Chapter 1 Macromolecules of the Cell: Structure and Function of Proteins and Nucleic Acids

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The Macromolecules of the Cell

Overview of Biological Macromolecules

Cells are composed of a diverse array of macromolecules, primarily synthesized from a limited set of small molecules. These macromolecules include proteins, nucleic acids, polysaccharides, and lipids, each with distinct monomeric units and biological roles.

Proteins: Polymers of amino acids, responsible for catalysis, structure, transport, signaling, and defense.
Nucleic Acids: Polymers of nucleotides, essential for storage, transmission, and expression of genetic information.
Polysaccharides: Polymers of sugars, involved in energy storage and structural support.
Lipids: Diverse group, not true polymers, but important for membrane structure and energy storage.

Kind of Molecule	Number Present	Names of Molecules	Role in Cell
Amino acids	20	See list in Table 3-2	Monomeric units of all proteins
Asymmetric bases	5	Adenine, Guanine, Cytosine, Thymine, Uracil	Components of nucleic acids
Sugars	varies	Ribose, Deoxyribose, Glucose	Components of RNA, DNA, energy metabolism
Lipids	varies	Fatty acids, Cholesterol	Components of membranes, energy storage

Table of common small molecules in cells

Proteins: Structure and Function

Diversity of Protein Function

Proteins are the most functionally diverse macromolecules in the cell, performing a wide range of tasks:

Enzymes: Catalyze biochemical reactions.
Structural proteins: Provide support and shape (e.g., collagen, keratin).
Motility proteins: Enable movement (e.g., actin, myosin).
Regulatory proteins: Control cellular processes (e.g., transcription factors).
Transport proteins: Move substances across membranes (e.g., hemoglobin, ion channels).
Signaling proteins: Mediate communication (e.g., hormones, growth factors).
Receptor proteins: Detect and respond to signals.
Defensive proteins: Protect against pathogens (e.g., antibodies).
Storage proteins: Store amino acids or ions (e.g., ferritin).

Amino Acids: The Monomers of Proteins

Proteins are linear polymers of 20 standard amino acids, each with a common structure: a central (α) carbon, an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain).

General structure of amino acids and isomerism

L- and D-isomers: Most amino acids exist as L- and D-isomers, but only L-amino acids are incorporated into proteins. Glycine is unique in lacking chirality and thus does not have separate L and D forms.

Structures of the 20 amino acids

Amino Acid	Three-Letter Abbreviation	One-Letter Abbreviation
Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
Cysteine	Cys	C
Glutamine	Gln	Q
Glutamic acid	Glu	E
Glycine	Gly	G
Histidine	His	H
Isoleucine	Ile	I
Leucine	Leu	L
Lysine	Lys	K
Methionine	Met	M
Phenylalanine	Phe	F
Proline	Pro	P
Serine	Ser	S
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
Valine	Val	V

Amino acid abbreviations table

Peptide Bond Formation and Protein Structure

Amino acids are joined by peptide bonds through dehydration (condensation) reactions, forming polypeptides with directionality (N-terminus to C-terminus).

Peptide bond formation between amino acids

Polypeptide: Linear chain of amino acids.
Protein: A functional molecule, which may consist of one or more polypeptides.

Levels of Protein Structure

Proteins exhibit hierarchical structural organization, each level stabilized by specific bonds and interactions.

Level of Structure	Basis of Structure	Kinds of Bonds and Interactions Involved
Primary	Amino acid sequence	Covalent peptide bonds
Secondary	Folding into α helix, β sheet, or random coil	Hydrogen bonds between NH and CO groups of peptide bonds in the backbone
Tertiary	Three-dimensional folding of a single polypeptide chain	Disulfide bonds, hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic interactions
Quaternary	Association of multiple polypeptides to form a multimeric protein	Same as for tertiary structure

Table of protein structure levels Diagram of primary, secondary, tertiary, and quaternary protein structure

Primary Structure

The primary structure is the unique sequence of amino acids in a polypeptide, determined by the gene encoding the protein. This sequence dictates all higher levels of structure.

Secondary Structure

Secondary structure refers to local folding patterns stabilized by hydrogen bonds between backbone atoms. The two main types are:

α Helix: A right-handed coil with hydrogen bonds between every fourth amino acid.
β Sheet: Extended strands connected by hydrogen bonds, can be parallel or antiparallel.

Alpha helix structure Beta sheet structure

Common motifs include β-α-β motifs, hairpin loops, and helix-turn-helix motifs.

Common secondary structure motifs

Tertiary Structure

Tertiary structure is the overall three-dimensional shape of a single polypeptide, stabilized by interactions among R groups (side chains). These include hydrophobic interactions, hydrogen bonds, ionic bonds, van der Waals forces, and disulfide bridges.

Types of bonds in tertiary protein structure

Quaternary Structure

Quaternary structure arises when two or more polypeptide chains (subunits) associate to form a functional protein complex. The arrangement and interaction of these subunits are critical for protein function.

Hemoglobin quaternary structure

Fibrous and Globular Proteins

Fibrous proteins: Extended, repetitive secondary structure (e.g., silk fibroin, keratin in hair).
Globular proteins: Compact, complex tertiary structure (e.g., enzymes, hemoglobin).

Keratin structure in hair

Nucleic Acids: Structure and Function

Nucleic Acid Components

Nucleic acids are polymers of nucleotides, each composed of a phosphate group, a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base (purine or pyrimidine).

Nucleotide structure: phosphate, sugar, base

DNA: Deoxyribonucleic acid, stores genetic information.
RNA: Ribonucleic acid, involved in gene expression and regulation.

Nucleotide Nomenclature

Nucleotides are named based on their base, sugar, and number of phosphate groups (e.g., AMP, ADP, ATP).

Adenosine and its phosphorylated forms

Bases	RNA Nucleotide	DNA Nucleotide
Adenine	Adenosine monophosphate (AMP)	Deoxyadenosine monophosphate (dAMP)
Guanine	Guanosine monophosphate (GMP)	Deoxyguanosine monophosphate (dGMP)
Cytosine	Cytidine monophosphate (CMP)	Deoxycytidine monophosphate (dCMP)
Uracil	Uridine monophosphate (UMP)	—
Thymine	—	Deoxythymidine monophosphate (dTMP)

Table of bases, nucleosides, and nucleotides

Polynucleotide Structure

Nucleotides are joined by 3',5'-phosphodiester bonds, forming a sugar-phosphate backbone with directionality (5' to 3').

DNA and RNA polynucleotide chains

Base Pairing and Double Helix

DNA is typically double-stranded, with complementary base pairing (A-T, G-C) and antiparallel strands. RNA is usually single-stranded but can form local double-stranded regions via intramolecular base pairing.

Complementary base pairing in DNA DNA double helix structure

Hydrogen bonds: Two between A and T (or A and U in RNA), three between G and C.
Antiparallel orientation: The two DNA strands run in opposite directions (5' to 3' and 3' to 5').

Nucleic Acid Synthesis

Nucleic acids are synthesized using a template strand, ensuring correct base pairing and sequence fidelity. DNA replication and transcription rely on complementary relationships between purines and pyrimidines.