EXAM 2 Flashcards
What is a catalyst?
- something that increases the rate (speed) of reaction\
- but does not under go any permanent chemical change as a result
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- but does not under go any permanent chemical change as a result
What do postive, negative and zero values mean in the gibbs energy equation?
How does delta G change when a reaction is or isnt at equilibrium?
What are ways in which an unfavorable reaction completes
What is the difference between a transition state and an activation energy state?
What are ways where an activation energy barrier can be overcome?
- Raise the temperature
- stablize the transition state (via enzyme)
What is the induced fit model?
- When a substrate binds the enzyme chages shape so that the subsrate is forced into the transition state
- accomplished via four strategies
- substrate orientation
- Straining of substrate bonds
- creating a favorable microenvironment
- covalent and/or noncovalent interacions between enzyme and substrate
What is covalent cataylsis?
- actual definition
- enzyme covalently binds the transition state (eletron transfer)
- strategy that involves covalent interactions between enzyme and substrate
What is acid base catalysis?/
- actual def
- Partial proteon transfer to the substrate
- noncovalent interactions between the enzyme and substrate
What is approximation (Catalysis strategy) ?
Remember, binding occurs in three dimensions
if eletrons and /or proteins must be exchanged, proper spatial orientation and close contact (proximity) of the reactant molecules must occur
If both pieces of the puzzle are captured and held in the proper orientation right net to each other, they are more likely to react with one and other (also known as entropy reduction)
What is eletrostatic catalysis?
stabilization of unfavorable charges on the transition state by polarizable side chains in the enzyme and/or metal ions
Why do we need proteases?
Recycling
regulation
defense
What are the qualities of chymotrypsin?
- the active site is an example of catalytic triad (repersented by yellow streaks)
- serine (S195) = a nucleophile
- Histidine (H57) = a base (proteon acceptor)
- Aspartic Aaid (D102) = an acid (proton donor)
- N terminus becomes the alkoxide ion
-
Oxyanion hole stablizes the tetrahedral intermediate (transition state)
- serine (S195)
- glycine (G193)
- Specitiy (S1) pocket determines placement of cut
- At asp 189 = trypsin
- at val 216 or val 190 = elastase
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What purposes do carbonic anhydrases serve?
- physiology releveance
- pH regulation
- Enzyme pathway regulation
- Medical application
- artifical lungs
- industrial application
- CO2 scrubbers for reduction of greenhouse gases
What are qualities for the carbonic anhydrases?
- The active site contains a ZN++ ion
- coordinated to 3 histadines and a water
- H2O facilitates the transition state
- deprontonated
- catalytic strategy of aproximation
- Entry channel determines size of substrate
- co2 is small and weakly polar
What is the reaction mechanism for Carbonic Anhydrases
- Water bind to Zn++, lowering pKa. At physiological pH, water loses a proton
- Catalytic strategy of approximation as subsrate enters
- Nucleophillic additions (add functional group to CO2_
- Release of product and regeneration of enzyme (histadine proteon shuttle)
what are the three kinestic trends possible ?
What are characteristics of a reaction rate of an irreversible reaction?
What is teh reaction rate for a reversible reaction?
What is the michaelis menten kinetics model and various varibles associated with it?
What is the michaleis mention equation and special applications of it?
What is the specificity constant and what can it tell you about your enzyme?
true of false: Michaelis-mentin kinetics can be used to describe multiple binding sites but as long as their cooperative.
what can the lineweaver-burk plot tell you?
true or false: Inhibtors must be reversible.
False; they can both reversible and irreversible
What are the three types of Reversible inhibition?
- Use nonocvalent interactions to bind
- results in
- Competitive
- Noncompetitve
- allosteric
- Uncompetitive
- allosteric
What are characteristics of competitive inhibition?
What are characteristics of Non-competitive inhibition?
What kind of inhibiton is this?
What are different irreversible inhibtors, their specficity for active sites, and their textbook examples?
What are metabolic enzymes regulated by?
- Compartmentalization = different locations
- Enzyme COncentration = On/Off switch
- Enzyme activity = Volume Control
- Hormone Signals And Second Messengers = Master regulators
What is the difference between substrate level control and feedback control?
- Substrate level acts on the reactions that created it.
- Feedback controls targers a different step in the pathway
How do activators and Inhibtors effect product formation
What are isozymes and name an example of one?
- mix and matched subunits
- Catalyze the same reaction but with different effcienceies
- TIssue specifiicty: compartmentalized isozymes
- development: temporal expression of isozymes
What are examples of reversible covalent modifications
- Add 1 functional groups to activate/inactive the enyme
- Post-translational modifications create nonproteinogenic amino acids
Common additions
- Lipids
- myristic acid and farnesyl
- Nucleic acids
- ADP-ribose
- Proteins
- ubiquitin
- Carbohydrates
- the great soure of diversity to the proteome
- O- vs. N- linakges
- Composition of sugars
- Branched vs. UNbranched
- Length of oligosaccharide
- the great soure of diversity to the proteome
- small moleules - gamma- carboxylation
- small molecules - sulfation
- ex: tyrosine and PAPs “3’ phosphoadenosine-5’ phosphosulfate” via the enzyme tyrosyl protein sulfotransferae becomees tyrosine w/ sulfor group and 3’5’ ADP
- Small molecules
- acetylation
- via NATs, KATs, KDACs
- Methylation
- activates or inactivates
- Phisphorylation
- acetylation
How does phosphorylation work?
- reversible covalent modification
- thermodynamics: ATP hydrolysis can dribe unfavorable reactions ((deltaG = -50 kh/mol)
- kinetics: PHysiologically processdictate reaction rate (msec-hrs/ rxn)
- Cell processes: ATP amounts dictated by metabolism (energy charge)
- signal transduction amplification (catalytic turnover)
- Shape and charge complementarity: each phosphate adds (-2)charge and 3+ (H-bonds)
Kinases: ADD phosphates
Phosphatases: remove phasephate
note: name of a kinase on which aminoacid the phospahte will be added
WHat is allostery?
- Allosteric binding does not occur at the active site
- Heteroallostery: effector binds at the allosteric site
- Homoallostery: cooperativity
What is the role of ACTase in metabolism?
ACTase is inhibited by CTP
BInding of CTP prefers the T/inactive state
Binding of ATP prefers the R/active state
how does enzyme amount affect protein synthesis?
- PRotein synthesis regulation on/off switch
- Two levels of control are possible
- transcription regulation @ promoters
- Hsitones control transcription
- histones acetylation promotes transcription
- histone phosphorylation rpevents transcription
- histone methylation either promotes or prevents transcription
- Euchromatin is ON open for transcription
- Heterochromatin is off closes
- no transcription
- Hsitones control transcription
- Translation regualtion @ UTRs
- mRNA levels do not correlate to proteins levels
- ex: gene silencing Argonaute without RBP protein is miRNA dependent Recruitment
- with RBP, Argonaut works with Independent miRNA recruitment
- transcription regulation @ promoters
Why is irreversible covalent modification so important ?
- PRoteolytic activation
- many important enzymes begin life as zymogens
- proteases:
- digestive enzymes
- collagenase (Development)
- Caspases (APoptosis)
- Collagen
- Blood clotting factors
- insulin/hormones
- proteases:
How does the protelyic activation of chymotrypsin occur?
What are the basic qualties of a lipid ?
- polar head group = hydrophilic
- Non polar tail = hydrophobic
- it essential a hydrocarbon + carboxyl
- Primary hydrophobic determinant
- Saturated fatty acids
- CONTAIN NO double bond
- straight
- Unsaturated fatty acids
- CONTAIN DOUBLE BONDS
- kinked or bent
- Fatty acids form micelles (ball of lipids with hydrophillic ehads on the outside and tails pointed in the inside)
How are fatty acids named?
- “n-“ =unsaturated
“cis-“ or “trans-“ = type of double bond(s), each one indicated - “nothing mention if saturated”
“delta#” after which carbond (counted from the carboxyl end) the double bond is located - Next part reperents number of carbons in hdrocarbon chain
- “an” = saturated
”en” = 1 double bond
“di-en” 2 double bonds
“tri-en” 3 double bonds
“tetra-en” 4 double bonds - “-oic acid” = protenated/acid
“oate” = deprotenated/ conju. base
IF parentheses are used
- (#:#)
- first number = number of carbons
- second number = number of double bonds
Ex: n-hexadecanoic acid
- 1 = n ; saturated
- 2= “nothing” no double bonds because saturated
- 3 = Hex ; 6 carbons
- 4 = an ; w/o double bond (saturated)
- 5 = oic acid
ALL-cis-delta9delta12delta15-octadecatrienoate
- 1 = all ; unsaturated
- 2= “cis” double present and which direction bent
- 3 = octadeca ; 18 carbons
- 4 = tri ; 3 double bonds (unsaturated)
- 5 = deprotonated (conj. base)
What are characteristics of omega fatty acids and how are they named differently
- omega-3 fatty acids
- are named for the position of the double bond closest to the methyl (omega) end of fatty acid
- two omega fatty acids cannot be synthesize by humans
- La/linoleic Ac (18:2/omega-6)
- ALA/linolenic ACID (
- ALA is inefficiently converted to two other omega fatty acids
- EPA (20:5/omega-3)
- DHA (22:6/omega-3)
- OMega fatty acids are important because
- they are used in cell membrane other imprtant lipids
- are a common energy source
- promote good health by improving cardiovascular health
What is triacycleglycerol?
polar head = glycerol
hydrophobic tails = 3 fatty tails
what are waxes?
Waxes are similiar to TAgs but have an alchol rather than a glycerol
What is archaeabacteria?
archaeal lipid membranes contain branched fatty acids
what are the three categories of cell membrane lipids foudn in lipid structures?
- phospholipids = contains phosphates
- Glycolipids = contains sugars
- Cholesterol = carbon rings
What is the general structure of phospholipids?
- common sugar alcohols added are
- amino acids
- serine
- sugar-alcohols
- inosito, glycerol
- Organics
- ethanolamine, choline,
- amino acids
- Sphingomyelin
- attaches a fatty acid to an amine
- which creates a sphingosine
What are characteristics of glycosphingolipids?
- important for ABO blood type antigens
- cell signaling
- found in plants and bacteria but rarely in animals
How do sterols apply to lipid structure ?
cholesterol adds rigity to structure
What is the lipid bilayer structure and the fluid mosaic model?
- lipid bilayer
- A 2-D liquid that allows lateral movement of proteins and lipids
- a permeability barrier
- FLuid mosaic model
- Cell membranes are made up of several different types of structures that allow for their flexible natures
- a composite of lipids, proteins, and carbohydrates
- base is the lipid bilayer
- carbohydrates decorate lipids and proteins but are only presented on the surface not in contact with the cytosol
- integral membranes proteins span the entire width of the lipid bilayer
- Peripheral membrane proteins span only part of the width of the lipid bilayer
- membrane proteins constitute ~30% of the proteasome
- Cell membranes are made up of several different types of structures that allow for there flexable natures
- asymmetrical in structure
- Cell membranes are made up of several different types of structures that allow for their flexible natures
How does the integral membrane, peripheral membranes proteins
- Integral membrane proteins
- Can be inserted cotranslational
- membrane proteins have lots of hydrophobic amino acids displayed on their surfaces
- good features for living in a hydrophobic environment
- bad feature if the cytoplasm of the cell is aqueous
- Can be inserted cotranslational
- Peripheral membranes proteins
- Membranes anchors are hydrophobic
- ex:
- S palmitocysteine
- C terminal S-faresylcysteine methyl ester
- Glycosyl phosphatidylinoitsol (GPI) anchor
What do membrane proteins do?
Receive external signals
trasnmot signals into cytoplasm
transmit signals to anoter cell
allow solutes through the membrane
help determine membrane thickness and rigidity
What accounts for membrane fluditiy and flexability?
- Lipids are 2-D fluids, allowing only lateral movement of componenets
- IN bacteria rigidity of the membrane is determined by fatty acid composition
- heavily affected by hot and cold states due to degree of saturation
- in humans, rigidity of the membrane is determined by cholesterol content
What does a glyceraldhyde look like
What does ribose look like
What does glucose look like
what does galactose look like?
what does dihydroxyacetone look like
What does ribulose look like?
What does fructose look like
What does D mannose look like?
What are the monosaccharide chemical modifications ?
- glycosides
- formed when one or more hydroxyls are replaced
- esters
- phosphorylation
- Oxidation and reduction
- alcohols
- N-linkages
- amino sugars
- nucleotides
- O linkages
- Methylation
- Toxins
What are characterisitics of fucose?
- glaactose derivative
- only L_monosaccharide made and used by mammals
- Part of A/b?o blood antigens
- excess free fucose in blood = liver damage, cancer, diabetes, heart disease
How does phosphorylation realted to modifed monosaccharides?
- Part of nucleic acids
- important reactive intermediates in carbohydrate metabolism
- adds negative charge
- phosphate from ATP
- the name tells you were to put the phospahte
How does oxiddation relate to modified monosaccharides ?
reducing sugars are oxidized at the carbonyl
make acids and alctones
(example below shows antiquated diabetes urine test)
How does reduction related to modified monosaccharides?
Reduction at the carbonyl makes alditols
sorbital can cause cataracts if it accumlates int he lens of the eye
How are aminosugars related to modifed monosaccharides ?
How are modified monosaccharides related to methylation?
Same reaction that creates polysaccharides but with a non sugar
????? literally only thing on slide look up more
How are glycosides related to modified monosaccharides ?
- Formed when one or more hydroxyls are replaced
- some important toxins are o linked glycosides
- Ouabain
- amydalin
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What are the essential monosaccharides?
What does maltose look like?
What does sucrose look like?
What does lactose look like?
WHat are the roles of polysacchrides?
- Role 1 = glucose storage
- amylopectin/ glycogen (branches) / amylose (unbranched)
- Role 2 = aids in structure
- Cellulose in plants
- chitin is the one structural polysacchride that essentially is universal
- Role 3 = protein diversity
- glycoproteins
- proteins wt > sugar Wt
- on memebranes for cell adhesion
- on soluble proteins for cell singaling
- erythropoetin is a glycoprotein for RBC prod. GlcNac indicates energy store
- Glycoaminoglycans
- dugar wt > protein wt
- repeating dissacharide unit
- sugar component of proteoglycans
- cartilage
- blood clotting
- ex
- heparin, chitin, chindrotin sulfate, keratan sulfate, and hyaluronic acid
- Mucins
- sugar wt > protein Wt
- Lubrication = protection + hydration
- glycoproteins
- note:
- glycolipids decroate cell memrbane and are used to recognize (self/other)
- One small addition can be matter of life or death
