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NWHSU biochem exam 2

QuestionAnswer
What do enzymes do? Increase reaction rate by lowering the activation energy (Biocatalyst)
Are enzymes used up in reactions? Nope, nope!
How much of an enzyme is needed to effect a reaction? Just a small amount is necessary and can have a big effect
Enzymes vs. inorganic catalysts Very specific!, Substrate (reactant) & Reaction, Mild conditions (pH, Temp, P)
Vast majority of enzymes are.. proteins
Enzymes end with.. "-ase"
Many enzymes require what component to perform proper functioning? a non-amino acid component
Can enzymes function as polypeptides Oh, you bet!
Name for a functional enzyme Holoenzyme
Polypeptide component of an enzyme Apoenzyme
Organic substance Coenzyme
Inorganic substance Cofactor
Reaction formula without an enzyme S ---------> P
Reaction formula WITH an enzyme E + S <---> E + P OR E + S <---> ES <---> EP <---> E + P
Importance of enzyme kinetics? To help us understand and predict enzymatic reactions & factors affecting them To study the reaction rate vs [S] relationship
The independent variable.. (X) [S]
The dependent variable.. (Y) V-naught (Vo)
Non-reversible enzyme regulation includes.. (3 subtypes) Proteolytic Cleavage Hormones: insulin glucagon Proteases in digestive tract: trypsin, chymotrypsin Blood clotting cascade
Types of proteolytic cleavage hormones- insulin, glucagon proteases in digestive tract- trypsin, chymotrypsin blood clotting cascade
Glutamate Carboxylase, involved in the formation of blood clots is dependent on.. Vitamin K
cofactors required for the proper functioning of the coagulation cascade.. (blood clotting) Ca2+, phospholipid & Vitamin K
Vitamin K antagonists, competing for Vit. K binding site 1.) Dicoumarol 2.) Warfarin-> Coumadin (blood thinner)
What are glycolipids? membrane lipids carrying oligosaccharides
Example of a glycolipid blood types- determined by variations of small oligosaccharides
glycolipids are ___________ in the membrane hydrophobic
glycolipids are ___________ on the surface of RBC's hydrophilic
Lipopolysaccharides are found.. in the outer membrane of gram-negative bacteria
Lipopolysaccharides- immune system reacts to.. Lipid A (the endotoxin) of the lysed cells
Is there variation in the polysaccharide formation of lipopolysaccharides? Slight variations occur- "serotypes"
where do polysaccharides of pathogens bind? to host surface structures
The Sugar Code leads to formation of.. many unique polymers that have specific (non-covalent) interactions with binding proteins (like a lock & key!)
Reasons for multitude of oligosaccharides: 1.) large # of building block types (~20-30 monosaccharides) 2.) # of building blocks not restricted a.] alpha or beta configuration b.] 1->1, 1->2, 1->3, 1->4, 1->6 c.] # of branches, types of branches
Lectins are often.. Receptors
Lectins are proteins with.. specific binding sites for specific oligosaccharides
Lectins are specific for.. cell to cell recognition, transfer of hormone signals, adhesion between cells
Oligosaccharides (comonents of a variety of glycoproteins/glycolipids on the outer surface of plasma membranes, interact with lectins in the.. extracellular milieu
viruses that infect animal cells (think influenza, etc) bind to.. cell surface glyoproteins as the 1st step in infection
bacterial toxins (think cholera & pertussis) bind to.. surface glycolipids before entering a cell
some bacteria, like H. pylori, adhere to.. animal cells where they colonize or infect the cells
Selectins (lectins) in the plasma membrane of certain cells mediate.. cell-cell interactions like those of neutrophils with endothelial cells at an infection site
Mannose 6-phosphate receptor/lectin of the trans Golgi complex binds.. the oligosaccharide of lysosomal enzymes, targeting them for transfer into lysosomes
Functions of carbohydrates: source of energy (glucose), storage of energy, protection/shape (cell wall) & for adhesion, signaling (glycocalyx)
Carbohydrates structure: polyhydroxy-aldehydes or ketones (carbonyl groups) --> (CH2O)n, may contain P, S, N ; oligosaccharides (small polymers- aka: disaccharides, trisaccharides, etc --> nutrients) or polysaccharides (aka- very large polymers)
Ketose Any of a class of simple sugars (monosaccharides) containing a ketone group.
Aldose Any of a class of simple sugars (monosaccharides) containing a aldehyde group.
Simple sugars end in.. "ose" (for carbohydrates)
name for 3 carbon atoms.. triose
name for 4 carbon atoms.. tetrose
name for 5 carbon atoms.. pentose(one of 2 most important groups)
name for 6 carbon atoms.. hexose (one of 2 most important groups)
name for 7 carbon atoms.. heptose
D-sugar H O \ // C | H-C-OH <-- "OH" ON THE RIGHT | CH2OH aldo-triose, chiral center, D-Glyceraldehyde D-carbohydrates occur in nature
L-sugar H O \ // C | HO-C-H <-- "OH" ON THE LEFT | CH2OH L-Glyceraldehyde
Mirror images = enantiomers
Draw glucose structure.. H O \ // C | H-C-OH | HO-C-H | H-C-OH | H-C-OH <--For L-Glucose, switch H w/ OH | CH2OH D-glucose, other config combos @C2-C5 = diastereomers, total possibilies with 4 chiral C's: 2^4=16
Draw D-glyceraldehyde structure.. H O \ // C | H-C-OH {D-Aldose} | CH2OH
Draw D-Mannose structure.. H O \ // C | HO-C-H | HO-C-H | H-C-OH | H-C-OH | CH2OH {Aldose}
Draw D-Galactose structure.. H O \ // C | H-C-OH | HO-C-H | HO-C-H | H-C-OH | CH2OH {Aldose}
Draw D-Ribose (RNA) strucure.. H O \ // C | H-C-OH | H-C-OH | H-C-OH | CH2OH {Aldose}
Which structures are epimers of D-glucose? D-mannose & D-galactose (differ in configuration at the 1st carbon)
Draw Dihydroxyacetone structure.. CH2OH | C=O | CH2OH {ketose}
Draw D-fructose structure.. CH2OH | C=O | HO-C-H | H-C-OH | H-C-OH | CH2OH {ketose}
Monosaccharides with non-chiral C1 can undergo.. spontaneous cyclization where C1 becomes chiral with 2 options of configuration
Alpha cyclic structure of monosaccharide = (First carbon) C-OH in opposite direction as CH2OH (Carbon 6)
Beta cyclic structure of monosaccharide = (First carbon) C-OH in same direction as CH2OH (carbon 6)
When a linear monosaccharide becomes cyclic it is called a.. hemiacetal (aldose) or hemiketal (ketose)
Hemiacetal's & Hemiketal's are.. compounds that are derived from aldehydes and ketones, respectively
what are alpha & beta anomers? either of a pair of cyclic stereoisomers (designated α or β) of a sugar or glycoside, differing only in configuration at the reducing carbon atom
Haworth Perspective Formula.. OH & H on far right can switch places, when OH is down = alpha, when it is up = beta
what do conformational formulas do? provide possible chair forms of a molecular structure.
Disaccharides are formed when.. two monosaccharides undergo a condensation reaction which involves the elimination of a small molecule, such as water, from the functional groups only.
What happens when disaccharides undergo hydrolysis? they cleave to fro two monosaccharides
Are hydrolysis & condensation reactions enzyme catalyzed? You betcha.
Common disaccharides.. Lactose & Sucrose
Pseudonym for sucrose.. table sugar
Why are peeps lactose intolerant? due to lack of hydrolytic enzyme lactase which can break the Beta 1->4 bond
3 disaccharides? Maltose, lactose, sucrose
Maltose building blocks? glucose, alpha-configuration, 1->4 connection
Lactose building blocks? galactose & glucose, beta-configuration, 1->4 connection
Sucrose building blocks? Glucose & fructose, alpha1 & beta2 configuration, alpha1<->2Beta connection
Hemiacetal (hemiketal) formation spontaneous equilibrium, 2 possible outcomes (alpha or beta)
acetal (ketal) formation enzyme-catalyzed goes to completion, 1 outcome, (alpha, beta, 1, 2, 3...)
hemiacetal (hemiketal) rxn partners -OH + C=O (aldehyde, ketone)
Acetal (ketal) rxn partners hemiacetal (ketal) + -OH
hemiacetal (hemiketal) outcome NO H2O formation
acetal (ketal) outcome H2O formation
hemiacetal (hemiketal) breaking spontaneous
Acetal (ketal) breaking enzyme-catalyzed
Commonly used for regulatory purposes.. feedback inhibition
mechanism for feedback inhibition allosteric regulation
what type of response is typical for a multi subunit protein a sigmoid response
allosteric enzymes are.. enzymes that change their conformational ensemble upon binding of an effector, which results in an apparent change in binding affinity at a different ligand binding site.
allosteric enzymes consist of.. catalytic unit, regulatory unit, substrate & positive modulator
Where is reversible covalent modification (regulation) common? quite common in higher organisms
ATP = adenosine tri-phosphate
ADP = adenosine di-phosphateP
phosphorylation reaction.. Enz--(Protein Kinase)--> {{need to fix}} **In the reverse reaction use Protein Phosphates instead of Kinase.
Example of enzyme phosphorylation: (reversible covalent modification) Glycogen-Phosphorylase
Function of Glycogen-Phosphorylase? (reversible covalent modification) release of glucose from glycogen (glucose polymer), gets activated when the blood glucose is low
Phosphorylase Phosphatase associated with.. Insulin (blood glucose increase)
Phosphorylase kinase associated with.. (fight/flight, exercise) epinephrine, glucagon (low blood glucose)
Reversible covalent modification (regulation) typical for bacteria? Methylation
Are monosaccharides reducing agents? Are they sweet? They sure are! & Yes.
Why do we use Benedict's reagent/Fehling's reaction? it is a chemical compound that can detect glucose or fructose. (used to test for simple sugars) Only occurs when the ring opens
Reducing Sugars "rule" Sweet tasting carb's (sugars) -mono, di, trisaccharides- are reducing carbohydrates, meanwhile, polysaccharides are non-reducing
Exception to the reducing sugars "rule" Neither ring can open--> non-reducing (but tastes sweet)
Are disaccharides reducing sugars? Are they sweet? mostly yes & yes
Are trisaccharides (molasses) reducing sugars? sweet? yes & yeees
Are polysaccharides reducing? Sweet? nope & nooope
Used in clinistix? glucose oxidase, tests for presence of glucose
Glycoproteins are greater than or equal to.. oligosaccharide attached to a protein
Glycoproteins are found.. in cytoplasmic membranes & soluble proteins
Glycoprotein functioning.. functions in support, adhesion (communication & cell-cell adherence), movement and regulation.
Glycoprotein examples Blood types & Antibodies, hormones, milk proteins (secreted proteins)
Oligosaccharide linkages.. glycosidic bonds
Types of glycoconjugates proteoglycans, glycoproteins
Proteoglycan structure polysaccharide connected to 1 or more proteins
where are proteoglycans located in the extra cellular matrix
what do proteoglycans interact (non-covalently) with? glycocalyx on cell surfaces
3 types of reversible inhibition: Mixed, competitive, & noncompetitive inhibition
LB-Plot for mixed inhibition Lines intersect in the 2nd quadrant, Vmax decrease, Km increase
Noncompetitive inhibition LB-Plot Lines intersect on the x-axis, Vmax decreases, Km stays the same
Effect of pH on enzyme activity As pH increases, enzyme activity increases until it reaches an optimal point in which enzymes denatures and as pH increases, the enzyme loses its effectiveness
Effect of temperature on enzyme activity As the temperature increases, enzyme activity increases until it reaches an optimal point in which the enzyme denatures and loses its effectiveness
How do enzymes work in cells? in groups, as part of pathways or cycles
Name for product of one enzyme RXN that became the substrate of another RXN metabolites
Are all enzymes regulated in cells? Nope, only key enzymes.
Types of enzyme regulation (modulation) inhibition & activation
Enzyme regulation overview: {{Look up in notes, helpful!}}
Michaelis-Menten Equation: Vo = Vmax [S]/Km + [S]
Independent variable in MM Equation [S], ("X" variable)
Dependent variable in MM Equation Vo, ("Y" variable), the rate of rxn/velocity of rxn
Constant in the MM Equation Vmax, (theoretical maximal velocity)
In MM Equation Km is.. @ 1/2Vmax
1/2Vmax in MM Equation Km
Lineweaver Burke Equation 1/Vo = Km/Vmax * 1/[S] + 1/Vmax
Line equation Equal to the Lineweaver Burke Equation: y = mx + b y = 1/Vo m = Km/ Vmax x = 1/[S] b = 1/Vmax
Competitive inhibition LB-Plot Lines intersect @ the Y-intercept
Competitive inhibition Vmax & Km Vmax = unchanged & Km = increase
Competitive inhibition equation E + S <---> ES ---> E + P I= inhibitor, S= substrate, E= enzyme, P= product
Where does I bind in Competitive inhibition? @ the active site, thus preventing binding of S
Structure of the inhibitor in Competitive inhibition Inhibitor has a similar structure to Substrate
Uncompetitive inhibition equation E + S <---> ES <---> E + P
Uncompetitive inhibition LB-Plot Lines don't intersect
Uncompetitive inhibition Vmax & Km Both decrease
What kind of bond is commonly used in biochemistry? glycosidic bond = acetal or ketal, involving one or more carbohydrates EXAMPLES.. monosaccharide-monosaccharide monoxaccharide-lipid monosaccharide-amino acid
Types of polysaccharides: 1.) HOMOPOLYSACCHARIDES (1 type of building block- monosaccharide), can be branched or unbranched. 2.) HETEROPOLYSACCARIDES, can be branched or unbranched
Building block of a homopolysaccharide Glucose!
Detail of the reducing & nonreducing ends of a homopolysaccharide Rings & cannot be opened
How does Amylopectin react in starch? refuses to branches in starch (glycogen)
Cellulase details? 1.) Cellulase is the enzyme that breaks the B1-->4 bond in cellulose., 2.) Not found in any higher organisms, 3.) Used by ruminating animals, originates from bacteria in (rumen?)
Lactase details? breaks down a B1-->4 bond
2 heteropolysaccharides are found in the cell walls of bacteria? Muramic acid & N-acetylmuramic acid
Where is peptidoglycan found? It is a polysaccharide in bacterial cell walls, unbranched and hetero
How does peptidoglycan "kind of branch"? through cross-linking with oligopeptides
How is peptidoglycan inhibited? biosynthesis of peptidoglycan is inhibited by certain antibiotics (e.g. penicillin)
So, what's that Chitin stuff all about? Funny you asked, it is a tough, protective, semitransparent substance, primarily a nitrogen-containing polysaccharide, forming the principal component of arthropod exoskeletons and the cell walls of certain fungi.
What are glycosaminoglycans? long unbranched polysaccharides consisting of a repeating disaccharide unit.
Glycosaminoglycans: Hyaluronate details? Extracellular- a) joint lubrication b) jelly like consistency c) associated with lots of H2O
Glycosaminoglycans: Heparin details? -regulation of blood clotting (blood thinner)
Polysaccharide breakdown- Starch: (homo) monosaccharide | linkage | function ------------------------------------------- glucose | alpha 1->4 | store energy in alpha 1->6 plants
Polysaccharide breakdown- Glycogen: (homo) monosaccharide | linkage | function ------------------------------------------- glucose | alpha 1->4 | store energy in alpha 1->6 animals
Polysaccharide breakdown- Cellulose: (homo) monosaccharide | linkage | function ------------------------------------------- glucose | beta 1->4 | plant cell walls
Polysaccharide breakdown- Dextran: (homo) monosaccharide | linkage | function ------------------------------------------- glucose | beta 1->3 |biofilm formation of bacteria
Polysaccharide breakdown- Peptidoglycan: (hetero (unbranched)) monosaccharide |linkage| function ------------------------------------------- n-acetylglucosamine|B1->4 |bacteria cell walls n-acetylmuramic acid
Polysaccharide breakdown- Hyaluronate: (hetero (unbranched)) monosaccharide | linkage | function ------------------------------------------- Glucosamine | beta 1->3 |xtracellular matrix n-acetyl- | beta 1->4 |->joint lubrication glucosamine | (alt.) |
Polysaccharide breakdown- Heparin: (hetero (unbranched)) monosaccharide | linkage | function ------------------------------------------- sulfated iduronic|alpha 1->4| prevent blood acid & sulfated | | clotting glucuronic acid
Glutamate carboxylase involved in blood clotting is... Vitamin K dependent
feedback inhibition is an example of _______ inhibition. reversible, non covalent
which of the following describes the typical feedback inhibition the best? allosteric
proteases in the small intestine get activated by proteolytic cleavage of C- and/or N-termini
carbohydrates are poly ___________ compounds -hydroxy carbonyl
A heptose consists of _____ carbons 7
Mannose is a _______ of glucose epimer
The carbonyl group depicted is located on carbon #... CH2OH | C=O | H-C-OH | H-C-OH | CH2OH 2
Created by: Pbandjulia on 2013-02-26



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