Lecture 2 Flashcards
What are enzymes
biological catalysts
- all proteins except some RNAHo
By how much can a catalyst increase the rate of a reation
10^20
Rate of reaction depends on what
activation energy (delta G)
What is activation energy
amount of energy required to start the rxn
- puts reactant in same transition state
- lower for enzyme catalyzed rxn
active site in enzyme catalyzed rxn
small portion of enzyme surface where substrate is bound
substrate in enzyme catalyzed reaction
reactant binds to active site of enzyme
enzyme substrate complex
held together by hydrogen bonding, electrostatic attractions, and van der waal interactions
Lock and key model
substrate binds to portion of enzyme w complementary shape
Induced fit model
binding of substrate induced change in conformation of enzyme that results in complementary fit
How do enzymes work
- concentration of enyzme usually lower than concentration of substrate
- rate of catalyzed rxn depends on substrate concentration
when are enzymes working at max rate
at saturation when all enzymes are bound to the substrate
What factors affect rate of reaction
- temp
- pH
- enzyme concentration
- substrate concentration
- presence of controlling molecules
how doe pH affect rate or rxn
- every enzyme is most active at particular pH
- pH influences ionization of functional group
How does temp affect rate of rxn
- every enzyme has optimal temp
- increase temp = increase rate of rxn
what happens to enzymes @ high temps
noncovalent bonds begin to break which affects enzyme structure and function
at what temp do noncovalent bonds begin to break
50 - 55º c
enzyme concentration and rate of rxn
- directly proportional
- if enough substrate, enzymes will double with wil cause Vm to double
substrate concentration and rate of rxn
rate of enzyme depends on substrate concentration
- @ low substrate concentration, adding more substrate increases rate f reaction
- constant rate (vmax) is reached when enzyme is completely saturates with substrate
the higher the Km value..
the lower the affinity for substrate
the lower the Km value…
the higher the affinity for substrate
Reversible inhibitor
substance that binds to enzyme to inhibit it, but can be released
competitive inhibitor
- reversible
- binds to active site and blocks access by substrate
noncompetitive inhibitor
binds to site other than active site, inhibits enzyme by chaging conformation
irreversible inhibitor
substance that causes inhibition that cannot be reversed
competitive inhbition
substrate must compete with inhibitor for active site
- more substrate required to reach given rxn velocity
allosteric enzymes
oligomer whose biological activity is affected by other substances binding to it
- change the enzymes activity by altering conformation of 4 degree structureal
allosteric effector
substance that modifies behavior of allosteric enzyme
- can be allosteric inhibitor or activator
Zygomens
inactive precursos of enzyme where proteolytic cleavage of one or more covalent bonds transforms it into active enzyme
examples of zygomens
digestive enzymes, complement proteins, blood factors and capses in apoptosis
Chymotrypsinogen origin
- synthesized and stores in pancreas
what is Chymotrypsinogen
single polypeptide chain of 245 amino acid residues cross linked by five disulfide bonds
what happens when Chymotrypsinogen is secreted into the small intestine
the digestive enyzme trypsin cleaves a 15 unit polypeptide from the N terminal end to give it to pi-chymotrypsin
apoptotic signals
signals that initiate apoptosis - can be hormones, growth factors, viral infections, toxins, extensive DNA damage
what can get activated during apoptosis
proteases called caspases
what are regulatory proteins
when several proteins act to control the activity of other proteins in the cell
when are G proteins activated
during signal transduction once a hormone binds its receptor and the receptor activates the G protein
What is transducin
a regulatory G protein in retinal rods and cones that is involved in transduction of the visual signals
Isozymes
different structural forms of a protein that catalyze the same reaction
Cofactors
enzymes that require partners
prosthetic groups:
cofactors that are non-amino acid groups bound to enzymes
inorganic cofactors
ions permanently bound to enzymes
coenzymes
small carbon containing molecules - not permanently bound
B6 vitamins
coenzymes involved in amino group transfer from one molecule to another
- important in amino acid biosynthesis
What is a lipid
heterogenous class of naturally occurring organic compounds
are lipids soluble in water
no, they are insoluble in water, but soluble in aprotic organic solvents
open chain form lipids
fatty acids, triaglycerols, sphingolipids, phosphacylglycerols, glycolipids, lipid soluble vitamins, prostaglandins, leukotrienes, and thrombaxens
cyclic chain form lipids
cholesterol, steroid hormones, and bile acids
Fatty acids
unbranched-chain carboxylic acid, most commonly of 12 - 20 carbons
which is more rare: cis fatty acids or trans
trans
triaglycerols
ester of glycerol wirh 3 fatty acids
- can be hydroluzed by base to yield glycerol and soaps
- lipases are enzymes that hydrolyze esters in triglycerides
Phosphoacylglycerols
- second most abundant group of naturally occuring lipids - found in plant and animal membranes
Phospholipases
enzymes that hydrolyze specific bonds in phospholipids
waxes
- complex mixture if esters of long chains carboxylic acids and alcohols
- found as protective coatings for plants and animals
Sphingolipids
- contain sphingosine
- found in plants and animals
- abdundant in nervous system
- bares structureal similarity to phospholipids
Glycolipids
compound in which carb is bound to -OH of the lipid
What are most glycolipids derived from
ceramides
what are gangliosides
glycolipids with complex carb moiety that contains more than 3 sugars
Functions of membrane proteins
- transport substances across membrane
- act as receptor sites, and site of enzyme catalysis
Lipid bilayers
- polar surface of bilayer contains charged groups
- hydrophobic tails lie in the interior of the bilayer
Steroids
a group of lipids that have fused ring structure of 3 six membered rings, and 1 five membered rings
Integral proteins
embedded in lipid bilayer
perpheral proteins
only loosely associated with the membrane
Passive transport
driven by concentration gradient
simple diffusion
molecule or ions move through an opening
facilitated diffusion
molecule or ions is carried across a membrane by a carrier protein
active transport
substance moved against concentration gradient
primary active transport
transport is linked to hydrolysis of ATP or other high energy moleculee
example of primary active transport
Na/K ion pump
secondary active transport
driven by concentration gradient established by primary active transport
channel proteins
integral membrane proteins that form a channel
ion channels
channel protein with hydrophillic pores
when are gates in channel proteins opened
when protein is stimulated to change shape by chemical signal or electrical charge difference
Vitamin A
serves as site of primary photochemical reaction in vision
Vitamin D
regulates calcium (and phosphorus) metabolism
Vitamin E
serves as antioxidant, necessary for reproduction in rats and may be necessary for reproduction in humans
Vitamin K
has a regulatory function in blood clotting
Retinol
- ## vitamin A
What is a precursor for vitamin A
beta - carotene
Rhodopsin
- pigment required for vision
- active molecule is retinal reacts with the protein opsin to form rhodopsi m
what is the active molecule in retinal
vitamin a aldehyde
How does vitamin E work
as an antioxidant - traps HOO and ROO radicals formed as result of oxidation by O2 of unsaturates hydrocarbon chains in membrane phospholipids
What is the chemical composition of vitamin K
long unsaturated hydrocarbon side consisting of repeating isopropene units
What are prostaglandins
family of compounds that have 20 carbon skeleton of prostanoic acid
where was prostaglandin first discovered
in seminal fluid from a prostatwe
what is the metabolic precursor for prostalandin
arachinodonic acid (20 carbon atoms; 4 double bonds) `
Leukotrienes
- cmpnds derived from arachnidonic acid
- found in WBC
- consists of 3 conjugated double bonds
What are leukotrienes important in
constriction of smooth muscle ** ESP in lungs
what are carbohydrates
a polyhydroxyaldehyde or polyhyrdroxyjeton, or a substance that gives these compounds on hydrolysis
what are monosaccharides
a carb that cannot be hydrolyzed to a simpler carb
what is the general formula for a carb
CnH2nOn
- n can vary from 3 - 8 *
what are the simplest types of monosaccharides
trioses
what makes a cyclic hemiacetal
cyclization of sugars whihc happens to make interactions b/n funtional groups on distanct carbons
hemiketal
cyclization using C2 to C5
during cyclization, the carbonyl carbon is the new chiral center and becomes…
anomeric carbon
Sorbitol Pathway
minor pathway for glucose metabolism
- importan in uncontrolled diabetic eye where high glucose levels exist and aldose reductase activity is significant
What does rising level of sorbitol do
affects osmotic balance in lens which leads to a diabetic cataract
normal levels of glucose in the lens leads to what
aldose reductase activity is very low and very little sorbitol is formed
Glycoside
a carb in which -OH of the anomeric carbon is replaced by -OR
Glycosidic bond
bond from the anomeric carbon to the -OR group
Polysaccharide
when many monosaccharides are linked together
cellulose
- polysaccharide of glucose with Beta 1,4 glycosidic linkages
- very stable, good for structural components
Starch
-polysaccharide of glucose w alpha, 1-4- glycosidic linkages
- unbranched or moderately branched
- storage of glucose in plants
Glycogen
- highly branches polysaccharide of glucose with alpha- 1,4- glycocidic bonds and branches created by alpha - 1,6 glycosidic bonds
- storage of glucose in animals
Glycosaminoglycans
polysaccharides based on repeating dissacharide where one of the monomer is an amino sugar and the other has a negative charge due to a sulfate or carboxylate group
Heparin
natural anticoagulant
Hyaluronic acid
component of vitreous humor of the eye and lubricating fluid of the joint
Chondoitin sulfate and keratin sulfate
components of connective tissue
exergonic reactions
breakdown of complex molecules releases energu
endergonic reaction
formation of single product from smaller reactants requires energy
what it metabolism
sum total of the chemical reactions of biomolecules in an organism
anabolic reactions
complex molecules are made from simple molecules, and energy input is required
catabolic reactios
complex molecules are broken down to simpler ones and energy is released
when does ATP release a large amount of energy
when it is hydrolyzed
equation for the hydrolysis of ATP
ATP + H20 –> ADP + pi + free energy
