Cell Biology: Comprehensive Review of Key Concepts
Key Concepts in Cell Biology
Water has hydrogen bonds that allow it to have special properties like cohesion (water molecules stick to each other), adhesion (water molecules stick to other surfaces), and surface tension.
Monomers form polymers via dehydration synthesis; in hydrolysis, polymers are broken down into monomers.
Nucleic acids are what make up DNA and RNA and hold a lot of genetic information. They are made up of nucleotides, which are composed of a deoxy/ribose, a phosphate, and a nitrogen base.
Amino acids make up a protein, and the specific order of the polypeptide determines the protein’s structure and function.
Sugar monomers bond to form complex carbohydrates.
Lipids are nonpolar and can vary in saturation (which affects the structure and function). They are most commonly seen as the cell membrane.
Carbohydrates are sugars and polymers of sugars (usually ends in the suffix -ose). There are multiple hydroxyl groups and a carbonyl group. If the carbonyl group is at an end, the sugar has an aldehyde and is known as an aldose sugar. If the carbonyl group is in the middle, the sugar has a ketone so it is a ketose sugar.
Monosaccharide – simple sugar – generally has a formula that is a multiple of the unit CH2O, 1:2:1 ratio. Glucose (C6H12O6), is the most common monosaccharide (important in glycolysis). Another common example is fructose.
Lipids are the only class of macromolecules that DO NOT form polymers. Non-polar molecules and hydrophobic – no affinity for water (avoids water). Mostly hydrocarbons. Important storage molecule. Most energy-rich (9 calories per gram). Important for insulation in animals. Fats are made up of glycerol and three fatty acids joined by an ester bond/linkage forming a triglyceride/triacylglycerol. Separate from water.
Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon. Fatty Acids are long chains of carbon attached to a carboxyl group and can be saturated or unsaturated. Saturated Fatty Acids have no double bonds between carbon atoms, contain a maximum number of hydrogen atoms, usually found in animals and solidify at room temperature (examples include lard and butter). Unsaturated Fatty Acids have one or more double and/or triple bonds between carbon atoms and are liquids at room temperature (examples are typically from plants, fish, and vegetable oils).
Phospholipids are one of the fatty acids of a triglyceride, replaced by a phosphate group. 1 glycerol, 2 fatty acids, and 1 phosphate group. A major component of the cell membrane called the phospholipid bilayer. The head is hydrophilic (attracts water) and contains the glycerol and phosphate group. The tail is hydrophobic (avoids water) and contains two fatty acids, one is unsaturated and the other is saturated). Phospholipid assembles into the bilayer found in cell membranes when added to water.
A steroid is a carbon skeleton made up of 4 fused rings. Although they have different structures than most lipids, steroids still classify as lipids because they are hydrophobic and insoluble in water. Every steroid has 4 linked carbon rings and many have short tails. Cholesterol is a type of steroid with a short tail, as well as a hydroxide functional group attached to it. This steroid is an important component of animal cell membranes. Any steroid with a hydroxide functional group is also classified as an alcohol, thus why they are called sterols.
Proteins are made of 20 different monomer amino acids joined by peptide bonds (also called “polypeptides”) which are covalent bonds. The structure of the amino acids have specified chemical and physical properties that determine their function so a slight change in structure at the primary stage can lead to the change in both a protein’s structure and function. (4 calories per gram) When two amino acids are joined together by dehydration synthesis, it is called a dipeptide. Polymers of amino acids are polypeptides and are formed when many amino acids join through dehydration synthesis. The folding of one or more polypeptides forms a protein. Some amino acids are polar and other are nonpolar; in addition, some are acidic and others basic.
Enzymes catalyze a chemical reaction by lowering the activation energy required. Enzymes interact with substrates at its active site but are only functional in certain conditions; otherwise, they denature.
Reactions can be inhibited by competitive inhibitors (which will bind to the enzymes’ active sites) or by noncompetitive inhibitors (which bind to allosteric sites to change the shape/activity of the enzyme).
Every enzyme has an optimal pH, temperature, and substrate concentration before it slows down activity and denatures.
There are two parts of photosynthesis. First, chlorophylls utilize light energy to charge electrons in photosystems I and II. Those electrons are transferred to power the production of carbohydrates in the Calvin cycle.
Cellular respiration produces ATP. Fermentation will occur in the absence of oxygen. Electron transfers result in the formation of a proton gradient, which results in the storage of energy in ATP, which is then used throughout the organism.
Paracrine signaling consists of a signaling molecule being released into the intracellular space between molecules when they are close by.
Endocrine signaling happens over long distances.
Signal Transduction Pathways consist of three stages: Reception, Transduction, and Response.
Reception is the process by which a ligand binds to a receptor on the cell membrane, such as an Ion-gated channel or a G-protein coupled receptor.
Transduction amplifies the signal by converting it to a form that the cell recognizes.
The response can activate gene transcription or whatever the cell response was meant to be.
Negative Feedback works to reduce the stimulus (ex. insulin regulation of glucose).
Positive Feedback works to increase responses (ex. oxytocin to help with contractions in childbirth).
The cell cycle has 3 stages of interphase (G1, S, G2), followed by mitosis (produces identical daughter cells).
Cell cycle checkpoints at the end of G1, G2-M transition, and metaphase prevent cell abnormalities.
Prophase
This is where the action begins. As a cell prepares to divide, it enters prophase, in which the nucleoli—spherical structures inside the nucleus that contain RNA and protein—disappear and the chromatin of the nucleus condenses into tightly-packaged chromosomes. Note that because the DNA was duplicated in S-Interphase, each chromosome now contains two copies of the cell’s DNA.
The membrane that surrounds the genetic material of the cell (known as the nuclear envelope) then disappears, and a mitotic spindle is created as the microtubule organization centers (MTOCs) move toward opposite ends of the nucleus. These MTOCs are specialized structures that control the arrangement of a protein called tubulin into long microtubules that can manipulate the positioning of the cell’s genetic material. The mitotic spindle is simply the term for the overall structure of microtubules that guide this material.
As the MTOCs move apart, the microtubules they’ve built increase in length and connect to the centromeres of the chromosomes via a region called the kinetochore. The MTOCs are then capable of moving the chromosomes toward or away from the poles of the cell by shortening or lengthening the microtubules.
Metaphase
During metaphase, the fully-formed chromosomes are aligned by the microtubules at the center of the cell in a plane known as the metaphase plate. Then, the attached microtubules retract, splitting each chromosome into its individual sister chromatids. These resulting chromatids still have a centromere each, however, and therefore are referred to as individual chromosomes from this point forward.
Metaphase ends as soon as the original chromosomes are split.
Top tip: to determine the number of chromosomes at any time during the process, simply count the number of centromeres.
Anaphase
After the initial separation of the chromosomes, the new chromosomes (the split chromatids) are pulled to the poles of the cell via the shortening of the microtubules. At the end of this phase, each pole contains a complete set of identical chromosomes.
Since the DNA copies made during the S phase of interphase have now split, the chromosomes at the poles consist of single chromatids with only a single copy of the parent cell’s DNA.
Telophase
To wrap up the division process, normal cell organelles start to re-build and the newly-formed daughter cells begin to take shape for their own interphase. Nuclear envelopes develop around the genetic material at each pole, the chromosomes unwind and return to loosely-floating chromatin, and the nucleoli appear once more.
While the nucleus reforms, the dividing cell undergoes cytokinesis, which refers to the splitting of the unit and the division of cytoplasm across the two new cells. A cleavage furrow develops at the center of the dividing unit and cinches closed like a drawstring, leaving two separate cells with enclosed cell membranes.
Final result: two diploid daughter cells containing identical genetic material to the parent cell.
Because meiosis has the special task of creating new sex cells for reproduction, its process is unique, though similar to mitosis in many ways. Meiosis essentially goes through the stages of mitosis twice, with some key variations.
Perhaps the most important thing about meiosis is that it enables the independent assortment of genetic material. The determination of which chromosomes end up in which gametes is random, allowing for natural variation in the gene pool. It is this variation and biological diversity that keeps species naturally resilient.
Now that you’re inspired by the beauty of natural genetic diversity, let’s discuss how it happens.
Prophase I
This phase begins similarly to prophase in mitosis, with the nuclear envelope breaking down and the chromatin condensing into chromosomes. In meiosis, however, homologous chromosomes pair up into groups of four chromatids (known as tetrads or bivalents) in a process called synapsis.
During synapsis, genetic material may cross over between non-sister homologous chromatids (chromatids that are not connected by a centromere and are therefore not part of the same chromosome).
Metaphase I
Next, homologous chromosome pairs are arranged at the metaphase plate. Instead of a line of single chromosomes, as in mitosis, meiosis sees a line of pairs. Microtubules from each pole then attach to the kinetochore of one chromosome from each pair.
Anaphase I
This next phase starts as soon as the tetrads begin to separate. Like in mitosis, the separate chromosomes are pulled by the microtubules to opposite ends of the cell. Unlike mitosis, however, these chromosomes still comprise two sister chromatids.
Telophase I
The first half of the process completes with the formation of nuclear membranes around the chromosomes at the poles. Unlike in mitosis, the cleavage furrow does not yet develop. Note that once this process repeats to form the final four daughter cells, the resulting cells will be haploid.
Prophase II
The fun starts again with prophase II, in which the two newly-formed nuclear envelopes break down again and the mitotic spindle forms. This time, there is no crossing over.
Metaphase II
Metaphase II is nearly identical to metaphase in mitosis, with single chromosomes aligning at the metaphase plate. In this case, however, there is half the number of chromosomes present as in mitosis.
Anaphase II
Just like metaphase II, anaphase II mirrors the happenings of anaphase in mitosis, but with half as many chromosomes. Each single chromosome is pulled apart by microtubules and the new chromosomes (formerly sister chromatids) are pulled to opposite poles.
Telophase II
The entire process wraps up in telophase II. Four new nuclei form and cytokinesis occurs to form the four final cells. Note that the resulting cells’ chromosomes comprise only one chromatid each, and even when these are replicated during the S phase of interphase the haploid cell will still only contain half the number of chromosomes of the parent cell.
Final result: four haploid daughter cells, each containing copies of half the genetic material of the parent cell.
Meiosis
Meiosis has two parts to form haploid gamete cells. Each gamete receives a haploid (1n) set of chromosomes after the homologous chromosomes separate. This is when crossing over may occur to increase genetic diversity.
Mendelian genetics can help predict outcomes of single-gene traits from parent to offspring.
Some traits do not follow Mendel’s laws and therefore will not fit within these predictions. They are more difficult to track, as they are less likely to separate from each other.
There are three major sources of genetic diversity: crossing over in prophase I of meiosis, independent assortment (2^23 combination in humans!) in metaphase I of meiosis, and random fertilization.
Genetic disorders are caused if an allele mutates or a sequence changes (nondisjunction).
As a eukaryotic organism grows, its cells are constantly dividing and creating new cells according to the “genetic blueprint” of its DNA. The processes by which these new cells are developed are known as mitosis and meiosis. Mitosis is the method by which somatic (or non-reproductive) cells are created, while meiosis is the method that creates gametes (reproductive cells like sperm and eggs). Keep in mind: prokaryotic cells do not have membrane-bound organelles like nuclei, and therefore do not undergo mitosis and meiosis as eukaryotic cells do (instead, they undergo binary fission). Throughout our discussion of mitosis and meiosis, we will be talking only about eukaryotes.
Before we get into the specifics of each process, let’s go over some AP® Biology background information that will help us understand the differences between them.
Chromatin, Chromatids, and Chromosomes
These are essentially the three forms of a cell’s genetic material. Chromatin is its loosest, least-organized form, which usually floats freely around inside the defined envelope of the nucleus. Chromatids are formed from condensed chromatin and serve as one-half of each chromosome. In its most complete form, two identical “sister chromatids” are joined together by a centromere to form a full chromosome.
Diploid vs. Haploid Cells
Cells come in essentially two “flavors”: diploid and haploid. As the names imply, a diploid cell contains two sets of genetic information in homologous chromosome pairs, while a haploid cell contains only one set of genetic information in single copies of each chromosome.
Non-reproductive somatic cells are diploid cells, containing two sets of chromosomes. Human cells, for example, have 23 chromosome pairs (46 total chromosomes), with one set of genetic information inherited from each of that human’s parents.
Reproductive gametes, on the other hand, are haploid cells, containing only one set of chromosomes. In humans, egg and sperm cells contain only 23 chromosomes. When gametes combine during sexual reproduction, the sets of chromosomes from both parents provide the chromosome pairs for future diploid cells.
Now that we’ve reviewed the necessary AP® Bio background, let’s get to the meat of this section: the actual processes of mitosis and meiosis.
The process of cellular mitosis occurs in four primary phases: prophase, metaphase, anaphase, and telophase. A fifth “phase,” known as interphase, is the state in which a somatic cell spends most of its lifespan.
Note: you will not need to know the names of these phases for the AP® Biology exam, but you will still be required to describe the steps.
Take a look at how each of these phases breaks down.
Interphase
Not necessarily a true “phase” of mitosis, interphase is the normal, non-division state of somatic cells. If you throw a prepared slide of cells under a microscope, chances are the majority of them will be sitting in interphase, looking relatively inactive and uninteresting. If a cell is not in interphase, it is undergoing mitosis (which is sometimes referred to as “M phase”).
Interphase itself is split into three stages, as follows:
- G1: cell simply grows
- S phase: cell continues growing, starts duplicating DNA
- G2: growth continues while cell prepares for mitotic division
DNA and RNA store genetic information. Chromosomes in prokaryotes are circular while ones in eukaryotes are linear. Bases are purines (G and A) with a double ring structure and pyrimidines (C, T, U) with a single ring structure.
DNA replicates from 5’ to 3’ and is semi-conservative. Helicase unwinds the DNA while topoisomerase prevents coiling. RNA primers initiate DNA polymerase’s DNA synthesis on the leading and lagging strands. Ligase combines the fragments in the lagging strand.
After transcription (copying of DNA to RNA), a GTP cap and poly-A tail are added and introns are removed.
Translation creates proteins by ribosomes reading mRNA and tRNA matching amino acids to codons.
Mutations in DNA lead to a protein losing functions, having more functions, or no change at all.
Gel Electrophoresis separates DNA fragments by size while PCR amplifies DNA segments. DNA sequencing determines the order of nucleotides in a DNA molecule.
Bacterial transformation introduces DNA to bacterial cells.
Evolutionary fitness is measured by reproductive success.
Competition is what creates natural selection.
As environments change, different selective pressures are put on populations that affect phenotypes.
Evolution is also driven by random events like mutations and genetic drifts.
The Hardy-Weinberg equation (see formula sheet!) is used to predict equilibrium frequencies.
Fossil age can be estimated using carbon-14 dating, geographical data, and identifying the age of rocks surrounding it.
Organisms are linked thanks to common ancestry, and they keep evolving.
Phylogenetic trees and cladograms both show relationships between lineages.
Extinction provides newly available niches.
Variation affects population dynamics.
Homeostasis is how organisms respond to external events to maintain internal equilibrium.
A net gain in energy allows growth in an organism.
Endotherms can use thermal energy to maintain internal temperatures, while exotherms cannot.
Some factors, like population size, population change over time, and carrying capacity, limit populations. These relationships are represented in an s-curve.
Simpson’s Diversity Index calculates the diversity in an ecosystem.
The more biodiversity an ecosystem has, the more resilient it is to disruptions.
There are many kinds of species interactions: commensalism, mutualism, parasitism, predator-prey, competition, etc.
When you go up a trophic level, only 10% of the energy is transferred; most energy is lost in the form of heat from one trophic level to another.
Cell size is very important to its survival, especially the surface area-to-volume ratio. The SA should be big enough to be able to exchange materials and eliminate waste products. (High SA, smaller volume = ideal ratio for cells!)
Phospholipid bilayers are semipermeable membranes. For nutrients that are unable to pass on its own, they require channel proteins, which can facilitate either passive or active transport. Particles in passive transport follow a concentration gradient (high to low), while those in active transport go AGAINST the gradient (low to high).
Organisms like plants, prokaryotic cells, and fungi, have cell walls, which act as a permeability barrier as well as maintain cell structure and function.
Cellular Respiration is a chemical process with the following equation: C6H12O6 + O2 → H2O + CO2. All organisms, including those capable of photosynthesis, go through the process of cellular respiration. The overall reaction breaks down a carbohydrate, most frequently modeled by glucose, and converts the energy stored in that molecule into the most basic cellular energy, ATP.
Cellular Respiration is broken down into three major steps which are dependent on one another: glycolysis, the Krebs cycle, and the electron transport chain. While glycolysis takes place in the cytoplasm of the cell, the Krebs cycle and the electron transport chain take place inside of the mitochondria.
Glycolysis is the most evolutionarily conserved process in cellular respiration. The process takes place in all living organisms in almost the exact same way. Fundamentally, glycolysis involves breaking down glucose, which possesses 6 carbons, into two 3-carbon molecules of pyruvate.
In the process, a small amount of energy is released due to the breaking of bonds. This is captured as 2 molecules of ATP. Similarly, the breaking of bonds releases a few electrons that are picked up by electron carriers, NADH. These electrons will be dropped off to the electron transport chain later.
Before pyruvate can continue on into the mitochondria to enter the Krebs cycle, pyruvate oxidation takes place. Oxidation is the loss of electrons. In this process, pyruvate becomes a 2-carbon molecule called acetyl CoA. A molecule of carbon dioxide is released from each pyruvate molecule that is oxidized.
The Krebs Cycle takes place in the mitochondria. In this cycle, similarly to the Calvin Cycle, a number of enzymes process a number of reactions number of highly specific enzymes break down acetyl CoA in reactions that create a number of electrons and a little bit of energy. The process results in the creation of a lot of electron carriers (around 8) such as NADH and FADH2. These electron carriers will allow a lot of ATP production in the electron transport chain. 2 ATP are also produced in the Krebs Cycle.
When hydrogen ions are dropped off by electron carriers to the electron transport chain, the hydrogen ion is pumped across the plasma membrane to form a high concentration gradient of hydrogen ions. These will be used by ATP synthase.
The electron travels through the electron transport chain on a number of electronegative proteins. It eventually ends up binding with oxygen, the final electron acceptor. When oxygen accepts the electron, it forms a bond with hydrogen ions and water is created.
The concentration gradient of hydrogen travels through ATP synthase, in the same way as it does in photosynthesis, the kinetic energy is used to phosphorylate ADP into ATP. This process is called chemiosmosis, as ions are moving down their concentration gradient. This process produces somewhere between 30 and 40 ATP molecules. Don’t worry, you don’t need to know specific numbers! Just know that a TON more ATP is produced through this process than through either glycolysis or the Krebs cycle.
Another important aspect of the electron transport chain is the recycling of electron carriers. This takes place when they drop off their electron and can then be refilled in glycolysis or the Krebs cycle. If these carriers were not emptied, the cycle would not be able to continue.
FERMENTATION-In organisms without access to oxygen, anaerobic respiration takes place. This happens in a number of bacteria, and in other organisms when oxygen is being used up faster than it can be inhaled (think crazy workout).
Without oxygen, the Krebs cycle and electron transport chain cannot take place, because there is no final electron acceptor. Instead, electron carriers must be recycled elsewhere.
This happens through the process of fermentation.
Organisms find other molecules to drop off their electrons. Some examples include creating lactic acid, ethanol, and carbon dioxide. This is how beer and wine are fermented by various bacteria and yeast. In humans, our body produces lactic acid when oxygen is in short supply, such as in a tough workout. This can create sore muscles the next day.
Photosynthesis
The process of photosynthesis is an essential AP® Biology concept to understand. Photosynthesis is the means by which most of the plant life on Earth gets its energy. All animals receive nutrients either from plants or from animals that get their energy from plants. This means that plants are the basis for all of the ecosystems on Earth, making photosynthesis a very important process. So, in order to understand how photosynthesis happens, biologists have to break it down into two parts, the light and dark reactions.
1. Light Reaction (or the Light-Dependent Reactions)
This is the first step in the process of photosynthesis. The light reaction is the process by which the leaf of a plant will absorb energy from the sun (in the form of photons) and will transfer it into electron carriers and energy (in the form of Adenosine Triphosphate, or ATP).
First, light will enter the leaf and will be absorbed by pigments within photosystem II, which is the first half of the light reaction. After the light is absorbed by the pigments, the photon is bounced around inside the photosystem until it reaches the pigment that is correct for that wave of light. Once it reaches that pigment, it will excite an electron and will move the electron up to the primary electron acceptor.
After reaching the primary electron acceptor, the electron will be moved to photosystem I. It will be transported across what is known as the electron transport chain. All you need to know about the ETC is that the electron will move down it and as it moves down it will transfer energy, which is used by the plant to combine ADP and a phosphate group into ATP.
Once the electron reaches photosystem I (just remember that photosystems go in reverse, II is first and I is second), it is excited by another photon and the electron again is bounced to a primary electron acceptor. Only this time when the electron falls, it is used to combine two hydrogen ions and one NADP+ ion to create NADPH. This will be used later on in the dark reactions to further the process. Once the NADPH has been made, the ATP and the NADPH move into the dark reactions, the second part of the cycle.
The next and final process of photosynthesis is the Calvin cycle. This is the process that takes the NADPH, ATP and CO2 and converts them into G3P (which can be turned into glucose, the basic unit of energy). This process is a cycle, so part of the product, G3P, will be used to start and end the cycle.
The cycle starts with three five-carbon chains that have a phosphorus attached to each of them using some of the ATP, creating three RuBPs. After this, carbon dioxide is fixed (carbon will be added) to the RuBP and will create three unstable six-carbon compounds. Then the compound will fall apart and will make six three-carbon chains. Next, an electron will be donated to the three carbon chain and it will create the end product, 6 G3Ps. One of these G3Ps will be removed from the cycle and the other five will be used to repeat the cycle and create the five-carbon chain. Finally, after enough G3P is made, it will be turned into glucose and thus photosynthesis is complete.