Lecture 1: Foundations of Biochemistry (Chapter 1)

Flashcards cover foundational concepts from biochemistry, cell structure, molecular building blocks, thermodynamics, energy coupling, enzymes, and evolution based on Lecture 1 notes.

What is the focus of biochemistry as a discipline?

The chemistry of living matter, including macromolecules, energy transformation, metabolism, signaling, and the storage and transfer of genetic information.

What are macromolecules and why are they important in biochemistry?

Highly ordered polymers that assemble into complex cellular structures; their sequence determines unique 3D structures and biological activity.

What is the universal building block of life?

Cells.

What limits the size of cells?

Diffusion governed by surface area-to-volume ratio; larger organisms compensate with many specialized cells.

Name invariant cellular components vs. variant components.

Invariant: cell membrane, ribosomes, DNA, and RNA. Variant: mitochondria, chloroplasts, and the nuclear membrane.

What are the three domains of life?

Bacteria, Archaea, and Eukarya.

How are life forms categorized into five kingdoms?

Monera (unicellular prokaryotes), Protista (unicellular eukaryotes), Fungi (unicellular/multicellular), Plantae (multicellular plants), Animalia (multicellular animals).

What is the difference between bacterial ribosomes and eukaryotic ribosomes?

Bacterial/archaeal ribosomes are smaller but perform the same function—protein synthesis from RNA.

What is the nucleoid?

Region in bacteria containing one or more long circular DNA molecules.

What distinguishes Gram-positive from Gram-negative bacteria in terms of cell envelope?

Gram-positive: thick peptidoglycan layer. Gram-negative: outer membrane with LPS, periplasm, and porins.

Which organelle processes, packages, and targets proteins in the cell?

Golgi complex.

Which organelle generates ATP by oxidation of fuels?

Mitochondrion.

Which organelle harvests sunlight to generate energy and carbohydrates in plants?

Chloroplast.

In plants, which organelle degrades and recycles macromolecules and stores metabolites?

Vacuole.

What is the site of energy-yielding and energy-consuming reactions separation in cells?

Spatial organization within the cell helps maintain homeostasis by separating these processes.

What are the main energy sources for living systems?

Light (photosynthesis) and chemical fuels (oxidation of nutrients).

How many elements are essential for life and which are predominant?

About 30 elements; major ones include C, H, O, N, P, and S.

What are functional groups in biomolecules?

Hydrocarbon derivatives where hydrogen is replaced by functional groups (e.g., amino and carboxyl groups in amino acids).

What are the four main building blocks of biochemistry?

Sugars (monosaccharides), lipids (fatty acids), amino acids, nucleotides.

What types of isomerism exist in biomolecules?

Structural isomers; stereoisomers (enantiomers and diastereomers); geometric isomers (cis/trans).

What are enantiomers?

Non-superimposable mirror images; identical physical properties except for polarized light; may have different biological activity.

What are diastereomers?

Stereoisomers that are not mirror images and may have different physical/chemical properties.

What is geometric isomerism?

Cis/trans isomers around a carbon–carbon double bond with no rotation; they are distinct compounds.

Why does biomolecule binding depend on 3D structure?

Macromolecules have stereospecific binding pockets; only certain stereoisomers fit and bind (e.g., hexokinase binds D-glucose).

What percentage of drugs are chiral and what percentage are racemic?

About 56% of drugs are chiral; about 88% of chiral drugs are sold as racemic mixtures.

What are the first and second laws of thermodynamics?

1) Energy cannot be created or destroyed; it can be interconverted. 2) Systems tend toward greater disorder (entropy) in spontaneous processes.

Are living organisms open or closed systems?

Open systems that exchange matter and energy with their surroundings.

What is free energy and the ΔG equation?

ΔG = ΔH − TΔS; reactions proceed toward equilibrium (ΔG = 0) under appropriate conditions.

Why is stepwise metabolism advantageous?

To overcome activation energy barriers; enzymes lower barriers; energy is captured progressively (e.g., as ATP).

What is ATP and why is it important?

Adenosine triphosphate; hydrolysis provides cellular energy; contains two high-energy phosphoanhydride bonds.

How does ATP couple to drive reactions?

Energy from ATP hydrolysis is transferred to activate another metabolite (group transfer) to drive endergonic steps.

What are the main features of enzymes?

Biological catalysts that lower activation free energy, accelerate reactions under mild conditions, provide high specificity, regulate, and couple reactions to ATP.

What is the Central Dogma of Molecular Biology?

DNA → RNA → Protein.

How does natural selection relate to mutations?

Mutations occur randomly and are usually deleterious, but some confer advantages that are propagated in a population.

What does the endosymbiotic theory propose for mitochondria and chloroplasts?

Mitochondria arose from engulfed aerobic bacteria; chloroplasts from engulfed cyanobacteria; gene transfer to the host nucleus over time.

Which combination is believed to be the original genetic material and origin of mitochondria?

RNA as the original genetic material; origin of mitochondria from aerobic bacteria.

What are the key features that define living organisms?

Complex and highly organized, able to extract and transform energy, capacity for self-replication (growth and reproduction), self-regulation with maintenance of homeostasis.

Summarize the key differences between prokaryotic and eukaryotic cells.

• Prokaryotes: Simple, no membrane-bound organelles or nucleus, circular DNA in nucleoid, smaller ribosomes (e.g., bacteria, archaea).
• Eukaryotes: Complex, contain membrane-bound organelles and a nucleus, linear DNA in chromosomes, larger ribosomes (e.g., fungi, plants, animals).

What are the primary roles of the four main classes of biomolecules in living systems?

• Sugars (monosaccharides): Energy source, structural components (e.g., cellulose in plants).
• Lipids (fatty acids): Energy storage, membrane structure, signaling.
• Amino acids: Building blocks of proteins, enzymatic functions, structural support, transport.
• Nucleotides: Genetic information storage (DNA, RNA), energy currency (ATP), signaling molecules.

What properties of ATP facilitate its high-energy hydrolysis?

The electrostatic repulsion between the negative charges on the phosphate groups, the resonance stabilization of ADP and P_i (inorganic phosphate) compared to ATP, and the increased solvation (hydration) of the products.

How do enzymes contribute to metabolic regulation within a cell?

Enzymes can be regulated by allosteric control, covalent modification, levels of synthesis/degradation, and compartmentation. This ensures that metabolic pathways operate efficiently and respond to cellular needs.

Explain the 'RNA world hypothesis' and why DNA likely superseded RNA as the primary genetic material.

The 'RNA world hypothesis' suggests that early life used RNA for both genetic information storage and catalysis. DNA took over because its double-stranded structure makes it more chemically stable and less susceptible to degradation and mutation, providing a more reliable long-term archive for genetic information.

What is the difference between monomers, polymers, and macromolecules?

Monomers are small molecules that can join together to form larger chains called polymers. Macromolecules are very large molecules, typically polymers, that are essential to life, such as proteins, nucleic acids, and polysaccharides.

What are Macromolecules?

Large molecules (like proteins, nucleic acids) that are essential for life.

What are Polymers?

Large molecules made up of repeating smaller units called monomers.

What does Invariant mean?

Constant or unchanging components or features.

What does Variant mean?

Components or features that can vary or differ.

What does Anuclear mean?

Lacking a cell nucleus.

What is Activation Energy?

The minimum energy required for a chemical reaction to start.

What are Structural isomers?

Molecules with the same chemical formula but different bonding arrangements of atoms.

What are Stereoisomers?

Molecules with the same chemical formula and bond connectivity but different spatial arrangements of atoms.

What are Enantiomers?

Stereoisomers that are non-superimposable mirror images of each other.

What are Diastereomers?

Stereoisomers that are not mirror images of each other.

What is a Racemic mixture?

A mixture containing equal amounts of two enantiomers.

What is the 1st Law of Thermodynamics?

Energy cannot be created or destroyed, only transferred or transformed.

What is the 2nd Law of Thermodynamics?

The total entropy (disorder) of an isolated system always increases over time for spontaneous processes.

What is Gibbs Free Energy?

A thermodynamic potential that measures the 'useful' or available energy in a system to do work at constant temperature and pressure (\Delta G).

What is Enthalpy?

The total heat content of a system (\Delta H).

What is Entropy?

A measure of the disorder or randomness within a system (\Delta S).

What is Reaction Rate?

The speed at which a chemical reaction proceeds, or how quickly reactants turn into products.

What does Degradative mean?

Pertaining to processes that break down complex molecules into simpler ones, often releasing energy.

What is ATP?

Adenosine triphosphate; the primary energy currency of the cell.

What is a Metabolite?

Any substance made or used during metabolism.

What is Hydrolysis?

A chemical reaction in which water is used to break down a compound into two or more smaller compounds.

What is Chemical Coupling?

The process of linking an energy-releasing (exergonic) reaction with an energy-requiring (endergonic) reaction to make the overall process favorable.

What is a Catalyst?

A substance that increases the rate of a chemical reaction without being consumed in the process.

What is ATP Group Transfer?

The transfer of a phosphate group from ATP to another molecule, often to provide energy or activate the recipient molecule.

What is the Central Dogma?

The fundamental concept that genetic information flows from DNA to RNA to protein.

What are Mutations?

Random, heritable changes in the DNA sequence of an organism.

What is the difference between cytoplasm and cytoskeleton?

The cytoplasm refers to all the material within a cell, enclosed by the cell membrane, including the cytosol (fluid portion) and organelles. The cytoskeleton, on the other hand, is a dynamic network of protein filaments and tubules within the cytoplasm that provides structural support, helps maintain cell shape, and is involved in cell movement and intracellular transport.

How do bacterial cytoskeleton proteins contribute to the distinct peptidoglycan structures of Gram-positive and Gram-negative bacteria?

Bacterial cytoskeleton-like proteins (such as MreB) guide the synthesis and insertion of the peptidoglycan cell wall. These proteins help ensure the proper deposition of peptidoglycan. Gram-positive bacteria have a thick peptidoglycan layer, while Gram-negative bacteria have a thin one.