Sex and Cells

An Informal Introduction to Biology

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Primer

Welcome all! If somehow you’ve stumbled across this blog post, please note that this is not an authoritative guide to introductory biology. This document is a study resource, created by me (not a biologist) to prepare for a final exam taught by the wonderful Dr. Claytor at the University of North Carolina Chapel Hill.  You can reach me at my school email with any comments or suggestions.

I. Introduction

Biology is the study of life. It is an exploration of the structure and function of all living things. Life and biology generally bear several similarities to the world of Computer Science. Upon closer inspection, life appears to work a lot like a computer. For living things to function, they must break up complicated tasks into many well-defined sub-tasks. In the same way that computers divide functionality into different components (e.g., CPU, RAM, etc), so to do living things employ a sort of compartmentalization.

We divide biology into five major themes to make it a little more palatable.

1. Evolution
2. Flow of Information
   • This topic involves the exchange of genetic material between organisms.
3. Structure and Function
   • What do components of life look like, and what do they do?
4. Transformation of Matter and Energy
   • Life is matter fueled by energy. As a result, the interactions between these two concepts are vital.
5. Interactions Between Systems
   • Here, we refer to biological systems, both big and small. These can be ecosystems or hormonal systems.

So, we can say that life follows a kind of hierarchy. We organize living things and their components from small to big meaningfully. We aim in this exploration to develop a top-to-bottom understanding of the basics of biology. This task isn’t easy. Biology is a big field spanning an endless number of topics. Therefore, as we work our way up the scales of life, we may be forced to take the occasional detour. These diversions are necessary to avoid leaving out vital Biological processes that may be needed later.

We’ll organize this document into four primary sections.

Structure

1. Cells
2. Sex
3. Systems
4. Societies

Notice that we try our best to group concepts by relative scale. Before we jump into cells, however, we need a good definition of life. What makes a thing a “living thing” anyway? We say a thing is “alive” if it meets specific criteria (or rules). There is no official set of rules for life – but generally, biologists agree that living things must be able to “respire, grow, excrete, reproduce, metabolize, move, and be responsive to the environment” [1]. These rules imply that things like our friend the Amoeba are living things, but viruses, for example, don’t make the cut. As a result, biology excludes any hunk of matter not conforming to these criteria.

II. Cells

Cells are the smallest unit of life. Cells are both alive and make up living things. Therefore, huge living things like yourself contain many tiny living things. Neat! But before we dive into cells, we need to talk about the non-living stuff that makes up cells.

A. Organic Molecules

Organic molecules are the building blocks of cells. We define an organic molecule as any chemical compound (a bunch of atoms bound together) in which a carbon atom is bound to a hydrogen atom. Small organic molecules are monomers and can combine into larger organic molecules called polymers. Together, these molecules bind to provide the raw material of life.

One exceptional type of organic molecule, the amino acid, acts as the building block for proteins. Proteins are a type of macromolecule (or large molecule) that perform an incredible variety of tasks in living things. We’ll get back to proteins later. All amino acids contain three essential components: an amino group, an acidic carboxyl group, and an R-Group. These are the general chemical components of all amino acids. For example, if we looked at a diagram of any of the 20 amino acid variants, we could spot all these different parts. The R-Group is like the thumbprint of each amino acid. That is, each amino acid is primarily distinguishable by its unique R-Group.

Take a look at an abstracted amino acid in the figure below.

We also say that amino acids have four levels of structure organized by scale.

B. Macromolecules

We’ll now examine three critical macromolecules (our next step up on the ladders of scale). Each macromolecule contains a unique monomer. Proteins, as mentioned earlier, are formed from long chains of amino acid monomers. Carbohydrates, or simple, starchy sugars, are comprised of the monomer monosaccharides. These monosaccharides can combine in a dehydration reaction and decouple via hydrolysis. The key takeaway is that dehydration combines  molecules – and hydrolysis breaks them apart.

Any gym bros reading this might be able to guess our last macromolecule. That’s right, Fats! Fats are lipids, another sub-class of organic molecules. that primarily store energy in organisms. Unlike our previous macromolecules, fats do not have a unique monomer. Fats are hydrophobic (water-fearing) because they repel water. This fact is intuitive to anyone who leaves a can of grease out to congeal overnight. In the morning, you’ll probably discover water left on top of the can and hardened fat left on the bottom.

One other special kind of lipid is the phospholipids. These molecules are hydrophobic and make up the outer membrane of cells. A double layer of these lipids keeps water in and out of the cell!

We’ll mention one more particular macromolecule: DNA. DNA contains nucleotide monomers and uses hydrogen bonds to hold a double helix shape. We’ll have plenty more to say about DNA a little later.

C. The Cell Membrane

Now, we get the barrier of the cell: the cell membrane. This vital structure controls the passage of materials in and out of the cell. We say the cell membrane has selective permeability, which is just a fancy way of saying it only lets some specific stuff in or out. Proteins embedded in the lipid layer of the membrane give it a fluid mosaic property. Therefore, the cell membrane is highly flexible and dynamic.

There are a few different ways that things can cross the cell membrane. One such mechanism is passive transport – the diffusion of substances across a membrane without energy. This process occurs when a substance moves from an area of high concentration to low concentration. A classic example of diffusion occurs when you leave a hot pan out on the stove to cool. Heat moves from the pan (an area of high energy concentration) to the surrounding air (low energy concentration).

The lipid-bilayer structure of the cell membrane keeps out polar and charged molecules. A polar molecule is any molecule that has opposite charges on either end. Water (H2O) is one such example of a polar molecule. Therefore, molecules like O2 and CO2 can easily cross the cell membrane, while polar molecules can not. However, water can cross the cell membrane through a process known as osmosis. Cells must maintain the correct balance of water. Therefore, H2O can only cross the cell membrane in certain instances.

So when does water cross the cell membrane? The answer depends on the relative tonicity of the surrounding medium. Tonicity refers to the ability of a surrounding solution to cause a cell to gain or lose water. We say a cell is isotonic when tonicity is equal in and out of the cell. A cell is hypertonic when solute concentration is higher outside a cell and hypotonic under the opposite conditions.

We stated earlier that diffusion can occur without energy because substances like to travel from areas of high to low concentration. But can molecules move the other way, from low to high concentration? The answer is yes, albeit with help. Facilitated diffusion is the movement of substances from low to high concentration aided by transport proteins. These transport proteins provide the energy (e.g., ATP) required to overcome the friction caused by the diffusion gradient.

Cells can inject or remove large particles by endocytosis and exocytosis.

D. Cell Signaling

Cells are rarely acting alone. Most cells are part of larger, complex structures with functions that far exceed the capabilities of a single living thing. So, to achieve this superior functionality, cells must work together. Teamwork requires communication.

The vast array of cells in the human body communicate by two primary mechanisms: chemical and electrical signaling. Chemical signals create slow, long-lasting responses in the body. These signals might include a prompt to the testes to produce more testosterone or a series of signals that start an immune response. Electric signals, by contrast, are fast-acting and short-lasting. These signals target the muscles, neurons, and other rapid-fire structures in the body.

Hormone signals, as alluded to earlier, are chemical signals. These messages rely on target cells, or cells outfitted with specific receptors that allow them to respond to chemical messages produced from disparate body parts. Hormone receptors can appear on both the inside and outside of the cell membranes. These receptors are sites that allow hormone signals to bind to the cell.

These cells are a bit like the watchtower guards of the body. We’ll break down the stages of hormone signaling into three parts, reception, transduction, and response. At a high level, we can think of each stage like this: “A message is received, a message is processed, and a response message returns from the cell.”  

We can further divide hormone signaling into water-soluble and lipid-soluble hormones. In water-soluble hormone signaling, hormones are polar and thus can not cross the cell membrane. In lipid-soluble signaling, messages pass through the cell exterior into the cytoplasm. We provide more details regarding these different processes in the figure below.

E. Enzymes

We’ll now briefly discuss enzymes, some of the unsung heroes of life on Earth. Cells require several chemical processes to perform essential functions. These reactions occur quite slowly by default in nature. Even ordinary biological processes (e.g., the conversion of starches into sugars) could take thousands of years without intervention!

Here’s where enzymes come into play. Enzymes are proteins that bind to the active sites of substrates (or reactants) in chemical reactions. By lowering the activation energy required for chemical reactions to occur, enzymes dramatically increase reaction speed.

F. Cellular Respiration

Now, let’s discuss cellular respiration, an essential component of all living things. First, we need to brush up on some chemistry. In chemical reactions, we say that an oxidation occurs when an atom loses an electron. By contrast, reduction occurs when an atom gains an electron. We can remember these terms with the nuemonic OILRIG. The processes always go hand in hand. When one atom loses an electron, another must gain an electron. Therefore, these processes are known as redox reactions. These terms will come into play when discussing energy transfer during chemical reactions.

Now, we are prepared to talk about cellular respiration. Cellular respiration is the primary process by which cells make energy. Almost all organisms on Earth use some form of cellular respiration, even plants! We’ll specifically examine a few different flavors of energy when talking about the kinds of energy organisms produce. Namely, we’ll look at chemical/potential and thermal/kinetic energy. The commonality between these subclasses is that they all represent the same thing: the ability to perform work.

Cellular respiration converts chemical energy from nutrients into energy-poor ATP. Glucose and oxygen transform into carbon dioxide, water, and ATP. This process occurs on a higher level every time you take a breath! We can write the chemical equation for this process as such:

\[C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy}\]

This conversion is a multi-staged process where the energy produced during previous stages fuels subsequent processes. This movement of energy from one reaction to the next is known as energy coupling, where the reaction releasing energy is considered exergonic and the reaction receiving energy is endergonic. Cells fuel endergonic reactions by breaking down ATP stores, creating kinetic energy.

Energy moves through the cell during respiration on “shuttles” called cofactors. These “exergy taxis” move electrons from reactants to product molecules. We’ll see how cofactors come into play during ATP synthesis shortly.

Let’s walk through the three stages of cellular respiration in eukaryotic cells. Please note that the figures for ATP production are approximations. In a real-world scenario, the number of ATP molecules produced during a round of cellular respiration will vary.

1. Stage One: Glycloysis
   • A glucose molecule is split into molecules of pyruvic acid.
   • Location: Cytoplasm
   • Inputs: [NAD+, Glucose]
   • Outputs: [Pyruvate, 2-NADH, 2-ATP]
2. Stage Two: The Krebs Cycle (A.K.A. The Citric Acid Cycle)
   • Pyruvate from the stage is broken down into carbon dioxide.
   • Location: Mitochondrial Matrix
   • Inputs: [Acetyl-CoA (Converted from Pyruvate)*, NAD+, FAD]
   • Outputs: [NADH, FADH2, 2-ATP]
3. Stage Three: Oxidative Phosphorylation
   • Location: Inner Mitochondrial Membrane
   • Inputs: [NADH, FADH2, Oxygen]
   • Outputs: [Water, 28-ATP]

* Coenzyme A converts pyruvate into acetyl-CoA between stages one and two.

Oxidative phosphorylation is vital enough to be discussed separately. During the previous stages, the cofactors NAD+ and FAD reduce (receive electrons) to form NADH and FADH2. These cofactors are like cargo bays that fill up with electrons to be dumped somewhere else in the cell. During oxidative phosphorylation, our cofactors are oxidized to produce molecules of ATP. Hence the name, oxidative phosphorylation.

Electrons movement within the mitochondria occurs along the electron transport chains. These structures are simply a collection of proteins and other molecules in mitochondria that enable redox reactions. Ultimately, approximately 26 molecules of ATP are created by ATP synthase from ADP and phosphate as electrons move down the electron transport chains. We call this process chemiosmosis in the context of oxidative phosphorylation. The movement of H+ ions down the electron transport chains creates a proton gradient. ATP synthase allows H+ ions to move from low to high concentration along this graduate. This release of energy fuels the conversion of ADP into ATP.

We also mention that glycolysis produces an additional two molecules of ATP during the third stage of cellular respiration. The process oxidizes glucose into lactate (pyruvate) without oxygen. This process is known as fermentation. That burning sensation in your muscles at the end of a hard workout is an example of fermentation. Lactic acid builds up more rapidly than your body can remove. Here, cells attempt to create energy in an anaerobic environment.

G. Photosynthesis

Photosynthesis is a bit like the hippie cousin of cellular respiration. Similarly, photosynthesis is a two-staged chemical reaction that involves the production of energy-rich products from reactants. This process, as you may have guessed, occurs in plants. Specifically, photosynthesis occurs in the chloroplasts of plant cells – where carbon dioxide and water convert into glucose and oxygen. Again, we can write a general equation for this reaction like so:

\[6CO_2 + 6H_2O + \text{light energy} \rightarrow C_6H_{12}O_6 + 6O_2\]

Photosynthesis broadly takes place within the stroma of chloroplasts. Here, two sub-processes happen simultaneously: the light-dependent reactions and the Calvin cycle.

Light-dependent reactions take place in the thylakoid membranes of chloroplasts. During this process, light energy from the sun helps split water molecules into oxygen, protons, and electrons. This reaction releases oxygen, and high-energy electrons travel through the electron transport chain. Energy-carrying molecules ATP and NADPH produced during these reactions carry on to the Calvin Cycle.

Photosystems I and II are the components of the light-dependent reactions responsible for absorbing energy from the sun. Ironically, photosystem II is the first of these systems to come into play. This system extracts oxygen molecules from water within the thylakoid membranes. Photosystem I has a slightly more niche role. Here, electrons are ‘boosted’ or ‘excited’ so NADP+ can reduce to NADPH. Below is a rather complicated diagram of these two systems at work. Try to understand their high-level differences.

The Calvin Cycle, the last stage of photosynthesis, occurs in the fluid surrounding the thylakoids (stroma). ATP and NADPH provide the energy necessary to convert CO2 from the air into glucose ($C_6H_{12}O_6$). The carbon in this glucose molecule is stolen directly from the CO2 in the air via carbon fixation. In total, 18 ATP and 12 NADPH molecules create just one molecule of glucose!

III. Sex

So far, we’ve worked our way up the scales of life to the cellular level. We learned about the raw material making up cells and their chemical reactions – including a few fundamental cellular processes. But this is starting to get a bit drab. How can we make the leap from single cells to multi-cellular life?

Our second section is a broad exploration of reproduction and inheritance in nature. The title “Sex” is, therefore, a bit of a misnomer. We will employ an anthropocentric bias in the topics that follow. Specifically, we will explore how humans reproduce and pass on genes from generation to generation. Thankfully, many concepts like reproduction are universal. Living things, in fact, must reproduce to be considered living. Therefore, even as our conversations skew towards human beings, the general concepts we learn will apply to many other living things.

There are two modes of reproduction. Asexual reproduction is the production of an exact genetic copy of an organism produced by a single living thing. This method is popular among single-celled creatures. Sexual reproduction, by contrast, involves the production of new offspring by two organisms combining their unique genetic information. As human beings, we are primarily interested in the ladder method.

A. Mitosis

All human beings begin life as single, fertilized cells. This microscopic organism contains all the genetic material to create a human being. The code for every organ, follicle of hair, synapse in your brain, and so on, is packed into a near-invisible point in space and time. This code exists as strands of DNA densely woven into 23 pairs of chromosomes in human embryo cells. This cell will divide into daughter cells through a process called mitosis. Cell reproduction is a recursive process for those familiar with the term.

Human embryonic cells are eukaryotic cells and pass through three phases of interphase preceding mitosis during cell division. These stages do not have a definite start or finish. Cell division is a continuous process happening all the time. During G1 Phase, cells grow in size and prepare for DNA replication. Next, during the S Phase (or “synthesis” phase), chromosomes duplicate to form two identical sets of DNA. Therefore, mitosis does not increase the genetic diversity of cells – and should be considered an asexual process. G2 is the last stage preceding mitosis. During this step, the cell grows and makes all final preparations before cell division.

Mitosis contains many steps and sub-steps. For the sake of simplicity, we will overview only the most critical stages of this process.

1. Prophase
   • Copies of chromosomes from interphase begin to condense and become visible. Our chromosomes now contain a pair of sister chromatids, which join together at a point called a centromere. Outside the nucleus, a structure called a spindle begins to form and pull chromosomes apart.
2. Prometaphase
   • The nuclear envelope breaks down, and the spindle fibers latch onto chromosomes. All the machinery is now in place to rip apart chromosomes.
3. Metaphase
   • Chromosomes line up down the middle of the cell. This step is critical. Our cell is going to divide along the equator in a little bit. Therefore, this “matching” procedure ensures that each new cell receives an exact copy of each chromosome.
4. Anaphase
   • Finally, chromosomes are ripped apart and pulled towards opposite poles of the cell. We now have two copies of all the chromosomes aligned at the top and bottom cytoplasm.
5. Telophase
   • Two new nuclear envelopes begin to form around the cell’s polls.
6. Cytokinesis
   • Finally, the cell’s cytoplasm splits into two complete daughter cells.

Differentiation is the process that allows cells to take on specialized roles following cell division. Cells in the human body perform a vast array of functions. Therefore, not every cell divides continuously throughout the human life span. Some non-dividing cells (such as nerve and muscle cells) lack a “go-ahead” signal during the G1 phase of interphase. This exclusion prevents these cells from dividing by mitosis. As a result, the loss of nerve or muscle cells can be especially devastating in human beings.

Uncontrolled cell division may lead to the formation of a tumor. Typically, cells in the body divide as needed. However, these structures responsible for managing cell division rates erode naturally over time. Sometimes these uncontrolled growths begin to spread to other parts of the body, hogging vital resources and interfering with fundamental bodily functions. Malignant tumors are also known as cancer.

B. Meosis

We’ve now learned how a human embryonic cell can divide and differentiate into the collection of cells that make up a full-fledged human being. But we said that mitosis is an asexual reproductive process, don’t human beings reproduce sexually? Admittedly, we skipped a step. Meosis is the process by which huamn sex cells (gametes) divide to help form zygotes after fertilization.

Human sex cells (i.e., sperm and eggs) are considered haploid cells. The ‘ha-‘ prefix indicates that these cells contain half of the chromosomes required to create a complete genome. Zygotes (fertilized egg cells) are diploid cells, with “di-“ meaning “two.” Intuitively, these cells contain the complete set of 46 chromosomes that program for a human being. Of our 46 total chromosomes, 44 are considered autosomes. The remaining two are sex chromosomes and can code for females (XX) or males (XY).

Meiosis consists of two divisions, and unlike mitosis, does lead to an increase in genetic diversity. Meiosis consists of two identical rounds of cell division leading to the formation of 4 new sex cells. Once again, let’s walk through the most essential stages of meiosis.

1. Prophase I
   • Chromosomes line up within the cell to form pairs of homologous chromosomes. During this stage, chromosomes can swap genetic material in a process called crossing over.
2. Metaphase I
   • Chromosomes line up in pairs at the cell’s equator identically to metaphase in mitosis. Now, however, chromosomes line up randomly via independent assortment. These independent arrangements of chromosomes promote an increase in genetic diversity.
3. Anaphase I
   • Pairs of chromosomes are pulled apart by the spindle fibers of the cell, while sister chromatids remain joined together.
4. Telophase I and Cytokinesis
   • The cell finally divides into two, with each new cell containing half the number of chromosomes as the original cell.

This process represents one more time during prophase II, metaphase II, anaphase II, and telophase II to create 4 haploid cells.

C. DNA & RNA

Now, we’ll talk about how genetic information is stored and read within the cell. Here, we are interested in the flow of information, (i.e., what messages pass throughout a cell and how they are transferred). T Cells store genetic data on organic molecules and use this information as a recipe to make other things.

Let’s talk about the hard drives of the cell: DNA. DNA (deoxyribonucleic acid) is the genetic code of life. This molecule is encoded using four unique states represented as nucleotides – each composed of a sugar, a phosphate group, and a nitrogen base. These nucleotides come in four varieties: adenine (A), thymine (T), cytosine (C), and guanine (G). Nucleotides bind together using phosphodiester bonds and take on a distinctive double helix shape held together by weak hydrogen bonds.

Through careful observation, scientists have discovered that A nucleotides always pair with T, and G pairs always pair with C. Variations in these simple base pairings account for the diversity of all living things on Earth. DNA sequences can even code for the structure and function of non-living things, such as viruses.

RNA is a complementary molecule to DNA involved in the translation and reproduction of DNA. RNA contains the A, C, and G bases but swaps out thymine (T) for uracil (U). Whereas DNA acts as a genetic blueprint, RNA is responsible for carrying out the genetic instructions it encodes. We’ll talk about two types of RNA, mRNA and tRNA. tRNA has two critical sites: an anticodon site, where juxtaposing nucleotides assemble from mRNA, and an amino acid site.   Ultimately, DNA and RNA work in unison to create proteins throughout a multi-staged process. DNA transcribes into RNA during a transcription phase. Transcription takes place in the nucleus of eukaryotic cells. An enzyme called RNA polymerase attaches to the promoter region of DNA. This protein marks the “head” of a sequence. Think of RNA polymerase like a translation device, mapping each nucleotide in a template strand to a corresponding RNA nucleotide. The enzyme works its way down the DNA until it comes to a terminator, a codon that marks the end of the strand. We call the final output strand RNA transcript.

Next, messages carried by RNA decode in the ribosomes during the process of translation to make proteins. Let’s take a look at this process in action.

Namely, sequences of base pairs map to different amino acids. This procedure is analogous to encoding and decoding data on your computer. We define a group of three DNA or RNA nucleotides to be a codon. Each codon can code for a specific amino acid or stop sequence during translation. The stop sequence marks the end of the translation process. There are three stop codons, UAA, UAG, and UGA, and one start codon, AUG.

Messenger RNA (mRNA) carries messages encoded in DNA through the cell. Translation RNA (tRNA) is responsible for fetching corresponding amino acids by matching anticodons to the codons of an mRNA strand. We show this process in the diagram below.

Let’s summarize the two main processes that pass genetic information throughout the cell. DNA acts as long-term storage read and copied by RNA polymerase into mRNA during transcription. Next, these mRNA strands then bind to ribosome molecules in the cytoplasm. Here, multiple “blocks” of tRNA code for unique amino acids bound to the mRNA strand. The ribosome moves over the strand like a reader or pointer. All the while, proteins are produced for every three nucleotides processed and are added to the back of the growing peptide chain analogously to an append operation. Translation begins at a start codon and terminates at a stop codon.

The final output of this entire process is a long, complex polypeptide chain that folds up into a protein. This protein goes on to serve any number of functions throughout the body.

We provide a summary of each stage of information transfer within a cell below.

Stage	Components	Location
Transcription	DNA, RNA, mRNA, RNA Polymerase	Nucleus
Translation	mRNA, tRNA, Ribosomes, Proteins, Amino Acids	Cytoplasm

D. Mutations

All the time, errors in transcription or translation lead to a corruption of genetic information. These errors typically occur by exposure to a mutagen. A few different kinds of mutations can occur. A missense mutation involves substituting a single base in a DNA strand for another. This mistake can result in a specific codon coding for a different amino acid or cause no visible change (silent mutation). A nonsense mutation occurs when a stop codon is introduced earlier in the DNA sequence, leading to a prematurely truncated protein. Lastly, a frameshift mutation offsets an entire DNA sequence by a base pair. This last type of mutation is particularly devastating, as now every single codon might code for a new amino acid.

We must emphasize, however, that mutations are not inherently good or bad. Mutations are simply random perturbations to a genetic sequence that occur regularly. These random errors are a vital component of life. Darwinian evolutionary theory argues that natural selection evolves species by selecting the fittest mutations over time. This phenomenon leads to evolution and eventually speciation (creation of new species) over time.

We’ll work through a few examples of mutations in the diagram below.

E. Inheritance

Up to this point, our conservations remain at the cellular level. Now, we begin working on the scale of individuals. As discussed previously, each organism carries with it a unique genotype (genome) that encodes its physical features (phenotype). When two mates reproduce via sexual reproduction, they produce offspring with a mix of traits. When discussing inheritance, we seek to predict with what probability an offspring of two parents will have a specific set of characteristics. We will work in a highly idealized setting here. Often, predicting the exact traits an offspring will have is made incredible by the sheer number of genes in the human genome. Still, even in complex settings, the basic principles of inheritance continue to apply.

A punnet square is a device used to enumerate all possible combinations of gametes two parents can create for a given trait given their unique alleles. We write alleles using either uppercase or lowercase letters. Each parent carries exactly two alleles for any given trait. For example, an individual with blue eyes could express the “BB” phenotype – assuming a single allele code for this trait. Letter choice here is arbitrary so long as the letters are the same.

We’ll make a few assumptions when working with punnet squares. For now, each parent carries exactly two alleles for a given trait. Secondly, capital-lettered alleles are dominant to lowercase alleles. Let’s go back to the eye color example. Consider four individuals with three unique sets of alleles for eye color. We’ll say that the “dominant” phenotype is blue, and the “recessive” trait is brown for this trait. One thing we don’t assume is that each allele from each parent is equally likely to be passed to the gamete. This phenomenon illustrates the law of independent assortment.

Alelles	Eye Color
BB	Blue
Bb	Blue
bb	Brown

Notice how even one large “B” is enough to dominate over the recessive “b.” We’ll say that individuals who carry two identical “cased” alleles are homozygous, and those possessing dominant and recessive alleles for a trait are  heterozygous. Let’s look at a complete punnett square representing a cross between two pea plants. Pea plants were the first organisms studied in such a way. Again, note how plants with just one uppercase “G” are green in color.

This experiment isolates the inheritance of one trait using a monohybrid cross. However, we can construct our punnet square to handle an infinite number of traits. Below is an example of dihybrid-cross, or cross isolating two traits. Note that our chart gets exponentially more complex. For this reason, we typically look at only one trait at a time using a Punnett square.

F. Human Reproduction

Earlier, we explored meiosis - the general method by which sex cells divide. Now, we zoom back a bit to view the human reproductive process as a whole. Specifically, we are interested in how human reproductive organs facilitate sexual reproduction and genetic inheritance.   Human sex cells come in male (sperm) and female (egg) varieties. These cells each contain one-half the entire human genome in 23 chromosomes donated from each parent. For these cells to fuse into a zygote, fertilization must occur. Humans utilize internal fertilization (fertilization within the body), as do most other mammals. But before fertilization occurs, sex cells must develop in the bodies of males and females.

We start from the female perspective. Egg cells release from a follicle in the ovary. This follicle then becomes a corpus lute, which secretes hormones that aid in pregnancy. The egg is transported from the ovary to the uterus via the oviduct, where normal implantation may occur. Oogenesis, or the creation of new egg cells, starts at birth and ends after puberty.

Now for the guys. Sperm are the sex cells of males. Sperm development occurs in the testes, which are kept outside the body at a slightly lower temperature. New sperm form through spermatogenesis within the seminiferous tubules. On the journey towards the outside of the body, sperm travel through the testes, epididymis, vas defers, ejaculatory duct, and urethra sequentially. Several glands, including the prostate and bulbourethral glands, additionally support semen production and ejaculation.

The release of LH and FSH hormones by the pituitary gland precipitates semen production. High testosterone lowers LH and FSH. The balance of hormonal signals in men and women keeps each respective system in homeostasis (balance).

Approximately once a month, an egg is prepared for fertilization during ovulation, a stage in the mental cycle in females. Menstrual cycles are controlled by hormones, including regular dips and spikes of specific hormonal signals during different times of the month. The menstrual cycle contains four primary stages.

1. Menstrual Phase
   • The horomones estrogen and progesterone fall. Menstrual bleeding occurs during the shedding of the old uterine lining (endometrium).
2. Follicular Phase
   • An increase in FSH released by the pituitary gland precedes the production of new follicles, each containing an immature egg.
3. Ovulation Phase
   • Rising estrogen levels correlate with a drop in LH. Next, ovulation occurs as the dominant follicle releases an egg from the ovary via ovulation.
4. Luteal Phase
   • The emptied follicle turns into a new structure called the corpus luteum responsible for producing progesterone and estrogen. The uterine lining is now at maximum thickness and prepared for implantation. The corpus luteum will degrade and disappear at the end of the menstrual cycle if the egg is unfertilized.

 

IV. Systems

We now begin the first of two brief sections. Systems are a universal concept in biology. A system is any collection of functional apparatuses interacting within a shared space. Life at all scales relies on systems to perform a plethora of functions. We have already explored a few of these structures. Energy production systems generate ATP within the cellular and human reproductive systems and enable the continuity of human life. We will examine one more system that lacks a clean fit within our previous sections.

A. The Human Immune System

In living things, internal mechanisms actively maintain balance with an external environment. The human immune system ensures the proper function of bodily processes by responding to external threats through several sub-systems. Human beings have two primary mechanisms against disease-causing agents (pathogens). These responses include innate immunity and passive immunity.

Innate immunity includes all the mechanisms humans acquire at birth. These defenses include skin, mucous membranes, stomach acid, natural killer cells, and other layers of protection. Innate immunity is fast immunity and responds, if not instantly, very quickly to foreign threats.

Acquired immunity occurs as humans gain exposure to new diseases over time. This form of immunity is slow. White blood cells (lymphocytes) identify and destroy foreign pathogens. T cells and B cells target antigens, or any substance that causes a bodily response. B cells specifically produce antibodies,  proteins that latch on to antigens. Upon detecting a foreign invader, B, and T cells proliferate through the body via clonal selection. Initial responses to a novel disease are typically slow. However, cellular “memory” allows the body to fight the same disease in subsequent encounters quickly. We say that adaptive immunity is specific and has memory.

Adaptive immunity fights disease using a dual defense mechanism. This system employs humoral and cell-mediated immune responses. The humoral immune response involves the production of antibodies by B cells to fight extra-cellular pathogens. T-cells destroy infected cells by apoptosis via the cell-mediated response system. Cytotoxic T cells target cancer cells specifically.

V. Societies

We now arrive at our last stop on this introductory tour of biology. This section tackles the last rung on the scales of life. We’ll consider societies to be groups of living things living together within the confines of a closed system. This broad definition encompasses different species living together in communities and the processes by which they adapt to their environments over time.

A. Evolution of Populations

The Darwinian theory of evolution states that species evolve by selecting desirable traits within a population over time. This concept is also known as the survival of the fittest. Individuals with greater fitness reproduce a pass of their genes to future generations. Variation within a population results from sexual reproduction and random genetic mutations. This phenomenon calls back to our discussions of DNA. Darwin noted differences between the beaks of fiches. These slight variations of shared features are homologies.

Evolution can only occur at the population level. Individuals can not evolve throughout a lifetime. We can tell if a species is evolving using criteria developed by the scientists Hardy and Weinberg. These requirements are as follows.

1. Mutations occur.
2. Gene flow exists.
3. Individuals do not mate at random.
4. Relatively small population size.
5. Selection of individuals.s

Here, gene flow refers to the movement of genetic material from one population to another. Any species that fails to meet any of these criteria is not evolving.

We consider five types of natural selection in the chart below.

Variant	Description
Directional Selection	Favors the average phenotype over time.
Stabilizing Selection	Favors extreme phenotypes at one end of the distribution of the population.
Disruptive Selection	Favors individuals with phenotypes at both extremes of the population distribution.
Sexual Selection	Selects for traits that improve the odds of mating success.
Balancing Selection	Favors the heterozygote at a given locus.

VI. Bibliography

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10123176/.