Premed · Premed · General Biology 1

Lecture 4: Biological Macromolecules II — Proteins and Nucleic Acids

General Biology I — Molecular & Cellular

Learning Objectives

By the end of this lecture, students will be able to:

1. Describe the structure of amino acids and explain how peptide bonds form
2. Distinguish among the four levels of protein structure and explain the forces stabilizing each
3. Explain how protein structure relates to function and describe denaturation
4. Describe the structure of nucleotides and the differences between DNA and RNA
5. Explain the role of ATP as the energy currency of the cell

Lecture Content

I. Proteins — Overview

Proteins are the most structurally and functionally diverse class of biological macromolecules. Built from amino acid monomers linked by peptide bonds, they carry out an astonishing range of cellular tasks. As enzymes, proteins catalyze virtually every chemical reaction in the cell--DNA polymerase copies DNA, lactase breaks down lactose, and thousands of others keep metabolism running. As structural elements, proteins like collagen, keratin, actin, and tubulin provide shape and mechanical support to cells and tissues. Transport proteins such as hemoglobin carry oxygen through the bloodstream, while membrane channels and carriers shuttle ions and molecules across the plasma membrane. Antibodies (immunoglobulins) defend the body against pathogens. Protein hormones like insulin and their corresponding receptors mediate cell signaling. Motor proteins--myosin, kinesin, and dynein--convert chemical energy into mechanical movement. Storage proteins like casein in milk and ferritin for iron sequestration hold reserves of nutrients. And transcription factors regulate gene expression by binding DNA. In short, proteins are the primary executors of the genetic instructions encoded in DNA.

II. Amino Acid Structure

All twenty standard amino acids share a common core architecture: a central alpha carbon bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable R group (side chain). It is the R group that distinguishes one amino acid from another, determining its chemical properties and behavior within a protein. Amino acids are classified by their R groups into four categories. Nonpolar (hydrophobic) amino acids--including glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine--tend to cluster in the interior of proteins, away from water. Polar (uncharged) amino acids such as serine, threonine, cysteine, tyrosine, asparagine, and glutamine can form hydrogen bonds; cysteine is particularly notable because its sulfhydryl group can form covalent disulfide bonds with another cysteine. Positively charged (basic) amino acids--lysine, arginine, and histidine--carry a positive charge at physiological pH, while the negatively charged (acidic) amino acids aspartate and glutamate carry a negative charge.

All amino acids except glycine are chiral, meaning they exist in two mirror-image forms. Biological systems use exclusively the L-isomer. At physiological pH (approximately 7.4), amino acids exist as zwitterions, carrying both a positive charge on the amino group (-NH3+) and a negative charge on the carboxyl group (-COO-).

III. Peptide Bonds and Polypeptides

A peptide bond is the covalent linkage that joins amino acids in a protein. It forms through a dehydration synthesis reaction between the carboxyl group of one amino acid and the amino group of the next, releasing a water molecule. The peptide bond has partial double-bond character, which makes it planar and rigid, while the bonds flanking it (characterized by the phi and psi angles) permit rotation, giving the polypeptide chain its flexibility.

A polypeptide is a chain of amino acids linked by peptide bonds. It has inherent directionality: one end carries a free amino group (the N-terminus) and the other a free carboxyl group (the C-terminus). By convention, protein sequences are written from N-terminus to C-terminus. A short chain of fewer than about fifty amino acids is typically called a peptide, while longer chains are referred to as polypeptides or proteins. A functional protein may consist of a single polypeptide or of multiple polypeptide chains (subunits) working together.

IV. Levels of Protein Structure

Protein architecture is described at four hierarchical levels, each building upon the last.

Primary structure is simply the linear sequence of amino acids in a polypeptide, dictated by the gene that encodes it. This sequence is absolutely critical--even a single amino acid change can dramatically alter function. Sickle cell disease provides a stark example: the substitution of valine for glutamic acid at position 6 of beta-globin causes hemoglobin molecules to polymerize under low-oxygen conditions, distorting red blood cells into a sickle shape.

Secondary structure refers to local, regularly repeating folding patterns that arise from hydrogen bonds between backbone atoms (specifically, between the N-H of one peptide bond and the C=O of another). The two most common secondary structures are the alpha helix, a tightly coiled structure stabilized by hydrogen bonds between every fourth amino acid along the backbone, and the beta pleated sheet, in which segments of the polypeptide lie side by side (in parallel or antiparallel orientations) and are connected by hydrogen bonds. Loops and turns connect these elements and often reside on the protein surface.

Tertiary structure is the overall three-dimensional shape of a single polypeptide chain, determined by interactions among the R groups of its amino acids. Hydrophobic interactions drive nonpolar side chains into the protein interior, away from water. Hydrogen bonds, ionic bonds (salt bridges), and van der Waals forces all contribute, along with covalent disulfide bonds between cysteine residues, which are the strongest of the stabilizing forces. Tertiary structure is what gives a protein its biological activity--an enzyme's active site, for instance, is a pocket or cleft whose precise three-dimensional geometry is a direct consequence of tertiary folding.

Quaternary structure describes the arrangement of two or more polypeptide subunits into a functional complex. The same types of interactions that stabilize tertiary structure--hydrophobic interactions, hydrogen bonds, ionic bonds, and sometimes disulfide bonds--hold the subunits together. Hemoglobin, with its two alpha and two beta subunits, and collagen, with its triple helix of three polypeptide chains, are classic examples. Not all proteins possess quaternary structure; many function as single polypeptide chains.

<image>A four-panel figure showing the hierarchy of protein structure. Panel A: Primary structure — a linear chain of amino acids with single-letter codes, showing peptide bonds connecting them, with the N-terminus on the left and C-terminus on the right. Panel B: Secondary structure — a ribbon diagram showing an alpha helix (coiled ribbon) with hydrogen bonds as dashed lines between backbone atoms, and a beta pleated sheet (flat arrows) with hydrogen bonds between strands. Panel C: Tertiary structure — a complete 3D protein fold (globular shape) with labeled interactions: hydrophobic core, disulfide bond (S-S), ionic bond, and hydrogen bond. Panel D: Quaternary structure — hemoglobin with four subunits (two alpha in blue, two beta in red) each containing a heme group.</image>

V. Protein Folding and Denaturation

A protein must fold into its correct three-dimensional shape to carry out its function, and this process is far from trivial. Chaperone proteins such as Hsp70 and the barrel-shaped chaperonins (like GroEL/GroES in bacteria) assist nascent polypeptides in folding correctly by providing a sheltered environment that prevents inappropriate aggregation with other molecules.

Denaturation is the loss of a protein's three-dimensional structure--and therefore its function--caused by disruption of the non-covalent interactions that maintain its shape. Heat, extreme pH, organic solvents, detergents, and heavy metals can all cause denaturation. Importantly, denaturation does not break the peptide bonds; the primary structure remains intact. In some cases, denaturation is reversible--if the denaturing agent is removed, the protein may refold spontaneously. In other cases, such as frying an egg, denaturation is irreversible.

Misfolded proteins can be dangerous. When proteins fail to achieve or maintain their proper conformation, they may aggregate into insoluble masses that damage cells. Prion diseases, including mad cow disease and Creutzfeldt-Jakob disease, are caused by a misfolded form of the prion protein that propagates by inducing normal copies to adopt the pathological conformation. In Alzheimer's disease, the accumulation of misfolded amyloid-beta peptides into plaques and the aggregation of hyperphosphorylated tau protein into tangles contribute to neurodegeneration.

VI. Nucleic Acids — Overview

Nucleic acids are the molecules responsible for storing, transmitting, and expressing genetic information. The two types--DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)--are both polymers of nucleotide monomers.

VII. Nucleotide Structure

Each nucleotide consists of three components. The nitrogenous base carries the genetic information and comes in two varieties: the double-ringed purines, adenine (A) and guanine (G), and the single-ringed pyrimidines, cytosine (C), thymine (T) (found only in DNA), and uracil (U) (found only in RNA). The pentose sugar is deoxyribose in DNA (lacking a hydroxyl group at the 2' position) or ribose in RNA (retaining that 2'-OH). One to three phosphate groups are attached at the 5' carbon of the sugar.

VIII. DNA vs. RNA

DNA and RNA differ in several key respects. DNA uses deoxyribose sugar and the bases A, T, G, and C; RNA uses ribose and replaces thymine with uracil. DNA is typically double-stranded and forms the famous double helix, while RNA is usually single-stranded, though it can fold into complex secondary structures. Functionally, DNA serves as the long-term repository of genetic information, while RNA participates in gene expression and regulation. DNA is also the more chemically stable of the two, in part because the absence of the 2'-OH on deoxyribose makes DNA more resistant to hydrolysis.

The DNA double helix consists of two antiparallel strands (one running 5' to 3', the other 3' to 5') wound around each other. Complementary base pairing holds them together: adenine pairs with thymine through two hydrogen bonds, and guanine pairs with cytosine through three. The sugar-phosphate backbone forms the outer rails of the helix, while the bases are stacked on the inside. The helical twist creates major and minor grooves that serve as important sites for protein-DNA interaction.

Several types of RNA fulfill distinct roles. Messenger RNA (mRNA) carries genetic information from DNA to the ribosome. Transfer RNA (tRNA) ferries amino acids to the ribosome during translation. Ribosomal RNA (rRNA) is both a structural and catalytic component of ribosomes themselves. A growing roster of additional RNA species--including snRNA, miRNA, siRNA, and lncRNA--play vital regulatory roles in gene expression.

<image>A two-panel figure. Panel A: Structure of a nucleotide showing the phosphate group attached to the 5' carbon of the pentose sugar, the nitrogenous base attached to the 1' carbon, and the 3'-OH group. Deoxyribose and ribose are compared side by side with the 2' position highlighted (H vs. OH). Panel B: DNA double helix showing antiparallel strands with sugar-phosphate backbone, complementary base pairs (A-T with 2 H-bonds, G-C with 3 H-bonds), major and minor grooves, and 5' to 3' directionality labeled on each strand.</image>

IX. ATP — Adenosine Triphosphate

ATP is a nucleotide derivative that serves as the primary energy currency of the cell. It consists of the nitrogenous base adenine, the sugar ribose, and a chain of three phosphate groups. Energy is stored in the phosphoanhydride bonds between the phosphate groups--bonds that are high-energy because the closely spaced negative charges on the phosphates repel one another. When ATP is hydrolyzed to ADP (adenosine diphosphate) and inorganic phosphate (Pi), approximately 7.3 kilocalories per mole of free energy is released. This energy is not wasted as heat; instead, it is harnessed through energy coupling to drive endergonic reactions--reactions that would not proceed spontaneously on their own.

The human body turns over a staggering 200 to 300 moles of ATP per day, yet at any given moment the total amount of ATP in the body is quite small. This means ATP is continuously recycled: ADP and Pi are reassembled into ATP by the processes of cellular respiration (and, in photosynthetic organisms, by photosynthesis). While ATP is the most widely used energy carrier, other nucleotide triphosphates--GTP, CTP, and UTP--play important roles in specific metabolic pathways.

X. Other Important Nucleotide Derivatives

Several nucleotide-derived molecules merit mention. NAD+/NADH and FAD/FADH2 are electron carriers that shuttle high-energy electrons through the metabolic pathways of cellular respiration. Cyclic AMP (cAMP), derived from ATP by the enzyme adenylyl cyclase, serves as a crucial second messenger in cell signaling cascades. Coenzyme A (CoA), which contains a nucleotide component, carries acetyl groups in metabolism and is essential for the citric acid cycle and fatty acid oxidation. These molecules illustrate a recurring theme in biology: evolution has repurposed the nucleotide as a versatile molecular building block, using it not only for information storage but also for energy transfer, electron transport, and cellular communication.

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