9/15 Viral Replication and Glycolysis Study Notes

Viral Replication: Latency and Lytic Cycles

Latent (Lysogenic) Stage

Definition: A stage where a virus is present in host cells but not actively replicating or causing symptoms. It integrates its genetic material into the host chromosome.
- Example: Chickenpox virus (Varicella-zoster virus) remains dormant in the body after initial infection, residing quietly in the dorsal root ganglia.
Mechanism of Integration:
- Instead of immediately destroying the host chromosome and taking over the cell, the viral DNA physically integrates into the host chromosome.
- Terminology: For animal viruses, the integrated viral DNA is called a provirus. For bacteriophages (viruses infecting bacteria), it's called a prophage.
- The virus becomes a physical part of the host cell's DNA.
Passive Replication:
- The virus is not actively making new virus particles. However, when the host cell replicates its DNA before dividing, it also copies the integrated viral DNA.
- Therefore, every time the host cell divides, both daughter cells inherit the viral DNA. The virus is passively replicated.
Absence of Symptoms: During latency, the host shows no signs or symptoms of viral infection because the virus is not expressed (repressed by specific viral genes).
Induction (Reactivation): The latent virus can re-enter the lytic cycle due to various triggers.
- Triggers: Stress is a major trigger. Stress can impair host cell function (e.g., altered eating, sleep, stress hormones), making the cell unhealthy.
- Viral Strategy: If the host cell's functioning declines or it's on the verge of dying, the virus must 'escape' to survive. If the cell dies with the virus integrated, the virus dies too.
- Process: The virus excises itself from the host chromosome, becomes an active virus, takes over the host cell's machinery, and begins replicating. This re-entry into the active state is called induction.
  - For a prophage, spontaneous induction occurs approximately every $10,000$ replications, or it can be triggered by external factors like UV light.
- Example: The chickenpox virus can reactivate years later, causing shingles, especially under stress. Cold sores (herpes virus) also exhibit this pattern of latency and reactivation.

Lytic Cycle

Definition: The active replication cycle where the virus takes control of the host cell's machinery to produce many new virus particles, ultimately leading to the lysis (bursting) of the host cell and release of progeny viruses.
Process (General Overview):
1. Absorption/Attachment: Virus binds to host cell receptors.
2. Penetration: Viral genetic material enters the host cell.
3. Synthesis: Virus immediately takes over cell machinery ( $ATP$ , ribosomes, nucleic acids, amino acids) to synthesize viral components (genetic material and proteins).
4. Assembly: Viral genetic material and proteins self-assemble into new, fully functional virus particles.
5. Release: The cell lyses, releasing a large number of viruses that can then infect other nearby cells.
Strategy: The lytic cycle is advantageous when there are many hosts available, aiming to rapidly produce a large "army" of viruses.

Entry Mechanisms into Host Cells

Bacteriophages: Directly inject their genetic material inside of the bacterial cell.
Other Viruses:
- Non-enveloped viruses: Trick cell receptors into allowing them entry.
- Enveloped viruses: Can use the receptor trick or directly fuse with the host cell membrane.

Impact of Lysogenic Viruses on Host Cells (Bacterial)

Example: Diphtheria:
- The bacterium Corynebacterium diphtheriae itself is not toxic.
- However, when it's infected by a specific virus that enters the lysogenic stage, the integrated provirus (prophage) carries and codes for the toxin responsible for diphtheria disease.
- This is a common phenomenon in bacteria, and these integrated viruses can confer new traits to the host.
Implications for Human Health:
- The human body contains billions of bacteria, many of which can be infected by lysogenic viruses.
- These prophages can alter the bacterial traits, potentially affecting human health (positively or negatively), even though the viruses are not directly infecting human cells.
- This is an emerging field of study, exploring links to heart disease, Multiple Sclerosis (MS), and other conditions.

Glycolysis: Breaking Down Sugars

Introduction

Definition: Glycolysis (from "glyco" referring to sugars, and "lysis" meaning to break down) is a metabolic pathway that breaks down sugars, particularly glucose, to produce energy.
Importance: It's a foundational process for all cells (microbes, humans, plants, algae, amoebas) to obtain energy.
Focus: The emphasis is on understanding the flow of the process rather than memorizing complex structures, compound names, or enzymes.
Location: Occurs in the cytoplasm of the cell; does not require any special structures or organelles, making it universal for all replicating cells.
Oxygen Requirement: Glycolysis does not require oxygen (it's an anaerobic process).

The "Billion Dollar Bill" Analogy

Glucose as a "Billion Dollar Bill": Glucose is a large energy source, but it's too big and "unusable" directly by the cell. It's like a billion-dollar bill that can't be used to buy a coffee or fill a gas tank.
ATP as Usable Currency: Cells need to break down glucose into smaller, usable energy units, which are $ATP$ molecules.

Steps of Glycolysis

Glycolysis is broadly divided into an energy investment phase and an energy payoff phase.

Starting Molecule: We begin with one molecule of glucose, a $6$ -carbon sugar.
Energy Investment Phase:
- Step 1: An $ATP$ molecule is used. A phosphate group from $ATP$ is added to the glucose molecule. $ATP$ becomes $ADP$ (adenosine diphosphate). Result: a $6$ -carbon sugar with one phosphate.
- Step 2: Another $ATP$ molecule is used. A second phosphate group from $ATP$ is added to the $6$ -carbon sugar. $ATP$ becomes $ADP$ . Result: a $6$ -carbon sugar with two phosphates.
- Instability: This $6$ -carbon molecule with two phosphates is inherently unstable and immediately splits in half.
- Outcome: Two molecules of Glyceraldehyde-3-phosphate ( $G3P$ ) are formed. Each $G3P$ molecule has $3$ carbons and $1$ phosphate.
- Net ATP used: So far, $2$ $ATP$ molecules have been consumed. This investment is like putting energy into lighting a bonfire (gasoline) to get a much larger energy release later.
Energy Payoff Phase: (This process happens twice, once for each $G3P$ molecule)
- Step 3: An inorganic phosphate ( $P_i$ ), not from $ATP$ , is added to each $G3P$ molecule.
  - To make space for the new phosphate, a hydrogen atom ( $H$ ) is removed from the molecule.
  - Hydrogen as Energy: Hydrogens represent energy because they consist of a proton and an electron. Moving electrons generates energy (like electricity).
  - Electron Carriers: The removed hydrogen (with its electron) is picked up by an electron carrier molecule called $NAD^+$ (Nicotinamide adenine dinucleotide).
  - $NAD^+$ accepts the hydrogen and its electron, becoming $NADH$ .
  - Significance of $NADH$ : $NADH$ will carry these high-energy electrons to the electron transport chain, where the majority of $ATP$ is generated.
  - Outcome: Each $G3P$ becomes a $3$ -carbon molecule with $2$ phosphates (let's call it $3C-2P$ ). Since we started with two $G3P$ , we now have two $3C-2P$ molecules and two $NADH$ molecules.
- Step 4 (and subsequent steps): The phosphates added in previous steps are gradually removed and transferred to $ADP$ molecules to create $ATP$ .
  - This direct transfer of a phosphate group from a substrate to $ADP$ to form $ATP$ is called substrate-level phosphorylation.
  - From each $3C-2P$ molecule, $2$ $ATP$ s are generated. Since there are two $3C-2P$ molecules, a total of $4$ $ATP$ s are produced in this phase.
- Final Product: The $3$ -carbon molecules ultimately become pyruvate (two molecules).

Net Yield of Glycolysis (per glucose molecule)

Net ATP:
- Used: $2$ $ATP$ (investment phase)
- Produced: $4$ $ATP$ (payoff phase)
- Net gain: $2$ $ATP$
$NADH$ : $2$ $NADH$
Pyruvate: $2$ molecules of pyruvate
Conclusion: While glycolysis directly produces only a small amount of $ATP$ ( $2$ net), its primary importance lies in producing pyruvate (which can proceed to the Krebs cycle) and, critically, $NADH$ , which fuels the electron transport chain for massive $ATP$ production.

Three Ways to Make ATP

Substrate-Level Phosphorylation:
- Mechanism: Direct transfer of a phosphate group from a high-energy substrate molecule to $ADP$ to form $ATP$ .
- Yield: Makes a small amount of $ATP$ (e.g., $2$ net $ATP$ in glycolysis). Not enough for complex organisms to survive on alone.
- Occurs in: Glycolysis, Krebs cycle.
Photophosphorylation:
- Mechanism: Energy from sunlight (photosynthesis) is used to add a phosphate to $ADP$ to form $ATP$ .
- Yield: No $ATP$ produced by humans or animals.
- Occurs in: Photosynthetic organisms like plants, algae, and diatoms.
Oxidative Phosphorylation:
- Mechanism: The vast majority of $ATP$ is made here. Electrons (carried by $NADH$ and $FADH_2$ from glycolysis and the Krebs cycle) are passed down an electron transport chain. The energy released drives the pumping of protons, creating a gradient that powers $ATP$ synthase to produce $ATP$ . This process requires oxygen.
- Yield: Produces a large amount of $ATP$ (over $30$ $ATP$ molecules).
- Occurs in: Animals, plants, and many microbes (in mitochondria for eukaryotes, cell membrane for prokaryotes). It's why humans breathe oxygen.
- Key Role of Glycolysis: Glycolysis produces $NADH$ , which is essential for fueling the electron transport chain in oxidative phosphorylation.