metabolism

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Questions and Answers

What effect does the size and charge of R groups have on the bonds within the backbone?

They increase the likelihood of double bond formation.

They enable free rotation around all bonds.

They have no effect on the bonds.

They can hinder rotational movement. (correct)

Which angles increase as the carbonyl or amide nitrogens rotate clockwise?

Φ and Ψ angles increase. (correct)

Φ and Ψ angles decrease.

Φ and Ψ angles alternate randomly.

Φ and Ψ angles remain constant.

In a protein structure, what role do aromatic amino acids play?

They serve as the primary energy source for proteins.

They can be stacked to generate stabilizing forces. (correct)

They enhance the flexibility of the protein backbone.

They create hydrogen bonds exclusively.

What configuration of Φ and Ψ angles is indicated in the conformation shown?

180° and -180° Signup and view all the answers

How does the charge state of a protonated/deprotonated amino acid affect its behavior?

It influences the interactions with other molecules. Signup and view all the answers

What phenomenon occurs when aromatic amino acids are stacked?

They generate stabilizing forces. Signup and view all the answers

What is the consequence of rotational hindrance in peptide bonds?

It leads to fixed angles for Φ and Ψ. Signup and view all the answers

What primarily affects the stability of protein architecture?

Hydrophobic interactions and stacking of aromatic residues. Signup and view all the answers

What is the effect of covalent modification on enzyme activity?

It can completely activate or inactivate the enzyme. Signup and view all the answers

Which of the following is NOT a common modification in covalent regulation of enzymes?

Reduction of hydroxy groups Signup and view all the answers

What is the primary function of ATP in the cell?

To act as the energy currency Signup and view all the answers

Which of the following describes allosteric regulation?

It is a feedback control mechanism modifying enzyme activity. Signup and view all the answers

Which role do NADH and NADPH play in metabolic processes?

They serve as coenzymes in redox reactions Signup and view all the answers

How do competing metabolic pathways minimize interference with each other?

By being localized within different cellular compartments Signup and view all the answers

What type of enzyme regulation involves hormonal signals?

Hormonal regulation Signup and view all the answers

What is released during the hydrolysis of ATP?

Inorganic phosphate (Pi) Signup and view all the answers

Which method is NOT a form of regulating enzyme activity?

Regulation by amino acid sequence Signup and view all the answers

Which of the following statements about NAD+ is true?

NAD+ serves as a cofactor for various enzymatic reactions Signup and view all the answers

What is the relationship between ATP and ADP?

ATP contains more phosphate groups than ADP Signup and view all the answers

What do catabolism and anabolism require for their regulation?

Tight and separate regulation Signup and view all the answers

Where does the energy for cellular activities primarily come from?

ATP hydrolysis Signup and view all the answers

What is the significance of penicillin’s structure in its function as an antibiotic?

It resembles the transition state of the normal cleavage reaction. Signup and view all the answers

Which type of coenzyme directly activates a substrate by forming a covalent bond?

Only activation-transfer coenzymes. Signup and view all the answers

In what way does the presence of an enzyme dramatically affect a reaction rate?

It can enhance reaction rates by as much as $10^{11}$ times. Signup and view all the answers

What cellular function do coenzymes primarily assist with?

Catalysis of chemical reactions. Signup and view all the answers

What occurs when penicillin binds to glycopeptidyl transferase?

The enzyme becomes irreversibly inactivated. Signup and view all the answers

What characteristic differentiates activation-transfer coenzymes from oxidation-reduction coenzymes?

Oxidation-reduction coenzymes often involve electron transfer reactions. Signup and view all the answers

What role do coenzymes usually have in the human body?

They participate in catalyzing specific reactions. Signup and view all the answers

How does the reaction rate in the absence of enzyme compare to the rate with enzyme present?

The reaction rate can increase by orders of magnitude with enzyme presence. Signup and view all the answers

Which of the following groups is associated with hydroxyl?

–OH Signup and view all the answers

What type of compounds are nucleophiles?

Electron-rich compounds Signup and view all the answers

Which of the following is NOT an example of an electrophile?

Negatively charged ions Signup and view all the answers

Which amino acid substitution is likely to lead to a permanent alteration in enzyme activity due to phosphorylation?

S → K Signup and view all the answers

What is the primary impact of reversible covalent modifications on enzymes?

They alter catalytic activities of enzymes. Signup and view all the answers

Which functional group is primarily modified in enzyme phosphorylation?

-OH groups in Ser, Thr, or Tyr Signup and view all the answers

Which of the following best describes cationic imine in terms of electrophilicity?

Electron-deficient species Signup and view all the answers

Which substitution at a serine side chain is least likely to affect enzyme activity?

S → L Signup and view all the answers

At which pH does half of the molecules of an amino acid with a charged side chain exist in a charged state?

At pH equal to its pKa Signup and view all the answers

What happens to the charge on the side chain of histidine when the pH increases?

The charge goes from positive to neutral Signup and view all the answers

Which of the following solutions is considered neutral?

Pure water Signup and view all the answers

Which of the following pH values indicates the most acidic solution?

1 Signup and view all the answers

What charge does a carboxylic acid group have at physiological pH?

Negative Signup and view all the answers

At which pH range do human blood and tears generally fall?

pH 7.35 to 7.45 Signup and view all the answers

What occurs to the pH level when there is an increase in $[H^+]$ concentration?

The pH level decreases Signup and view all the answers

Which of the following represents a basic solution on the pH scale?

8 Signup and view all the answers

In terms of amino acid charge, what is the significance of the pKa value?

It represents the equilibrium point of protonation and deprotonation Signup and view all the answers

What is the expected charge of a hydroxyl ion ($OH^-$) at high pH?

Negative Signup and view all the answers

Which of the following is a characteristic of weak acids in relation to pH and pKa?

Weak acids partially dissociate, affecting pH near their pKa Signup and view all the answers

Which of the following statements is true regarding amino acids at physiological pH?

Some amino acids can be positively, negatively, or neutrally charged Signup and view all the answers

Which of the following would likely lead to a decrease in $[OH^-]$ concentration?

Addition of a strong acid Signup and view all the answers

Which of the following substances would have a higher concentration of $H^+$ than $OH^-$?

Gastric juice Signup and view all the answers

Study Notes

Metabolism: An Overview

Metabolism encompasses all life-sustaining chemical reactions in organisms
Its main purposes are converting food to energy, converting food to building blocks for molecules like proteins, lipids, and nucleic acids, and eliminating metabolic wastes
It involves hundreds of enzymatic reactions organized into discrete pathways
These pathways involve many specific chemical intermediates transforming substrates to end products
Catabolism is oxidative and exergonic, breaking down complex molecules to release energy
Anabolism is reductive and endergonic, building complex molecules requiring energy

Structure of BS2003 - Biochemistry II

Students are provided with a booklet, "Essentials and Beauty of Biochemistry," as foundational material
Pre-recorded lectures are made available electronically, allowing for flexible learning
Weekly tutorial sessions and online coffee sessions are provided for clarification
The first online coffee session, on August 13th at 8:30 AM, is scheduled to address questions and reinforce learning outcomes
Practical course content related to carbohydrate catabolism, and lipids and fatty acids is covered in weeks 8 and 9, respectively

BS2003 - Biochemistry II - Learning Outcomes

Identifying classes of organic molecules in food
Describing metabolic processes of proteins, carbohydrates, and nucleic acids, and fatty acids,
Classifying key catalysts involved in metabolic processes
Determining relationships between pathways related to the digestion and synthesis of amino acids, fatty acids, and nucleic acids, as well as carbohydrates

Metabolic Fuels and Dietary Components

The body requires synthesizing the components it cannot acquire from the diet and protecting itself from toxins from the environment
It metabolizes dietary components through pathways such as fuel oxidation, fuel storage and mobilization, biosynthesis, and detoxification.
Our diet provides energy in the form of calories from elements like carbohydrate, fatty acids, and proteins.

Carbohydrates: Monosaccharides

Monosaccharides typically exist in ring structures, with a carbonyl group reacting with a hydroxyl group within the same molecule
Rings formed are five or six-membered
The anomeric carbon is a result of intramolecular bonding from the carbonyl group and the hydroxyl group
These molecules also undergo mutarotation, a process where the a and ß positions spontaneously interconvert when the ring opens and closes

Carbohydrates

A disaccharide contains two monosaccharides linked by an O-glycosidic bond
Oligosaccharides contain 3 to roughly 12 monosaccharides
Polysaccharides have tens or thousands of monosaccharides
Starch and glycogen are examples of branched polymers of glucosyl residues
Polysaccharides can be found as components in the cell walls, and in animals, as energy storage molecules.

The Three Key Polysaccharides Made From Glucose Monosaccharides

Cellulose, starch, and glycogen differing in linkage and branching
Cellulose — used for structural support
Starch — energy storage in plants
Glycogen — energy storage in animals

Energy Content of Food Constituents

Energy content of fat, glycogen, protein, glucose is discussed in kJ/g and total amounts in a human
Important advantages of storing energy in fatty acids compared to sugars or amino acids relate to fatty acid structure and their suitability form storage tissue

Saturated and Unsaturated Fatty Acids

Fatty acids can be saturated or unsaturated, based on the presence or absence of double bonds in the carbon backbone
Melting point varies based on the degree of saturation—saturated are typically solid at room temperature, while unsaturated are typically liquid
Trans fats differ from naturally occurring fatty acids, and are often used in food substitutes

Amino Acids and Peptide Formation

Twenty amino acids are building blocks of proteins
Amino acids differ in their side chains, which contain various atoms, and groups
Amino acids are categorized based on their properties

The Acidic and Basic Amino Acids

The pKa values differentiate acidic and basic amino acids
It correlates with their ability to gain or lose a proton
The isoelectric point (pI) identifies the pH at which the net charge of an amino acid is zero

Dissociation of Side Chains of Amino Acids

Describes how the amino acid side chains can gain or lose protons depending on the pH of the environment
pKa values indicate at what pH half the molecules in the solute will become ionized

Enzymes as Catalysts

Enzymes are proteins that catalyze chemical processes including creating more products
Enzymes speed up reaction rates by lowering the activation energy needed to initiate a reaction
Enzymes are not consumed, meaning they are not consumed during the transformation of substrates to products

Antibiotic Penicillin as a Transition-State Analog

Penicillin is a transition analog, tightly binding to an enzyme creating a specific enzyme-substrate complex
This binding site is irreversible, inhibiting the normal function of the enzyme involved in bacterial cell wall synthesis

Coenzymes in Catalysis

Coenzymes, non-protein organic molecules, function similarly to amino acid side chains
Two general types are oxidation-reduction coenzymes and activation-transfer coenzymes
Thiamine pyrophosphate (TPP), coenzyme A (CoA), biotin, or pyridoxal phosphate are examples of activation-transfer coenzymes derived from vitamins

Regulation of Enzyme Activity

Enzyme activity, crucial for maintaining equilibrium in biological systems
Methods like allosteric regulation, covalent modification, proteolytic cleavage by isoenzymes, enzyme availability, and compartmentalization, are explained
Hormonal regulation as a final mechanism modifying enzyme activation and activity

Allosteric Interaction

Allosteric interaction describes a sigmoid plot between the reaction rate and substrate concentration
Example of homotropic interaction includes hemoglobin, where binding of one oxygen molecule changes the subsequent binding affinity for oxygen molecules within the same enzyme
The altered affinity of different oxygen-binding sites for oxygen is crucial for the function of hemoglobin, to increase binding in regions with high oxygen demands within the body

Regulation by Covalent Modification

Reversible, covalent changes in enzymes altering their activities
Phosphorylation of specific amino acid side chains within the enzyme (Ser, Thr, Tyr) is common regulation method
The change in side chain chemistry directly affects the overall function of the enzyme

Regulation By Compartmentation

Compartmentalization within compartments limits diffusion of substances.
Selective permeability of compartmental membranes control the rate of movement of metabolites
This compartmentalization creates distinct areas within cells where specific metabolic reactions are regulated, ensuring appropriate metabolic function.

Mitochondria and chloroplasts are crucial for energy generation
Photosynthesis in chloroplasts and cellular respiration in mitochondria convert energy from one form to the other
Cellular respiration is also related to ATP production within the mitochondria and the usage of energy within the cell

Metabolism Overview

Catabolism is the breakdown of complex molecules, releasing energy.
Anabolism is the synthesis of complex molecules, requiring energy
These processes are interconnected and regulated to maintain homeostasis

Transport and Fate of Major Carbohydrates and Amino Acids

Glucose, proteins, amino acids, and other metabolites are transported throughout the body
Organs such as the liver and kidneys, are central in transporting and converting metabolites
Metabolism within the different parts of the body are coordinated, ensuring regulated transportation and utilization of metabolites

Energy Relationship Between Pathways

The process of catabolism and anabolism are simultaneous
Catabolism is oxidative and releases chemical energy in the form of ATP and NADPH
Anabolism is reductive, using the energy from catabolism to synthesize complex molecules such as proteins, nucleic acids, and carbohydrates

NADH and NADPH as Sources of Free Energy

Coenzymes NADH and NADPH are crucial in transferring electrons and hydrogen during biochemical reactions. The oxidation of NADH and NADPH are associated with energy release
NADH and NADPH are involved in driving important cellular processes like biosynthesis, synthesis, and energy transfer

ATP Serves in a Cellular Energy Cycle

ATP serves as the primary energy currency in the cell
Hydrolysis of ATP releases energy, which powers many cellular processes like biosynthesis, muscle contraction, active transport, and osmotic work

Corresponding Pathways of Cata- and Anabolism

Pathways are regulated to ensure they proceed efficiently and independently
Reactions are localized or separated within compartments to prevent conflicting processes and maintain appropriate metabolic function

Multienzyme Systems Carrying out Metabolic Pathway

Multienzyme systems facilitate and organize sequential reactions
The organization can take several forms: physically separate soluble entities, multienzyme complexes, or membrane-bound structures
Multienzyme systems increase efficiency of metabolism by concentrating enzymes and controlling processes

Metabolic Pathways Are Compartmentalized Within Cells

Compartmentalization of metabolic pathways in cells isolates enzymes and other components involved in metabolic reactions
Different compartments within cells house different metabolic reactions, e.g., glycolysis in the cytosol, citric acid cycle and oxidative phosphorylation in mitochondria

State of Reduction of Carbon Atoms in Biomolecules

The level of reduction of carbon atoms in molecules determines their potential to release energy when oxidized

Biochemical Reaction Types

Nucleophilic substitutions, nucleophilic additions, carbonyl condensations, eliminations, oxidation and reductions are the common types of transformations within biochemistry

Nucleophilic Substitution

Carbonyl carbons, protonated imines, and phosphates are common examples of electrophiles, commonly interacting with nucleophiles to form covalent bonds

Quiz Regarding Biochemistry

Several multiple-choice questions and explanations were not included regarding this topic

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Description

Explore the fundamentals of metabolism, including the critical processes of catabolism and anabolism. This quiz covers the essential pathways and reactions involved in converting food into energy and building blocks for cellular function. Ideal for students studying Biochemistry II.