Podcast
Questions and Answers
Why does the ketose family have half the number of stereoisomers compared to the aldose family for a given number of carbon atoms?
Why does the ketose family have half the number of stereoisomers compared to the aldose family for a given number of carbon atoms?
- The ketone functional group in ketoses eliminates a chiral center present in aldoses. (correct)
- Ketoses are only found in L-isomeric forms, reducing the variety.
- Cyclization of ketoses is less favorable, limiting the diversity of cyclic forms.
- Ketoses are less stable than aldoses, leading to fewer possible structures.
In a Fischer projection, horizontal lines represent bonds angled away from the viewer, while vertical lines represent bonds angled towards the viewer.
In a Fischer projection, horizontal lines represent bonds angled away from the viewer, while vertical lines represent bonds angled towards the viewer.
False (B)
During the cyclization of an aldose sugar like D-glucose, which carbon atom typically attacks the carbonyl carbon, and what new functional group is formed as a result?
During the cyclization of an aldose sugar like D-glucose, which carbon atom typically attacks the carbonyl carbon, and what new functional group is formed as a result?
The 5th carbon atom attacks the carbonyl carbon, forming a hydroxyl group.
The only triose sugar in the ketose family is ______.
The only triose sugar in the ketose family is ______.
Match the following monosaccharides with their classification:
Match the following monosaccharides with their classification:
How does the length of a saturated fatty acid affect its melting point?
How does the length of a saturated fatty acid affect its melting point?
Unsaturated fatty acids have a positive correlation between their length and melting point.
Unsaturated fatty acids have a positive correlation between their length and melting point.
What is the primary function of triacylglycerols (TAGs) in the body?
What is the primary function of triacylglycerols (TAGs) in the body?
The process of splitting a triacylglycerol into three fatty acids and glycerol is called ______.
The process of splitting a triacylglycerol into three fatty acids and glycerol is called ______.
During beta oxidation, what molecule is generated every two carbons that are cleaved from a fatty acid?
During beta oxidation, what molecule is generated every two carbons that are cleaved from a fatty acid?
If an 18-carbon fatty acid undergoes beta oxidation, how many molecules of acetyl-CoA will be produced?
If an 18-carbon fatty acid undergoes beta oxidation, how many molecules of acetyl-CoA will be produced?
Carbohydrates are better suited for long-term energy storage compared to triacylglycerols due to their higher energy density.
Carbohydrates are better suited for long-term energy storage compared to triacylglycerols due to their higher energy density.
Match the energy storage molecule with its characteristic.
Match the energy storage molecule with its characteristic.
Why do multiple branches in glycogen provide an advantage for animals?
Why do multiple branches in glycogen provide an advantage for animals?
What role do the surrounding amino acids in the enzyme pocket play in an enzymatic reaction?
What role do the surrounding amino acids in the enzyme pocket play in an enzymatic reaction?
Lipids are defined primarily by their chemical structure, particularly the presence of a glycerol backbone.
Lipids are defined primarily by their chemical structure, particularly the presence of a glycerol backbone.
What is the primary difference between amylose and glycogen in terms of structure?
What is the primary difference between amylose and glycogen in terms of structure?
In the enzymatic process represented as E + S ↔ ES → EP ↔ E + P, the conversion of ES to EP is always an irreversible reaction.
In the enzymatic process represented as E + S ↔ ES → EP ↔ E + P, the conversion of ES to EP is always an irreversible reaction.
In the omega naming system for fatty acids, the position of the last double bond is determined by counting backwards from the ______ carbon.
In the omega naming system for fatty acids, the position of the last double bond is determined by counting backwards from the ______ carbon.
In an enzymatic reaction, what is the significance of ensuring that the enzyme is regenerated at the end of the process?
In an enzymatic reaction, what is the significance of ensuring that the enzyme is regenerated at the end of the process?
Match the following characteristics with the appropriate polysaccharide:
Match the following characteristics with the appropriate polysaccharide:
In the enzymatic reaction E + S ↔ ES → EP ↔ E + P, ES and EP represent reaction ________.
In the enzymatic reaction E + S ↔ ES → EP ↔ E + P, ES and EP represent reaction ________.
Which of the following is a key distinction between ether and ester linkages in lipids?
Which of the following is a key distinction between ether and ester linkages in lipids?
Match the energy states with their relative stability and impact on the enzymatic reaction:
Match the energy states with their relative stability and impact on the enzymatic reaction:
Cis-bonded fatty acids are less common in biological systems than trans-bonded fatty acids.
Cis-bonded fatty acids are less common in biological systems than trans-bonded fatty acids.
A fatty acid is designated as 20:2n-6. What does this naming convention indicate about the fatty acid's structure?
A fatty acid is designated as 20:2n-6. What does this naming convention indicate about the fatty acid's structure?
How do enzymes increase the rate of a reaction?
How do enzymes increase the rate of a reaction?
The ΔG of a reaction provides information about the kinetics of the reaction.
The ΔG of a reaction provides information about the kinetics of the reaction.
What is the significance of geometric and electronic complementarity in enzyme-substrate interactions?
What is the significance of geometric and electronic complementarity in enzyme-substrate interactions?
Enzymes use ________ to separate and concentrate bio-components in specific subcellular sections.
Enzymes use ________ to separate and concentrate bio-components in specific subcellular sections.
Match the following terms related to enzyme function with their correct description:
Match the following terms related to enzyme function with their correct description:
What is the primary function of the active site in an enzyme?
What is the primary function of the active site in an enzyme?
Stabilizing the transition state too much can increase the efficiency of an enzyme.
Stabilizing the transition state too much can increase the efficiency of an enzyme.
Besides expression or substrate availability, what other mechanism provides a layer of control over enzyme activity?
Besides expression or substrate availability, what other mechanism provides a layer of control over enzyme activity?
Which of the following is NOT a general characteristic of enzyme binding sites?
Which of the following is NOT a general characteristic of enzyme binding sites?
To react, molecules need to collide with high enough ________ and the correct orientation.
To react, molecules need to collide with high enough ________ and the correct orientation.
In a Lineweaver-Burk plot, what does the slope of the line represent?
In a Lineweaver-Burk plot, what does the slope of the line represent?
$V_{max}$ is a constant value published for every enzyme, as it is an intrinsic property of the enzyme itself, independent of experimental conditions.
$V_{max}$ is a constant value published for every enzyme, as it is an intrinsic property of the enzyme itself, independent of experimental conditions.
Define the term 'turnover number' ($K_{cat}$) in enzyme kinetics.
Define the term 'turnover number' ($K_{cat}$) in enzyme kinetics.
The catalytic efficiency of an enzyme is defined as ______.
The catalytic efficiency of an enzyme is defined as ______.
Which type of reversible enzyme inhibitor binds only to the enzyme-substrate (ES) complex?
Which type of reversible enzyme inhibitor binds only to the enzyme-substrate (ES) complex?
How does a competitive inhibitor affect $K_m$ and $V_{max}$?
How does a competitive inhibitor affect $K_m$ and $V_{max}$?
Noncompetitive inhibitors impact $K_m$, but do not impact $V_{max}$.
Noncompetitive inhibitors impact $K_m$, but do not impact $V_{max}$.
Match the type of reversible inhibitor with its effect on $K_m$ and $V_{max}$.
Match the type of reversible inhibitor with its effect on $K_m$ and $V_{max}$.
Flashcards
Aldose
Aldose
Has an aldehyde functional group on its backbone.
Ketose
Ketose
Has a ketone functional group on its backbone.
Fischer Projection
Fischer Projection
Vertical lines are dashes (away), horizontal lines are wedges (towards).
Sugar Forms
Sugar Forms
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Cyclization of Aldoses
Cyclization of Aldoses
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Enzyme Pocket Geometry
Enzyme Pocket Geometry
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Enzyme Catalysis
Enzyme Catalysis
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Enzymatic Reaction Equation
Enzymatic Reaction Equation
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Enzyme Regeneration
Enzyme Regeneration
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Cofactor
Cofactor
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Amylose (Starch)
Amylose (Starch)
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Glycogen
Glycogen
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Lipids
Lipids
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Ether Linkages
Ether Linkages
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Fatty Acids
Fatty Acids
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Polyunsaturated Fatty Acid
Polyunsaturated Fatty Acid
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Omega Naming (Fatty Acids)
Omega Naming (Fatty Acids)
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Naming Fatty Acids
Naming Fatty Acids
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Saturated Fatty Acids & Melting Point
Saturated Fatty Acids & Melting Point
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Unsaturated Fatty Acids & Melting Point
Unsaturated Fatty Acids & Melting Point
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Triacylglycerols (TAGs)
Triacylglycerols (TAGs)
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Function of TAGs
Function of TAGs
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Lipolysis
Lipolysis
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Beta-oxidation
Beta-oxidation
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Carbohydrate Energy Storage
Carbohydrate Energy Storage
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Beta Oxidation: Last Step
Beta Oxidation: Last Step
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Enzyme Compartmentalization
Enzyme Compartmentalization
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Catalysts
Catalysts
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Activation Energy
Activation Energy
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Transition State
Transition State
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Enzyme Active Site
Enzyme Active Site
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Geometric and Electronic Complementarity
Geometric and Electronic Complementarity
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Enzyme Regulatory Site
Enzyme Regulatory Site
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Allostery
Allostery
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Enzyme Specificity
Enzyme Specificity
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Transition State Stabilization
Transition State Stabilization
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Lineweaver-Burke Plot
Lineweaver-Burke Plot
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Turnover Number (Kcat)
Turnover Number (Kcat)
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Catalytic Efficiency
Catalytic Efficiency
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Enzyme Inhibitor
Enzyme Inhibitor
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Competitive Inhibitor
Competitive Inhibitor
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Uncompetitive Inhibitor
Uncompetitive Inhibitor
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Noncompetitive Inhibition
Noncompetitive Inhibition
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Mixed Inhibition
Mixed Inhibition
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Study Notes
Lecture 11: Carbohydrates
- Glucose metabolism is important for respiration and energy
Functions of Carbohydrates
- Energy storage is a primary function
- Achieved with large polymers
- Protein targeting
- Proteins recognize and associate with carbohydrates
- Chains can recruit proteins to different locations
- Cell identification and recognition
- Carbohydrates act as physical structures on protein/cell/receptor surfaces
- Influence physical interactions
- Blood type determination
- Unique carbohydrate sequences on cell surfaces determine blood type
- Square/circle shapes represent carbohydrate monomers
- Differing branches represent different cell surface carbohydrates, each unique to a blood type
- Immune issues during blood mixing arise from immune cells recognizing carbohydrate chains as foreign, leading to binding interaction
Structure and Components
- Cell walls and insect shells contain carbohydrates
- Chains of carbs have structural uses
- Act as components in other biomolecules
- Antibiotics, enzyme cofactors, and nucleic acids
- Serve as Lubrication in joints
- Glucose is a monosaccharide
- Sucrose is a disaccharide
- Amylose is a polysaccharide/starch
Basic Knowledge
- Monosaccharides, disaccharides, and polysaccharides exist
- Monosaccharides have a basic cyclic ring structure
- Glucose and fructose
- Aldoses have a functional aldehyde group
- Ketoses possess a functional ketone group
- C3: triose
- C4: tetraose
- C5: Pentose
- C6: Hexose
Basic Trioses
- Trioses contain 3 carbon sugars
- Glyceraldehyde has two stereoisomers
- D and L
- The Hydroxyl is in different place in space
- Hydroxyl on right (D)
- Hydroxyl on left (L)
- Ketoses always have one less chiral center
- Dihydroxyacetone has no D or L due to the absence of a chiral center, but is a ketose.
- Vertical lines in the Fischer Projection represent dashes angled away
- Horizontal lines indicate wedges angled towards viewer
- Longer Fischer sugars can transition to cyclic molecules
Ketose Family
- Biochem generally focuses on D sugars
- Ketose family is stunted
- Dihydroxyacetone is the only triose
- Chirality dictates the unique structure names at the other two carbs
Aldose Family
- There are 8 possible hexoses instead of 4 from the ketose versions
Cyclization
- Sugars can be linear or cyclic and interconvertible
- During cyclization
- Aldoses: the carbonyl on D-glucose is the target
- The 5th carbon attacks the 1st carbon
- The carbonyl becomes a hydroxyl group and the oxygen from the 5th hydroxyl becomes part of the ring
- The oxygen shows where the anomeric carbon is
- The hydroxyl can point up or down becomes the C1 which becomes a chiral center or anomeric form
- Alpha is on the opposite side of C6
- CH2OH and OH are opposite
- Beta is on the same side as C6
- CH2OH and OH are on same side
- For D-sugars, C6 is above the ring and always the same -Alpha is down (trans) -Beta is up (cis)
- Cyclization is reversible
- Anomers interchange with mutarotation (relinearize and recyclize)
- Beta switches to Alpha
- Mutarotation requires a hydroxyl and no other group on its anomeric carbon
- In ketoses
- A 5-membered ring is smaller where the same hydroxyl attacks an earlier carbon making C2 the anomeric carbon instead of C1
- Pyranose form sugars
- Have the basic sugar structure and there is an oxygen in a ring and the rest are carbons (6 membered)
- Furan Form Sugars
- Have the same criteria as above, but 5 membered
- Most sugars will be in pyranose form but a small percentage of sugars will be in furanose form
- Furanose Sugars are unstable
- Stacked hydroxyls are unfavorable
Glycosidic Bond Formation
- Monosaccharides are combined with a glycosidic bond between monomers
- Glycosidic bonds are covalent
- Occurs between hemiacetal group of one carbohydrate
- A hydroxyl group (often C4) on another carbohydrate molecule
- condensation or dehydration occurs (water molecule is popped out)
- Notation indicates involved carbons and anomeric forms
- The name indicates carbon origin, destination, and α/β arrangement
- Example is 1-4 α-glycosidic bond
Disaccharides
- Naming scheme
- Even with beta or alpha both you indicate the numbers
- Lactose and maltose
- One monomer can relinearize and switch to alpha or beta if the reducing anomeric carbon has a hydroxyl open to change
- Sucrose
- Cannot linearize
- It would require breaking the glycosidic bond before any mutarotation
Polysaccharides
- Important for 2 different functions in biological systems through different glycosidic bonds
- Energy storage
- Protection and structure
Important Polysaccharides
Cellulose (structural polysaccharide)
- Has with β-d-glucose that provides structure in plants
- Glucose links in a β-1,4-linkage with an alternating structure
- Every other glucose flips relative to the previous one
- This occurs to maximize interactions and forms a linear chain
- Chains stack due to their structure
- Interchain happen between different chains
- Intrachain interactions happen within the one chain
- Combined interactions create lateral and vertical stabilization creating high tensile strength which makes for a very fibrous structure
Chitin (structural polysaccharide)
- It utilizes β -D-glucose polysaccharides with modifications on each glucose residue before placement, (acetamide group added on C2)
- Offers more opportunities for Hydrogen bonding because of N's
- Chitin is stronger than cellulose, providing bulk strength
- Beetles and hermit crabs make use of this structure
Energetic Polysaccharides
- Forms of glycosidic bonds distinguish energetic from structural
- B-1,4 in structural
- A-1,4 in energetic
- Lacks hydrogen-hydrogen interchain bonds
- Results in helical structures without tensile strength
Starch (amylose)
- Has α-D-glucose used for energy storage in plants
- Helical structure has roughly 8 glucose residues per turn
- Standard 1,4 linkage and no branches
- Human enzymes break α linkages to use energy
Glycogen
- Utilizes α -D-glucose for energy storage in animals
- Main linkages occur in 1,4 linkages but after 8-10 residues a 1,6 linkage occurs
- Multiple branches speed up breakdown and utilization, which benefits animals
- Enzymes bind to non-reducing ends
- Rate of glucose release is faster
- Human enzymes more easily break alpha linkages
Lecture 12: Lipids
- Lipids have organic compounds not soluble in water
- Classifying characteristic based on solubility and not structure
Lipid Uses
- For a variety of options based on structure
- Energy storage: longer term compared to carbohydrates
- Structural components: found in cell membrane
- Signaling molecules: exist intracellulary and intercellulary
- Storage lipids have neutral charge
- phospholipids, sphingolipids are some of the membrane lipids
Ether vs Ester Linkages
- Ether more difficult to break
Fatty Acids
- Carboxylic acids
- Aliphatic chains
- Can be saturated or unsaturated according to bonds
- Polyunsaturated contains more than one double bond
- Cis-bonded more common than trans
Naming Fatty Acids
- Use omega naming - Number carbons in fatty acid (from eg. 18 - Number of double bonds (eg. 3) - Position of the last bond (eg. 3) - Omega carbon is last carbon in the chain, count backwards from the omega carbon to find the first carbon in double bond. Example: 18:3n-3 3 Double bond 3 Omega carbon
Fully Saturated Fatty Acid
- 18:0 is example
Melting Points
- Saturated
- Positively correlated
- Longer length the higher the melting point
- Unsaturated
- Negatively correlated - Longer lengths lower melting point - Cis double bonds cause a bend and makes it harder to align with each other - Less stable intermolecular forces
Triacylglycerols (TAGs)
- Body stores with fatty acid
- Esters derived from glycerol and three fatty acids
- Constitutes about 90 percent of dietary lipids
- Storage - Major form of energy storage in humans - Carbs (glycogen) = short term - TAGS = long term
- Simple have one fatty acid and mixed have multiple
- Ester linkages links fatty acids to glycerol
TAG Catalysis
- Two Phases
- Lipolysis - Splits TAGS into fatty acids and a glycerol
- Fatty acid break down in beta oxidation - Oxidizes to reduce NAD/FAD and Generate acetyl-CoA - Fatty acids cycle - Depending on length of chain (more energy with longer chains) Every two carbons an Acetyl-CoA is produced The last step splits into Acetyl-CoA 18 Carbon chain yields 9 Acetyl-CoA
Energy Storage
- Carbohydrates
- Short term and hard to store
- Hydrophilic = significant increase in pressure but easier transport
- Lipids
- Long term that is easy to store
- Hydrophobic lower in osmotic pressure and harder transport
- Higher is better and lipids are better
Lipoproteins
- Lipidproteins consist of composite structres with a monolayer (tails point in) with apolipoproteins
Eicosanoids
- Hormones derived from acid
- autocrine and paracrine
- immune response
- inhibit with COX - Aspirin is example - Irreversible inhabitation that stays bound
Sterols
- subset to steroids
- global hormones and nuclear receptors
Lecture 13: Membranes
- Phospholipids bilayers
- As long as there are enough then Self assemble
- membrane permeability needs ion channels
Molecule Permeability
Small nonpolar molecules pass easily
Glycerophospholipids
- polar head structure ece
- inner fatty tail leaflet
Pip2 Signaling
- phospholipids sitting laterally in inner leaflet, they are laterally diffusing (moving around)
- can bump into Pi3K
- signals and adds phosphate to pi
Sphingolipids
- Polar head outter leaflet end
- Fatty acid Tail with scaffold and hydrophobic end
Phospholipid Diffusion
Transverse Diffusion lateral diffusion
Transverse and Lateral Diffusion
- flips from outer leaflet
- nonpolar enviornment
- simply moves from the leaflet
Diffusion Assymetry
- Cell membranes actively maintain distribution
- Cell membranes that are different in composition
- electric enviornmnets for structure
- if ps seen outside means targted for something
Maintaining Assymetry
Flippase: to inside Floppase: to outside Scarmble Indiscrimant to inside
Saturation and Temperature
Saturation: rigid Insaturation: fluid Regulation
ABOVE: heat saturated BELOW: Cold unsaturated
-
choleseterol moderates fludiity and creates bonding
-
lipid anchors exist on the surface of the cell membreane covalente
-
helps associate proteins to the membreane
Lecture 14: Enzymes
- Oxidation of glucose with enzymes is highly exergonic
- Catalysis for protein
Comparentailization
- Bio comparents that have processing efficency increases metabolites and have correct enyzme
Catalyst
- Catalyst lowers actovation enegry becoming products
- activation energy is high when the reaction has to go pass through transitions
Enzyme Sites
- Binding or catalytic +Substrate +geometric and binding
Regulatory
- Binding molecules
- change efficiencies
- prodes a third ayer
Characteristics
Alloestery changes activity spaces that are small complentariy
Design Challenge
- binds to target - bings w solution - soltion to stable target
The Enyzmatic Process
- Sometimes has reaction but can also go back for uncatylzed and catlyzed
- two indermediates where recycled which es > e+s is always driven which is why it works
Starts with Enymes
- always has one end - regenerated in a process - peptid
Transition
- stabilizes
- binds to product
Polypeptide
- Amino acids residues are chain Hole: Change from o has strong bond
Destaizling
- decreases activation w two ways to do it
- deastablzies
Steric Hindrandce
- binds
- hinders
- analogs w inhibitors models
Stererospecific
Steric bond with shape
- effect with systems
Reaction Specicity
limits to subsrtrrate all product types
Temperature Specifity
Temp = 37
- starts and denatures, the protein structure will be the type
- in low temp the lower effeicncy of the enzyme is in the lower amunt of sufficient molucukes from the energy
- denaturation can a lter the active site too
PH
optimal ranges with the right acitvity at 5
Enzymes
- oxidoreductases which move electron and reduces atom
- lactate
- Transferases where groups go from molecule
- functional groups where transferse
- hydrolases
- single water usage pep tide = hydro
Lyases
-
bond forms through remval
-
lyase is used forms product from subtrtes bond formation
-
isomerases where structures rearrange
Enzymes have orientation
Acidity
with rna through catalysis
- acid catalysis which donwates and stbalzie
- basic catalsis which allows high funaction
can be used to form a teiad
Covalant catalysis
- where active often forms bonds
- by nulciophile
- chanvges new
can be eleectric to chnage stabalziaiton.
metals
used cations for structre stabilization
RNaase
- non specfici cuts uracil
Histindie
acts to stable. catalylsi the reaction while lys is the phosphate. the h makes the O bcome a much better catalysr
Proeteae
use of catalysts to attack.
base:
high strengths charges where acid is present.
chymotrpysin
recognitions used to cleave peptide
Catalytic
-
His stabaizlsed
-
ser attacks ser is there bond oxyianion is stabilzed and hydrogen bonding
-
Carbonyl bond formed
-
histindone makes group water active with stabilizeation with Hist hist with base hydorcide with act stabilizeed aminos is there ser stabilizon and carbyul
all dissociates and origan
Kintetics Of Enzymes"
lecture: michel
Key facts
- enzymes used in reaction
- products and how it work
- prodices are true in the reacyion
- reaction
Assemptions
- fast and slow
- prodcuts are 0
State : whats measured for easy
what equals out from it is from system find vmx which equation
- how it affects and does it effect the product
- it increases and affects product
Linewave
we use to linear with enzyme
- turnovber rater, and to find product
Inhibition of Enymes
- interfere with subsrte
- reversubke by binding an ehzyme
What kind of Inhibition are you Non allusteric, Km up Alluesteroc Km doan Mixed Allusteric P. km
- Competitive with KM up
- Mixed is to Km
Noncompetitive Inhibition
mechanism as mixed inhibitors and can bind the same to all E or es. Km is the inhibitor disassociation
- decreases the dissociation to km and the maximum is not affevtced Mixed: a site that e bmds it is for or es.
What binds to
- COmp: e and s. uncompetition:
- e+ and s
- Non competiton bounds to both
- Mixed can eiter
Cometpeivi vs non. All steric effects Km and vMxa with el, i and es i
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