Biomidterm II - Nov 11th Flashcards
Describe myoglobin
- Only in cardiac myocytes and skeletal muscle fibers of vertebrates
- The major function of myoglobin is to facilitate
oxygen diffusion in muscles and act as oxygen storage - Myoglobin is not essential for muscles under normal conditions
Describe the shape / size of myoglobin
- Contain 153 amino acids (sperm whale myoglobin). First protein with known X-ray structure.
- Human myoglobin contains 154 amino acids
- Contain 8 helices: A-H and short inter helices region such as CD, EF and GH
Describe the heme group of myoglobin
- Heme is a porphyrin derivative
containing four pyrrole groups
(Proline side chain is a
pyrrolidine group) - Heme occurs in many proteins:
myoglobin, hemoglobin,
neuroglobin, cytochrome c etc - Heme sits in a hydrophobic
pocket - Oxygenation alters the
electronic state of the Fe2+-
Heme complex and causes the
color change
What helps hold heme in place in the myoglobin?
- Val E11 and Phe CD1 stabilise the heme group: The amino acids Valine (Val E11) and Phenylalanine (Phe CD1) create a hydrophobic pocket that stabilises the heme within myoglobin, ensuring it stays embedded in the protein and can bind oxygen effectively.
How do you calculate for oxygen binding property of myoglobin?
How do you calculate for oxygen binding property of myoglobin as a function of partial pressure
Describe the oxygen binding curve of myoglobin
- As more oxygen gets dissolved in the blood (pO2 increases) more myoglobin are saturated (YO2 increases)
- pO2 = the amount of total oxygen in the blood that is dissolved
- k = the partial pressure of oxygen when 50% of myoglobin are saturated (have oxygen bound to their heme group)
Describe the function of hemoglobin
*Located in red blood cells
* Structurally (homologue) related to myoglobin
*But only 18% of residues are identical in myoglobin and in the alpha or beta subunits of hemoglobin
*Functions for O2 transport
Describe hemoglobin as a tetramer
In C₂ symmetry, there is a single axis of symmetry around which the structure can be rotated by 180 degrees to yield an identical configuration
In a binding affinity curve for hemoglobin and myoglobin:
- _____ binding curve
always shows a cooperative
binding: binding of one
ligand affects the other
ligand binding sites - _____ binding curve
always shows an
independent binding:
binding of one ligand does
not affect the other ligand
binding sites
Sigmoidal
Hyperbola
Describe the Hill equation
Describe how the Hill plot tells how hemoglobin binds the first
and the next O2 so differently
Why does hemoglobin have such a binding property?
( lower O2 concentrations, low O2 binding affinity, at higher O2
concentrations, higher O2 binding affinity )
Structure and Subunit Interaction: Haemoglobin is made up of four subunits, each containing a heme group that can bind one O₂ molecule. When one O₂ molecule binds to one of these heme groups, it causes a conformational (shape) change in the haemoglobin molecule. This structural shift increases the affinity of the remaining subunits for O₂.
Describe the T and R state of hemoglobin
Haemoglobin shifts between two key structural states to manage its oxygen-binding properties:
T State (Tense State):
- This is the low-affinity form, where haemoglobin binds oxygen weakly. It’s stabilised by salt bridges and hydrogen bonds, which create a “tense” structure resistant to oxygen binding.
- The T state predominates in low-oxygen areas like body tissues, facilitating oxygen release to meet tissue demand.
R State (Relaxed State):
- In the high-affinity R state, haemoglobin binds oxygen more readily. When one oxygen molecule binds to a haemoglobin subunit in the T state, structural changes break salt bridges, shifting the entire molecule into the R state.
- This conformation is favoured in high-oxygen environments like the lungs, where haemoglobin can fully load with oxygen for transport.
Describe the role of porphyrin in hemoglobin
- Structure: Porphyrin is a ring-shaped molecule made of four pyrrole units, holding an iron (Fe²⁺) atom at its centre.
- Oxygen Binding: The iron atom binds oxygen reversibly, allowing haemoglobin to transport oxygen in the blood.
- Stabilisation: Porphyrin stabilises the iron in its Fe²⁺ state, preventing oxidation to Fe³⁺, which cannot bind oxygen.
- Conformational Changes: When oxygen binds to iron, it induces a structural shift in haemoglobin, facilitating the transition between the T (tense) and R (relaxed) states and regulating oxygen affinity.
Describe the Changes at the alpha1-beta2 interface during
the T–>R transition in hemoglobin
How do both Both alpha and beta chains C-termini form
ion pairs
(Arg 141alpha and His 146beta)
Describe the Bohr effect
The Bohr effect is a physiological phenomenon where an increase in carbon dioxide (CO₂) concentration and a decrease in pH (increased acidity) lead to a reduction in hemoglobin’s affinity for oxygen. This effect facilitates oxygen release in metabolically active tissues, where CO₂ production and acidity are high. As a result, hemoglobin delivers more oxygen to tissues that need it most, enhancing overall oxygen transport efficiency in the body.
What is the role of Bisphosphoglycerate in hemoglobin?
BPG Stabilises the T State: 2,3-bisphosphoglycerate (BPG) binds tightly to the T state of hemoglobin, occupying a specific channel and stabilising this low-affinity conformation, which shifts the equilibrium away from the high-affinity R state.
Narrowing of the Binding Channel: The binding channel for BPG in hemoglobin is much wider in the T state, allowing for effective binding, while it becomes narrower in the R state, making it difficult for BPG to bind and facilitating higher oxygen affinity.
Enhanced Oxygen Release: By stabilising the T state, BPG promotes the release of oxygen in tissues with high metabolic activity, where oxygen demand is greater, ensuring efficient oxygen delivery tailored to the physiological needs of the body.
How are O2 and CO2 transport through the blood
How many ways can CO2 be transported?
- About 7-10% of CO₂ is transported dissolved in plasma, where it remains in its molecular form.
- Approximately 20-25% of CO₂ binds to hemoglobin and other proteins, forming carbamino compounds that facilitate its transport.
- The majority, around 70-75%, is converted into bicarbonate ions through a reaction with water, allowing for efficient transport in the plasma
Describe Mutations that Alter Hb’s Structure & Function
Is there a significant overlap in between areas with sickle cell anemia and malaria? and why?
Yes, there is a significant overlap between areas affected by sickle cell anemia and malaria, particularly in sub-Saharan Africa and parts of India and the Mediterranean. This overlap exists because the sickle cell trait provides a protective advantage against malaria; individuals with the trait are less likely to suffer severe forms of the disease. As a result, the prevalence of the sickle cell trait has increased in regions where malaria is endemic, illustrating how genetic traits can evolve in response to environmental pressures.
- How many alpha-helices are there in a myoglobin protein?
- What ion does the myoglobin protein bind?
- Which amino acid holds the metal ion in the myoglobin?
- Number of α-Helices: Myoglobin contains eight α-helices (labeled A through H) that form its compact structure.
- Ion Bound by Myoglobin: Myoglobin binds an iron (Fe²⁺) ion, which is crucial for its function in oxygen binding.
- Amino Acid Holding the Metal Ion: The metal ion (iron) in myoglobin is held in place by a histidine residue, specifically the proximal histidine (His93), which coordinates directly to the iron atom in the heme group.
When the partial pressure of oxygen in venous blood is
30 torr, the YO2 value for myoglobin is ______ given
that the k value is 2.8 torr.
a) 0.55
b) 0.91
c) 2.8 torr
d) 0.95
e) none of the above
Describe carbohydrates
Describe the function of carboydrates
❑Mainly act as energy resource
❑Protection as structural materials
❑Intercellular communication
❑Stabilization of protein structures
Describe monosaccharides
Describe Aldose (containing 3 to 6 carbon atoms)
Describe Ketose (containing 3 to 6 carbon atoms)
Describe Cyclic monosaccharide structures and anomeric forms
Describe how ketose relates to D-enantiomers and epimers
Describe how Howarth projections represent sugars
Haworth projections are a two-dimensional representation of cyclic monosaccharides that effectively convey stereochemical information.
- Cyclic Structure: They depict sugars in their cyclic forms (pyranose or furanose) as flat rings, with each vertex representing a carbon atom.
- Anomeric Carbon: The anomeric carbon is clearly marked, with the orientation of the hydroxyl group indicating whether it is in the α (downward) or β (upward) configuration.
- Substituent Orientation: Other substituent groups are shown with their positions indicating stereochemistry, and hydrogen atoms are often omitted for simplicity.
Describe the Two anomeric forms of cyclic sugars
The two anomeric forms of cyclic sugars are alpha (α) and beta (β), distinguished by the orientation of the hydroxyl group (-OH) on the anomeric carbon:
- Alpha (α) Anomer: The -OH group on the anomeric carbon is positioned downward (trans to the CH₂OH group) in the Haworth projection. For example, α-D-glucose features this configuration.
- Beta (β) Anomer: The -OH group is positioned upward (cis to the CH₂OH group), as seen in β-D-glucose.
- These forms can interconvert in solution through mutarotation, where the cyclic structure temporarily opens to allow the hydroxyl group to change orientation, impacting the sugar’s properties and biological functions.
Are monosaccharides in planar confirmation?
Describe how sugars are modified to produce aldonic and uronic acids
Describe how sugars are modified to produce alditols and deoxy sugars
Describe sugar acetylation
Describe sugar phosphorylation
Describe N-Acetylneuraminic for complex modification of sugars
- N-Acetylneuraminic acid (Neu5Ac) is a nine-carbon sugar, also known as sialic acid, that plays a vital role in the modification of glycoconjugates like glycoproteins and glycolipids.
- Structure and Composition: It contains an N-acetyl group and is characterized by its cyclic form, which includes a carboxyl group, a hydroxyl group, and an acetamido group.
- Biological Significance: Neu5Ac is crucial for cell-cell recognition, immune response modulation, and neurological functions, often found at the terminal positions of glycan chains, enhancing cell adhesion and preventing immune detection.
- Complex Sugar Modification: Through the process of sialylation, Neu5Ac modifies glycoproteins and glycolipids, impacting their stability, biological activity, and overall functionality, contributing to a diverse range of glycan structures with specific biological roles
Describe how the anomeric group of a sugar can condense
with an alcohol to form alpha or beta-glycoside
Describe N-glycosidic bonds
Found in:
- Nucleotides: In DNA and RNA, an N-glycosidic bond connects the nitrogenous base (adenine, thymine, cytosine, guanine, or uracil) to the 1’ carbon of the sugar (ribose in RNA or deoxyribose in DNA).
- Glycoproteins: N-glycosidic bonds link sugars to the amino group of asparagine residues in glycoproteins, forming N-linked glycosylation.
Describe cellulose
Describe chitin
What is the main storage polysaccharide in plants?
What is the main storage polysaccharide in animals?
Glycoconjugates are molecules that consist of carbohydrates covalently bonded to other types of biomolecules, such as proteins or lipids. This combination allows glycoconjugates to play essential roles in cell recognition, signalling, and structural integrity. Key types and roles include:
Proteoglycans: These are heavily glycosylated proteins, containing large carbohydrate (glycosaminoglycan) chains. Proteoglycans are abundant in connective tissue, providing structural support and participating in cellular signalling pathways
Describe Peptidoglycans
What are the two types of bacterial cell walls?
Describe NAG and NAM
N-Acetylglucosamine (NAG): This amino sugar has a six-carbon structure with an acetyl group at the amino position. It forms part of the repeating disaccharide units in peptidoglycan, linking to NAM through β-1,4-glycosidic bonds.
N-Acetylmuramic Acid (NAM): Similar to NAG but contains a lactic acid side chain at the C3 position, NAM also alternates with NAG in the peptidoglycan structure. Its unique side chain allows for peptide cross-linking, enhancing the rigidity and strength of the bacterial cell wall.
Describe pentaglycine
Structure and Function: Pentaglycine provides flexibility and connectivity in the peptidoglycan layer, contributing to its structural integrity and rigidity.
Linkage with Lysine and D-Alanine: Pentaglycine links the side chain of a lysine (Lys) residue from one tetrapeptide to the D-alanine (D-Ala) of a neighboring tetrapeptide, forming covalent cross-links.
Cross-Linking Importance: This interaction enhances the strength and resistance of the peptidoglycan structure, which is essential for bacterial survival against osmotic pressure.
Describe penicillin as and antiobiotic and beta-lectamase as an antagonist
Penicillin is a beta-lactam antibiotic that inhibits bacterial cell wall synthesis by targeting penicillin-binding proteins (PBPs), which are essential for cross-linking peptidoglycan layers.
Beta-Lactamase Resistance: Some bacteria produce beta-lactamase enzymes that hydrolyze the beta-lactam ring in penicillin, rendering it ineffective.
Combination Therapy: To combat this resistance, penicillin is often combined with beta-lactamase inhibitors, such as clavulanic acid, which protect penicillin from degradation, enhancing its effectiveness against resistant bacteria.
This combination therapy improves the treatment of infections caused by beta-lactamase-producing bacteria, maintaining the utility of penicillin in clinical settings.
Describe glycoproteins
What are the two types of glycoproteins
- O-linked glycoproteins: carbohydrate is linked to the protein through OH group the side chain of serine, threonine or tyrosine
- N-linked glycoproteins: carbohydrate is linked to the protein through the side chain of Asparagine (N)
Describe Glycoprotein biosynthesis in Eukaryotic cells
Glycoprotein biosynthesis in eukaryotic cells involves several key steps:
- Protein Synthesis: The process begins with the transcription of the gene encoding the glycoprotein into mRNA, followed by translation into a polypeptide chain in the cytoplasm. A signal peptide directs the nascent protein to the endoplasmic reticulum (ER).
- Glycosylation: In the ER, the polypeptide undergoes co-translational translocation and folding, followed by N-glycosylation, where an oligosaccharide is attached to asparagine residues. O-glycosylation occurs in the Golgi apparatus, adding sugars to serine or threonine residues.
- Golgi Modifications and Transport: The glycoprotein is transported to the Golgi apparatus, where it undergoes further modifications and sorting for its final destination, such as the plasma membrane or secretion outside the cell.
Describe the most common form of O-linked glycoproteins
O-linked carbohydrates can include any single or short carbohydrate group linked via oxygen.
O-linked oligosaccharides specifically refer to more complex, branched sugar chains attached through oxygen, often with intricate biological roles.
Describe N-linked glycoproteins
Describe N-linked Protein Glycosylation In The ER
Describe the Biosynthesis Of N-linked Glycoproteins
Describe N-linked Glycosylation In ER And Golgi
Describe lipid functions
Describe the four classes of lipids
Describe fatty acids
Compare Saturated vs. Unsaturated Fatty Acids
When naming common biological fatty acids, if the acid is listed as 18:3n-3 what does that mean?
- The 18 = total number of carbons in the acid
- The 3 = number of double bonds
- The second 3 = position of last double bond from terminal methyl group
Describe hydrogenation of unsaturated fats
Hydrogenation Process: Hydrogenation is the chemical process of adding hydrogen to unsaturated fats, often converting oils into a more solid form. This process is typically achieved by exposing the fat to hydrogen gas at high temperatures in the presence of a metal catalyst (usually nickel).
Formation of Trans Fats: Partial hydrogenation can cause some of the natural cis configurations of double bonds in unsaturated fats to flip into trans configurations. This creates trans fats, which have a straighter molecular shape, allowing them to solidify at room temperature.
Health Implications: Trans fats are associated with negative health effects, as they can raise ____ (bad) cholesterol and lower ____ (good) cholesterol, increasing the risk of cardiovascular diseases.
LDL
HDL
Describe Triacylglycerols
Structure: Triacylglycerols (also called triglycerides) are lipid molecules consisting of three fatty acid chains attached to a glycerol backbone. Each fatty acid is linked to glycerol through an ester bond, forming a stable structure.
Function: Triacylglycerols serve as the body’s primary form of long-term energy storage. They are stored in adipose tissue and can be broken down during fasting or energy-demanding activities to release fatty acids and glycerol for fuel.
Properties: Triacylglycerols can be solid (fats) or liquid (oils) at room temperature, depending on the types of fatty acids they contain. Saturated fats are more likely to be solid, while unsaturated fats are usually liquid.
Describe Glycerophospholipids
Structure: Glycerophospholipids are composed of a glycerol backbone, two fatty acid chains, and a phosphate group that is often further modified with additional polar head groups (such as choline, ethanolamine, or serine). This amphipathic structure allows them to form bilayers in aqueous environments.
Function: They are essential components of cell membranes, contributing to membrane fluidity and integrity. The hydrophobic tails face inward, while the hydrophilic head groups face outward, creating a barrier that separates the internal and external environments of the cell.
What are the common classes of glycerophospholipids (based on their polar head group)
What are Sphingolipids and how are they important for higher animals?
Cell Membrane Structure and Fluidity: Sphingolipids, including gangliosides and ceramides, are essential for maintaining cell membrane integrity and fluidity. Their unique structures contribute to the formation of lipid rafts, which support various membrane proteins and signalling pathways, particularly in neurons.
Cell-Cell Recognition and Communication: Gangliosides play a crucial role in cell-cell interactions, mediating immune responses and neuronal communication. They serve as recognition molecules that influence how cells respond to pathogens and communicate during tissue development and repair.
Regulation of Cellular Processes: Ceramides are important for regulating processes such as apoptosis and inflammation. They act as signalling molecules that can trigger programmed cell death, crucial for tissue homeostasis, and are involved in inflammatory responses linked to diseases like obesity and neurodegeneration
Describe Sphingolipids
Structure: Sphingolipids are composed of a sphingosine backbone, a long-chain fatty acid, and a polar head group. Unlike glycerol-based lipids, sphingolipids contain a single fatty acid linked to the sphingosine through an amide bond, which gives them unique properties.
Function: They play critical roles in cellular signalling and recognition. Sphingolipids are essential components of cell membranes, particularly in the nervous system, where they contribute to the formation of myelin sheaths that insulate nerve fibres.
Types: Key subclasses of sphingolipids include ceramides, sphingomyelins (which contain a phosphocholine head group), and glycosphingolipids (which have sugar residues).
Describe cholesterol
Describe Vitamin D2 & D3 as Sterol Derivatives
Chemical Structure: Vitamin D2 (ergocalciferol) and D3 (cholecalciferol) are sterol derivatives derived from cholesterol. D2 is produced by UV irradiation of ergosterol, while D3 is synthesised in the skin upon UVB exposure.
Biological Functions: Both vitamins are essential for calcium and phosphorus metabolism, promoting bone health by enhancing the absorption of these minerals in the intestine. They regulate parathyroid hormone levels, support bone mineralisation, and help maintain bone density. Additionally, Vitamin D plays a role in immune function, influencing the activity of immune cells and reducing inflammation, which may have implications for chronic disease prevention and overall health
Just look at this
Membrane lipids are divided ____ between the inner and outer leaflet
Describe the inner v.s outer leaflet
Composition Differences: The inner and outer leaflets of the plasma membrane differ in their lipid and protein compositions. The outer leaflet predominantly contains sphingolipids and phosphatidylcholine, which contribute to a positive charge on the extracellular side. In contrast, the inner leaflet is rich in phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol, which play key roles in intracellular signalling and membrane dynamics.
Functional Roles: The distinct compositions of the leaflets contribute to their specific functions. The outer leaflet is involved in cell recognition, signalling, and interactions with the extracellular environment, while the inner leaflet is crucial for anchoring cytoskeletal proteins and facilitating intracellular communication.
Asymmetry Importance: The asymmetry between the inner and outer leaflets is vital for maintaining membrane integrity and functionality. This asymmetry affects membrane fluidity, stability, and the ability to respond to external signals, ensuring proper cellular processes such as apoptosis and vesicle trafficking
Describe fluid-like lipid bilayers
Describe glycans
= Glycans are complex carbohydrates composed of sugar molecules that are linked together to form larger structures, such as oligosaccharides and polysaccharides. They play crucial roles in biological processes, including cell recognition, signalling, and the formation of structural components in cells and tissues.
What are the three types of membrane proteins
What are the four classes of membrane anchored proteins
Describe Prenylated proteins
Describe Palmitoylated proteins
Describe Myristoylated proteins
Myristoylated proteins are proteins that have a myristoyl group (a 14-carbon saturated fatty acid) covalently attached to their N-terminal glycine residue, which helps anchor them to cell membranes. This lipid modification facilitates membrane association, influencing protein localization, stability, and interactions in various cellular processes, including signal transduction.
Describe GPI-anchored proteins
Describe integral proteins
Describe the three types of transmembrane proteins
Describe Transmembrane Segments that Contain
Either alpha-helices or beta-barrels
Describe beta-barrel proteins
Describe bacteriorhodopsin
Describe glycophorin A
Describe the topology of membrane proteins
Describe the Properties of Membrane Proteins
(alpha-helix TM Segment)
Where does N-Glycosylation occur (specific, include location parameters for the protein sequence)
Describe the roles of signal recognition particles and signal peptides in polypeptide synthesis
Describe signal peptide cleavage
Describe translocon
- Translocon embedding of TM proteins happens in four steps:
1. Signal peptide on end of chain attaches to wall of translocon
2. Protein (peptide chain) is fed through translocon until the hydrophobic stop transfer signal halts production
3. Signal peptidase cleaves the signal sequence
4. Peptide sequence moves laterally through the translocon and embeds itself into the membrane
What are the three types of vesicles involved in intracellular transport
Describe membrane fusion phase of vesicle
How do SNARE proteins participate in membrane fusion
Does the lipid membrane allow free diffusion of most substances?
What are the two types of membrane transport
Describe the two ionophores involved in passive transport
How do you calculate the electrochemical potential
Describe Kcs A
What are the five types of ATPases / transporters required for active transport
- F-Type = ATP synthase (pump proton, make ATP)
- V-Type = Pump proton into lysosomes, endosome, (for degredation reasons?) use ATP
- A-Type = found in archaea and work like F-types but pump anions instead of proteins
- ABD = Legit just pinball arms that throw molecules from one side to another
Describe Na/K ATPases
In the Na⁺/K⁺ ATPase cycle, E2-P * 2K⁺ represents a specific conformational state of the enzyme. Here’s what it means:
E2: The enzyme is in a conformation that favours the binding and release of potassium (K⁺) ions on the extracellular side of the membrane.
P: Indicates phosphorylation of the enzyme, providing energy for ion transport.
* 2K⁺: Two potassium ions are bound to the enzyme in this state, ready to be transported into the cell.
This step is part of the mechanism allowing the Na⁺/K⁺ pump to maintain ion gradients across the cell membrane.
Describe the six steps involved in the active transport done by Na/K ATPases
Describe uniporters, symporters and antiporters
Tell me what each digit means in the classification number below:
Tripsin: EC 3.4.21.4
Describe oxidoreductases
Describe transferases
Describe hydrolases
Describe lyases
Describe isomerases
Describe the general properties of enzymes
What makes enzyme catalysis highly specific?
Describe stereospecificity in enzymes
Describe chymotrypsin
Chymotrypsin is a digestive enzyme that plays a crucial role in the breakdown of proteins in the small intestine. It is a type of serine protease, meaning it cleaves peptide bonds in proteins using a serine residue in its active site.
Chymotrypsin specifically targets peptide bonds adjacent to large, aromatic amino acids such as phenylalanine, tryptophan, and tyrosine. By breaking these peptide bonds, it helps to degrade proteins into smaller peptides, which are then further broken down into amino acids by other enzymes. This process is essential for protein digestion and the absorption of amino acids, which are used for various physiological functions, including tissue repair and enzyme synthesis.
Describe enzymatic cofactors
What are the 5 mechanisms of catalysis
Metal ion catalysis: This mechanism involves the use of metal ions, often as cofactors, to facilitate the reaction. Metal ions can stabilize negative charges on transition states, participate in redox reactions, or help in the binding of substrates to the enzyme.
Proximity and orientation effects: This effect refers to the enzyme’s ability to bring substrates into close proximity and orient them correctly to increase the likelihood of a successful reaction. By concentrating the reactants and positioning them optimally, enzymes enhance reaction rates.
Preferential binding of transition state complex: Enzymes often bind the transition state of the reaction more tightly than the substrates or products. This preferential binding lowers the activation energy and makes the reaction more efficient.
Describe keto-enol tautomerisation
Describe RNase A as an acid-base catalyst.
And how many S-S in RNase A ?
- RNase A is an enzyme that acts as an acid-base catalyst in the cleavage of RNA molecules. It catalyzes the hydrolysis of the phosphodiester bond in RNA through a two-step mechanism, where His12 and His119 act as key acid-base catalysts. These histidine residues alternately donate and accept protons to facilitate the reaction, helping to stabilize the transition state.
- As for the number of S-S bonds in RNase A, there are two disulfide bonds (S-S) in its structure. These bonds help maintain the enzyme’s stable three-dimensional conformation, which is essential for its catalytic activity.
Describe the phosphate ester break in RNase A
Describe covalent catalysis
Covalent catalysis: This involves the formation of a temporary covalent bond between the enzyme and the substrate. The enzyme acts as a nucleophile and forms a covalent intermediate, which lowers the activation energy for the reaction. The enzyme then helps to break the bond and release the product.
Describe the decarboxylation of acetoacetate
Describe metal ion cofactors that act as catalysts
What are the two types of enzymes containing metal ions
How can catalysis occur through proximity and orientation effects?
Proximity and orientation effects in enzyme catalysis involve bringing substrates together and positioning them in the correct orientation within the enzyme’s active site. While simply concentrating substrates can slightly speed up a reaction (up to five times), the real catalytic benefit comes from the enzyme’s ability to properly orient the substrates. This alignment minimizes entropy and allows for more efficient bond formation or breaking, greatly reducing activation energy. By restricting substrate motion and ensuring optimal orientation, enzymes can accelerate reactions by up to 10^7 times, making them much more efficient than in solution.
How can enzymes catalyze reactions by preferentially binding the transition state
Describe the catalytic mechanism of lysozyme
How is lysozyme involved in bacterial cell walls
Describe lysozyme surfaces
What side chains are involved in substrate binding of lysozymes
What are the five steps of lysozyme catalysis via a covalent intermediate
How do you determine the polysaccharide binding sites on lysozyme
What is the structure of (NAG)4
The strong binding of the δ-lactone analog of (NAG)₄ (a tetra-saccharide derivative of N-acetylglucosamine) suggests that the D-ring of the substrate adopts a half-chair conformation when interacting with the enzyme lysozyme. This conclusion is supported by crystal structure data, which reveal that the enzyme binds the substrate in a way that forces the D-ring of the sugar to adopt this specific conformation.
In the context of the complex with lysozyme, the half-chair structure of the D-ring is crucial for the enzyme’s ability to cleave the glycosidic bond in the polysaccharide. The half-chair form of the ring is a transition-state-like structure that helps facilitate the hydrolysis reaction, as it allows for better positioning of the substrate in the active site and promotes the optimal orientation for bond cleavage. The crystal structure provides direct evidence that lysozyme’s active site stabilizes this conformation, enabling the enzyme to effectively catalyze the breakdown of the (NAG)₄ substrate.
This structural insight into the enzyme-substrate interaction highlights how enzymes can influence the conformation of their substrates, often stabilizing transition-state-like structures that are key to accelerating the reaction. The half-chair conformation of the D-ring in this case is a critical factor in the enzyme’s mechanism and efficiency in breaking down glycosidic bonds in the polysaccharide
How does mass spectrometry confirm covalent intermediates of lysozyme-NAG
How does the lysozyme bond cleavage get confirmed by isotope labelling
Describe the catalytic mechanism of serine proteases
What is the role of Ser and His residues in chemical labelling (think DIPF and S195)
How were Ser and His residues identified by chemicals labeling
How do Ser195, His57 and Asp102 form a catalytic triad in trypsin
How is substrate binding pocket responsible for substrate specificity
What are the four steps in the mechanisms of serine proteases
Describe oxyanion holes and the attack of Ser195 O on the carbonyl C tetrahedral
How was the first tetrahedral state of trypsin directly observed
How was the second tetrahedral state directly observed in crystal trypsin structures
How are proteases synthesized?
Describe reaction coordinate diagrams
Describe enzyme kinematics
What equation explains how enzymes catalyze reaction by preferentially
binding transition state
What are the properties of first order reactions
What are the properties of second order reactions
Describe the early days of biological catalyst research
Describe the Michaelis-Menten equation
What did George Briggs and John Haldane assume about [ES]
What is the revised Michaelis-Menten equation proposed by Briggs and Haldane
Describe typical Michaelis-Menten enzymes
Typical Michaelis–Menten enzymes follow classical kinetics, where reaction rates (v) depend on substrate concentration ([S]) and exhibit a hyperbolic curve. Their key parameters are
Vmax , the maximum reaction rate, and Km , which reflects substrate affinity. These enzymes operate via simple substrate-enzyme interactions without cooperative or allosteric effects, exemplified by enzymes like chymotrypsin and carbonic anhydrase.
Describe the Significance of Michaelis constant (Km)
The Michaelis constant (Km) is a key parameter in enzyme kinetics that represents the substrate concentration at which an enzyme achieves half of its maximum reaction velocity (Vmax). It provides insight into the enzyme’s affinity for its substrate:
- A low Km indicates high substrate affinity, as the enzyme reaches half Vmax at low substrate concentrations.
- A high Km indicates low substrate affinity, requiring higher substrate concentrations to achieve the same reaction rate.
- Km is significant in understanding enzyme efficiency and behaviour under physiological conditions, helping to predict how enzymes function within metabolic pathways and respond to changes in substrate availability.
Describe the catalytic constant (Kcat). How is Kcat/Km is a measure of the catalytic
efficiency
Describe Km, kcat and kcat/Km of example enzymes
Describe the lineweaver-burk equation
Describe the complexity of enzymatic reactions
Describe common bisubstrate reactions
Describe sequential bisubstrate reactions
Describe ping-pong bisubstrate reactions
