclooxygenase) by Asprin (acetlysalicylate) inhibits production of prostaglandins.
Trypsinogen is activated either by trypsin or by the duodenal enzyme:
b) Alanine aminotransferase
d) Pancreatic lipase
- The presence of amino acids in small intestine from digestion releases cholecystokinin (CCK). This hormone causes the release of pancreatic zymogens (trypsinogen, proelastase, etc..) and the contraction of the gall bladder to deliver bile to the duodenum.
- Trypsinogen is activated either by trypsin or enteropeptidase. Trypsin can act as an activator for all zymogens of pancreatic proteases.
Which enzyme is derived from osteoblasts and its serum level rises in bone conditions with increased osteoblastic activity?
a) Lactate dehydrogenase
b) Alanine transaminase
c) Alkanine phosphatase
d) Acid Phosphatase
- Alkaline phosphatase is abundant in bone, placenta, intestine and hepatobilary system, with each system containing a different isoenzyme (bone and liver being the most abundant). The serum in the bone enzyme is present in rickets, osteomalacia, hyperparathyroidism, osteitis deformans, neoplastic diseases and healing fractures.
- Enzymes for clinical lab testings
- Plasma cholinesterase-organophosphate poisoning
- Alanine transminase (ALT)- liver disease
- gamma-glutamyl transferase (GGT)- liver and kidney bilary obstruction.
- Creatine kinase - first enzyme to appear after heart attack
- Levels of lipase and amylase elevated in acute pancreatitis and it is the main differential diagnosis tool for patients with severe abdominal pain.
Which of the following equations is correct?
a) Haloenzyme + cofactor = cohaloenzyme
b) Apoenzyme + cofactor = haloenzyme
c) Coenzyme + cofactor = enzyme
d) Coenzyme + apoenzyme = coapoenzyme
- Apoenzyme + cofactor = haloenzyme
- Cofactors (coenzymes) are organic molecules or small metal ions required for the activity of an enzyme. The cofactor binds to the associated protein (apoenzyme, the inactive enzyme) and forms the haloenzyme (fully functional)
- Ions can be Iron, copper, zinc, magnesium, nickel, potassium etc...
Which of the following functions as a coenzyme vital to tissue respiration?
a) Pyridoxial phosphate
c) Thiamine pyrophosphate
Thiamine pyrophosphate functions as an coenzyme vital to tissue respiration. It is required as a cofactor for the enzyme pyruvate dehydrogenase, which catalyzes the oxidative decarboxylation of pyruvate, to form acetyl-CoA, which then enters the Krebs cycle for generation of energy.
In your practice you see quite a few HIV/AIDS patients. These patients have a virus that has the unique ability to:
a) produce (+) ssRNA from a (-) ssRNA molecule
b) Produce (-) ssRNA from a (+) ssRNA molecule
c) Produce DNA from an mRNA molecule
d) Produce dsRNA from an ssRNA molecule.
- Produce DNA from an mRNA molecule using the enzyme reverse transcriptase (found in retroviruses) is a DNA polymerase that uses RNA as a template. The retrovirus makes cDNA (complimentary) to incorporate into host DNA.
- The drug AZT is a competitive inhibitor of HIV reverse transcriptase.
- Reverse transcriptase is one of the enzymes used in genetic engineering, in which the enzyme can be used to obtain a copy of a particular gene from the relevant mRNA
Ribosomes are surrounded by a membrane and form a separate cellular compartment.
In bacteria, they are either free-floating in the cytoplasm or attached to the plasma membrane, and in eukaryotes they are either free floating in the cytoplasm or bound to the membrane of the endoplasmic reticulum.
a) both are true
b) both are fale
c) first is true, second is false
d) first is false, second is true
- First is false, second is true
- Ribosomes are protein synthesizing machines of a cell that are catalytically active. Here, amino-acids are linked together in the order specified by mRNA to form a polypeptide chain or protein.
- 70s ribosomes are sites of protein synthesis (translation) in bacterial cells and chloroplasts, formed by two rRNA subunits (30s and 50s) and 55 proteins.
- 80s ribosomes are sites of synthesis (translation) in the cytoplasm of eukaryotes and composed of two rRNA subunits (40s and 60s) and 84 proteins.
Genetic recombination experiments depend heavily upon the action of which two enzymes?
- Restriction endonucleases and DNA ligases
- The nucleases are used to cleave both the DNA to be cloned and a plasmid DNA, then they will be joined together by the DNA Ligase (restriction enzymes are site specific).
- Southern blotting is a technique used to detect mutations in DNA and can also identify DNA restriction fragments. Combines the use of restriction enzymes and DNA probes.
- First organism used for DNA cloning was E. Coli.
All of the following are true except one, which is the exception?
a- the replication of DNA involves some RNA intermediates
b- The replication of DNA involves DNA ligase linking DNA molecules together
c- The replication of DNA requires unzipping of the DNA molecule
d- The replication of DNA involves the building of new ssDNA strand from 3' to 5'
- The replication of DNA involves the building of new ssDNA strand from 3' to 5'
- DNA polymerase reads a single strand of DNA from the 3' end to the 5' end forming a new complimentary strand from the 5' end to the 3' end. DNA polymerase forms about 1000-5000 base long multiple segments (Okazaki fragments) which are joined by DNA ligase to form a continuous strand.
- DNA polymerase can only add nucleotides to a pre-existing piece of nucleic acid primer provided by RNA polymerase.
- Topoisomerases are responsible for unwinding supercoiled DNA to allow DNA polmerase access to replicate the genetic code. The enzyme DNA gyrase then formed the supercoiled structure one for replication fork has passed.
Which of the following enzymes are NOT involved in the unwinding, unzipping and rezipping the DNA molecule during replication?
- Polymerases are used in the replication ITSELF
- The hydrolysis of DNA will yield: Phosphoric acid, Dexyribose (sugar) and Nitrogenous base (ATGC)
- The hydrolysis of RNA will yield: Phosphoric acid, Ribose (sugar) and a Nitrogenous base (AUGC)
- Helicases: unwind the helix
- Toposomoerases: Responsible for unwinding the supercoiled DNA to allow DNA polymerase access to replicate the genetic code.
Which of the following is contained in a nucleoside?
-Two of the above
-All of the above
- Two of the above, without the phosphate group is is called a nucleoside, with the phosphate group is is called a nucleotide (single base sugar phosphate). The bonds between nucleotides form polynucleotide chains, the link of the phosphate group of one and the sugar of the next is a phosphodiester bond.The catabolism of a nucleotide does not yield ATP, like the catabolism of lipids, carbs and proteins.
- Humans obtain nearly all of their pyrimidines and purines from endogenous synthesis.
Which of the following are the same in RNA and DNA molecules?
-both purines and pyrimidines
-neither purines or pyrimidines
- The purines (A and G) are the same
- In DNA the pyrimidines are T and C, while in RNA they are U and C
- The purines consumed in diet in form of DNA and RNA are excreted as Uric acid with Xanthine oxidase as the enzyme that forms it.
- UV light produces pyrimidine dimers in DNA, which then interferes with replication and transcription.
Which of the following RNA mutations is least likely to have significant effect on the product protein?
-the elimination of the third nucleotide of a codon
-the elimination of the first nucleotide of a codon
-a substitution of third nucleotide of a codon
-a substitution of the first nucleotide of a codon
- a substitution of third nucleotide of a codon, due to the "wobble effect"
- Initiation codon AUG
- Termination codons UAA, UAG, UGA
A sequence of DNA reads "A-T-T-G-C-A". How many hydrogen bonds would you expect to see holding this sequence to its complementary strand?
- 14 - 2 in each, A-T pairing and 3 in each G-C pairing
- hydrogen bonding holds the DNA double helix together.
A sequence of DNA is "T-A-G-T-A-T-C-A-T". What would the complementary RNA sequence be?
- Uracil substitutes for wherever thymine would be
- Purines are the larger of the two types
- The melting temperature of the double helix is a function of the base composition with the higher GC content (raises the melting temperature)
- A + G = T + C, sum of purines equals sum of pyridines.
All of the following statements concerning the backbone of DNA are true except one, which is the exception?
- It is constant throughout the molecule
- it consists of deoxyriboses linked by "phosphodiester bridges" or "phosphodiester bonds"
- It is hydrophobic
- It is highly polar
- It is hydrophobic, Backbone of DNA is highly hydrophilic.
- hydroxyl groups of sugar residues form hydrogen bonds with water
- backbones of RNA and DNA are highly polar
Which types of RNA is the least abundant in the cell?
- Messenger RNA
- transfer RNA
- Ribosomal RNA
- Ribosomal RNA is the most abundant, followed by transfer RNA
- Messenger RNA: (mRNA) carry genetic code from DNA nucleus to ribosomes where polypeptides are synthesized (translation), mRNA is the template for protein synthesis and contains the codon
- Transfer RNA: (tRNA) carries amino acids to ribosomes for linkage in specific orders, amino-actyl-tRNA synthase ensures correct aa is attached to tRNA with the right codon, no error checking occurs.
- Ribosomal RNA: (rRNA) major component of ribosomes, physical and chemical structures which protein molecules are actually assembled.
- Transcription: is the process which DNA serves as the template for the assembly of all RNA types, uses RNA Polymerase.
Sugars that contain aldehyde groups that are _____ to carboxylic acids are classified as ____ sugars.
- Oxidized, reducing (includes lactose, maltose, glucose, galactose and fructose)
- Reducing sugar test, used to screen for diabetes. Glucosuria is glucose in the urine cause by low insulin, high blood sugar impaired tubular reabsorption, etc...
- Sucrose is NOT a reducing sugar because it does not contain free anomeric carbon to be oxidized.
Which of the following glycosaminoglycans can be found functioning in synovial fluid?
- Hyaluronic acid
- The most abundant heteropolysaccharides in the body are glycosaminoglycans (GAGs). They are long molecules of modified disaccharides N-acetyl-galactosamine or N-acetyl-glucosamine
- Hyaluronate: synovial fluid, vitreous humor, ECM. schock absorbing and large polymers.
- Chondroitin sulfate: Cartilage, bone, heart valves. MOST ABUNDANT GAG!
- Heparin sulfate: basement membranes, components of cell surfaces. higher acetylated glucosamine than heparin.
- Heparin: Component of intracellular granules of mast cells lining skin, liver and lungs. Anticoagulant, more sulfated than heparan sulfate.
- Dermatan sulfate: skin, blood vessels, heart valves
- Keratan sulfate: Cornea, bone. MOST HETEROGENOUS.
Which intestinal enzyme breaks down the O-glycosidic bond between glucose and fructose?
-none of the above
- Final digestion of disaccharides is to get broken down to monosaccharides in the small intestine and absorbed by enterocytes.
- an O-glucosydic bond is when oxygen is involved, if nitrogen is involved it is a N-glycosidic bond.
- D-glucose is the most important of aldohexoses
Glucose, Fructose and Galactose are classified as?
- Monosaccharides (ribose, mannose, xylose), can be classified by the amount of carbons they contain (triose, tetrose, pentose and hexose, etc..)
- Aldoses have an aldehyde as their most oxidized functional group and Ketoses have a keto group.
- Naming of simple sugars is similar to the naming of amino acids, they are based on the absolute configuration of glycerolaldahyde. The symbols L and D are based on the constituents around a specific chiral carbon.
Which of the following polysaccharides is a hydrolyzed by glucan transferase?
- The 2 most important polysaccharides are starch and glycogen
- Starch: a large insoluble carb and most important energy store in plants, Large number of a-glucose, amylose is hydrolyzed by alpha amylase (parotid and pancreas)
- Glycogen: branched polymer is 10k to 40k glucose residues held together by alpha-1,4 glycosidic bonds, it is especially abundant in the liver. Its cleavage depends on glucantransferase and amylo-alpha-1,6 glucosidase.
- Cellulose: most common organic compound on earth, not digestible by humans, dietary fiber, roughage, hydrophilic bulking agent for feces
- Glycan: refers to polysaccharide and oligosaccharide.
The ground substance of the ECM is made up of:
- Type II collagen
- Type III collagen
- Proteoglycan molecules
- Proteoglycan molecules, consist of a core protein with GAGs attached in brushlike fashion. 95% polysaccharide and 5% protein.
- Functions include lubricant, EXM, being a molecular "sieve".
- Glycoproteins: serve as enzymes, hormones, antibodies and structural proteins. Part of cell membranes and involved in cell to cell interactions.
- Glycolipids: (sphingolipids) in cell membrane an extents to the outer, derived from ceramide and include cerebrosides, globosides and dangliosides (nervous tissue)
The most abundant Glycosaminoglycan in the body is.
- Keratan sulfate
- Chondroitin sulfate (chondro=cartilage), connective tissue, ground substance of blood vessels, bone and cartilage. Provides strength, flexibility and shock absorption.
- It is the ground substance of ECM provides a porous pathway for nutrients and oxygen to cells whole holding the tissue together.
- Hyaluronidase: enzyme that Splits hyaluronic acid and lowers viscosity while increasing permeability.
- Heparin contains the largest portion of sulfate (more than heparan sulfate), while hyaluronic acid contains the least portion of sulfate.
- GAGs are unbranched acidic polysaccharides that consist of repeating disaccharide units.
Dextrans are (A)____ of (B)_____ produced extracellularly by bacteria and yeast. The enzyme used to produce dextrans is (C)_____, and the substrate is (D)______. A side product of dextran production is (E)____, which is formed into (F)______ and stored intracellulary as reserve nutrients.
(C) Dextran synthase/glucosyl transferase/fructosyl transferase
- (A) polysaccharides
- (B) Glucose
- (C) glucosyl transferase (dexran sucrase)
- (D) Sucrose
- (E) Fructose
- (F) Levans (fructans)
Dextrans are polysaccharides of glucose produced extracellularly by bacteria and yeast using the enzyme glucosyl transferase
(dextran sucrase) with the substrate being sucrose (table sugar).
A few bacteria like Strep mutans produce dextran from sucrose, a sticky polymer of glucose molecules produced outside the cell wall by glucosyl transferase and forms a glucocalyx
essential for cariogenicity.
(levans) also promote adhesion to surfaces of teeth and dental plaque and they're reserve nutrients for bacteria.