Cell Biology

In Cell Biology, teams answer questions and/or perform lab tasks relating to cell biology and cellular biochemistry. The event was most recently run nationally in Division C in 2015 and 2016, and will return in 2021.

Overview
Cell Biology is an event about eukaryotic and prokaryotic cells. According to the rulebook, questions may include the following material: cell structure, function and classification, cellular respiration, protein synthesis, the cell cycle, DNA replication, RNA synthesis, viral structure and function, molecular genetics, DNA sequencing and analysis, DNA fingerprinting, and immunology. Some of these topics are tested only at the National level. Many of the topics are covered in AP Biology courses, but some tests will go into greater depth or may cover a broader scope of topics than an AP Biology course would. The event can be administered as a sit-down test, but it is usually a series of stations.

Strategy
An important strategy for this event is having trust between partners. Lots of time can be wasted debating the answer to a question instead of moving on, which can leave many questions unanswered. This lack of trust is often the difference between the partners placing or not placing in their event, or worse, not qualifying for a future tournament. This lack of trust can be combatted by practice. Learning how to divide the test to give each partner their strongest areas will help assure that the questions are more likely to be correct.

During the event, focusing on previous stations can negatively affect scores. Focusing on previous stations can take away focus from the current station. This may result in worse scores and a lowered chance of medaling. Participants are not able to change their previous work and it is not something to be worrying about when there are more important things to be done. Taking a deep breath and focusing on the work ahead helps the participant not worry and improve their scores.

It is important to learn the material thoroughly. Frequent study and practice can help cultivate confidence and develop team chemistry, as well as increase understanding of the subject matter.

Mnemonic devices can be extremely effective, especially in dealing with more complex topics. These methods allow for quick and accurate recollection of information throughout the event.

Finally, if time allows, utilize a technique for writing down brief summaries of unanswered questions and returning to them at a later point. Whether it be a rest station, tiebreaker station, or another regular station that is more quickly finished, it is far better to spend down time answering questions.

Quick Overview of Helpful Ideas
 * Start practicing early and efficiently
 * Use mnemonic devices to memorize complex concepts
 * Answer practice test questions to familiarize yourself with the test format

Enzymes
Enzymes are special proteins that regulate nearly every biochemical reaction in the cell. Proteins are built from amino acids, which have a carboxyl end (C-terminus), an amino end (N-terminus), an “R” group and a hydrogen, with carbon as the center.

There are four different levels of structure for an enzyme:
 * Primary Structure - the unique sequence of amino acids
 * Secondary Structure - coils and folds in the polypeptide chain (beta pleated sheet or alpha helix) due to hydrogen bonding
 * Tertiary Structure - determined by interactions among various side chains (R groups), including hydrogen bonding, ionic, hydrophobic, and van der Waals interactions, as well as disulfide bonds between two cysteines. Tertiary structure determines the unique shape of a protein and it determines the protein’s function.
 * Quaternary Structure - Results when a protein consists of more than one polypeptide chain; the same interactions from tertiary structure apply.

Enzymes function to:
 * Provide energy to cells
 * Build new cells
 * Aid in digestion
 * Break down complex molecules (“substrate” = reactant)
 * Catalyze reactions (speed up chemical reactions without being used up or altered)

The function of an enzyme is determined by its structure. The structure of an enzyme, especially its primary structure, is determined during protein synthesis. Other factors such as pH, temperature, and quantity also affect an enzyme's effectiveness.

The rate of enzymatic reactions is determined by the Michaelis-Menten equation, given by


 * [math] v = \frac{d [P]}{d t} = \frac{ V_\max {[S]}}{K_\mathrm{M} + [S]} .[/math]

Here, [math]V_\max[/math] represents the maximum rate achieved by the system, at saturating substrate concentration. The Michaelis constant [math]K_\mathrm{M}[/math] is the substrate concentration at which the reaction rate is half of [math]V_\max[/math].

Enzyme activity can be regulated through allosteric regulation, encompassing negative regulation (feedback inhibition) and positive regulation (subtract activation), as well as enzyme inhibitors, including reversible and irreversible inhibitors.

Membrane Structure
The cell membrane is a selectively permeable membrane that consists of a phospholipid bilayer in which proteins, lipids, and carbohydrates are embedded. The cell membrane follows the fluid mosaic model, which states that the phospholipid bilayer behaves more like a fluid than a solid, so lipids and proteins move laterally within the bilayer and the pattern or “mosaic” of lipids and proteins constantly changes.

The outer portion of the cell membrane is composed of the hydrophilic (water-loving) heads of the phospholipids which consist of a “variable” head group (a simple organic molecule molecule, ex: choline), a negatively charged phosphate group, and a glycerol. The “variable” head group associates with some proteins and allows cells to recruit certain proteins to the cell membrane, which is important for cell communication. Conversely, the inner portion is composed of the hydrophobic (water-fearing) tails of the phospholipids which consist of 2 fatty acid (hydrocarbon) chains.

Sphingolipids are another type of lipid found in the cell membrane; their metabolism produces bioactive signaling molecules that modulate fundamental cellular processes. The core of a sphingolipid is an amino alcohol called sphingosine.

The tight packing of phospholipids and the hydrophobic tails prevents larger (especially polar) molecules (amino acids, carbohydrates) and ions (sodium, potassium, calcium) from from passively diffusing into the cell.

The fluidity of the cell membrane is determined by a variety of factors:
 * Single and double bonds in the fatty acid tails, where saturated lipids composed of solely single bonds can pack more tightly, and where unsaturated lipids composed of chains with double bonds have kinks, resulting in a bent chain. The kinks introduce space, and thus a membrane filled with only saturated phospholipids would be solid rather than fluid-like at physiological temperature.
 * Presence of cholesterol (a sterol - steroid alcohol), which packs between phospholipids, reducing permeability (prevents water-soluble molecules from diffusing across) and increasing rigidity (four linked hydrocarbon rings + hydrocarbon tail + hydroxyl)

Functions of the cell membrane:
 * Define and compartmentalize the cell
 * Serve as the locus of specific functions
 * Control movement of substances into and out of the cell and its compartments
 * Play a role in cell-to-cell communication and detection of external signals

Proteins
Function of the proteins is to form channels in membranes that allow the passage of specific molecules or ions; act as enzymes to increase the rate of cellular reactions (and modify proteins in blood or extracellular space); act as receptors that detect the presence of specific molecules or ions in the external environment; and interact with proteins in other membranes, generating sites of attachment between membranes and cells

Integral membrane proteins - exposed to interior AND exterior


 * Form channels (or pores or pumps), receptors (that recognize & respond to hormones), or adhesion points


 * Also can be cell-surface markers, such as glycoproteins which have carbohydrates that act as labels attached to the external side (these labels allow cells to recognize each other and viruses use the labels as “docks” to enter and infect cells)


 * Can span membrane at least once and cross it several times


 * They are permanently embedded and can only be removed through expenditure of large amounts of energy or digestions

Peripheral membrane proteins - exposed to one side (interior OR exterior) provide structural support to membranes


 * Participate in transmitting cell signaling events


 * Alter the topology of membranes in the secretory pathway


 * Can be enzymes


 * Associate with the head groups of specific phospholipids or portions of integral membrane proteins (hence the name “peripheral”)

Unlike integral proteins, the association is impermanent - they can be easily removed by changing the composition of the membrane or the morphology or charge of the protein

Some proteins in the outer leaflet form covalent links (through the amino acids in their C-terminuses) with the head groups of phospholipids; these are the proteins that act as enzymes.

Carbohydrates
Membrane carbohydrates account for approximately 2-10 % of the mass of the cell membrane. They are confined mainly to the non-cytosolic surface on the extracellular surface of the cells. They are covalently bonded to proteins and lipids, forming glycoproteins/proteoglycans and glycolipids, respectively.

Cytoskeleton
Structural support (maintaining shape & preventing damage) for the cell membrane is provided by cytoskeleton.


 * Sits directly under the cell membrane and is composed of a “mesh” of actin filaments


 * Interacts with integral membrane proteins by limiting the diffusion of membrane proteins and providing a stable framework to which membrane proteins attach


 * Prevents damage to membranes when external forces pull or push on integral membrane proteins


 * Microtubules that form unique structures (ex: 9 + 2 arrangement for cilia)

Movement Across Membranes
An important ability of cells is to transport materials in and out of the cell via the cell membrane. Such movements generally fall under the categories of passive transport or active transport.

Passive Transport
Passive transport is the movement of molecules that does not require the energy of the cell. There are three primary forms of passive transport.

Simple diffusion is the movement of molecules down their concentration gradient (region of high concentration to region of low concentration) without the use of energy. The rrate of diffusion varies from membrane to membrane because of different selective permeabilities. Examples of items that pass easily include small, uncharged substances, such as the following:
 * Water
 * Lipids (due to nonpolarity)
 * Oxygen (due to nonpolarity)
 * Carbon dioxide
 * Some waste
 * Some amino acids

Osmosis is the passive diffusion of water down its concentration gradient (region of high concentration to region of low concentration) across selectively permeable membranes. Water will flow from a region with a lower solute concentration (hypotonic) to a region with a higher concentration (hypertonic). Water “dilutes” area with more solute and makes the area with less solute less watery until both areas have equal concentration of solute.

Facilitated diffusion is the diffusion of particles across a selectively permeable membrane with the assistance of the membrane’s transport proteins. Transport channels are specific in what they can carry and have binding sites designed for molecules of interest. These binding sites are designed in such a way that using these to transport particles requires no energy.

Active Transport
Active transport is the movement of particles across a selectively permeable membrane against its concentration gradient (from low concentration to high), requiring an input of energy (ATP). Active transport is vital to the ability of cells to maintain particular concentrations of substances despite environmental concentrations.

Some processes associated with active transport include the following:
 * Endocytosis - a process in which substances are brought into cells by the enclosure of the substances into a membrane-created vesicle
 * Pinocytosis - involves the transport of solutes or fluids
 * Phagocytosis - the movement of large particles or whole cells (ex: phagocytes are immune cells which engulf bacteria and viruses and eliminate them with lysosomal enzymes)
 * Exocytosis - a process in which a vesicle functions like a trash chute by escorting the (packaged) substance to the plasma membrane, fusing with the membrane, and ejecting the substance outside the cell

The sodium-potassium pump is a major pump in animal cells. Through this transport, 2 potassiums are moved in for every 3 sodium out against their respective concentration gradients. This makes sure that cells have a very high concentration of potassium and a very low concentration of sodium at all times (diffusion wants to move sodium in and potassium out to equalize)

Tonicity

 * Hypertonic - when the concentration of solute molecules outside the cell is higher than the concentration in the cytosol, the solution outside is hypertonic to the cytosol (and cytosol is hypotonic to outside solution), so water diffuses out of the cell until equilibrium is established
 * Hypotonic - when the concentration of solute molecules outside the cell is lower than the concentration in the cytosol, the solution outside is hypotonic to the cytosol (and cytosol is hypertonic to outside solution), so water diffuses into the cell until equilibrium is established
 * Isotonic - when the concentrations of solutes outside and inside the cell are equal, the outside solution is said to be isotonic to the cytosol, so water diffuses in and out of the cell at equal rates and there is no net movement of water

Tonicity can be understood in different ways for animal cells and plant cells. In an animal cell:
 * In a hypertonic environment, water rushes out of the cell to establish equilibrium and cell shrivels
 * In a hypotonic environment, water rushes into the cell to establish equilibrium and cell lyses (bursts)
 * Isotonic environment is IDEAL

By contrast, in a plant cell:
 * In a hypertonic environment, water rushes out of the cell to establish equilibrium and cell becomes plasmolyzed (shrinking of cell’s cytoplasm away from the cell wall)
 * In an isotonic environment, water diffuses in and out at equal rates but cell is flaccid
 * A hypotonic environment is IDEAL because water rushes into the cell to establish equilibrium and fills the central vacuole, causing it to press against the cell wall and create turgor pressure (a turgid plant cell is best)

Some cells prefer a hypotonic environment, so as cells accumulate water, they must pump excess water out in order to maintain a lower concentration of water in the cytosol (maintain osmotic pressure). A contractile vacuole is an organelle that uses energy to collect excess water and then contract, pumping water out of the cell (found in paramecium).

Cell Cycle
In animals, autosomal cells are diploid (2n), with two copies of each chromosome. Germ cells, on the other hand, are haploid (n), containing only one copy of each chromosome. Eukaryotic cells replicate through the cell cycle, a specific series of phases during which a cell grows, synthesizes DNA, and divides. Derangements of the cell cycle can lead to unchecked cell division and may be responsible for the formation of cancer.

Preparation

 * Interphase - DNA is chromatin (chromosomes not visible), cell spends most time here (90%)
 * G1 phase (presynthetic gap) - Cell grows to mature size and makes sure it has all material necessary for DNA synthesis, also obtains nutrients and begins metabolism
 * G1 checkpoint (aka restriction point)- Cell irreversibly commits to the cell division process and goes into S phase (if all conditions favorable) or advances into G0. Growth factors (and other external influences) play a role in carrying the cell past the G1 checkpoint. The cell (1) must be of appropriate size, (2) have adequate energy reserves, (3) no damage to DNA.
 * G0 phase (inactive phase) - Cell makes the decision to exit cycle after G1 and does not replicate DNA or divide (ex: fully developed cells in the central nervous system)
 * S phase - DNA is replicated (synthesized) so that each daughter cell will have a complete set of chromosomes after the parent cell divides; transition to S phase is signaled by cyclins and CDKs. Following S phase, each chromosome consists of two identical chromatids that are bound together at a specialized region known as the centromere.
 * G2 phase (postsynthetic gap) - Cell grows more and prepares for division by making sure that it has the material (ex: doubles of organelles) necessary for the physical separation and formation of daughter cell
 * G2 checkpoint - Bars entry into mitotic phase if conditions not met. The cell checks for DNA integrity and DNA replication, and if errors or damage are detected, the cell will pause to allow for repairs; if the damage is irreparable, the cell may undergo apoptosis. If no problems are found, CDKs signal beginning of mitotic cell division.

Depending on the type of cell, either meiosis or mitosis can proceed.

Mitosis
Mitosis, taking up 10% of the cell cycle, divides an autosomal cell into 2 diploid (2n) daughter cells.


 * Prophase - Nucleus and nucleolus disappear; chromosomes appear as two identical, connected sister chromatids; mitotic spindle (made of microtubules) begins to form; centrioles move to opposite poles of the cell (plant cells do not have centrioles)
 * Metaphase - the sister chromatids line up along the middle of the cell, ready to split apart
 * M checkpoint (spindle checkpoint) - occurs near the end of the metaphase stage of mitosis and determines whether all the sister chromatids are correctly attached to the spindle microtubules; mitosis will not proceed until the kinetochores of each chromatid pair are firmly anchored to at least 2 spindle fibers arising from the opposite poles of the cell
 * Anaphase - The sister chromatids split and move via the microtubules to opposite poles of the cell (pulled by the spindle apparatus so that each pole of the cell has a complete set of chromosomes
 * Telophase - the nuclei for the newly split cells form; the nucleoli reappear, and the chromatin uncoils
 * Cytokinesis - Newly formed daughter cells split apart. Animal cells are split by the formation of a cleavage furrow, plant cells by the formation of a cell plate

Meiosis
Meiosis, divided into two stages, divides one diploid (2n) cell into 4 haploid (n) daughter cells. It occurs in cells of gonads to produce gametes (part of process of sexual reproduction).

Meiosis I

 * Prophase I - Each chromosome pairs with its homolog. Crossover (synapsis) occurs in this phase. The nuclear envelope breaks apart and spindle apparatus begins to form.
 * Metaphase I - Chromosomes align along the metaphase plate matched with their homologous partner. This stage ends with the separation of the homologous pairs.
 * Anaphase I - Separated homologous pairs move to opposite poles of the cell.
 * Telophase I - Nuclear membrane reforms; process of division begins.
 * Cytokinesis - After the daughter cells split, the two newly formed cells are haploid (n).

Following meiosis I, cells enter a period of rest called interkinesis or prophase II. No DNA replication occurs during this stage.

Meiosis II

 * Prophase II - Nuclear envelope breaks apart and spindle apparatus begins to form.
 * Metaphase II - Sister chromatids line up along the equator of the cell.
 * Anaphase II - Sister chromatids split apart and are called chromosomes as they are pulled to the poles.
 * Telophase II - The nuclei and the nucleoli for the newly split cells return.
 * Cytokinesis - Newly formed daughter cells physically divide.

DNA Structure
DNA (deoxyribonucleic acid) has a double helix shape of uniform width, discovered by Rosalind Franklin’s photos. Nucleotides are the polymers of DNA, and are made up of a nitrogen-containing base, a phosphate group, and a deoxyribose sugar.

The nucleotides that compose DNA can have four different nitrogen-containing bases: two pyrimidines (single ring - thymine and cytosine), and two purines (double ring - adenine and guanine). Base pairing rules state that adenine bonds with thymine, using 2 hydrogen bonds, and guanine bonds with cytosine, using 3 hydrogen bonds. Chargaff’s rule states that amount of Adenine equals the amount of Thymine (equal percentages) and amount of Guanine equals the amount of Cytosine (equal percentages)

The backbone of DNA is made up of covalently bonded deoxyribose sugars, which have 5 carbons, and phosphates.

DNA (in eukaryotic cells) wraps around proteins:
 * histone proteins - maintain shape of chromosome & aid in tight packaging of DNA
 * nonhistone proteins - control activity of specific regions of DNA

Prokaryotic Cells


Prokaryotic cells are single-celled microorganisms most often containing a cell wall, but lacking membrane-bound organelles found in Eukaryotes. Eukaryotic cells contain a nucleus, plasma membrane, and membrane-bound organelles.

Prokaryotic Cells contain:
 * Cell Membrane: Functions in transport, the movement of substances in and out of the cell, and in energy production (breakdown of large molecules, photosynthesis).
 * Cell Wall: Gives structural strength (rigidity) to the cell.
 * Capsule: Jelly-like substance which protects the cell wall from environmental damage.
 * Nucleoid: Contains a single circular molecule of DNA.
 * Cytoplasm: Region surrounding the nucleoid and within the cell membrane. Contains ribosomes and RNA (site of protein synthesis).
 * Vacuole: Site of photosynthesis (storage).
 * Flagellum: Protein fiber the functions in movement.

Eukaryotic Cells
Eukaryotic Cells contain:
 * Cell Wall: Found in plant cells, provides protection and support. Prevents the cell from bursting when turgid.
 * Plasma Membrane: Control substances coming in and out of the cell. Selectively permeable. Consists of a phospholipid bilayer and various embedded proteins.
 * Cilia: Sweeps materials across the cell surface.
 * Flagellum: Enables a cell to propel and move in different directions (uncommon).
 * Cytoplasm: Contains the organelles of the cell (see table below).

Cell Structure and Organelles
During animal cell division centrioles replicate and centrosome divides. Two resulting centrosomes and centrioles move to opposite ends of the nucleus. From each centrosome, microtubules grow into a spindle which is responsible for separating replicated chromosomes in the daughter cells.

Resources and Study Materials

 * Albert's Molecular Biology of the Cell (6th Edition). Most higher-level tests will draw from this textbook.
 * Campbell Biology (11 Edition); alternatively, any college-level biology textbook.
 * Any high school biology teacher, and especially the AP/IB Biology teacher (if available). Seek out these teachers as they can be important and at times invaluable resources for learning difficult or confusing material. Teachers also can aid in answering questions that may arise during study.
 * AP Biology CD. Most AP Biology teachers have an interactive CD that comes with the textbook that they use. If possible, borrowing the CD can provide another portable resource.
 * AP Biology review books, inlcuding Cliff's AP Biology (less detailed) and Barron's AP Biology (more detailed).
 * Old tests. Event members should ask the coach for old tests from previous invitationals as most invitationals provide the test and answers after the competition is over. The Test Exchange on this site is also an excellent source for additional practice tests.
 * Review, study, and practice often. Trust, respect, and understanding communication is key to an effective partnership.

Links

 * CELLS alive!
 * UW Department of Pathology Cytogenetics
 * The Biology Project