lecture_11_full_3

Announcements

• No lecture or student hours on Friday of this week.

• Pre- and post-class questions are to be submitted as usual, allowing for continuous engagement and comprehension assessment.

• Please note that the lecture recording from Fall 2024 will serve as the primary content for this week's discussions.

• There are designated times to review exam questions (located in 200 Burrill Hall):

  • Today: 3:30-5:00 PM

  • Tuesday: 10:30-Noon

  • Thursday: 9:30-11:00 AM

Cellular Respiration Overview

Phase 2: Pyruvate Oxidation and Krebs Cycle

• During this phase, there is a significant transition of energy from glucose to pyruvate and subsequently to the Krebs Cycle. The full oxidation of one glucose molecule encompasses several critical steps that ultimately convert energy into forms usable by the cell.

Problems at the End of Krebs Cycle

• NAD+ Replacement Issues:

  • In certain conditions, NAD+ may not be adequately replaced, leading to an accumulation of NADH. As NADH accumulates, it impairs cellular respiration efficiency, as NAD+ is crucial for several metabolic pathways.

  • FADH2 also requires re-oxidation, and if not accomplished, it contributes to energy transfer inefficiencies where energy carried by cofactors is not efficiently converted to ATP.

• Dependence on Oxygen:

  • Although aerobic respiration requires oxygen, the Krebs Cycle itself functions without it. However, it is essential for connecting to the Electron Transport Chain (ETC), where oxygen serves as the final electron acceptor, maintaining the flow of electrons through the chain.

Oxidative Phosphorylation

Electron Transport Chain (ETC)

• The process begins when NADH donates electrons; this not only regenerates NAD+ but also allows NAD+ to partake in critical redox reactions.

• The electrons travel down a series of carriers, and as they progress, they release energy that is harnessed to pump protons across the inner mitochondrial membrane. This activity creates an electrochemical proton gradient essential for ATP synthesis.

Last Steps of ETC

• The final electron carrier in the chain transfers electrons to oxygen, which combines with protons to form water, a byproduct of cellular respiration.

• FADH2 bypasses Complex I during the process, leading to fewer protons being pumped into the intermembrane space, which results in a lower contribution to the creation of the electrochemical gradient compared to NADH.

ATP Production Theoretical Calculation

• The theoretical ATP yield from the complete oxidation of glucose can be summarized as follows:

  • 2 ATP from Glycolysis.

  • 4 ATP from 2 NADH produced during Glycolysis (2 ATP each).

  • 2 ATP (GTP, which can be converted to ATP) from the Krebs Cycle.

  • 24 ATP from 8 NADH generated in Krebs Cycle (3 ATP each).

  • 4 ATP from 2 FADH2 produced in Krebs Cycle (2 ATP each).

• Total: This culminates in a total theoretical yield of 36 ATP per glucose molecule under ideal conditions.

Fermentation and Metabolic Regulation

Fermentation in Anaerobic Conditions

• Under anaerobic conditions, glycolysis remains active while the Krebs Cycle and oxidative phosphorylation cease, leading to ATP being generated solely through glycolysis. In this scenario, pyruvate may be converted into fermentation products, effectively regenerating NAD+ without producing additional ATP per glucose molecule.

• Such conditions can lead to the accumulation of various fermentation products that also influence cellular metabolism.

Types of Fermentation

• In Yeast:

  • Fermentation converts pyruvate into ethanol and carbon dioxide, a process exploited in brewing and baking.

• In Muscle Cells:

  • The conversion of pyruvate to lactic acid occurs, which can lead to muscle fatigue under strenuous activity.

Regulation of Pathways

• Metabolic pathways that involve catabolism and biosynthesis require tight regulation to ensure energy efficiency. The regulation is influenced by:

  • The amount of specific enzymes present in the cellular environment.

  • The activity levels of allosterically regulated enzymes that respond to cellular energy states.

Allosteric Regulation Mechanisms

• Allosteric regulators are essential as they bind to sites outside of the active site on enzymes, leading to changes in enzyme activity:

  • Positive Regulators: Generally increase enzyme activity, enhancing metabolic flux.

  • Negative Regulators: Decrease enzyme activity, providing feedback to prevent overproduction of certain metabolites.

Feedback Inhibition

• An example of feedback inhibition is when ATP binds to phosphofructokinase (PFK), inhibiting glycolysis when energy levels are sufficient. Conversely, ADP (or AMP) binding to PFK activates glycolysis to promote ATP production when energy is low.

Structure and Function of DNA

Central Dogma of Molecular Biology

• DNA is fundamental in encoding genetic information that directs protein synthesis, following the central dogma pathway:

  • DNA → RNA (Transcription): The process wherein DNA is transcribed to mRNA.

  • RNA → Protein (Translation): The conversion of mRNA into a polypeptide chain at ribosomes.

Discovery of DNA's Function

• In the 1940s, it was established that inheritance resides in chromosomes composed of DNA, overcoming the earlier misconception that proteins were the genetic material due to their complex structure.

Structure of DNA

Chargaff’s Rules

• Chargaff elucidated base pairing rules, indicating that the concentration of adenine (A) equals thymine (T) and that of cytosine (C) equals guanine (G).

X-ray Diffraction Insights

• Pioneering work by Rosalind Franklin and Maurice Wilkins yielded critical insights into the helical structure of DNA, which were fundamental to Watson & Crick's comprehensive model.

• DNA comprises complementary base pairs, which are linked by hydrogen bonds, creating the double helix structure vital for its function.

DNA Replication and Its Mechanics

Stages of DNA Replication

• Key stages include:

  • Determining the starting point (origin of replication).

  • Strand separation facilitated by helicase enzymes.

  • Addition of short RNA primers to initiate synthesis.

  • Synthesis of new strands by DNA polymerases that extend primers.

  • Cleanup and sealing of newly synthesized strands by various enzymes.

Leading and Lagging Strands

• DNA is replicated in the 5' to 3' direction; the leading strand is synthesized continuously, while the lagging strand is constructed in discontinuous sections termed Okazaki fragments.

Enzyme Roles

• Primase: Synthesizes the RNA primers that are necessary for DNA polymerase action.

• DNA Ligase: Seals nicks created between Okazaki fragments once the RNA primers have been replaced by DNA.

Key Terminology and Processes in DNA Replication

• The use of nomenclature, such as “X-Dependent Y-Synthesizing Enzyme,” provides clarity in discussing enzymatic roles in replication.

• Understanding nuclease activity is crucial; types of nucleases, including exonucleases and endonucleases, play vital roles in maintaining DNA integrity and allowing for repair mechanisms.

Proofreading Mechanisms

• DNA polymerases possess 3'→5' exonuclease activity, which allows for the correction of errors during DNA synthesis, significantly enhancing replication fidelity and cellular stability.

DNA Organization

Chromatin Structure

• DNA is compactly organized into chromatin; nucleosomes form the basic structural units wherein DNA is wrapped around histones.

• Supercoiling and further organizational modifications result in higher-order structures that facilitate efficient DNA packaging within the cellular nucleus.

Eukaryotic Chromatin Complexity

• Chromatin exists in two main forms: euchromatin, which is active and loosely packed for accessibility; and heterochromatin, which is inactive and densely packed, playing a crucial role in gene regulation and expression.

Summary of DNA Processes

DNA Transcription and Processing

• RNA polymerase is responsible for transcribing DNA into RNA, involving processes such as promoter recognition and elongation.

• Post-transcriptional modifications include important steps like capping, polyadenylation of the 3' end, and intron removal to produce mature mRNA ready for translation.

Protein Translation

• The synthesis of proteins involves the collaboration of mRNA, tRNA, and rRNA at ribosomes. The genetic code, composed of triplet codons, dictates the sequence of amino acids in polypeptides, ultimately determining protein function.