Question | Answer |
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 |