bio ap

really bad

Null Hypothesis

States that there is no statistically significant difference between two groups in an experiment. If the calculated chi-square value is greater than the critical value, the null hypothesis can be rejected, suggesting that any observed effect is likely due to real differences rather than chance.

Chi-square test

A statistical test that is used to compare the observed results to the expected results in an experiment. Best used for raw data.

Degrees of Freedom

Found by subtracting 1 from the number of possible outcomes. Used with p-value, which is the probability that the observed data would be random(0.05), to find the critical value in the chi-square table.

Mean

Average of the data.Calculated by summing all values and dividing by the number of values.

Median

Midpoint of the set. Middle of a sorted data set.

Standard Error of the Mean

A way to measure the variability/spread of a data set. The larger the SEM, the greater the variability.

Water

Possess polar covalent bonds, which allow it to from hydrogen bonds with other water molecules.
Results in:

Cohesion(Surface Tension) - molecules sticking to themselves

Adhesion(capillary action) - molecules sticking to other substances that are hydrophilic/polar.

High specific heat - capacity to absorb energy, which can cause cooling

Expanding upon freezing due to h-bonds(makes ice lighter than water)

Universal solvent

pH

Measures concentration of H+ ions in a solution. A pH less than 7 is acidic, greater than 7 is basic, and equal to 7 is neutral.

Buffer

A solution that helps maintain relatively constant pH levels in living cells. Can form acids or bases in response to changing pH levels.

Carbohydrates

Carbon, Hydrogen, Oxygen(CHO, often in a 1:2:1 ratio)

Polymers made up of sugar monomers, which can be used to store energy (starch or glycogen) or be of structural support (cellulose)

Dehydration Synthesis

Also known as a condensation reaction, it is when two molecules, often monomers, form covalent bonds and release water.

Hydrolysis

Reaction in which water is added to break apart two molecules, often monomers.

Lipid

Composed up of Carbon, Hydrogen, Oxygen, and sometimes Phosphorous. Serve for storing energy, cell membranes, and insulation. Composed up of fatty acid monomers.

Unsaturated fatty acid

Has a double bond, liquid at room temperature, and often originates from plants(ex. olive oil)

Saturated Fatty Acid

No double bond(max # of C-H bonds) room temperature and usually originate from animals.(butter)

Phospholipids

Important in cell membranes, made up of a glycerol molecule, two fatty acids, and a phosphate group. Due to the monomers being polar and making up the “tail”, there is a hydrophobic tail, and there is a hydrophilic head due to phosphate being polar. The head interacts with the water, and the inside repels water.

Steroids

Lipid with 4 carbon-based rings, often used for signaling. ex. cholesterol, testosterone, estrogen, vitamin D, cortisone.

Protein

Polymer of amino acid. Can have Primary, secondary, tertiary, and quaternary structures.

Made up of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur.

Amino Acid

Consists of an amino group, a carboxylic acid group, a hydrogen atom, and a variable R-group, all attached to a central carbon atom. Can be altered by mutations, affecting protein structure.

Primary Structure

Amino acids that are joined by peptide bonds(formed by dehydration synthesis), and the order of such amino acids determines the function of the protein.

Secondary Structure

When hydrogen bonds form between adjacent amino acids in the polypeptide chain, resulting in helixes and pleated sheets.

Tertiary Structure

The 3-dimensional folded shape of the protein, often determined by the hydrophilic/hydrophilic interactions between r-groups in the polypeptide. Also includes disulfide bridges between sulfur atoms.

Hydrophilic r-groups will often be on the surface of the protein, making contact with the watery cytosol, while hydrophobic r-groups will be in the interior of the protein.

Picture a crumpled paper ball for structure.

Quaternary Structure

When a protein consists of multiple polypeptide chains known as subunits, which are joined together to form the complete protein.

ex. hemoglobin has 4 subunits

picture multiple crumpled paper balls together.

Nucleic Acids

DNA and RNA, polymers of nucleotides. consists of the elements Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorous.

Nucleotide

Monomer, consists of a 5-carbon sugar(deoxyribose/ribose), a nitrogenous base(A,G,C,T/U), and a phosphate group. 5’ end will have the phosphate group, and the 3’ is a hydroxyl group, allowing for new nucleotides to be added.

Pyremidines

Thymine, uracil, and cytosine.

Purines

Adenine and guanine.

Ribosomes

Function in protein synthesis(translation), made up of Ribosomal RNA(rRNA),

Endoplasmic Reticulum

A series of membrane channels in eukaryotic cells.

Rough endoplasmic reticulum has bound ribosomes and function in protein synthesis. Smooth endoplasmic reticulum does not have ribosomes and function in lipid synthesis and substance detoxification.

Golgi Complex

A stack of flattened membrane sacs(cisternae) that controls the modification and packaging of proteins for transport. Often found near the Rough ER and modifies proteins from bound ribosomes into their final conformation and packages them into vesicles for transport.

Lysosomes

Membrane-bound sacs containing hydrolytic enzymes that function in digesting macromolecules, disposing of cell parts, aid in apoptosis, or destroying bacteria and viruses.

Vacuole

Function in food or water storage, water regulation, or waste storage until the waste can be eliminated. By filling up space in plant cells, vacuoles provide the plant with turgor pressure and support.

Mitochondira

Double membrane bound structure that had a double membrane, one smooth outer membrane and a highly folded inner membrane that increases surface area. Center of mitochondria, within inner membrane, is known as the matrix, and it is where the Krebs cycle(citric acid cycle) occurs.

Chloroplasts

Found in photosynthetic organisms, has double membrane structure. smooth outer membrane, and membranous sacs called thylakoids that are stacked into grana. liquid inside chloroplast is known as the stroma. Thylakoids facilitate the light reactions, while the dark reactions(calvin cycle) happen in the stroma.

Centrosome

Helps microtubules assemble into spindle fibers needed in cell division. found in animal cells.

Endosymbiont hypothesis

States that membrane bound organelles, such as the mitochondria and chloroplasts, were once free living prokaryotes that were absorbed by larger prokaryotes, which then became dependent on another.

Evidence: they have their own DNA, that is similar to prokaryotic DNA.

They have their own ribosomes, similar to prokaryotic ribosomes..

They replicate via binary fission, similar to bacteria.

Surface Area to Volume Ratio

As the diameter increases, the ratio will decrease. Larger cells have a lower ratio, and thus are less efficient when it comes to exchange of materials with the environment. can be increased by folding membranes.

Passive Transport

Movement of molecules from areas of higher concentration to areas of lower concentration. Does not require energy. Also known as diffusion.

Facilitated Diffusion

Passive transport that uses a membrane protein, often used for polar or charged molecules, or ions with channel proteins.

Active Transport

Moves molecules from areas of low concentration ot areas of high concentration. Requires input of energy, often ATP, to power protein pumps.

Hypotonic

solution that has a lower concentration of solute. water will flow out, solute will come in.

Hypertonic

A solution that has a higher concentration of solute. Water will flow in, solute will go out.

Isotonic

Solution has the same concentration of solute as another solution.

Enzyme

Biological catalysts, which speed up chemical reactions happening in cells. Have 3-d protein structure that is specific to their function.

Temperature correlates with the number of collisions between enzyme and substrate, affecting reaction speed, and can also disrupt bonds in enzyme and change active site shape if it is too high.

pH can result in disrupted bonds and a change in tertiary structure.

These changes are known as denaturization.

Active Site

Interacts with the substrate(reactant). Shape of active site is specific to the shape of the substrate. Any charged R-Groups in the active site must also be compatible with the substrate.

Increase the concentration of substrate will increase the rate of a reaction, up until all active sites are saturated.

Competitive Inhibitors

Substances that are similar in shape to substrates and compete with substances for active sites of an enzyme, decreasing reaction rate.

Noncompetitive(allosteric) inhibitors

Substances that do not bind to the active site but a different site on the enzyme, known as an allosteric site, which can affect its function and adjust the rate of chemical reactions.

Cofactors/coenzymes

increase the efficiency of reactions catalyzed by enzymes, usually by binding to the active site/substrate, enhancing binding of substrate to the active site.

Endergonic reactions

reactions that have products with a higher free energy level (think of potential energy, energy that molecules contain) than its reactant are considered energetically unfavorable.

these absorb energy, such as the adding of a phosphate to ADP(phosphorylation).

Exergonic reactions

reactions that have products with a lower free energy level (think of potential energy, energy that molecules contain) than its reactants. are considered energetically favorable.

these release energy.

Activation Energy

Difference between the energy level of the reactants and the transition state of the reaction. Higher activation energies result in slower reactions, while lower activation energies result in faster rates. Enzymes speed up reactions by lowering activation energy.

They do this by:

bring substrates together in proper orientation

destabilizing chemical bonds in the substrate by bending it

forming temporary ionic or covalent bonds with the substrate.

Coupled reactions

Many reactions are coupled and allow for the controlled transfer of energy between molecules, leading to more efficiency.

Essentially is just using energy released by exergonic reactions to power endergonic reactions, such as the breakdown of ATP into ADP + phosphate + energy, which can power other endergonic reactions, such as glucose + fructose + energy yielding sucrose.

Free Energy change

difference between free energy of the products and the free energy of the reactants

Heterotroph

Organisms that consume other organisms to aobtain organic molecules

Autotrophs

Organisms that can produce their own organic molecules from inorganic molecules. Autotrophs that use light energy are known as photoautotrophs.

Oxidation

A molecule losing hydrogen atoms

Reduction

Molecule gaining hydrogen atoms.

Light-Dependent reactions

Energy from sunlight to split water, producing oxygen, gas, protons, and high-energy electrons, releasing oxygen into the atmosphere. The protons and electrons are used to power the production of ATP and NADPH(energy carriers), which are sent to the Calvin cycle. Occurs in the thylakoids.

Photophosphorylation

The process by which light energy is used to drive the production of ATP.

Chlorophyll

Light-absorbing pigment that captures the energy of photons from the sun, which excites electrons from water. Found in PSI and PSII.

Photolysis

Energy from sunlight to split water, producing oxygen, gas, protons, and high-energy electrons, releasing oxygen into the atmosphere.

Electron Transport Chain of the Light Dependent Reactions

Energy from the photons is used to boost the electrons to a higher energy level in PSII, which are then transported from and to carriers through a series of redox reactions, in which the energy is slowly released, similar to “falling down a hill”.

These lost electrons are used to pump H+ ions intp the thylakoid space, building a proton gradient.

In PSI, these electrons get re-energized and accepted by another carrier, which eventually reduced NAD+ to NADPH, which goes to the calvin cycle.

Using the proton gradient formed, ATP synthase is powered, which adds a phosphate group to ADP, through a process known as chemiosmosis.

Calvin Cycle Step 1: Carbon Fixation

Carbon fixation; the enzyme Rubisco adds one molecule of CO2 to the 5-carbon molecule RuBP, producing an unstable intermediate, which breaks down into two 3 carbon molecules known as 3PGA.

Calvin Cycle Step 2: reduction

ATP and NADPH are used to reduce the G3P, which produces 3 carbon molecule known as G3P, which can be used to make sugars.

Calvin Cycle Step 3: Regeneration

ATP is used to regenerate RuBP from the G3P.

Final Electron Acceptor for light-dependent reactions

NADP+

Glycolysis

Occurs in the cytosol, and can be performed by all living organisms(form of anaerobic respiration).

Glucose and 2 NAD+ are inputs. During Glycolysis, Glucose is oxidized, and NAD+ is reduced to NADH, using 2 ATP molecules. 4 ATP are produced overall, resulting in a net gain of 2 ATP, and Glucose is cleaved into two 3-carbon pyruvate molecule.

No carbon dioxide is released.

Oxidation of Pyruvate

Occurs in the Mitochondrial Matrix

Pyruvate is oxidized(loses a hydrogen atom), and the NAD+ electron carrier is reduced(gains hydrogen atom) and become NADH. As this happens, one carbon in pyruvate is released as CO2, leaving behind a 2-carbon acetyl group. Coenzyme A attached to this group, which delivers it to the krebs cycle.

This will occur two times for every molecule of glucose that enters glycolysis, since glycolysis produces two molecules of pyruvate.

Krebs Cycle(Citric Acid Cycle)

Occurs in Mitochondrial Matrix.

Acetyl Coenzyme A is attached to a 4 carbon intermediate, forming a 6-carbon molecule. This molecule goes through a series of reactions, which releases two CO2 molecules, and regenerates the 4-carbon intermediate.

During one turn of the Krebs, cycle, 3NAD+ are reduced to NADH, FAD+ is reduced to FADH2, and one molecule of ATP is produced through substrate-level phosphorylation.

When it is done, all the carbon that was originally in glucose at the start of glycolysis has been released as CO2, since 2 Acetyl Coenzyme A are produced from one glucose.

Oxidative Phosphorylation

Occurs in Mitochondrial Membrane.

NADH and FADH2, which were produced during glycolysis, pyruvate, and Kreb Cycle, get oxidized into NAD+(to be used in glycolysis) and FAD+, releasing their hydrogen atoms and electrons. As the electrons travel through the ETC, they release energy, and this energy is used to pump H+ out of the matrix and into the intermembrane space, creating a gradient that can power ATP synthase. As Protons flow from the intermembrane space into the matrix, the shape of ATP synthase is changed, which catalyzes the production of ATP.

At the end of the ETC, the remaining electrons get combined with oxygen, the terminal electron accepter, to produce two molecules of water.

34 ATP in total are generated.

Fermentation

Occurs in cytosol, when there is no oxygen present.

Because there is no oxygen present, Oxidative phosphorylation cannot occur due to there being no terminal electron acceptor, resulting in a blockage of the ETC.

Fermentation is carried out to regenerate NAD+(for glycolysis) and keep glycolysis running so that ATP is continuously produced, preventing the death of a cell.

Alcohol Fermentation

Pyruvate is reduced to an alcohol, typically the 2-carbon Ethanol and carbon dioxide, and NADH is oxidized to NAD+.

Lactic Acid Fermentation

Pyruvate is reduced to the 3-carbon molecule Lactic Acid, and NADH is oxidized to NAD+. No carbon dioxide is produced. This can occur in muscle cells if they do not have enough oxygen to carry out oxidative phosphorylation and can be harmful if it builds up.

Ligand

A chemical signal, such as a protein, cholesterol, ions, etc., that interact with specific target cells that respond to the presence of the ligand.

Can be hydrophobic or hydrophilic, with hydrophilic ligands being unable to cross the membrane and can only interact with cell membrane receptors, which can then trigger a series of chemical reactions with the cell.

Hydrophobic ligands can slide between phospholipids, bind to intracellular receptors in the cytosol, and then cross the nuclear membrane and bind to DNA, changing gene expression.

Autocrine Signaling

Cell secretes a ligand, which then binds to a receptor on the cell that secreted it, triggering a response.

In short, Cell signals itself.

ex. cancer cells, which release its own hormones that stimulate growth and division.

Juxtacrine signaling.

Signaling that depends on direct contact between the cell that is sending the ligand and the cell that is receiving and responding to it.

ex. antigen cells in the immune system, which signal helper T cells through direct cell-to-cell contact.

Paracrine signaling

Cell secretes a ligand that travels a short distance, signaling cells in the nearby area. Only affects cells that are in the vicinity of the cell that is sending the signal.

ex. Neurotransmitters, since they travel a short distance across a synapse to communicate with nearby cells.

Endocrine signaling

Ligands that travel a long distance between the sending and receiving cells, known as hormones.

ex. Insulin, produced by the pancreas, travels through the circulatory system to signal cells all over the body.

Signal Transduction

Begins with a chemical message(ligand).

Reception, Transduction, Response

Reception

First step of signal transduction; ligand binds to a specific receptor on/in the target cell. Upon binding, the receptor’s shape changes, which triggers transduction on the inside of the cell.

Transduction

A series of chemical reactions triggered by the reception that helps a cell choose the appropriate response.

Signaling Cascade(signal amplification)

A series of chemical reactions in which one molecule activates multiple molecules, amplifying the cell’s response to a signal.

Kinase

Enzyme that transfers phosphate groups to other molecules, activating them.

Phosphatases

Can remove phosphate groups from other molecules, which inactivates them.

Secondary Messengers

Secondary messengers are small intracellular molecules produced or released by enzymes in response to an extracellular signal. They amplify and transmit the signal within the cell by activating specific target proteins or pathways.

Response

Final step of signal transduction; ultimate result generated by ligand.

ex activation of genes by steroid hormones, initiation of cell process, such as division or apoptosis.

Negative Feedback

Returns a system to its original condition and helps maintain homeostasis(maintenance of a stable state).

ex. if body temperature is too high, cell signaling processes will trigger the release of sweat, which cools the body and helps return it to homeostasis.

Positive Feedback

Magnifies cell processes.

Ex. oxytocin stimulates contractions of uterine muscles during childbirth, and this contraction of muscles releases more oxytocin, which also increase muscle contraction, leading to a continuously amplifying signal.

Interphase

longest phase of the cell cycle. Cell grows so that it has enough material to divide between two daughter cells. DNA is also replicated.

G1 Phase

Cell grows and prepares for DNA replication, and some organelles are replicated.

S(Synthesis) phase

DNA is replicated.

when it begins, each chromosome consists of one chromatid. After replication is complete, each chromosome has 2 chromatids held by one centromore, in contrast to the single chromatid before replication. Cell contains twice as much DNA.

G2

Cell continues to grow and prepares materials needed for mitosis

Prophase

Nuclear membrane dissolve and chromosomes condense and become visible.

Spindle fibers begin to form

metaphase

Spindle fibers have fully attached to the centromeres of each chromosome. Chromosomes align along equator of cell, with the center of the mitotic spindle known as the metaphase plate.

Anaphase

Each chromosome splits at its centromere as opposing spindle fibers begin to shorten. Sister(identical) chromatids are pulled towards opposite ends, resulting in twice as many chromosomes but same amount of DNA.

telophase

2 new nuclear membranes form, with each nuclei containing the same number of chromosomes and genetic information as the parent cell.

Cytokinesis

Division of cytoplasm along with all cellular contents, between two daughter cells.

In animals, a cleavage furrow is formed, which partitions the cytosol between 2 new cells, while in plants, a cell plate is built, providing a new cell wall for each daughter cell.

G0 phase

Cells that have exited the cycle and have either stopped dividing temporarily or permanently.

Cyclin-dependent kinases

Kinases that are inactive until they bind to cyclin proteins, a secondary messenger. Works together with cyclin to regulate cell cycle