397 Questions
How many protons are in the nucleus of a carbon atom?
6
How many electrons can the first shell of an atom hold?
2
Which element can form 4 covalent bonds by sharing its 4 outer shell electrons?
Carbon
What is the maximum number of covalent bonds that oxygen can form?
2
How many electrons are present in the outer shell of a hydrogen atom?
1
What is the atomic number of sulfur?
16
How many covalent bonds can sulfur form?
4
What determines if a bond is polar or not?
The type of atoms involved in the bond
How many covalent bonds can a phosphorous atom form based on the information provided?
4
Which type of bond involves electron sharing?
Covalent bonds
In a non-polar covalent bond, how are electrons shared?
Equally
What is the main difference between polar and non-polar covalent bonds?
The type of atoms sharing electrons
What type of connection do hydrogen bonds, Van Der Waals forces, and ionic bonds belong to?
Non-covalent bonds
What determines the electronegativity of an atom in a covalent bond?
The number of protons in the nucleus
In a covalent bond, if the electronegativity difference between two atoms is greater than 0.5, what happens?
The bond becomes polar
Which atom in the table forms a polar covalent bond with hydrogen?
Oxygen
In a water molecule, which part is more negative due to sharing electrons with hydrogen?
Oxygen
What type of bonds are responsible for dipole-dipole interactions between neighboring molecules?
Hydrogen bonds
What property of water allows it to dissolve neutral polar molecules?
Its hydrogen bonding capability
How do hydrophobic molecules behave when placed in water?
They aggregate together away from water
What term describes a molecule that repels water?
Hydrophobic
Which type of interaction can be attractive or repulsive in nature?
Van der Waals forces
What type of Van der Waals force occurs between two polar bonds?
Strongest dipole-dipole
How do hydrophilic molecules behave in passing through the phospholipid bilayer?
They cannot pass through
Which term refers to molecules having both hydrophilic and hydrophobic regions?
Amphipathic
What do dipole-induced dipole forces involve?
Permanent and induced dipoles
In Van der Waals forces, what happens when the van der Waals radius is optimal?
The forces become attractive
What defines a redox reaction?
Loss of Electrons = Oxidation, Gain of Electrons = Reduction
What are NAD+/NADH?
Nicotinamide Adenine Dinucleotide
What type of oxidoreductase is used in Dehydrogenases?
Ligases
In the Krebs cycle, what is oxidized to make Malate?
Oxaloacetate
What oxidizes H's and donates them to oxygen?
Oxidases
What are FAD/FADH2 in the context of enzyme reactions?
Flavin Adenine Dinucleotide, key players in electron transfer reactions
Which enzyme classification involves Isomerization reactions?
Isomerases
'LEO the lion says GER' represents a mnemonic for understanding:
'Losing Electrons: Oxidation, Gaining Electrons: Reduction'
'CAC' in 'Redox Example: CAC' refers to:
'Citric Acid Cycle'
'Oxidoreductases catalyze redox reactions'. What do they reduce according to the text?
'Oxygen'
Why is UDP a better leaving group than OH?
OH cannot stabilize negative charge as well as UDP.
In the context of hydrolases, what type of transferase enzyme is being used?
Phosphatases
Which molecule acts as a nucleophile in hydrolysis reactions catalyzed by hydrolases?
Water (H2O)
What enzyme class catalyzes hydrolysis reactions in biological systems?
Hydrolases
Which enzyme specifically hydrolyzes monophosphate esters like AMP?
Phosphatases
What type of enzyme hydrolyzes peptides to release smaller fragments?
Peptidases
What molecule acts as a nucleophile in hydrolase-catalyzed reactions?
Water (H2O)
What is the primary role of ATPases in biological systems?
Hydrolyzing ATP to release energy
What is the significance of 'X' in the naming convention 'X-ases' for enzymes like Peptidases?
It indicates the type of substrate being acted upon.
In the breakdown of fatty acids for energy (beta oxidation), which type of lyase catalyzes a reaction that removes atoms in a molecule to create a double bond?
Dehydratase
What is the molecule added by a hydratase, a type of lyase, during the breakdown of fatty acids for energy (beta oxidation)?
Water
What is the role of lyases in biological reactions?
Remove atoms to form a double bond
Which type of bond is commonly involved in the reactions catalyzed by hydratases during beta oxidation?
Pi (π) bond
In beta oxidation, what is removed by decarboxylases, which are a type of lyase enzyme?
Carbon dioxide
What physiological process involves the reactions catalyzed by amylase, hydratases, and decarboxylases?
Beta oxidation
Which enzyme class catalyzes reactions that involve group transfer through an intramolecular process?
Isomerase
What is the main function of ligases in catalyzing reactions?
Joining two molecules using ATP
Which enzyme class is responsible for dehydrating or eliminating water molecules from a substrate?
Lyase
What is the specific function of epimerases among isomerases?
Interconverting asymmetric carbons
In the context of enzyme classes, what do mutases specifically involve?
Rearrangement of groups within a molecule
"X"-ligases are examples of which specific type of ligase?
"X"-synthetases
"Synthase" and "synthetase" can be used synonymously with which term?
"Ligase"
"X"-transferase is most likely associated with which type of enzyme class based on the information provided?
"Transferase"
"Aconitate hydratase" is an example related to the isomerization of which two compounds in the Citric Acid Cycle (CAC)?
"Citrate and Isocitrate"
What type of bonds are formed between water molecules?
Hydrogen bonds
Which of the following is NOT an unusual property of water?
Low surface tension
How many other water molecules does each water molecule form hydrogen bonds with?
4
What property of water helps it dissolve many substances?
Polarity
At what temperature does water have its highest density?
4⁰C
Which type of bond is stronger, a hydrogen bond or a covalent bond?
Covalent bond
What property of water enables it to have a high specific heat capacity?
Hydrogen bonding between molecules
What is the pKa of the bicarbonate buffer system?
6.1
Which compartment has higher buffering power according to the text?
Intracellular fluid
What two components make up the bicarbonate-carbonic acid buffer system?
H+ + HCO3-
Which enzyme plays a crucial role in the equilibrium between H2CO3, H+, and HCO3-?
Carbonic anhydrase
Why is the bicarbonate buffer system considered more effective in extracellular fluid?
Carbonic anhydrase action
Which system has a major buffering capacity in the extracellular fluid?
Bicarbonate-carbonic acid system
What is the approximate concentration of bicarbonate ions in the intracellular compartment?
4-5 mmol/L
What is the purpose of the Henderson-Hasselbach equation?
To describe the properties of weak acids or bases
At a pH of 3.74 for acetic acid, what is the significance of the ratio of salt/acid?
Acid is in excess compared to salt
In what scenario would acetic acid buffer best?
At a pH of 6.74
What happens when the pH equals the pKa value for acetic acid?
The amount of salt and acid are equal
For acetic acid at a pH of 6.74, what does the ratio of salt/acid indicate?
Salt is in excess compared to acid
What does the Henderson-Hasselbalch equation calculate?
The pH of a solution given the pKa and concentrations of weak acids or bases
Which statement best describes the behavior of acetic acid as a buffer around its pKa value?
Italic_The buffering capacity would be optimal when the pH is close to acetic acid's pKa value_Italic
What is the primary role of carbonic anhydrase in the process described?
Catalyzing the formation of H2CO3 from water and CO2
At what pH level is the ratio of bicarbonate to carbonic acid determined according to the provided information?
7.4
Which organ system can modify the rate of bicarbonate excretion?
Renal system
What happens to H2CO3 when the red blood cell reaches the lungs based on the text?
It is converted to water and CO2 by carbonic anhydrase
What is the function of the HCO3-/Cl- transporter in red blood cells?
Importing bicarbonate into red blood cells
Which process allows the lungs to modify the rate of CO2 removal?
Increasing ventilation
What happens to HCO3- when reaching the lungs according to the text?
It is converted back into the red blood cell
Why is carbonic anhydrase considered important in the process described in the text?
To convert H2CO3 to CO2 and water
What allows for the modification of bicarbonate excretion by the kidneys?
Changes in blood pH levels
Which of the following best describes anabolism?
Building molecules from smaller subunits, requiring energy
Where does gluconeogenesis primarily occur in the cell?
Mitochondria
What is the primary purpose of ketogenesis in metabolism?
To produce glucose from non-carbohydrate precursors
Under anaerobic conditions, what is the end product of glycolysis?
Lactate
Which pathway involves the breakdown of glycogen into glucose?
Glycogenolysis
In metabolism, what is the primary function of lipogenesis?
To synthesize lipids from acetyl-CoA and malonyl-CoA
Where does beta-oxidation primarily take place in cells?
Mitochondria
When there is a lack of oxygen, pyruvate converts to lactate rather than?
Acetyl CoA
What is the primary purpose of gluconeogenesis?
Synthesizing glucose from non-carbohydrate precursors
What is a key function of the citric acid cycle (CAC) in energy production?
Producing NADH and FADH2 for the electron transport chain
What is the main site of gluconeogenesis in the body?
Liver
What molecules can serve as substrates for gluconeogenesis?
Various amino acids
What is the end product of fatty acid breakdown that can enter the citric acid cycle?
Acetyl CoA
What is the primary function of the pentose phosphate shunt described in the text?
Generating NADPH for fatty acid synthesis
In the context of energy production, what are fats broken down into?
Fatty AcylCoA
If fatty acids are not needed for energy, how are they stored for later use?
Converted to Triglycerides
What connection exists between excess glucose and fatty acid synthesis?
Divergence into Lipogenesis
What is the next step if more energy is required after breaking down fatty acids?
Oxidation in the Mitochondria
When making fatty acids in excess quantities, what role does ATP play in the process?
Direct fuel for fatty acid synthesis
Which organelle is responsible for the production of ketone bodies?
Cytosol
What is the final electron acceptor in the Electron Transport Chain (ETC) for the production of water?
Oxygen (O2)
Which pathway can lead to the production of Acetyl CoA that feeds into the Citric Acid Cycle (CAC)?
Beta-Oxidation of Fatty Acids
What compound is primarily responsible for driving ATP synthesis in the ETC?
H+ gradient
Which enzyme catalyzes the conversion of Fatty AcylCoA to Fatty Acids in the mitochondria?
Fatty AcylCoA Dehydrogenase
In which compartment does the Electron Transport Chain (ETC) occur within the mitochondria?
Matrix
Which of the following is NOT an irreversible reaction in glycolysis?
Conversion of Glyceraldehyde-3-P to Pyruvate
Where does gluconeogenesis primarily occur?
Liver and kidney
Why is gluconeogenesis particularly important during times of fasting?
To provide glucose for tissues when carbohydrate intake is low
Which process involves the synthesis of glucose from non-carbohydrate precursors?
Gluconeogenesis
What are the main regulated steps of glycolysis discussed in the text?
Conversion of Glucose to Pyruvate
What is the purpose of gluconeogenesis in metabolism?
To synthesize glucose from non-carbohydrate precursors
Which substrates feed into gluconeogenesis according to the text?
Glucogenic amino acids and lactate
What is the main difference between glycolysis and gluconeogenesis?
Glycolysis is catabolic, breaking down glucose, while gluconeogenesis is anabolic, synthesizing glucose.
What is the function of lactate dehydrogenase in the Cori Cycle?
Converts lactate to glucose in liver tissue
How does glycerol enter the gluconeogenesis pathway?
By being converted to DHAP in the liver
Which precursors can be used in gluconeogenesis besides lactate and glycerol?
Glucogenic amino acids
Why is lactate transported from tissues to the liver via the blood in gluconeogenesis?
To convert it back to pyruvate for glucose production
What role do glucogenic amino acids play in supporting gluconeogenesis?
They act as direct precursors for glucose synthesis
Which pathway is supported by the conversion of pyruvate to lactate under anaerobic conditions?
Glycolysis
What is the significance of the Cori Cycle in energy metabolism?
It allows for the utilization of lactate as a fuel source
Why is the synthesis of glucose from non-carbohydrate precursors important?
To maintain blood glucose levels during fasting
Which enzyme is responsible for carboxylation of pyruvate in the gluconeogenesis pathway?
Phosphoenolpyruvate carboxykinase
What is the main symptom associated with very rare inherited disorders of gluconeogenesis?
Drowsiness
Which glycolytic intermediate can continue through the reversible reactions of glycolysis in the gluconeogenesis pathway?
Phosphoenolpyruvate
In gluconeogenesis, which enzyme is involved in the conversion of fructose 1,6-bisphosphate to fructose-6-phosphate?
Fructose 1,6-bisphosphatase
Which enzyme in the gluconeogenesis pathway is involved in converting glucose-6-phosphate to glucose?
Glucose-6 Phosphatase
What is the metabolic condition usually associated with individuals presenting early in life with poor growth and development, drowsiness, tremors, and seizures?
Gluconeogenesis disorders
Which enzyme deficiency leads to the accumulation of fructose 1,6-bisphosphate in individuals with a metabolic disorder?
Fructose 1,6-bisphosphatase deficiency
Which molecule is converted from oxaloacetate to enter gluconeogenesis through the malate shuttle system?
Phosphoenolpyruvate
What is the primary function of the malate shuttle system in gluconeogenesis?
To transport oxaloacetate across the mitochondrial membrane
In the context of glycerol entering gluconeogenesis, what substance can glycerol be converted to?
Dihydroxyacetone phosphate
Which shuttle system is utilized when lactate is the substrate entering gluconeogenesis?
Aspartate shuttle
What is the final product of oxaloacetate conversion that allows for the continuation of gluconeogenesis?
Phosphoenolpyruvate
Which amino acid serves as the starting substrate for the malate shuttle system in gluconeogenesis?
Alanine
In the context of entering gluconeogenesis, what is lactate converted to before participating in this process?
Pyruvate
Which substance is shuttled out of the mitochondria to continue with gluconeogenesis after being converted from oxaloacetate?
What defines the internal energy of a system?
Potential energy of bonds
In thermodynamics, what does a reaction that releases heat indicate?
It is spontaneous
What does the Second Law of Thermodynamics state about systems?
Energy disperses unless hindered
Which term describes how energy is 'spread out' in a system?
Entropy
What directly measures the change in enthalpy when reactants form products?
Heat change in the system
Which type of reaction has a positive ΔH and is often not spontaneous?
Endothermic reaction
What is the primary factor that determines if a bond is polar or not?
Electronegativity difference
'Enthalpy' simplifies to represent the energy content of which component within a system?
'Potential energy'
What tends to indicate a spontaneous reaction based on the laws of thermodynamics?
Negative Gibbs Free Energy
Which factor makes a chemical reaction spontaneous according to the Laws of Thermodynamics?
Increase in entropy
What type of reaction is indicated by a positive Gibbs Free Energy value?
Endergonic reaction
Why does a chemical reaction need a spark?
To initiate the reaction by providing activation energy
What is the significance of ΔG=0 in a chemical reaction?
The reaction is at equilibrium
What does a negative ΔG value signify for a chemical reaction?
Exergonic, spontaneous
Which factor is taken into account by Gibbs Free Energy that affects the spontaneity of a reaction?
Enthalpy change
Why do exothermic reactions tend to be spontaneous?
They release heat and increase entropy
For which type of reaction would the Gibbs free energy change be most negative?
A (-) ΔHrxn and a (-) ΔSsystem
Under what condition would a reaction be considered non-spontaneous?
Always
In a hypothetical reaction with a positive ΔGoʼ value, when would the reaction be spontaneous?
When both A and B are at high concentrations
What impact do non-standard conditions have on the Gibbs free energy of a reaction?
Decrease it
Which reaction from the given list is likely to be the most spontaneous?
ATP + H2O à AMP + PPi
At what pH and temperature is the standard Gibbs free energy calculated?
pH 7, 298 K (room temperature)
How does increasing the concentration of reactants impact the spontaneity of a reaction?
Increases spontaneity
What role does RT ln have in calculating the non-standard Gibbs free energy change?
Accounts for temperature and pressure effects
In which situation does the text mention that reactions with a fairly large +ΔG can develop into exergonic reactions?
When reactants are increased compared to products
What strategy is commonly used to drive some endergonic reactions forward in glycolysis according to the text?
Increasing the concentration of reactants
How is it possible that a reaction with a positive ΔGoʼ still occurs in our bodies, as mentioned in the text?
By coupling it with other reactions
What is the significance of a positive ΔGoʼ value for a reaction like Glucose + Pi Glucose-6-phosphate in glycolysis?
The reaction is endergonic
Which type of reactions does the text specifically mention as a common strategy in biochemical and cellular situations?
Coupled reactions
What is the role of having significantly more reactants than products in driving reactions forward?
Shifting the equilibrium towards products
Which scenario allows reactions with large positive ΔG values to become exergonic?
Substantial excess of reactants
What type of reactions can develop into exergonic reactions if there is a significant difference between reactants and products?
Endergonic reactions
Why might a reaction with a positive ΔGoʼ still occur in our bodies?
By utilizing other available energy sources
Which common strategy is used to drive endergonic reactions forward in glycolysis and other biochemical processes?
Having substantially more reactants than products
What is the main key enzyme for transcription?
RNA polymerase
Which factor is essential for RNA polymerase to recognize where to start transcription?
Sigma factor
During transcription, in which direction does RNA polymerase work on the DNA template?
5' to 3'
What is the error rate of RNA polymerase in terms of nucleotides?
1 in every 104 nucleotides
In eukaryotes, which sequence is recognized by transcription initiation factors like TFII for RNA polymerase to start transcription?
TATA box
Which stage of transcription involves the creation of a new phosphodiester bond on the forming RNA strand?
Elongation
'Template strand' in transcription corresponds to which direction on the DNA sequence?
3' to 5'
'Non-template strand' in transcription corresponds to which direction on the DNA sequence?
5' to 3'
Where does transcription occur?
Nucleus
What region of a gene contains a consensus sequence?
Promoter region
What is the function of the Terminator region in transcription?
Specifies end of transcription
Which enzyme is responsible for synthesizing an RNA molecule from a DNA template?
RNA Polymerase
Which strand of DNA is transcribed into RNA during the transcription process?
Anti-sense strand
What is the main function of RNA in protein synthesis according to the text?
Serves as an intermediate for protein synthesis
Where does translation occur?
Ribosome
What is the role of tRNA in translation?
Carries amino acids to ribosomes
What happens when repressor proteins bind upstream sequences on DNA known as silencers?
Inhibit gene transcription
Which proteins bind upstream sequences called enhancers?
Activator proteins
What is the main function of elongation factors in transcription?
Assist RNA Polymerase in moving along DNA
In transcription, what is the role of various elongation factors?
Help reduce the likelihood of RNA Polymerase dissociating from DNA
What might occur if there was a mutation in a repressor protein binding site?
Enhance gene transcription
How do activator proteins influence transcription rates?
Enhance the rate of transcription
What is the consequence of elongation factors helping RNA Polymerase during transcription?
Faster movement along the DNA template
What is the role of chromatin remodeling complexes in eukaryotic elongation?
Navigate the chromatin structure for RNA polymerase
How does DNA topoisomerase function in eukaryotic elongation?
Removes supercoiling tension generated by RNA polymerase
What is the purpose of the 7-methyl guanosine cap added to pre-mRNA transcripts in eukaryotes?
Facilitates translation of the mRNA into proteins
What is the primary function of histone chaperones during eukaryotic elongation?
Partially disassemble & reassemble nucleosomes for RNA polymerase movement
During elongation, what occurs once approximately 25 nucleotides of RNA have been transcribed?
Addition of a 5' cap to pre-mRNA
What is the function of DNA topoisomerase in resolving super-helical tension during elongation?
Breaks phosphodiester bonds to allow DNA rotation
Which process occurs at Step 3 - Processing during eukaryotic elongation?
Splicing of introns in the pre-mRNA transcript
In cell regulation of protein synthesis, which factor determines the amount of a particular protein available to a cell?
Stability of mRNA transcript
What role do chromatin remodeling complexes play in transcription regulation?
Expose or obscure gene regulatory elements
Which modification tends to open chromatin and increase transcription during transcription regulation?
Histone acetylation
What is the main purpose of histone methylation in transcriptional regulation?
Promote transcriptional activation or repression
Which enzyme is responsible for histone acetylation during transcription regulation?
HAT (histone acetyltransferase)
What is the result of DNA methylation during transcription regulation?
Result in chromatin condensation
How do histone modifications impact the regulation of protein synthesis?
Regulate gene expression
How can the stability of an mRNA affect protein synthesis?
Increased mRNA stability leads to increased protein synthesis.
Which type of RNA can promote the destruction of mRNA transcripts?
miRNA
What is the role of specific proteins in relation to mRNA degradation?
They promote mRNA degradation.
Which cellular location requires translation on free ribosomes in the cytosol?
Nucleus
What is the process called when proteins are directed to the rough ER for translation?
Co-translational transfer
Which sequence is translated to bind a signal recognition particle (SRP) during protein targeting?
Signal peptide sequence
In co-translational transfer, where does translation initially begin before directing proteins to specific cellular locations?
Cytosol
What is the function of a specific amino acid signal in a polypeptide during protein translation?
Targets the protein for its intracellular location
What is the function of SRP when it binds to a SRP receptor?
Stops translation and directs the ribosome to the RER
What happens when a protein with a stop transfer sequence encounters the translocator?
Translation is paused
In the process of targeting a protein to cell membranes, what is discharged by the translocator into the ER membrane?
Polypeptide
What happens to the signal peptide sequence once the protein is in the RER?
It is removed
In proteins intended for cell membrane insertion, what feature is associated with the stop transfer sequence?
It triggers translation pausing
Which organelle is primarily involved in discharging polypeptides into the phospholipid bilayer during targeting?
Endoplasmic reticulum (ER)
What effect does the presence of a stop transfer sequence have on translation?
Induces translation pausing
0
Non-polar
What is the basis for nucleic acid according to the text?
DNA
Which biomolecule serves as the intermediate for protein synthesis according to the text?
RNA
What are the 3 components of a nucleotide, as stated in the text?
Monosaccharide, Phosphate, Nitrogenous base
Why does Adenine (A) always pair with Thymine (T) in DNA structure?
To maximize H-bonds between bases
According to Chargaff’s rule, why must the number of purines equal pyrimidines in DNA?
To keep the double helix structure intact
What is the 3D structure of DNA called as per the text?
Double helix
What holds the two DNA strands together in the double helix structure?
Hydrogen bonds
What is the role of purines in DNA structure?
Facilitating base-pairing efficiency
Which type of RNA directly degrades specific mRNA molecules to reduce gene expression?
miRNA
What is the main function of lncRNA in gene regulation?
Increase or decrease transcription
Which type of RNA is an adaptor between mRNA and amino acids during protein synthesis?
tRNA
What is the primary function of siRNA in gene regulation?
Promote mRNA degradation
Which RNA molecule is involved in splicing pre-mRNA?
snRNA
What is the function of mRNA in the context of gene expression?
Catalyze protein synthesis
What is the primary function of rRNA in protein synthesis?
Structural component of the ribosome
Which region of tRNA is responsible for pairing with the codon on mRNA?
Anticodon
According to the Wobble Hypothesis, why are there fewer tRNAs than possible codons?
Multiple tRNAs can pair with one codon
What is the purpose of the amino acid binding site on tRNA?
To bind the amino acid corresponding to the anticodon
Which RNA molecule directly carries the genetic information for protein synthesis?
mRNA
What role does the Wobble Hypothesis play in the translation process?
Allowing tRNAs to recognize multiple codons
Which statement best describes the importance of tRNA in translation?
tRNA ensures accurate amino acid insertion into proteins
Which part of a tRNA molecule binds to a specific amino acid?
Amino acid binding site
Why is it crucial that some tRNAs can tolerate a mismatch in the third position of a codon?
To allow for fewer tRNAs needed for protein synthesis
How does RNA differ from DNA chemically?
RNA has deoxyribose sugar instead of ribose sugar
What is the function of messenger RNA (mRNA) in the central dogma?
mRNA is used as a template for protein translation
What is the function of small nuclear RNA (snRNA) in the cell?
Forms the core of the spliceosome complex
Which type of RNA does not get translated into proteins?
Non-coding RNA
What is the primary role of non-coding RNA in cellular processes?
Regulate various cellular processes
What happens to pre-mRNA after it undergoes processing?
It becomes mature mRNA
How does tRNA contribute to protein translation?
By carrying amino acids to the ribosome
What is the structural difference between DNA and RNA?
DNA is always single-stranded while RNA is double-stranded
What is the role of ribose sugar in RNA?
It forms the backbone of the RNA molecule
What term describes the disruption in folding or shape of a protein due to the breakdown of bonds holding it together?
Denaturation
Which of the following could disrupt protein structure by disrupting hydrophobic, polar, and charged interactions?
Organic solvents
What kind of agents can denature proteins by either adding or removing hydrogens?
Reducing agents
Which heavy metals, based on their charge, are likely to bind to amino acid side chains within proteins?
Mercury (Hg+2)
What kind of interactions within a protein are disrupted when heavy metals bind to amino acid side chains?
Ionic bonds
Which type of agents can denature proteins by disrupting polar and charged interactions within the protein structure?
Salts
How does lead poisoning affect the synthesis of hemoglobin in the body?
Binds to enzymes needed for Hb synthesis, leading to decreased Hb production
In the context of enzymes, what is the significance of cofactors and coenzymes?
They enhance enzyme specificity and catalytic function
Why are enzymes necessary for biochemical reactions in the body?
To ensure reactions occur at a pace fast enough to support life
What is the primary role of enzymes in our body?
To catalyze biochemical reactions
Which type of protein do enzymes belong to?
Globular proteins
How do heavy metals like lead affect the shape of proteins?
Cause protein denaturation
What is the primary role of enzymes in specific reactions?
Decreasing the activation energy of the reaction
Why are enzymes considered highly specific in catalyzing reactions?
Only substrates of correct size and shape can bind to their active site
What is the biochemically recognized term for the minimal energy needed for a reaction to occur?
Free energy of activation (ΔG‡)
Which type of enzyme specificity is enforced by amino acids in the active site?
Size and shape-specific binding
What defines the transition state in a chemical reaction?
The point where reactants have the highest energy
Why is lowering the activation energy critical in biochemical reactions?
To make reactions occur more quickly
What is the enzyme-substrate complex known as?
ES complex
Which model describes the conformational change in the shape of the enzyme upon substrate binding?
Induced Fit model
In enzyme mechanisms, how may catalytic groups speed up reactions?
Acid-base catalysis
Which amino acid side chain acts as a general acid or base, facilitating the addition or removal of protons?
Histidine
What allows for electrostatic interactions to form between the correct substrate and enzyme?
Induced fit between substrate and enzyme
How does acid-base catalysis contribute to making a substrate more reactive?
Adding or removing protons from the substrate
Which type of catalysis involves the addition or removal of a proton from a substrate?
Acid-base catalysis
'Catalytic groups may speed up reactions in two main ways: Acid-base catalysis and...?'
'Covalent catalysis'
'Which side chains of amino acids facilitate adding or removing protons?' This question tests for:
'Types of amino acids'
Which amino acids are considered glucogenic?
Alanine and glutamine
What is the key enzyme involved in the conversion of alanine to pyruvate?
Alanine Transaminase (ALT)
Which process involves the immediate shuttling of pyruvate into mitochondria?
Lactate conversion
What is the primary function of glycerol kinase in metabolism?
Conversion of glycerol to glycerol-3-phosphate
In gluconeogenesis, which molecules serve as substrates?
Alanine and lactate
What is the fate of pyruvate once inside the mitochondria during gluconeogenesis?
Conversion to oxaloacetate
Which amino acid is converted to pyruvate through transamination involving PLP as a coenzyme?
Alanine
What is the significance of glucogenic amino acids in metabolism?
They can be converted into glucose or TCA cycle intermediates.
Which enzyme is responsible for the conversion of lactate to pyruvate in the cytosol?
Lactate dehydrogenase
What is the primary purpose of Gluconeogenesis?
Synthesize glucose from non-carbohydrate sources
Which two organs are primarily involved in the process of Gluconeogenesis?
Liver and Kidney
What are the substrates that feed into Gluconeogenesis?
Lactate, glycerol, ketogenic amino acids
What is the significance of the three irreversible reactions mentioned in the text with respect to glycolysis?
They prevent the reversal of glycolysis
Thinking Question: Is Gluconeogenesis merely a reverse of Glycolysis? Why or why not?
No, due to unique enzymes and bypass reactions
When Gluconeogenesis occurs in the liver and kidney during fasting, what is its primary role?
Supply glucose to other body tissues as an energy source
What makes Gluconeogenesis particularly important during times of fasting?
It provides glucose when dietary intake is insufficient
What is the role of oxaloacetate in gluconeogenesis?
Converted to phosphoenolpyruvate in the cytosol
Which shuttle system is used when lactate is the starting substrate for gluconeogenesis?
None of the above
In the malate shuttle system, where is malate converted back to oxaloacetate?
In the cytosol
Which substrate can enter gluconeogenesis by being converted to phosphoenolpyruvate?
Glycerol
What is the function of the malate-aspartate shuttle?
Shuttles malate across the inner mitochondrial membrane
Which compound is involved in the malate shuttle system for gluconeogenesis?
Alanine
What is the fate of phosphoenolpyruvate in gluconeogenesis?
Shuttled out of the mitochondria
Which substance needs a shuttle system due to its inability to cross the inner mitochondrial membrane?
Oxaloacetate
In gluconeogenesis, which enzyme is responsible for adding a CO2 molecule to pyruvate during reaction 1a?
Pyruvate carboxylase
Which enzyme is involved in bypass reaction 2 of gluconeogenesis, converting fructose 1,6-bisphosphate to fructose 6-phosphate?
Which glycolytic intermediate can continue through the reversible reactions of gluconeogenesis until reaching fructose 1,6-bisphosphate?
Phosphoenolpyruvate
Which enzyme catalyzes the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate in gluconeogenesis?
Fructose-1,6-bisphosphatase
Which of the following enzymes is NOT involved in gluconeogenesis?
ATP synthase
What is the endpoint of bypass reaction 3 in gluconeogenesis?
Glucose
Which disorder of gluconeogenesis typically presents with symptoms like poor growth, drowsiness, tremors, and seizures early in life?
Glucose-6-phosphatase deficiency
'Gluconeogenesis' primarily involves the synthesis of which molecule in cellular metabolism?
$\text{Glucose}$
What type of charge do amino acids have at pH = 7?
Net charge of zero
In the nitrogen cycle, where does the nitrogen come from that plants convert into amino acids?
From bacteria in roots of legumes and soil
What is the key role of plants in the nitrogen cycle in relation to amino acids?
Converting nitrogen into a usable organic form: amino acids
What happens once animals ingest plants containing amino acids?
Animals digest the amino acids and incorporate the nitrogen into their own proteins
At pH = 7, how do amino acids behave in terms of acidity and basicity?
Can act as either an acid or a base
What is the source of nitrogen that eventually returns back to the soil and atmosphere in the nitrogen cycle?
Decomposing plant matter
Why is it important for bacteria to convert nitrogen into forms assimilated by plants?
To assist in the production of essential amino acids in plants
What is the significance of amino acids being amphoteric?
Gives them the ability to act as both an acid or a base
Which subset of essential amino acids is known as branched chain amino acids (BCAA’s)?
Ile, Leu, Iso
Which of the following amino acids are considered essential and not made de novo in mammals?
Lys, Met, Phe
What is the main reason plant products are not usually considered complete proteins?
Lack of essential amino acids in proper amounts
Which amino acid classification group includes the phrase 'Any Help In Learning These Little Molecules Proves Truly Valuable'?
Essential amino acids
What do complete proteins contain in sufficient amounts to support health?
Essential amino acids
Why are histidine and arginine considered essential amino acids in infants but not in adults?
Adults can synthesize them de novo
Which protein source is generally not considered complete as it lacks certain essential amino acids?
Beans
What is the role of soy in the context of complete proteins?
Considered a complete protein despite low in Met
What is a characteristic of quinoa that sets it apart from other plant protein sources?
A complete protein despite being from a plant source
Which type of bonding can both the hydroxy and amido groups participate in?
Hydrogen bonding
In amino acid anabolism, what is the direct way nitrogen can be incorporated into an amino acid?
Direct incorporation
Which coenzyme is mentioned in the text with a function related to anemia, spina bifida, and cancer?
Folate
What is the primary function of histamine as outlined in the text?
Inflammatory response modulation
In transamination, which ketoacid is paired with glutamate for amino group transfer?
α-ketoglutarate
Which amino acid is paired with oxaloacetate in the context of transamination?
Aspartate
In amino acid anabolism, what is the specific indirect method that involves transferring an amino group from one amino acid to a ketoacid?
Transamidation
What is the unique property of proline that distinguishes it from other amino acids?
It cannot rotate freely around the α-C
Which amino acid group contains a sulfur atom and can form disulfide bonds?
Neutral Non-Polar amino acids
What is the role of the thiol group in cysteine?
It helps bind metals
Which two amino acids are noted for their ability to bind metals due to the presence of sulfur?
Cysteine and Methionine
What is the significance of having an OH group on Serine and Threonine?
They can be phosphorylation sites
Which category of amino acids is most likely to be involved in hydrophobic interactions within proteins?
Neutral Non-Polar amino acids
Which unique property of Cysteine makes it important in oxidative stress response?
Ability to form disulfide bonds
What is the primary function of the thiol group in Cysteine within proteins?
Stabilizing protein structures
What property makes Cysteine and Methionine suitable for binding metal ions within proteins?
Ability to chelate metal ions using sulfur atoms
Which coenzyme is required for transaminations as mentioned in the text?
PLP
Which liver enzymes are typically responsible for transaminations involving alanine and aspartate?
AST and ALT
Elevated levels of which enzymes in the blood may indicate liver problems?
ALT and AST
Which precursor family do the 20 amino acids belong to that share a common precursor with glutamate?
Pyruvate family
In transamidation, where does the N come from compared to transamination?
Amido instead of amino
Which molecule serves as the common precursor for the Glutamate family of amino acids?
Glutamate
What is required to add nitrogen to a molecule directly from ammonia according to the text?
$B3$ coenzyme
What is the function of transamidation compared to transamination based on the text?
'Direct incorporation' of nitrogen from amido groups
Which process adds nitrogen directly from ammonia to molecules?
Direct incorporation
Which enzyme is involved in the conversion of alpha ketoglutarate to glutamate, part of amino acid anabolism?
GDH
What is the main role of glucokinase in the context provided?
Converting excess glucose to glycogen in the liver
Why can't other tissues convert excess glucose to glycogen?
Absence of glucokinase in other tissues
What is significant about adding a phosphate group (P) to glucose?
It allows storage of glucose as glycogen
Why does hexokinase have a lower Km value compared to glucokinase?
Hexokinase has a higher affinity for glucose
Why is hexokinase inhibited by glucose-6-phosphate while glucokinase is not?
Hexokinase is allosterically regulated by G6P
What does a high Vmax value indicate for an enzyme like glucokinase?
High catalytic efficiency
What happens in the HK pathway until 'what happens'?
Energy production stops
What is the primary function of hexokinase and glucokinase in carbohydrate metabolism?
Converting excess glucose to glycogen for storage
In reversible noncompetitive enzyme inhibition, does binding to E or ES appear to have a higher affinity?
ES
For noncompetitive inhibition, is Vmax lower or higher in the presence of the inhibitor?
Higher
What happens in irreversible enzyme inhibition?
A covalent bond is formed between the inhibitor and the active site of the enzyme
How does Penicillin function as an inhibitor?
By forming a covalent bond with the active site
How does lead poisoning affect enzyme activity?
Changes the shape of the enzyme, preventing it from functioning
What is the primary consequence of lead poisoning in terms of heme synthesis?
Decreased heme synthesis
How does irreversible inhibition differ from reversible inhibition in terms of mechanism?
Reversible inhibitors form covalent bonds with enzymes
In reversible enzyme inhibition, what is the key characteristic of competitive inhibition?
Binds to the active site of the enzyme
What is the main reason Vmax does not change in competitive inhibition?
The concentration of active enzyme remains constant
In uncompetitive reversible enzyme inhibition, where does the inhibitor bind?
Enzyme-substrate complex
How does methotrexate exert its effect against cancer cells?
By inhibiting purine and pyrimidine production
What is the impact of uncompetitive inhibition on Vmax?
Vmax decreases
Why doesn't competitive inhibition affect Km?
It does not affect substrate binding affinity
What happens to product formation in the presence of uncompetitive inhibition?
Product formation is unaffected
What is a characteristic feature of irreversible enzyme inhibition?
'Locks' the enzyme into an inactive form permanently
What effect would an activator, which could be the substrate, have on the shape of the binding graph for multi-subunit allosteric enzymes?
Produce a left shift
In the context of allosteric inhibition, where does ATP bind when it is acting as an inhibitor?
Allosteric site
In the example of phosphofructokinase 1 (PFK1), what is the effect of ATP on enzyme activity?
Allosterically inhibits enzyme activity
What happens to the Km values for different binding sites when comparing ATP as an inhibitor vs. a substrate in allosteric inhibition?
The Km value for ATP as an inhibitor is higher
What does the term 'allosterically inhibited by ATP' imply about the regulation of phosphofructokinase 1 (PFK1)?
ATP binds to an allosteric site on PFK1
How does the binding of F-6-P to one subunit affect the binding of F-6-P to other subunits in phosphofructokinase 1 (PFK1)?
Enhances binding to other subunits
General Biochemistry 1-9 (including pre- and post-learning)
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