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