Cell Biology

Overview
Cell Biology is an event dealing with everything concerning eukaryotic and prokaryotic cells. According to the rulebook, questions will include the following material: cell structure, function and classification, cellular respiration, protein synthesis, cell reproduction, 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 many tests also go in greater depth or may cover a broader scope of topics than an AP Biology course. The test is given either as one written test or in a series of stations, which may include anything from demonstrations to actual specimens.

Strategy
An important factor in having success, besides knowing the material, is working well with your partner. Trusting your partner can be the difference when it comes to the rankings. When taking the test, don't get frustrated. Trust your partner, disagreeing on an answer could cause you and your partner to lose valuable time on the test. If you come to a station where neither you nor your partner knows the answer, just move on. Don't get hung up about past stations, it may hurt you when trying to think of the answers to the rest of the test. The main strategy that you and your partner can use is obvious. Learn the material! Study, study, study. Know things like the Krebs Cycle and protein synthesis like the back of your hand. Come up with mnemonic devices to help you remember complicated biology terms. For example, CKSMO (see-kay-smo) can be used to remember the key enzymes in the Krebs Cycle (Citric Acid, Ketogluteric Acid, Succinic Acid, Malic Acid, and Oxalocetic Acid). Learning techniques like this can allow you to spit out the information when needed during the test. One more technique that can be used during the test is to remember or write down questions that you were unable to answer. On most tests, there is usually a rest station or tiebreaker station. Instead of answering the tiebreaker questions, you can go back to the previous questions that you were unable to answer, which are far more important than the tiebreaker questions. Overall, know the material and gain trust and confidence in your partner.

Enzymes
3D structure, and protein’s structure determines its function (in this case, function is enzymatic protein)
 * has a carboxyl end (C-terminus) and an amino end (N-terminus), and an “R” group and a hydrogen (carbon is the center)
 * Structure:
 * Primary Structure - the unique sequence of amino acids
 * Secondary Structure - coils and folds in the polypeptide chain (beta pleated sheet or alpha helix)
 * Tertiary Structure - determined by interactions among various side chains (R groups). It is 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
 * sequence of amino acids (primary structure, which is determined by inherited info) determines a protein’s


 * Enzymes are special proteins that regulate nearly every biochemical reaction in the cell. Different reactions require different enzymes.


 * Enzymes function to:
 * Provide energy to cells
 * Build new cells
 * Aid in digestion
 * Break down complex molecules (“substrate” = reactant)
 * Catalysts (speed up chemical reactions without being used up or altered)
 * Factors that affect enzymes: pH, temperature, and quantity

Membrane Structure
Cell membrane - a selectively permeable membrane that consists of a phospholipid bilayer with proteins of various lengths and sizes interspersed and cholesterol among the phospholipids

Fluid mosaic model - 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

Function of the membrane is to prevent the loss of critical cellular material such as proteins, nucleic acids, carbohydrates, the building blocks of thos macromolecules (amino acids, nucleotides, and sugars), and ATP

Outer portion → hydrophilic (water-loving) head of the phospholipid which consists 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 → important for cell communication

Inner portion → hydrophobic (water-fearing) tail of phospholipid which consists of 2 fatty acids (long chains of hydrocarbons) chain with only single bonds is straight (saturated lipid - solid at room temp), can pack more tightly

Chain with a double bond has a kink, results in a bent chain (unsaturated lipid - liquid at room temp), introduces space because a membrane filled w/ only saturated phospholipids would solid rather than fluid-like at physiological temperature

Tight packing of phospholipids prevents larger molecules (amino acids, carbohydrates) from diffusing by themselves and hydrophobic-ness prevents ions (sodium, potassium, calcium) from diffusing by themselves so small, uncharged stuff is preferable.

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 a 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

Function of the cholesterol (a sterol - steroid alcohol) is to pack between phospholipids, reducing permeability (prevents water-soluble molecules from diffusing across) and increasing rigidity (four linked hydrocarbon rings + hydrocarbon tail + hydroxyl)

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
Passive Transport - does not require energy

(Simple) Diffusion

-the movement of molecules down their concentration gradient (region of high concentration to region of low concentration) without the use of energy rate of diffusion varies from membrane to membrane because of different selective permeabilities

-things that pass easily: small, uncharged stuff (ex: water, lipids (bc nonpolar), some waste, some amino acids, oxygen (bc nonpolar), carbon dioxide)

Osmosis

-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 area with less solute less watery until both areas have equal concentration of solute

Facilitated Diffusion

-the diffusion of particles across a selectively permeable membrane with the assistance of the membrane’s transport proteins -channels are specific in what they can carry and have binding site designed for molecules of interest → does not require energy

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

Sodium-potassium pump

-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)

-moves 2 potassium in for every 3 sodium out against their respective concentration gradients

-major pump in animal cells

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

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

Animal Cell

-in hypertonic environment, water rushes out of the cell to establish equilibrium and cell shrivels

-in hypotonic environment, water rushes into the cell to establish equilibrium and cell lyses (bursts)

-isotonic environment is IDEAL

Plant Cell

-in 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 isotonic environment, water diffuses in and out at equal rates but cell is flaccid

-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 (turgid plant cell is best)

Contractile vacuole

-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
growth factors (and other external influences) play a role in carrying the cell past the G1 checkpoint. It’s point at which the cell irreversibly commits to the cell division process and goes into S phase (if all conditions favorable) or advances into G0
 * Interphase - DNA is chromatin (chromosomes not visible), cell spends most time here (90%)
 * G1 phase - 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)

Conditions:
 * cell is appropriate size
 * cell has adequate energy reserves
 * no damage to DNA
 * cell can also halt the cycle and try to remedy problematic condition

G0 phase (aka 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

G2 phase - 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

Conditions:
 * assessment of cell size and protein reserves
 * ensure that all of the chromosomes have been accurately replicated without mistakes or damage
 * if there are problems with DNA, cell halts the cycle and tries to complete DNA replication or repair damaged DNA

No problems → CDKs signal beginning of mitotic cell division

occurs near the end of the metaphase stage of mitosis determines whether all the sister chromatids are correctly attached to the spindle microtubules cycle 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 or
 * Mitosis (10%) - divides into 2 diploid (2n) daughter cells; all cells of the body other than the cells of the gonads
 * 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 (aka spindle checkpoint)
 * 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 - divides into 4 haploid (n) daughter cells; occurs in cells of gonads to produce gametes (part of process of sexual reproduction), 2 divisions Intermission
 * 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).

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 (Rosalind Franklin’s photos)

Polymers of DNA = nucleotides (nitrogen-containing base + phosphate group + deoxyribose sugar)
 * Nitrogen-containing bases (4)
 * 2 Pyrimidines (single ring) - thymine and cytosine
 * 2 Purines (double ring) - adenine and guanine

Base pairing rules state that:
 * adenine bonds with thymine (2 hydrogen bonds)
 * guanine bonds with cytosine (3 hydrogen bonds)
 * Chargaff’s rule states that amount of A=T (equal %s) and amount of G=C (equal %s)

Deoxyribose sugar has 5 carbons
 * Backbone of DNA is made up of covalently bonded deoxyribose sugars and phosphates
 * DNA (in eukaryotic cells) wraps around proteins → histones (maintain shape of chromosome & aid in tight packaging of DNA) or nonhistone proteins (control activity of specific regions of DNA)

Cell Structure
which is responsible for separating replicated chromosomes in the daughter cells
 * Nucleus
 * most obvious organelle in any eukaryotic cell
 * enclosed in double membrane
 * communicates with surrounding cytosol via nuclear pores
 * Filled of nuclear chromatin-DNA and surrounding protein
 * Nucleolus
 * Inside the nucleus
 * Produces ribosomes which then leave the nucleus and go into the rough **endoplasmic reticulum where they’re critical to protein synthesis
 * Cytosol
 * “soup” where all organelles reside
 * where most of cellular metabolism occurs
 * mostly water, but full of proteins that control cell metabolism including **glycolysis, transcription factors, intracellular receptors, etc.
 * Cytoplasm- collective term for cytosol and organelles in it
 * Centrosome
 * AKA microtubule organizing center(MTOC)
 * area where microtubules are produced
 * Animal cell centrosome is small pair of organelles called centrioles
 * During animal cell division
 * centrioles replicate and centrosome divides
 * Two resulting centrosomes and centrioles move to opposite ends of the nuclears
 * from each centrosome, microtubules grow into a spindle
 * Centriole
 * Ring of nine groups of fused microtubules
 * 3 microtubules in each group
 * Microtubules and centrioles are part of the cytoskeleton
 * The centrioles in a complete animal centrosome are perpendicular
 * Golgi
 * Membrane Bound Structure with a single membrane
 * actually a stack of membrane bound vesicles that are important in packaging macromolecules for transport elsewhere in the cell
 * Stack of larger vesicles surrounded by smaller vesicles containing packaged macromolecules
 * Lysosomes
 * Membrane Bound
 * Common in animal cells
 * contain hydrolytic enzymes necessary for cell digestion
 * in white blood cells that eat bacteria, lysosomes are released into the vacuole around the bacteria and kill them
 * Necrosis- uncontrolled mass release of lysosomal contents into cell that cause cell death
 * Peroxisome
 * protect the cell from its own production of toxic hydrogen peroxide
 * Ex. white blood cells produce hydrogen peroxide to kill bacteria
 * Oxidative enzymes in peroxisomes break down hydrogen peroxide into water and oxygen
 * Secretory Vesicles
 * Cell secretions (hormones, neurotransmitters) are packaged in secretory vesicles at Golgi apparatus
 * secretory vesicles then transported to cell surface for release
 * Cell Membrane
 * Cell enclosed in membrane, a double layer of phospholipids-lipid
 * Exposed heads are hydrophilic, hidden tails are hydrophobic
 * This allows membrane to act as protective barrier to uncontrolled water flow
 * Proteins on membrane
 * receptors for odors, tastes, and hormones
 * responsible for controlled entry and exit of ions like sodium potassium, calcium, and chloride
 * Mitochodria
 * provide energy-power centers
 * about the size of bacteria
 * membrane bound-double membrane
 * outer membrane smooth, inner forms folds(cristae) which greatly increases the inner membrane’s surface area.
 * food(suger) is combined with oxygen to make ATP on these cristae
 * Vacuole
 * membrane bound sac
 * plays roles in intracellular digestion and release of cellular waste products
 * generally small in animal cells
 * large in plant cells
 * storing nutrients and waste products
 * helps increase cell size during growth
 * acts like lysosomes of animal cells
 * regulates turgor pressure in cell-water in vacuoles produce rigidity in plant
 * Cell Wall
 * Only found in plant cells
 * Rigid protective cell wall made of polysaccharides -usually cellulose
 * provides and maintains shape of cells and serves as protective barrier
 * fluid collects in vacuole and pushes against cell wall
 * this turgor pressure responsible for crispness of fresh vegetables
 * Chloroplasts
 * Specialized organelles found in higher plant cells
 * contain chlorophyll responsible for plants’ green color and absorbing energy from sunlight
 * energy used to convert water and carbon dioxide into sugars through photosynthesis
 * have a double outer membrane
 * within stroma are thylakoids appearing in stacks called grana
 * Smooth Endoplasmic Reticulum
 * vast network of membrane bound vesicles and tubules called endoplasmic reticulum
 * a continuation of the outer nuclear membrane and its varied functions suggest the complexity of the eukaryotic cell
 * named because of its smooth appearance in electron microscopy
 * plays different functions depending on cell type including
 * lipid and steroid hormone synthesis
 * breakdown of lipid soluble toxins in liver cells
 * control of calcium release in muscle cells
 * Rough ER
 * appears pebbled by ribosomes on its surface
 * proteins synthesized by ribosomes collect in rough ER for transport throughout the cell
 * Ribosomes
 * membrane bound
 * Packets of RNA and protein
 * the site of protein synthesis
 * comprised of two parts, large and small subunit
 * Cytoskeleton
 * maintains cell shape
 * primary importance is cell motility-internal movement of organelles
 * organized network of three primary protein filaments
 * Microtubules - Largest filaments. They mainly provide mechanical support, as well as organize the cytoplasm, move the cell, and separate chromosomes during telophase. 25 nm diameter.
 * Intermediate filaments - "Middle-sized filaments." This also has a main job of providing support for the cell when it comes into contact with other cells. 10 nm diameter.
 * Actin filaments (Microfilaments) - Smallest filaments. Most abundant protein in eukaryotic cells. This is used in muscle contraction, cell movement, cytokinesis, cell signaling, movement of organelles. 7 nm diameter.

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.

Diagram of the typical Prokaryotic Cell:



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
Cytosol: The fluid portion of a cell's cytoplasm.

Endoplasmic Reticulum (ER): The passageway for transport of materials within the cell, a network of intracellular membranes where secreting proteins are synthesized. Rough ER is the ER and ribosomes, this supplies raw materials for protein synthesis. Smooth ER is the ER without ribsosomes, this functions in the breakdown of fats attached to the rough ER in the Golgi Complex and synthesizes lipids.

Ribosomes: The site of protein synthesis, this is a cytoplasmic particle that contains RNA and proteins.

Golgi Apparatus: The "packing center" of the cell, this is a membraneous organelle that packages and sorts newly synthesized secretory proteins. Also does the final modifications of proteins and lipids.

Mitochondria: Consists of an outer membrane and a convoluted inner membrane, this is the site of aerobic cellular respiration and the site of ATP production.

Lysosomes: The "recycling center" of the cell, this contains enzymes to digest ingested material or damaged tissues.

Peroxisomes: Contains specialized enzymes whose functions involved hydrogen peroxide.

Chloroplasts: Store chlorophyll in a plant cell that is used in the photosynthesis light reaction.

Vacuoles: The storage in a cell, these increase the cell surface area.

Centrioles: Organize the spindle fibers during cell division.

Resources and Study Materials

 * Any AP Biology or College Biology Textbook. Usually it is only the first 7-10 chapters that contain the pertinent information. Openstax has a free Biology textbook for download. Campbell-Reece has an especially good biology textbook.
 * Your AP Biology teacher. Ask them any specific questions that you have or ask them to explain concepts that you don't understand.
 * AP Biology CD. Most AP Biology teachers have an interactive CD that comes with the textbook that they use. Ask them to use it, it helps a lot.
 * Cliff's AP Biology Book. This is probably the most useful book that you can use to refresh yourself on the major points of each subject area.
 * Also, Barron's AP Bio book goes into many of the specifics. (Read this book after you get a basic understanding of the topics in biology.)
 * Old tests. Ask your coach for old tests from previous invitationals. Most invitationals provide you with the test and answers after the competition is over.
 * Your partner. Work with your partner whenever possible. Trusting each other is the key to success.

Links

 * CELLS alive!
 * Harvard Dept of MCB - Biology Links
 * UW Department of Pathology Cytogenetics Image Gallery
 * The Biology Project