Chapter 5 - Part 2 Study Notes : Proteins and Nucleic Acids: Structure, Function, and Biological Importance

Proteins and Nucleic Acids

Introduction

Proteins and nucleic acids are two major classes of biological macromolecules essential for life. Proteins perform a wide variety of functions in cells, while nucleic acids store and transmit genetic information. This study guide summarizes their structure, function, and significance in biology.

Section 5.4: Proteins – Diversity of Structure and Function

Protein Structure Overview

Proteins are polymers made from amino acid monomers. Their structure determines their function, and they exhibit a remarkable diversity in both.

• Monomer: Amino acid

• Polymer: Polypeptide

• Functional Protein: One or more polypeptides folded into a specific 3D shape

Levels of Protein Structure

Proteins have four levels of structural organization, each contributing to their final shape and function.

• Primary Structure: The unique sequence of amino acids in a polypeptide chain. Example: The order of amino acids in insulin determines its ability to regulate blood sugar.

• Secondary Structure: Local folding of the polypeptide chain into structures such as alpha helices and beta sheets, stabilized by hydrogen bonds. Example: The alpha helix in keratin provides strength to hair and nails.

• Tertiary Structure: The overall 3D shape of a single polypeptide, formed by interactions among R groups (side chains), including hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges. Example: The globular shape of enzymes allows them to catalyze specific reactions.

• Quaternary Structure: The association of multiple polypeptide subunits into a functional protein complex. Example: Hemoglobin consists of four polypeptide subunits that work together to transport oxygen.

Amino Acids: Structure and Properties

Amino acids are the building blocks of proteins. Each amino acid has a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain).

• N-terminus: The end of a polypeptide with a free amino group.

• C-terminus: The end of a polypeptide with a free carboxyl group.

• Peptide Bond: The covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water. Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains (R groups), which affect protein structure and function.

• Non-polar (hydrophobic): Glycine, Alanine, Valine, Cysteine, Proline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine

• Polar (hydrophilic): Serine, Threonine, Tyrosine, Asparagine, Glutamine

• Charged (acidic/basic): Aspartic acid, Glutamic acid (acidic); Lysine, Arginine, Histidine (basic)

Type	Amino Acids
Non-polar	Glycine, Alanine, Valine, Cysteine, Proline, Leucine, Isoleucine, Methionine, Tryptophan, Phenylalanine
Polar	Serine, Threonine, Tyrosine, Asparagine, Glutamine
Charged	Aspartic acid, Glutamic acid, Lysine, Arginine, Histidine

Essential vs Nonessential Amino Acids

Some amino acids must be obtained from the diet (essential), while others can be synthesized by the body (nonessential).

• Essential amino acids: Cannot be synthesized by the body; must be obtained from food.

• Nonessential amino acids: Can be synthesized by the body.

Essential Amino Acids	Nonessential Amino Acids
Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine	Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine

Example: Combining beans and rice provides all essential amino acids for vegetarians.

Section 5.5: Nucleic Acids – Storage and Transmission of Hereditary Information

Nucleic Acid Structure

Nucleic acids are polymers made of nucleotide monomers. They store, transmit, and help express genetic information.

• Monomer: Nucleotide (composed of a pentose sugar, phosphate group, and nitrogenous base)

• Polymer: Polynucleotide (DNA or RNA)

Nucleotide Structure

• Pentose sugar: Ribose (RNA) or deoxyribose (DNA)

• Phosphate group: Forms the backbone of the nucleic acid

• Nitrogenous base: Purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil)

Type	Bases
Purines	Adenine (A), Guanine (G)
Pyrimidines	Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

DNA vs RNA

DNA and RNA differ in structure and function.

• DNA: Double-stranded, contains deoxyribose, bases are A, T, C, G

• RNA: Single-stranded, contains ribose, bases are A, U, C, G

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double	Single
Bases	A, T, C, G	A, U, C, G

Section 5.6: Genomics and Proteomics

Genomics and Proteomics in Biological Inquiry

Genomics is the study of whole sets of genes and their interactions, while proteomics is the study of the entire set of proteins produced by an organism. These fields have revolutionized biological research and medical applications.

• Genomics: Involves sequencing, analyzing, and comparing genomes.

• Proteomics: Involves identifying and studying proteins, their structures, and functions.

• Applications: Disease diagnosis, personalized medicine, biotechnology, and understanding evolutionary relationships.

Additional info:

• Protein denaturation refers to the loss of structure and function due to environmental changes (e.g., heat, pH).

• Mutations in protein-coding genes can lead to diseases such as sickle cell anemia, where a single amino acid change alters hemoglobin structure and function.

• Recent advances in mRNA vaccines (e.g., COVID-19 vaccines) utilize nucleic acid technology to stimulate immune responses.