MDCAT Biology High-Yield Review: Acellular Life, Bioenergetics, and Biological Molecules

Characteristics and Classification of Viruses

Viruses are defined as non-cellular, obligate intracellular parasites that lack their own metabolic machinery. Because they possess no independent metabolism, they must replicate exclusively inside host cells by hijacking the host's cellular machinery. The classification of viruses is complex and organized based on several distinct criteria: morphology, genome composition, host specificity, and the presence or absence of an envelope.

In terms of morphology and shape, viruses are categorized as helical, polyhedral or icosahedral, or complex. A primary example of a helical virus is the Tobacco Mosaic Virus (TMV). Icosahedral viruses include Adenovirus and Poliovirus. Complex viruses, such as the Bacteriophages (specifically T2 and T4), possess a distinct head and tail structure.

Viral genomes are highly varied, consisting of either DNA or RNA in single-stranded or double-stranded forms. Double-stranded DNA (dsDNA) viruses include Poxvirus, Herpesvirus, and various Bacteriophages. Single-stranded DNA (ssDNA) is found in the Parvovirus. Double-stranded RNA (dsRNA) characterizes the Reovirus. Single-stranded RNA (ssRNA) is found in a wide variety of pathogens, including HIV, Influenza, Poliovirus, and other Retroviruses.

Host specificity remains a critical classification tool. Bacteriophages specifically infect bacterial cells. Phytophages target plant cells, such as the Tobacco Mosaic Virus (TMV). Zoophages infect animals; notable examples include the Rabies virus, HIV, and Influenza. Furthermore, viruses are classified by the presence of an envelope. Enveloped viruses, such as HIV and Influenza, possess an outer layer derived from the host cell membrane. Naked viruses, like the Poliovirus, lack this outer membrane layer.

AIDS and the Pathogenesis of HIV

The Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS). It is an enveloped, positive-sense single-stranded RNA (ssRNA) retrovirus. Retroviruses possess a unique ability to reverse the central dogma of molecular biology. By using the enzyme Reverse Transcriptase, they synthesize DNA from an RNA template. The process follows the sequence: $\text{RNA} \rightarrow \text{cDNA} \rightarrow \text{mRNA} \rightarrow \text{Protein}$. In addition to Reverse Transcriptase, HIV contains the enzymes Integrase and Protease, which are essential for its replication cycle.

HIV specifically targets Helper T-lymphocytes, also known as CD4+ T-cells. Infection begins when the viral glycoprotein gp120 binds to the CD4 receptors on the host cell surface. Transmission of the virus occurs through unscreened blood transfusions, the sharing of infected needles or syringes, unprotected sexual contact, and mother-to-child transmission via the placenta, childbirth, or breast milk. It is important to note that HIV is not spread by casual physical contact, saliva, or insect vectors.

The clinical symptoms and pathogenesis of HIV infection include chronic fever, rapid weight loss, persistent diarrhea, and lymphadenopathy (swelling of the lymph nodes). As the infection progresses, there is a severe depletion of CD4+ cells, which cripples the immune system. This leads to the onset of opportunistic infections such as Pneumocystis jirovecii pneumonia, Tuberculosis, and Kaposi’s sarcoma.

Bioenergetics: Cellular Respiration of Various Substrates

While glucose is the primary respiratory substrate, cells can also utilize fats and proteins for energy. Glucose-6-Phosphate and Glyceraldehyde 3-Phosphate (G3P) enter cellular respiration at the start of Glycolysis. This process yields Pyruvate, which undergoes oxidation to Acetyl-CoA before entering the Krebs Cycle. The final stage is Oxidative Phosphorylation, which generates ATP. The standard energy yield for one molecule of glucose is approximately $30\text{–}32\,\text{ATP}$.

Lipids, or fats, are broken down into glycerol and fatty acids. Glycerol is converted into DHAP or G3P and subsequently enters Glycolysis. Fatty acids undergo a process called $\beta$-Oxidation within the mitochondria to produce Acetyl-CoA, which then enters the Krebs Cycle. Fats are highly efficient energy sources, yielding more than double the energy per gram ($\sim 9\,\text{kcal/g}$) compared to carbohydrates ($\sim 4\,\text{kcal/g}$). This high energy density is due to a significantly higher proportion of $\text{C–H}$ bonds in lipids.

Proteins serve as an energy substrate primarily during periods of prolonged starvation or extreme carbohydrate deficiency. Amino acids first undergo deamination, a process where the amino group ($-\text{NH}_2$) is removed and eventually excreted as urea. The remaining carbon skeletons enter the metabolic pathway at various points, such as Pyruvate, Acetyl-CoA, or Krebs Cycle intermediates like $\alpha$-ketoglutarate, succinyl-CoA, and oxaloacetate.

Biological Importance of Water

Water ($\text{H}_2\text{O}$) constitutes $60\text{–}90\%$ of cellular mass. Its life-sustaining properties arise from its polar structure and ability to form extensive hydrogen bonds. In a water molecule, oxygen is highly electronegative, creating a partial negative charge ($\delta^-$) on the oxygen atom and a partial positive charge ($\delta^+$) on the hydrogen atoms. This polarity allows water to act as a universal solvent, dissolving polar substances and ionic compounds by forming hydration shells around them.

Water is a vital chemical reactant in hydrolysis, where it is used to break covalent bonds in complex polymers, such as the peptide or glycosidic bonds broken during digestion. It also possesses a high specific heat capacity, meaning a large amount of energy ($4.184\,\text{J}$ or $1\,\text{cal}$) is required to raise the temperature of $1\,\text{g}$ of water by $1\,^\circ\text{C}$. This allows water to act as a thermal buffer, protectively stabilizing cellular temperatures against environmental fluctuations.

The high heat of vaporization of water means it absorbs substantial energy when evaporating, which facilitates evaporative cooling, such as sweating in mammals or transpiration in plants. Uniquely, water exhibits a density anomaly; it expands upon freezing to form a hexagonal crystal lattice. This makes ice less dense than liquid water at $4\,^\circ\text{C}$, allowing ice to float and insulate aquatic habitats.

Water molecules exhibit cohesion (sticking to each other via H-bonds) and adhesion (sticking to polar surfaces like xylem walls). Together, these forces facilitate capillary action and the transpiration pull in plants. Finally, water ionizes into $\text{H}^+$ and $\text{OH}^-$ ions. At $25\,^\circ\text{C}$, the concentration of these ions is $10^{-7}\,\text{M}$, which is essential for maintaining biochemical acid-base equilibrium and buffer action.

Carbohydrates: Structure and Categories

Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these compounds upon hydrolysis. They follow the general empirical formula $\text{C}_n(\text{H}_2\text{O})_n$. They are categorized into three main groups: monosaccharides, oligosaccharides, and polysaccharides.

Monosaccharides are simple sugars consisting of a single polyhydroxy unit. They have a sweet taste, are highly soluble in water, and cannot be further hydrolyzed. They are reducing sugars because they possess a free aldehyde or keto group. Key examples include Glucose (a hexose and an aldose sugar, $\text{C}_6\text{H}_{12}\text{O}_6$, which is the major blood sugar), Fructose (a hexose and a ketose sugar, known as the sweetest natural sugar), and Ribose (a pentose sugar found in RNA and ATP).

Oligosaccharides contain between $2$ and $10$ monosaccharide units joined by glycosidic bonds formed via condensation reactions. They are less sweet and less soluble than monosaccharides. Sucrose, or cane sugar, is a non-reducing sugar composed of Glucose and Fructose linked by an $\alpha$-1,2 glycosidic linkage. Lactose, or milk sugar, consists of Glucose and Galactose with a $\beta$-1,4 linkage. Maltose consists of two Glucose units with an $\alpha$-1,4 linkage.

Polysaccharides are high molecular weight polymers containing more than $10$ monosaccharide units. They are non-sweet, insoluble in water, and are non-reducing sugars. Starch is the storage form in plants, consisting of Amylose (unbranched with $\alpha$-1,4 linkages) and Amylopectin (branched with both $\alpha$-1,4 and $\alpha$-1,6 linkages). Glycogen is the highly branched storage form found in animal liver and muscles. Cellulose is a structural component of plant cell walls, consisting of linear, unbranched chains with $\beta$-1,4 linkages.

Protein Structure and Levels of Organization

Proteins are polymers of amino acids linked by peptide bonds ($-\text{CO-NH}-$). A peptide bond is formed through a dehydration condensation reaction between the carboxyl group of one amino acid and the amino group of the next. Every amino acid has a central $\alpha$-carbon bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom ($-\text{H}$), and a variable side group ($-\text{R}$).

The primary structure of a protein is the specific linear sequence of amino acids, which is dictated by the genetic code. The secondary structure involve the regular folding of the polypeptide chain, stabilized by hydrogen bonds along the backbone. This results in the formation of the spiral $\alpha$-helix or the $\beta$-pleated sheet. The tertiary structure is a complex 3D globular conformation formed by the folding of secondary structures. It is maintained by disulfide bonds ($\text{S–S}$), ionic bonds, hydrogen bonds, and hydrophobic interactions. The quaternary structure refers to the spatial arrangement of two or more polypeptide subunits. Hemoglobin is a prime example, consisting of two $\alpha$ and two $\beta$ chains.

Lipids and Biochemical Linkages

Lipids are a heterogeneous group of organic compounds that are insoluble in water but soluble in non-polar organic solvents like ether, chloroform, and benzene. Acylglycerols, or triglycerides, are esters composed of one glycerol molecule linked to three fatty acids via ester linkages ($-\text{COO}-$). These serve as the primary long-term energy storage in adipose tissue. Saturated fatty acids have no double bonds and are solid at room temperature (e.g., animal fats), while unsaturated fatty acids have one or more double bonds and are liquid at room temperature (e.g., plant oils).

Phospholipids consist of one glycerol, two fatty acids (the hydrophobic tail), and one phosphate group attached to an alcohol or choline (the hydrophilic head). These amphipathic molecules are the fundamental structural components of cell membranes, forming the lipid bilayer. Waxes are esters of long-chain fatty acids with high molecular weight long-chain monohydric alcohols. They form protective hydrophobic coatings on plant leaves (cuticle), insect exoskeletons, and animal skin or feathers to prevent water loss.

The key biochemical linkages to remember are: glycosidic linkages ($\text{C–O–C}$) for carbohydrates, peptide linkages ($\text{C–N}$ or $-\text{CO-NH}-$) for proteins, and ester linkages ($\text{C–O–C=O}$) for lipids such as triglycerides.