Midterm Flashcards
Define biochemistry
The science concerned with the chemistry of biological processes
The study of life at the molecular level
The application of chemistry to the study of biological processes at the cellular and molecular levels
Describe cells
Basic building blocks of life
Smallest living unit of a cell
Grow, reproduce, use energy, adapt, respond to their environment
Most cannot be seen with naked eye
Cell may be an entire organism of may be one of billions
What are bio-molecules?
Building blocks of cell
What are the major classes of small bio-molecules?
Simple sugars
Amino acid
Nucleotide
Fatty acid
Describe amino acids
Building blocks of protein
20 commonly occurring
Contains amino group and carbonyl group and r group
What do r groups do?
Determine the chemical properties of amino acids
Describe sugars
Make up carbohydrates
Basic unit is a monosaccharide
What are the functions of sugars?
Store fuel/energy in the form of starch or glycogen
Provide energy
Supply carbon for synthesis
Form structural components in cells and tissues
Intracellular communications
Describe fatty acids
Are monocarboxylic acids and contain even numbers of C atoms
Saturated and unsaturated
Components of several lipid molecules
What are the functions of fatty acids?
Storage of fuel/energy in the form of fat
Membrane structures
Insulation
Synthesis of hormones
Define metabolism
Total sum of the chemical reactions happening in a living organism
Anabolism and catabolism
Define anabolism and catabolism
Anabolism: energy requiring biosynthetic pathways
Catabolism: degradation of fuel molecules and the production of energy for cellular function
What is true about all biochemical reactions?
All are catalyzed by enzymes
What are the primary functions of metabolism?
Acquisition and utilization of energy
Synthesis of molecules needed for cellular structures and functions
Removal of waste products
What are some frequent reactions encountered in biochemical processes?
- Nucleophilic substitution: one atom of group substituted for another
- Elimination reactions: double bond is formed when atoms in a molecule are removed
- Addition reactions: two molecules combine to form a single product (hydration reaction)
- Isomerization reactions: involve intramolecular shift of atoms or groups
- Redox: transfer of electrons from a donor to an acceptor
- Hydrolysis: cleavage of double bond by water
How do cells remain organized?
Living cells are unstable and are in steady-state
A constant flow of energy prevents them from becoming disorganized
How do cells obtain energy?
Mainly by the oxidation of bio-molecules (electrons transferred from 1 molecule to another in doing so they lose energy)
Describe the transformation of energy from the sun to heterotrophs
Sunlight is captured phototrophs
Autotrophs use energy and electrons from inorganic molecules to reduce CO2 to organic compounds (carbon from CO2)
Heterotrophs oxidize these organic carbon sources to obtain energy and carbon (carbon from organic compounds)
How does life drive unfavourable reactions forward?
Uses chemical coupling
How does the complex structure of cells maintain high internal order?
- Synthesis of bio-molecules
- Transport Across membranes
- Cell movement
- Waste removal
How much of a cell is made up of H, O, N, and C?
> 95%
What are geometric isomers?
Configuration is restricted by double bonds
Different bond connectivity
What are stereoisomers and what are the two types?
Have the same bonds and atoms, different configuration around a chiral center
Enantiomers: mirror images
Diastereomers: stereoisomers that are not mirror images
What occurs when you change the configuration of a molecule?
It alters its ability to interact with proteins and therefore its biological activity
What does free energy depend on?
Depends on temperature, change in intrinsic energy of molecules, and change in entropy
What is occurring when 🔺G >0, <0, and =0
<0: spontaneous (exergonic)
>0: energy is required (endergonic)
=0: at equilibrium
* energy released by an exergonic reaction can drive an endergonic reaction *
What do enzymes do?
Accelerate reaction rates by lowering activation energy
Define catabolic and anabolic pathways
Catabolic: release energy and are used to produce ATP
Anabolic: hydrolyse ATP to synthesize cellular molecules
Define cohesion and adhesion
Cohesion: attraction to other water molecules
- responsible for surface tension
Adhesion: attraction to other substances
- water is adhesive to any substance with which it can hydrogen bond
- adhesion to hydrophilic substances
How does water storing heat effect its physical chemistry?
High specific heat and high heat of vapourization
Define specific heat and heat of vapourization
Specific heat: amount of heat that must be absorbed or expended to change the temperature of 1g of a substance 1C
Heat of vapourization: amount of energy required to change 1g of liquid water into a gas
Is water polar or non-polar? Why?
Polar with a dipole moment
Due to difference in electronegativity between oxygen and hydrogen
What are hydrogen bonds?
Non-covalent weak interactions
One H2O molecule can form up to four hydrogen bonds between hydrogen donor and each lone pair on electron acceptor
Attractive interaction between dipoles when the positive end is a hydrogen atom bonded to an atom of high electronegativity and the negative end of the other dipole is an atom with a lone pair of electrons
Why is water a good insulator?
Lots of heat is needed to break H-bonds and raise the water temperature
Why does water participate in many chemical reactions?
It is electron rich
It is a weak nucleophile
It is present in high concentrations
Define electronegativity
A measure of the force of an atoms attraction for electrons it shares in a chemical bond with another atom
What does the attraction between a bonding pair of electrons and a nucleus depend on?
Number of protons in the nucleus
Distance from the nucleus
Amount of screening by inner electrons
How does electronegativity effect polarity?
A small electronegativity difference leads to a polar covalent bonds
A large electronegativity difference leads to an ionic bond
What unique properties does hydrogen bonding in water give rise to?
Cohesion and adhesion
High specific heat and heat of vaporization
Ice is less dense
Versatile solvent
Why is water as effective solvent?
It can form hydrogen bonds
Water clings to polar molecules causing them to be soluble in water (hydrophilic)
Water tends to exclude nonpolar molecules (hydrophobic)
Define amphipathic
Molecules that contain one or more hydrophilic regions
Ex. Lipids
What is a micelle?
Hydrophobic tails at the centre forming a ball exuding water
What is the underlying principles to the solvent properties of water?
Electrostatic attraction of unlike changes
Eg the positive dipole of water for the negative dipole of another molecule
What are the different types of interactions?
Ion-dipole: KCl dissolved in water
Dipole-dipole: ethanol dissolved in water
Dipole dipole induced: weakens and generally do not lead to solubility in water
Define pH
Expressed hydrogen ion concentration in a solution
Define acids and bases
Acids: dissociate in water to increase the concentration of H
Bases: combine with H ions when dissolved in water thus decreasing H concentration
What do buffers do?
Act as a reservoir for hydrogen ions donating or removing them from a solution as necessary
Define buffers
A weka acid plus it’s conjugate base that cause a solution to resist changes in pH when an acid or base are added
How is the effectiveness of a buffer determined?
- The pH of the solution, buffers work best within 1 pH unit above and below their pka
- The concentration of the buffer; the more present the greater the capacity
How do buffers work?
If a strong acid is added to a buffer, the base component (X-) neutralizes it and the reaction goes to completion
If a strong bases is added, the acid component (HX) neutralizes it and the reaction goes to completion
What occurs during a titration?
Adding a strong base to a weak acid solution will progressively convert more and more HA to A-
What is buffer capacity?
The ability of a solution to resist change in pH
When does the most effective buffering occur?
Solution pH=buffer pka
At this point [weak acid]=[congujage base]
What are the 6 elements of life?
C, H, N, O, P, and S
What are organic molecules?
Chains of carbon atoms with other atoms or groups attached
Why is carbon the basic building block of life?
Can form an almost infinite number of compounds as a result of its capacity to make as many as four highly stable bonds
Can be tetrahedral, trigonal, or linear
Give the definition of a molecule
2 or more atoms, covalently bonded in specific proportions according to stoichiometry with a unique geometry
What are stereoisomers?
Isomers with the same molecular formula and same connectivity of atoms but different arrangement of atoms in space
What are the two types of stereoisomers?
Enantiomers: nonsuperimposable mirror images of each other
Diasteromers: are not mirror images of each other
What are constitutional isomers?
Isomers whose atoms have a different connectivity
What is a chiral molecule?
Not superimposable on its mirror image
Can exist as a pair of enantiomers
Why is chirality important?
The binding specificity of a chiral receptor site for a chiral molecule is usually only favourable in one way
What is a Fischer projection?
2D représentation of chiral molecules
Virtical lines represent bonds that project behind the plane of the paper
Horizontal lines represent bonds that project out of the plane of the paper
What are the functions of proteins?
Catalysis Chemical storage and transport Structure Mechanical work Information storage and retrieval Intercellular communication Défense
What is an amino acid?
A compound that contains both an amino group and a carboxyl group
What is an alpha amino acid?
An amino acid in which the amino group is on the carbon adjacent to the carboxyl group
How many common amino acids have a chiral alpha carbon atom?
19/20
Which amino acids have 2 chiral carbons?
Threonine and isoleucine
What form are proteins assembled in?
L
Most carbohydrates are D
How many amino acids are S and what are the ones that are R?
19/20
Cysteine
Describe amino acids
Colourless, crystalline, water soluble substances
R group gives individuality
What are some important properties of amino acids?
- They have the capacity to polymerize
- They have interesting acid base properties
- The have varied structure and chemical functionality
- They are chiral
What are ampholytes?
Act as either an acid or a base
Zwitterions
Have extremely high melting temperatures
What is a zwitterion?
Molecules that have both a positive and negative charge
No net charge
What is the Isoelectric point?
The pH at which the zwitterion is the prédominent form
pI=1/2(pka1 + pka2)
Why does the same carboxyl group have different pka values?
The pka is related to the dissociation constant ka
The equilibrium of proton dissociation from a chemical group is influenced by its chemical environment. Thus the dissociation constant of a carboxyl group is different when it is in a different chemical environment
What are the most useful and commonly used characteristics of amino acids?
Hydrophobicity Size Charge Secondary structure preference Alcoholicity Aromaticity
Why is hydrophobicity the most important characteristic of amino acids?
It is the hydrophobic effect that drives proteins towards folding
Why does hydrophobicity drive protein folding?
Water does not like hydrophobic surfaces
When a protein folds, exposed hydrophobic side chains get buried and release water of its sad duty to sit against the hydrophobic surfaces of these side chains
What make up the secondary structures of protein?
Alpha helices, beta strands, beta turns and loops
Name some types of protein modification
- Acetylation of N-terminal
- Proline and lysine oxidized to hydroxyproline and hydroxylysine
- Carboxylation of glutamate residues
- Glycosylation
- Phosphorylation
- Farnesylation
- Post-synthesis cleavage
- Glycation
What does post-synthesis modifications to protein structure do?
Add precision to the regulation of the protein activity inside and outside the cell
What are essential amino acids?
Amino acids that the body cannot metabolize or make on its own in sufficient quantities
Must be obtained through diet
What are steric interactions?
Two atoms cannot occupy the same region of space simultaneously
When two atoms are brought very close:
- electron clouds of atoms overlap
- Paulo exclusion principle begins to apply
How are short range repulsion and interatomic distance related?
Short range repulsion has an exponential dependence on interatomjc distance
What occurs when a peptide bond is formed?
The formation of a peptide bond results in the liberation of one molecule per two amino acids condensed
Too slow to be accomplished in a living cell without the aid of enzymes
What does the fact that a peptide bond is métastable mean?
The favoured reaction at RT in aqueous solution is hydrolysis of the peptide bond
However this is very slow so catalysis can occur via acid or base and is provided by proteolytic enzymes or pro teases
Why does a peptide bond have a partial double bond characteristic?
Délocalisation of Pi electron orbitals gives it this
How does resonance effect a peptide bond?
Causes it to be rigid, planar structure
What configuration are peptide bonds generally?
Trans is favourable configuration particularly with bulky R groups
What is involved in protein synthesis?
Coupling of ATP hydrolysis is involved
What are the terminals on a polypeptide called?
Amino or N terminus
Carboxyl or C terminus
What is the difference between an amino acid residue and a free amino acid
An amino acid residue is bound to an R group
What is an oligopeotide?
Peptides with only a few AA residues
What are some characteristics of the sequences of amino acids in a protein?
A unique characteristic of every protein
Encoded by the nucleotide sequence of DNA
A form of genetic information
Read from the amino terminus to the carboxyl terminus
How does a MALDI mass spectrometer work?
Ions are generated by a laser firing at the target plate
The time of firing of the laser and the arrival time of the ions at the detector are known, the relative masses can then be calculated
Only singly charged ions are generated, other types may generate multiply charges ions
What are sequence databases?
International databases of protein sequences
What is solid-phase peptide synthesis?
A clinical, three step process
Involves the successive addition of amino acids to create a linear peptide chain
The c terminus is covalently bound to a solid support or resin during synthesis
What three chemical reactions are repeated for each amino acid added to the peptide chain?
- Deprotection
- Activation
- Coupling
What are the steps to the merrifield solid phase synthesis technique?
- Anchoring C-terminal amino acid to the support resin
2 deblocking and condensation - Release of peptide from the resin
What are the fundamental properties of biological macromolecules?
Stereospecificity Structural flexibility Multivalency Allostery Reversible covalent modifications Weak interactions Cooperativity Modularity Combinatorics Polarity p
What functions do proteins preform?
Motor proteins Structural components of cells Enzymes Antibodies Hormones Hemoglobin/myoglobin Transport proteins in blood
What determines a proteins function?
3D structure
What are the four levels of protein structure?
Primary: amino acid linear sequence
Secondary: regions of regularly repeating confirmations of the peptide chain
Tertiary: the shape of the fully folded polypeptide chain
Quaternary: arrangement of 2 or more polypeptide chains into a multi-subunit molecule
How do sequences run in an protein?
N terminus to C terminus
What does the primary structure of proteins do?
Dictates the structure and function of the protein
Where do the first five amino acids reside?
In the lysozyme
How does bond rotation effect polypeptides?
Allows them to fold in water to assume complex 3D structures
What causes the secondary structure?
Occurs due to regularly spaced hydrogen bonds
What are the most common secondary structures?
Alpha helix and beta pleated
What is true about protein helices?
Always right handed and is stable due to hydrogen bonding
What holds an alpha helix together?
Held by h bonds between the h of the NH group and the O of CO on the fourth amino acid along the chain
What is a triple helix?
Three polypeptide chains woven together
Give a strong structure
Ex collagen, connective tissue, skin, tendons, and cartilage
What is membrane spanning?
Contains hydrophobic amino acids in the central region to allow the protein to cross a bi-layer membrane
What are helical wheels?
A tool to visualize the position of amino acids around an alpha helix
Allows for quick visualization of whether a side of a helix posses specific chemical properties
What are amphipathic helices?
These helices posses hydrophilic amino acids on one side and hydrophobic residues on the other
Can be used to associate a protein to a membrane
Describe beta sheets
Common form of secondary structure
Can join very distant parts of the protein together
Very stable due to hydrogen bonding
Polypeptide chains are arranged side by side with h bonds in. Eteeen and r groups extending above and below
What is a beta barrel?
B sheets ten to twist and inclinated
The amino acids side chains inside the barrel are very often b branches or hydrophobics
Why are alpha helices and beta sheets good?
Alpha helix is of the appropriate size to fit in the major groove of DNA
Beta sheets for very well into the minor groove of DNA double helix
- can also be used in DNA binding
What are the four types of bonds found in tertiary and quaternary protein structures?
- Disulfide bridges
- Salt bridges
- Hydrogen bonding
- Hydrophobic interaction
What occurs if one of the protein forces is changed?
The proteins nature was changed as all four forces can be used for a protein to function in its specific role
Said to be denatured
What is the tertiary protein structure?
Overall 3D shape that results from the folding of a protein chain
Depends mainly on attraction of amino acid side chains
Governed by non-covalent interactions and disulfide covalent bonds
What is a proteins native state?
The shape in which a protein exists naturally in a living organism
What is the quaternary protein structure?
The way in which two or more polypeptide subunits associate to form a single 3D protein unit
Caused by non-covalent forces
What is protein dénaturation?
The loss of secondary, tertiary, or quaternary protein structure due to disruption of non-covalent interactions and/or disulfide bonds but leaves peptide bond and primary structure intact
What causes dénaturation?
Heat- the weak side chain attractions in globular proteins are easily broken by heating
Mechanical agitation
Detergents- disrupts the association of hydrophobic side chains
Organic compound- interfere with h bonding
pH change- disrupts salt bridge
Inorganic salt- disrupt salt bridge in high concentrations
What did the anfinsen experiment find?
All information necessary for folding the peptide chain into its. Stove structure is contained in the primary amino acid sequence of the peptide and the native form of a protein has the thermodynamically most stable structure
What is an example of a quaternary structure?
Hemoglobin
What are the 3 classes of proteins?
Fibrous
Globular
Membrane
Describe fibrous proteins
Elongated molecules with well defined secondary structures and function primarily in a structural role
Hold things together
Contain polypeptide chains organized parallel along a single axis, producing long fibers and large sheets
Difficult to dissolve in water due to high percentage of hydrophobic amino acids
Define globular proteins
Does most of the catalytic work
Named due to compact 3D folding
More numerous than fibrous
What is alpha keratin?
Found in hair, finger nails, claws, horns and beaks
Sequence consists of 311-314 residue alpha helical rod segments capped with non-helical N and C termini
What is beta keratin?
Contains the much more extended beta sheet structure thus are much less flexible than helical alpha keratin
Found in structures like feathers and scales of birds and reptiles
What is fibroin?
Another beta sheet found in the fivers spun by spiders
Contain long regions of anti parallel beta sheets interrupted by periodic compactly folded regions
What are richardsons classifications of globular protein?
Antiparallel alpha helix proteins
Parallel or mixed beta sheet proteins
Antiparallel bet sheet proteins
Metal and disulfide rich proteins
How are globular proteins packed?
Most polar residues face outside of the protein and interact with solvent
Most hydrophobic residues face the interior of the protein and interact with each other
Cavities provide flexibility in protein conformation and dynamics
What are the different types of motion in globular proteins?
Atomic: random within short distances and arise from kinetic energies and are a function of temperature
Collective: motions of a group of atoms as a single unit in longer distances and slower
Conformational: motions of domains or segments in proteins which may occur in response to stimuli
What is levinghals paradox?
Illustrates that proteins must only sample through limited confirmations or folded by specific pathways
How did scientists resolve the idea of specific pathways?
- Are limited number of secondary structural elements
- Elements tend to form spontaneously during the co-translational folding of a protein
- Proteins fold via so-called folding landscapes where the proteins follow pathways of folding that lead to the correct 3D shape
- Folding intermediates may be important in such folding pathways
What occurs when unfolding conditions are reverted?
Many proteins have enough information stored in their sequence of amino acids to resold back to the same tertiary structure
Some get stuck along the way
What does molten refer to?
Fluctuating nature of interactions between secondary structures
What is the driving force behind the formation of molten globules?
Hydrophobic collapse
An unfolded polypeptide chain is often unstable in water because many non-polar residues may come in contact with water
Hydrophobic groups tend to come together to avoid water
Which amino acids do not favour helix formations?
Proline and glycine
Both have tendency to form turns
What is conformational entropy?
Unfavourable energy favours random chains conformation due to burying of hydrophobic residues interacting with water
Define enthalpy conformation
Favourable energy from intramolecular side groups interaction
What is the entropy contribution from the hydrophobic effect?
Favourable energy due to the burying of hydrophobic r groups
What is the general order of folding?
- Random polypeptide: hydrophobic residues stabilized by water forming a cage like structure
- Secondary structure starts to form
- Secondary structure are formed, domains, protein folded
What is a motif?
Simple combinations of a few secondary structure elements with specific geometric arrangement
What is a domain?
Polypeptide chain or part of polypeptide chain that can fold independently in stable tertiary structures
How amino acids to domains have?
50-300
Less that 50 difficult to fold stably
More than 300 difficult to fold correctly
What is the goal of protein separation?
Pure active form using a minimum number of steps and the shortest time possible
What does the solubility of protein in a aqueous solution depend on?
Size of protein
Surface charge on protein
Polarity of protein
pH and ionic strength of the solution
What is protein purification?
Separating proteins based on their ionic properties, their sizes, hydrophobicity, and affinity for certain molecules
What are the steps in protein purification called?
Fractionation
What is ion exchange chromatography?
Beads are charged and opposite charges remain in solution
What is size exclusion chromatography?
Proteins migrate as a function of their molecular mass
What is affinity chromatography?
Proteins are separated according to their ability to bind to a specific ligand that is connected to the beads of the resin
After bound protein is eluted by a solution containing free ligand
What is SDS-polyarcylamide gel electrophoresis?
Electrophoresis carried out in the presence of sodium docecyl sulfate (SDS) which is a detergent
How does SDS-polyacrylamide gel electrophoresis work?
SDS bonds to every protein in roughly the same proportion
SDS carries a negative charge which renders the intrinsic net charge of the protein insignificant
Every protein will have the same charge to mass ratio causing all to migrate towards cathode with a rate dependent on size
Small migrate faster than larger
What is isoelectric focusing?
A procedure that allows the pI of a particular protein to be determined, and that separates protein based on their respective pI values
What is 2D electrophoresis?
Allows separation of proteins by both size and isoelectric point
Each spot represents a different protein
What does reaction rate depend on?
Concentration of reactants: higher concentration = more collisions
Température: higher temp = greater energy per collision
Environment: solvent, pH, and catalysts
What does the law of mass action state?
The rate of a reaction is proportional to the product of the concentrations of the reactants
Any reversible chemical reaction will have associates with it an equilibrium constant
What must occur for a reaction to occur?
A collision must occur
Must have sufficient energy to break the necessary bonds and be of proper orientation
What is true about the activation energy of a reverse reaction in an exothermic reaction?
Larger than that if the forward reaction
What is a reversible reaction?
Any reaction that can proceed to a significant extent both in the forward and reverse directions
Define chemical equilibrium
The rate of the back reaction becomes equal to the rate of the forward reaction and the concentration no longer change
What would you expect if K=1, <1, and >1
=1: products=reactants at equilibrium
<1: more reactants than products at equilibrium
>1: more products than reactants at equilibrium
State le châteliers principle
If a system at equilibrium is disturbed, the position of equilibrium will shift in such a way as to counteract the disturbance
What occurs when you add or remove a reactant?
Adding a reactant or product will shift the position of equilibrium away from the increase
Removing a reactant of product with shift the equilibrium towards the decrease
Define thermodynamics
The relationship among various forms of energy and how energy effects matter in the macroscopic level
Why are thermodynamics important?
Essential for understanding why macromolécules fold into their native conformations, How metabolic pathways are designed, why molecules cross biological membranes
Tell us which will go forward and which won’t
Define chemical reactions
Substances change their chemical nature by changing the way in which their constituent atoms are bonded together to form compounds
Give an example of how a chemical reaction can increase the disorder of a system
If the reaction emits heat, the heat is dispersed in the form of thermal energy in the surroundings
Produces an increase in disorder which is a requirement for spontaneous change
Define entropy
A measure of disorder associated with the atoms or molecules that make up a substance and the dispersal of energy associated with those particles
How are entropy and disorder related?
Entropy is proportional to the number of ways in which the available energy can be distributed over the atoms or molecules of a system
What is the second law of thermodynamics?
There exists a thermodynamic function called entropy, denoted S, that has the property that for any process the change in entropy of the universe is greater than or equal to zero
Distinguish between kinetics and thermodynamics
Thermodynamics characterizes the energy associated with equilibrium conditions in reactions
Kinetics describes the rate at which a reaction moves toward equilibrium
What is free energy?
A measure of the available energy in the products and reactants
🔺G = -RTlnK
What is the first law of thermodynamics?
The energy of an isolated system is constant
Define open, closed, and isolated system
Isolated: doesn’t exchange energy or matter with the outside
Closed: exchanges energy but not matter
Open: exchanges energy and matter
What are extensive properties?
Thermodynamic properties that are directly related to the amount of stuff present
What are intensive properties?
Not directly related to mass
Why does entropy decrease in water?
Tends to form ordered structure surrounding apolar molecule causing a decrease in entropy because they are so ordered
What does the Gibbs equation show?
A reaction will be spontaneous if and only if 🔺G<0
🔺G = 🔺H - T🔺S
What occurs to a reaction if 🔺G = 1, <1, >1?
=1 K=1
<0 K>1 exergonic, we can do work
>0 K<1 endergonic, need to do work in order to make the reaction occur
What are couples reactions?
A single enzyme catalyzed 2 reactions, shoving them together
If G<0 then reaction 1 is driving reaction 2
What are the general principles of coupling reactions?
If two equations are added, their energetics add
An item that appears on the left and right side of the combined equation can be cancelled
What is ATP?
The free energy currency of the cell
What does the cells capacity to carry out ATP-driven reactions depend on?
Depends on the relative concentration of ATP - the driving force for the ATP hydrolysis reaction
Why is there a maximum amount of useful work that can be obtained from a chemical reaction?
More useful work out means less heat out
The liberation of heat by a reaction may be crucially important in ensuring that the reaction causes the entropy of the universe to increase
If too much of the heat liberated us converted to useful work the reaction may lose its spontaneity and stop
How can we monitor rate of a reaction?
Can be monitored by measuring the increase in the concentration of a reaction product with time
What is a rate law?
An equation expressing the rate of a reaction in terms of the molar concentrations of the species involved in the reaction
Often found to be proportional to the molar concentrations of the reactants raised to be a simple power
Powers are he orders of the reaction
Define the instantaneous rate of reaction
The initial rate of decrease in the concentration of a reactant, or increase in the concentration of a product
What are the four important factors that effect the rate of a reaction?
Concentration of reactants
Température
Action of catalyst
Surface area of solid reactants
What is the Arrhenius equation?
K = Ae^-Ea/RT
lnK=-Ea/RT + lnAo
What is an elementary step?
Any reaction that occurs as a result of a single molecular collision
What is molecularity?
The number of molecules involved in an elementary step
What is the rate-determining step?
The slowest step
What are the different types of catalysts?
Homogeneous: the catalyst and reactants are present in the same phase
Heterogeneous: the catalyst and reactants are in different phases
How do catalysts function?
Operate by lowering the activation energy for a reaction by changing the path of the reaction
May also increase the number of effective collisions
May add intermediates to the reaction
What do enzymes do?
Play key function in controlling rates of reaction, coupling reactions, and sensing the momentary metabolic needs of the cell
What is enzyme kinetics?
Addresses the biological roles of enzymatic catalysts and quantified the remarkable functions of biological enzymes
Describe the active site
Usually groove or pocket
Substrate fits with high specificity
What do enzymes do?
- Lower activation energy of forward and reverse reaction
- Reduce the time required to reach equilibrium
- Stabilize the transition state
- Conduct a specific reaction with no side products
Define substrate
The target of the enzymes action
The molecule that will undergo chemical change as a result of the enzyme
Define enzyme activity
A measure of the enzymes catalytic effectiveness as manifested by the rate of the reaction catalyzed
Define cofactors
A component that works with the enzyme in effecting catalysis
Any chemical factors that assist the activity of an enzyme catalyzed reaction
Define coenzyme
Related to go factor but generally used to describe molecules that are derived from B-vitamins
Define enzyme kinetics
A branch of enzymology that deals with mechanism as studied by factors that affect the rate of enzyme reaction
What are the 6 classes of chemical reactions that are catalyzed by enzymes?
- Oxide-reduction (oxidoreductases)
- Transfer of chemical groups (transferases)
- Hydrolysis (hydrolases)
- Removal of chemical groups (lyases)
- Isomérisation (isomerases)
- Linking two groups together (ligases)
What do oxidoreductases do?
It is a redox enzyme
Runs glycolysis in molecules
Ex. Lactate dehydrogenase
What does transferases do?
Transfer molecules back and forth
Ex. Alanine transaminase
Give an example of hydrolases
Diphosphate phosphohydrolase
What do lyases do?
Break down large molecules into parks
Ex. Pyruvste de carboxylase
What do isomerases do?
Moves functional groups back and forth
Ex. Alanine racemase
What do ligases do?
Put things together
Need energy and another molecule
Ex. L-glutamine synthetase
Why are enzyme reactions reversible in theory but not in practice?
Low levels of one of the reactants usually pushes the equilibrium in one direction
Enzymes increase the rate but does not alter the equilibrium
What three conditions must be met in order for a chemical reaction to take place?
- Must collide
- Must be enough energy for two molecules to react
- The molecules must be oriented correctly with respect to each other
What is the transition state?
A transitory molecular structure that is no longer the substrate but not yet the product
What is the energy barrier?
Without an enzyme the substrate requires a substancial amount of energy in order to reach the activation state and react
What factors influence enzyme activity?
Temperature pH Substrate concentration Product concentration Presence of inhibitors (or activators)
How do we measure enzyme activity?
- Detection of the products
- Accumulation/utilization of a co-factor
- Coupled reaction
What is true about enzymatic reactions and velocity?
- Vo is the rate of the reaction very early in when [P] is negligible
- Vo can be obtained by taking the slope of the graph of [p] vs time
- Vo barked as a function of [E]
- Vo increases as a function of [S] until E is saturated by S
- When E is saturated with S -> Vo=Vmax
What is the michaelis mentent equation?
Vo = Vmax[S]/Km + [S]
What conditions it eh michaelis menten equation based on and what does it describe?
- Steady state assumption
- Initial velocity assumption
- Rate law
Describes the relationship between reaction rate and substrate concentration
Can explain the saturation behaviour in catalyzed reactions
Define steady state
The state during which the enzyme-substrate complex remains constant or -d[ES]/dt = 0
Pre steady state is the state during which [ES] builds up
What is he equation for forward velocity? Reverse?
Vf=k1[E][S]
Vd=K-1[ES] + K-2[ES]
What is Km?
An estimate of the dissociation constant of E from S because at equilibrium K1[E][S] = K-1[ES]
Km = k-1 + K2/ K1
Small km means tight substrate bindingg and high means weak substrate binging
What is Vmax?
Asymptotically approached as the substrate is increased never reached in reality because it requires that all enzymes are bound with substrate
What is the turnover number?
Describes the number of substrates converted into products per enzyme, per unit time
When the enzyme is saturated with substrate [s]>[Et]
K2 = Vmax/[Et] = Kcat
How do you measure how perfect an enzyme is?
Kcat/Km
V = Kcat[Et][S]
The upper limit is the diffusion limit: the rate at which E and S diffusé together
What are the two main types of inhibition?
Reversible enzyme inhibitors: enzyme activity can be recovered by removing the inhibitor
Irreversible enzyme inhibitors: inhibitor bonds covalently to enzyme which is then irreversibly inactivated
What is competitive inhibition?
I is very similar to S Compete for the same bonding site Vmax stays the same Km is increases because I can bind to E , the amount of S required to reach 1/2Vmax will increase Can be used to determine Km and Ki Km = Km(1+[I]/Ki) Ki=[E][I]/[EI]
What is Ki?
A measure of the affinity if I for E the smaller Ki the more potent the inhibition
What is uncompetitive inhibition?
I only binds to ES not the free enzyme
Vmax is decreases since some of the E is converted into an inactive ESI complex
Km is decrease since I reduces the amount of E that can participate therefore ESI shifts the E+S->ES to the reigns leading to a decrease in Km
What is noncompetitive inhibition?
I and S bind to different sites of E
Km is unchanged but Vmax is decreased
What are the three types of irreversible enzyme inhibition?
Group specific
Active site directed reagents
Suicide inhibitors
What are the three main types of catalysis found in basic reaction mechanisms?
General acid base catalysis: transfer of protons between side chains of the enzyme and the substrate
Metal ion catalysis: use metal ions for catalysis
Covalent catalysis: the formation of a transient covalent bond between the enzyme and substrate
What are the different ways metal ions can act?
Stabilisé transition state
Help orient the substrate vs enzyme
Participate in transfer of electrons/protons between enzyme and substrate
What strategies are used to modulate enzymes?
Allostery - inhibition by product - activation by substrate/cofactor Bonding of regulatory subunits Covalent modification - phosphorylation on ser/thr/tyr Degradation of enzymes Limited proteolysis
Describe allostery
Bonding of an effective molecule to a separate site on the enzyme
Inhibition by the end product of a pathway
Ex ATCase
Describe regulatory subunits
cAMP is produced from ATP by the action of adenylate cyclase
The binding of cAMP to the regulatory subunits of PKA frees the catalytic subunits that are then fully active
What is regulation by covalent modification?
Specific amino acid side chains of several enzymes are the target of covalent modification
Ex. By phosphorylation
Addition of phosphate group by protein kinases or their removal by protein phosphatases is frequently used to modulate the activity of enzymes
What is regulation of enzyme stability?
Proteins are constanly being made and destroyed
The tight regulation of protein synthesis and degradation is a key factor in the regulation of enzyme activity
Ex. Ubiquitin and polyubiquitylated proteins with proteosomes
What is limited proteolysis?
Several enzymes are initially synthesized as inactive precursors
Activation of the enzymes is done by the cleavage of a limited number of peptide bonds
Cutting reveals active site
Ex. Pancreatic trypsin inhibitor
What are carbohydrates?
- The primary energy reservoir in the biosphere
- Used for energy storage and distribution
- Biosynthetic precursors to amino acids and nucleic acids
- Used on glycoproteins as addresses for intracellular traffic
- Antigenic
- Structural and mechanical components
Define monosaccharides
Simple sugars with multiple OH groups
Describe the L and D forms of monosaccharides
In d form the configuration of the chiral carbon with the highest number comes out of the plane of the paper and points to the right
In L form points to the left
What is mutarotation?
Alpha and beta anomeric forms intercovert
What are anomers?
Cyclic sugars that differ only in position of substituents at the hemiacetak carbon
In alpha OH groups opposite side from CH2OH
In beta same side
What are five important simple monosaccharides?
Glucose Mannose Galactose Fructose Ribose
Describe monosaccharides
Generally high melting, white, crystalline solids that are soluble in water and insoluble in nonpolar solvents
Sweet tasting, digestible, and nontoxic
