Biology Chapter: Importance of Carbon and Bonding

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Some Fundamentals

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The Importance of Carbon

• Carbon (C) is the most crucial atom in biological molecules.
• Carbon-containing compounds exhibit a wide range of diversity and stability due to specific bonding patterns.
• Carbon's valence is 4.
• It interacts and bonds with other atoms by sharing its 4 available electrons, forming a full set of 8 electrons (octet rule) in bonding.
• Biological considerations include some relevant atoms and their valences: Carbon (valence: 4), Hydrogen (valence: 1), Oxygen (valence: 2), and Nitrogen (valence: 3).

The Importance of Bonding

• Bonding can take the forms of single, double, or triple bonds.
• Stronger interactions require more energy to break.
• Bond energies are measured in calories.
• The strength of C=C bonds is greater than that of C-C bonds due to greater electrostatic attraction caused by the increased number of localized electrons between the two positive nuclei.

The Types of Bonding

• Ionic bonding: Based on the exchange of positive (+) and negative (-) charges, this type of bonding is the strongest.
• Covalent bonding: Involves sharing orbital electrons, making it strong.
• Di-sulfide bonding: A strong type of covalent bond.
• Hydrogen bonding: A milder type of bonding.
• Van der Waals forces: Relatively weak interactions.
• Hydrophobic interactions: Interactions that involve a preference for avoiding water.

Macromolecules

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Discovery of Cells

• Robert Hooke discovered and named "cells" in 1665.
• He was observing tiny hollow compartments.

Anatomy of a Cell

• Several cellular processes occur within the confines of membranes.
• Cell components like cilia, Golgi apparatus, rough ER, smooth ER, nuclear envelope, nuclear pores, ribosomes, mitochondria, cytosol, centrioles, lysosomes, cytoskeleton, microvilli, and secretory vesicles are involved in various cellular activities.

Importance of Self-assembly

• Synthesized macromolecules, like proteins, nucleic acids, and lipids, demonstrate self-assembly characteristics.
• Once synthesized, these molecules spontaneously organize into specific structures (shapes and conformations).
• Molecular chaperones facilitate the correct folding of proteins.
• Hierarchical assembly offers quality control at each stage of the assembly process, allowing greater structural precision.

Macromolecules of the Cell

• Four main types, namely proteins, nucleic acids, polysaccharides, and lipids, are the primary macromolecules in cells.
• They are derived from simple organic molecules through the assembly of monomers.
• Monomers are the building blocks of macromolecules.

Monomers are the Building Blocks of Macromolecules

• Monomers act as building blocks for macromolecules.
• The analogy is drawn using LEGO blocks as a way to depict the construction of intricate structures.

Most Biological Macromolecules in Cells

• Most biological macromolecules are constructed from approximately 30 common small molecules, also known as monomers.
• The table lists types of molecules, number present, their names, their roles in the cell, and image numbers for the structures.

Macromolecules Synthesis

• Macromolecules are assembled through a stepwise process of polymerization of monomers.
• The addition of each monomer is accompanied by the removal of a water molecule, creating a condensation reaction.
• Monomers must be in an activated state for successful bonding in the condensation process.
• Activation involves attaching monomers to a carrier molecule, while ATP (or related compounds) provides the necessary energy.
• Macromolecules display inherent directionality.

Important Atom in the Biological Realm

• Carbon (C) is the most crucial atom in the biological realm.

Macromolecules: Nucleic Acids

• Nucleic acids are linear polymers of nucleotides.
• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are two major types.

Nucleic Acid Components

• Purines (adenine, guanine) and pyrimidines (thymine, uracil, cytosine) are important components of nucleotides.
• Nucleotides contain a phosphate group, a sugar, and a nitrogenous base.
• DNA and RNA differ in their composition and roles within the cell.

Nomenclature

• Nucleosides are precursors, consisting of a sugar attached to a base.
• Examples include adenosine, guanosine, cytidine, uridine (RNA) and deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine (DNA).
• Nucleotides are nucleosides with one or more phosphate groups attached. Examples are AMP, ADP, and ATP.
• RNA and DNA are polymers of nucleotides.

Nucleotides are the Monomers of Nucleic Acids

• Nucleotides are the building blocks of nucleic acids.
• The table displays detailed information about different DNA and RNA nucleotides.

Phosphorylated Forms of Adenosine

• ATP, GTP, CTP, and TTP (or UTP) are examples of phosphorylated forms of adenosine.
• These act as activated monomers in nucleic acid synthesis

The Polymers Are DNA and RNA

• DNA and RNA are polymers of nucleotides that are connected together by phosphodiester linkages.
• Directionality from 5' to 3' end.

Nucleic Acid Synthesis

• Nucleotides (NTPs for RNA, dNTPs for DNA) are added to a template molecule to ensure correct sequence.
• A template molecule provides the information for correct base pairing.
• Complementary base pairs (A-T/U, G-C) are held together by hydrogen bonds.

Nucleic Acid Synthesis: Exceptions

• Some viruses replicate their RNA from pre-existing RNA molecules using RNA-dependent RNA polymerases (RNA replicases).
• Certain viruses (like retroviruses, HIV) encode reverse transcriptases, which synthesize DNA from RNA molecules. -this is not common in cells

Nucleic Acid Synthesis direction

• Synthesis of nucleic acids progresses in the 5' to 3' direction.
• New nucleotides are added to the 3' end of an existing chain.

Chargaff's Rules

• DNA from different cells within the same species consistently has similar proportions of bases.
• Proportions of bases vary between species
• In DNA samples examined, the number of adenine (A) is equal to the number of thymine (T), while the number of guanine (G) equals the number of cytosine (C).

DNA Base Pair Calculation

• Given a DNA sequence with a total of 500 base pairs and 27% of the nucleotides are G.
• The number of T nucleotides is 46% and approximately 230 nucleotides.

Functions of Nucleic Acids

• Inside cells, nucleic acids are produced by proteins, requiring a pre-existing DNA or RNA template.
• The presence of a template ensures that correct base pairing occurs to copy cellular information efficiently..

RNA Exception in Viruses

• Some viruses use RNA replicase to synthesize RNA from pre-existing RNA.
• Retroviruses employ reverse transcriptases to make DNA from RNA sequences.

RNA Folding

• RNA structures can be very intricate and highly complex.

RNA's Role in Intermediacy Between DNA and Protein

• RNA acts as an intermediary for information transfer between DNA and proteins.
• mRNA, rRNA, and tRNA perform different roles in the cell.

RNA-Folding/Structure Translates to Its Function

• RNA binding proteins (RBPs') structures affect their function (processing, stability, localization, translation, function, interaction, and stability).

Types of RNA Molecules Based on Structure/Function

• Various types of RNA, such as mRNA (messenger RNA), tRNA (transfer RNA), rRNA (ribosomal RNA) and other types of non-coding RNAs (ncRNAs) are identified based on their structures and roles; including regulatory or housekeeping.

Properties of RNA

• RNA molecules contain ribose sugar, uracil, and form linear structural elements.

True Characteristics of RNA

• RNA includes uracil and can take a single-stranded form

Nucleic Acids Hierarchical Assembly

• DNA is usually a double helix, while RNA mostly takes a single-stranded shape, but exceptions exist in certain viruses.
• Secondary and tertiary RNA structures, in addition to DNA quaternary structures, are crucial for their function.

Becker's World of the Cell

• Textbook Chapter 3 information. (pages 58-62).

Acidic Component in DNA and RNA

• The phosphate group within DNA and RNA is responsible for their acidic properties.

This quiz explores the fundamental role of carbon in biological molecules, highlighting its unique bonding properties and valence. Understand how carbon interacts with other elements and the significance of bond types in molecular structure. Designed for biology students, this quiz tests your knowledge on the key concepts of carbon chemistry.