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Academic Work

MIT Climate Grand Challenges

The agriculture sector (AS) in the US is primarily based on raising livestock and crops for consumption and accounts for approximately 10% of the total greenhouse gas (GHG) emissions; a breakdown of contributions includes manure management -13%, enteric fermentation -28%, and crop/soil management -59% [1]. Nitrous oxide (global warming potential [GWP] 298x of CO2) accounts for 58% of agricultural GHG emissions and methane (GWP 25x) 41% [2]. US, China, India, and Brazil account for a third of the total GHG emissions from agriculture [3]. Compounding the problem, food waste accounts for 6% of total anthropogenic GHG emissions [4]. Besides food production, the AS directly contributes to the biofuel economy; one-third of corn produced in the US in 2020 was used for ethanol production [5]. However, N fertilizer synthesis and N2O emissions contributed 61% to GHG emissions from corn production, greatly reducing biofuel climate gains [6]. Given the unprecedented extreme weather events broached by global warming within the last few decades, it is imperative that GHG emissions be significantly reduced to counter the effects of climate change. 

Book Chapters

Excerpt from Chapter: Introduction to Chemical Bonds (figs excluded due to copyright)

  • Learning Objectives

This chapter serves as an introduction to chemical bonds with a focus on the following concepts:

  1. To understand how electrons are arranged in an atom of an element and their role in chemical bonding.
  2. Be able to classify bonds as ionic or covalent by visualization through Lewis structures.
  3. Understand the concept of lattice energy for ionic compounds.
  4. Explore the role of electronegativity in bond formation.
  5. Be able to understand how the octet rule contributes to Lewis structures and resonance structures for molecules.
  6. Develop a sound understanding of how molecules are named based on the individual elements in a compound, i.e., nomenclature.

  • Why do elements react to form molecules?

At its most basic, the human body is made up of atoms of carbon, hydrogen, oxygen, nitrogen, and other elements that constantly form and break chemical bonds to maintain homeostasis, produce energy, and conduct chemical signaling. Thus, understanding how atoms react to form molecules is at the core of human physiology, as well as medicine. When scientists studying muscle relaxation discovered that our bodies produce NO (nitric oxide) as a neurotransmitter, it wasn’t long before the mechanism for how the drug nitroglycerin (C3H5N3O9) functions to alleviate symptoms of angina pectoris was understood. Nitroglycerin produces NO which causes muscles to relax and arteries to dilate allowing unrestricted blood flow to the heart. So what are the forces that hold nitrogen and oxygen together as a molecule? We discuss chemical bonding in detail below.

With the development of the periodic table and the principle of electron configuration, scientists began to unravel the explanation for atoms combining to form molecules. Let’s first briefly revisit the 4 basic models of an atom:

  1. The Thomson Atomic model (chocolate-chip model): atoms are spheres of positive charge with electrons embedded inside (see fig 5.1a).
  2. The Rutherford Atomic model: protons and neutrons are inside the nucleus and electrons are somewhere far away (see fig 5.1b).
  3. The Bohr Atomic model (energy-level model): protons and neutrons are in the nucleus while electrons are in discrete energy levels outside the nucleus (fig 5.1c). This model considers electrons as particles.
  4. The Quantum Atomic model: Schrodinger proposed electrons exist as waves and not particles. In this model, protons and neutrons are in the nucleus, while electrons are localized to different orbitals in an energy level shell. There are 4 shells that electrons can be localized to depending on the total number of electrons in an element (the greater the number of the electrons, the more shells needed to contain the electrons; see table below); the s shell exists as a single sphere, p shell has 3 degenerate (equal energy) orbitals, d shell has 5 degenerate orbitals, and f shell has 7 degenerate orbitals. Each orbital can only hold 2 electrons.

Shell

Number of orbitals

Total Capacity for Electrons

s

1

2

p

3

6

d

5

10

f

7

14

An electron density map explains where an electron probably is 90% of the time in this model (see fig 5.1d). The quantum model serves as the basis for explaining the electron configuration of atoms.

It is important to note that electrons fill lower-energy atomic orbitals first before filling higher-energy ones (Aufbau principle; German for “building-up”).

Let’s consider the electron configuration of the element sodium (Na) that has a total of 11 electrons. We start by filling up low energy shells to high energy shells (fill s before p), with 2 electrons per orbital in opposite spins, and half filling equal energy orbitals (each p orbital receives 1 electron first) before electrons are paired up (see fig 5.1 e’ and e).

Molecular Genetics for MCAT review guide

Cell Cycle

Every cell has a life cycle which is the period from the beginning of one division to the start of the next division. A cell’s life cycle is known as the cell cycle which involves cell growth and division to produce two new daughter cells. The cell cycle is divided into 2 phases; interphase and mitosis/meiosis. Interphase (inter- means between) is often referred to as the “resting” stage; however, the cell is actively growing and replicating DNA during this phase. Mitosis (somatic cells) and meiosis (gametes) refer to the actual physical division of the cell and its cytoplasmic contents and DNA. After cell division, some cells enter the G0 phase either temporarily (a signal may trigger the cells to enter G1; liver cells stay in G0 mostly dividing less than once a year) or permanently like mature cardiac muscle and nerve cells. Note that cells in G0 phase do not undergo DNA replication or cell division.

Side note: Not all cell types in the body regularly undergo cell division. Fully differentiated neurons rarely divide to produce new cells. Neurons primarily remain in the G0 phase of the cell cycle and devote their time and energy toward carrying out the normal functions of a neuron (producing neurotransmitters, maintaining the resting potential, etc.) rather than toward producing new neurons. Some cell types, such as skin and intestinal cells, have short lifespans or are lost to the environment and must regularly be replaced.

Before discussing the phases of the cell cycle, it is important to understand how chromosomes are counted. Inside the nucleus of a human somatic cell, there are 46 double stranded DNA molecules; each chromosome possesses a partner that codes for the same traits as itself. Two partners are called homologues and each homologue is donated by a parent to its offspring (basis of sexual reproduction). Diploid (Greek: di means twice) refers to any cell that has 2 sets of chromosomes and haploid (Greek: haploos means single) refers to any cell that has one set of chromosomes. In humans, the diploid number of chromosomes is 46 and the haploid number of chromosomes is 23. Most cells in human body are diploid and undergo mitosis; but the sex cells or gametes are haploid and undergo meiosis. Each parent contributes a gamete cell with one set of chromosomes that is paired with a set from another parent to produce a new diploid cell called a zygote. Thus, the offspring is genetically distinct from either parent. 

Interphase is the first phase of the cell cycle and it is sub-divided into 3 phases (G1, S, and G2). 

  1. G1 (Gap1): All cells undergo this phase. The cell grows in size by producing new organelles and proteins (rate of RNA and protein synthesis is high during this phase). This phase is the longest phase of the cell cycle. The G1 checkpoint at the G1/S transition ensures the presence of all necessary conditions: 
  1. Cell size- is the cell large enough for division?
  2. Nutrients-does the cell have energy reserves to continue towards division?
  3. Growth factors- is the cell receiving positive signals for division?
  4. Cell cycle regulators- cyclin-dependent kinases (CDKs) are activated by binding of cyclins. This complex activates downstream targets so that cells can continue towards division. Are cell cycle regulators present?
  5. Integrity of DNA- is the DNA damaged? 

If a cell doesn’t meet all the necessary conditions, it will either enter into the G0 phase or undergo apoptosis (cell death). Cells often repair DNA damage and continue with the cell cycle; if DNA damage is extensive, the cell will enter the irreversible process of apoptosis to ensure damaged DNA is not passed onto daughter cells and is important in preventing cancer.

  • S (synthesis): The cell replicates its genetic material during this phase. The original chromosome undergoes replication and the new duplicate is linked to the original chromosome by the centromere to form sister chromatids. Though chromosomes duplicate, the cell is still considered to have the SAME number of chromosomes (each chromosome is now made up of two identical sister chromatids). S phase is the second longest phase of interphase.
  1. G2: The cell continues to grow and synthesizes proteins required for chromosome migration (especially tubulin for microtubules). G2 typically occupies 10-20% of the cell life cycle. Near the end of this phase is the G2 checkpoint which ensures DNA is free of both damage and errors from replication. The G2 checkpoint checks for mitosis promoting factor (MPF; also knows as the cyclinB1-CDK1 complex). When the level of MPF is high enough, mitosis (in somatic cells) or meiosis (in gametes) is triggered.

Mitosis: This phase is characterized by nuclear division without change in the genetic material and occurs in almost every somatic cell (not in sex cells). Purpose of mitosis is,

  • To produce daughter cells that are identical to the parent cell.
  • Maintain proper number of chromosomes from one generation to the next. 

In a typical eukaryotic cell, mitosis is subdivided into 4 stages (PMAT🡪Prophase, metaphase, anaphase, telophase).

  • Prophase: The first sign of prophase is the disappearance of the nucleolus and nuclear membrane as the chromatin condenses into chromosomes. Centrioles in the microtubule organizing centers (MTOCs) move towards the opposite ends of the cell and form spindle fibers. These spindle fibers attach to the kinetochore protein complex in the centromere of the chromatid.
  • Metaphase: Chromosomes line up at the metaphase plate as the mitotic spindle fibers pull on sister chromatids via the kinetochores. 
  1. Anaphase: The centrosomes push outwards. The sister chromatids are split at the centromere and pulled apart to the opposite end of the cell by the microtubules in a process called disjunction. The microtubules shorten while the non-kinetochore microtubules elongate the cell. 
  2. Telophase: Nuclear membrane forms around each set of chromosomes (chromosomes decondense-cannot be seen under the microscope) and the nucleoli reappear. The cell begins to split along the cleavage furrow produced by the actin filament in a process known as cytokinesis and two distinct daughter cells form. The cells then re-enter interphase and the cell cycle starts again.

It is of interest to note that abnormal separation of chromosomes during cell division can lead to aneuploidy (either a gain or loss of chromosome). Trisomy is the most common form of aneuploidy; trisomy 21 (third copy of chromosome 21) results in Down syndrome. Polyploidy occurs when a cell has more than two copies of homologous chromosomes (lethal in humans).

Meiosis: In eukaryotic sex cells, each parent contributes half of its chromosomes to a gamete via meiosis (n) which combine to form a zygote (2n). Meiosis only occurs in sex cells in specialized sex organs called gonads (in males) and ovaries (in females). After DNA replication occurs in the S phase of interphase, the cell is called a primary spermatocyte or primary oocyte. During spermatogenesis, four sperm cells are produced from each diploid cell through meiosis. Oogenesis is different; it produces one ovum instead of 4. The other 3 cells are called polar bodies and they degenerate to conserve cytoplasm for the ovum. In the human female, replication takes place before birth, and the life cycle of all germ cells are arrested at the primary oocyte stage until puberty. Just before ovulation, a primary oocyte undergoes the first meiotic division to become a secondary oocyte. The secondary oocyte is released upon ovulation, and the penetration of the secondary oocyte by the sperm stimulates the second meiotic division in the oocyte. Note that meiosis gives rise to genetic variation which provides selective advantage to species that sexually reproduce. Two rounds of cell division occur in meiosis🡪 Meiosis I and Meiosis II. 

Meiosis I 🡪 divided into Prophase I, Metaphase I, Anaphase I, and Telophase I

  1. Prophase I: The nuclear membrane disappears, chromosomes condense to become visible, and centrosomes separate to opposing ends (similar to Mitosis). Unique to meiosis is the process of synapsis. Synapsis involves two sets of chromosomes that come together to form a tetrad (four chromatids); these tetrads cross over to exchange segments of DNA (containing several alleles) located on the homologous chromosome giving rise to genetic recombination (genetic variation). If crossing over does occur, the two chromosomes are “zipped” along each other where nucleotides are exchanged, and form what is called the synaptonemal complex. Under the light microscope, a synaptonemal complex appears as a single point where the two chromosomes are attached creating an ‘X’ shape called a chiasma. Genes located close together on a chromosome are more likely to cross over together, and are said to be linked.
  2. Metaphase I: Chromosomes line up (as tetrad) along the metaphase plate.
  3. Anaphase I: One pair of each tetrad separates to opposite end of the cell (homologs are pulled apart). Sister chromatids are still attached via a centromere. 
  4. Telophase I: Nuclear envelope forms around the separated chromosomes, chromosomes de-condense, and mitotic spindle breaks up. Cytokinesis simultaneously separates the cell into two daughter cells with each cell containing a haploid number of chromosomes (note that each chromosome has a duplicate at this point). The new cells are called secondary spermatocytes or secondary oocytes. 

Meiosis II: The duplicate chromosomes separate. Meiosis II has four stages, Prophase II, Metaphase II, Anaphase II, and Telophase II that are similar to mitosis. The product of meiosis II is 4 haploid gametes/daughter cells.

The table below summarizes the differences in Mitosis vs. Meiosis

Mitosis

Meiosis

Occurs in somatic (body) cells

Occurs in germ (sex) cells

Produces identical cells (1 cell🡪2 cells)

Produces gametes (1 cell🡪 4 cells)

Diploid🡪Diploid

Diploid🡪Haploid

Number of divisions: 1

Number of divisions: 2

Content Questions:

  1. Colchicine is an alkaloid drug that interferes with formation of spindle fibers. When a dividing cell is treated with colchicine, which cell cycle phase would the cells be stalled in?
  1. Interphase
  2. Anaphase
  3. Telophase
  4. Metaphase

Correct answer is D. The chromosomes would be stuck at the metaphase plate without the spindle fibers. Interphase does not require spindle fibers. Both anaphase and telophase occur after spindle fiber forms and attaches to chromosomes.