AP Bio

Null hypothesis

Hypothesis stating that there will be no difference between the groups in and experiment

Chi Squared

Formula that finds if the null hypothesis is true:

• Plug the values into the summation formula

• Then see what the degrees of freedom are, or the number of possible outcomes minus one

• Find on the chi-square table the place where the p value (0.05 unless said otherwise) and the degrees of freedom line up

• If the table value is less than your equation value, you can reject the null hypothesis

Standard deviation

Calculates how far away each data point is from the mean; a high number means data that ranges very far very frequently

Standard error of the mean

Calculates how well a mean represents a group of data; a higher SEM means that the mean is not very fitting for the diverse data

95% confidence interval

Made from adding 2x the SEM; if the bars overlap, you cannot say there is a significant difference between the groups

Hydrogen Bonds

Bonds that are formed by water and are caused by the fact that oxygen has a higher electronegativity than water; some results of this are:

• Water is more attracted to itself or “sticky” because its oxygens are attracted to other water’s hydrogens; this is how it goes up the stems of plants

• Water expands when it becomes solid and therefore ice floats on water

• Water can hold a very high amount of heat

• Water is a very good solvent because it has a positive and negative end to choose from

• Hydrogen bonds are between different water molecules, not the bonds linking the atoms in each water molecule

pH

• How much H+ is in something

• The more H+, the lower the pH

• A pH of 7 is neutral, below 7 is acidic, and above 7 is basic

• More H+ makes something more acidic

• If there is less H+, there is more OH- by converse

• Buffers are in cells to regulate pH by adding more or less H+

Buffers

Proteins in the cells that regulate pH

Degrees of freedom

The number of possible outcomes of an experiment minus one

Macromolecules

• Carbon, Oxygen and Hydrogen are in all kinds

• Sulfur is found only in proteins

• Phosphorus is in nucleic acids and lipids

• Nitrogen is in nucleic acids and protein

Dehydration Synthesis

Where water is produced while joining things in a reaction

Hydrolysis

Where water is used up while separating things in a reaction

Carbohydrates

• Polymers made of sugar monomers

• Can store energy or be used as structure

Lipids

• Hydrophobic molecules made of fatty acids

• These acids can be saturated or unsaturated

• Saturated fats have only C—H bonds and are solid at room temp

• Unsaturated fats have at least on C==C bond and are liquid at room temp

• Phospholipids and steroids are notable lipids

• Lipids contain phosphorus

Proteins

Formed by amino acids; each amino acid has an R group on top that determines what the amino acid will do; they have four different structures:

• Primary structure: A chain of amino acids connected by peptide bonds that link together

• Secondary Structure: The amino acids join into either an alpha helix or a beta sheet

• Tertiary Structure: The way the secondary structure folds; one method is having hydrophilic R groups on the surface of the protein and hydrophobic R groups on the inside

• Quaternary Structure: The way that the tertiary structure folds; not every protein has quaternary structure

Proteins contain sulfur and nitrogen

Nucleic Acids

• Ex. DNA and RNA;

• Made up of monomers called nucleotides;

• T, U, and C are purines and A and G are pyrimidines

• Nucleic acids contain nitrogen and phosphorus

Prokaryotic DNA

Circular chromosome located in the nucleoid; also contains DNA outside of thee chromosome called plasmids

Ribosomes

Protein making structures made up of rRNA; look like dots floating around in the cytosol; some are also in the rough ER

Endoplasmic Reticulum (not endoPLASTIC)

• Channels in eukaryotes that look like coral

• Rough endoplasmic reticulum has ribosomes in the membranes and makes proteins

• Smooth endoplasmic reticulum is used for synthesizing lipids

• You can tell it apart from the golgi apparatus because it touches the nucleus

Golgi apparatus

• A stack of sacs, each of which contains the enzymes needed to function

• Looks like ER but is farther from the nucleus

• After proteins have been made, it modifies and packages them for transport and makes them fully mature

Lysosomes

Sacs containing acidic enzymes; used for disposal of dead cells or old cell parts; you can tell them apart from vacuoles because they are usually smaller

Vacoules

• Store food or water in the cell

• In plant cells, they fill up with water and provide a lot of structural support

• You can tell them apart from lysosomes because they are typically bigger

Mitochondria

• They have two different membranes; inner and outer

• The center of a mitochondria has a fluid called the matrix

Chloroplasts

• Have a double membrane structure

• The thylakoids are stacked like pancakes

• The stroma is like the cytosol of the chloroplast

Surface Area

Some organelles fold up their membranes to maximize their surface area; look for the surface area equation on the test

Plasma membrane

• Made up of the phospholipid bilayer

• Steroids, proteins, and phospholipids can very freely move across the plasma membrane when it wants to be fluid

• Only small, hydrophobic molecules such as O2 can go through it

• Although a little water can get through on its own, aquaporins are proteins that allow water to get through in larger amounts

Cell wall

• Seen only in prokaryotes, plants, and fungi

• Outside the cell membrane

• Makes the cell more rigid

Passive transport

• Movement of molecules that takes no energy and moves them with their concentration gradient

• Diffusion is when you just let molecules go through the membrane with their gradient

• Some molecules need channel proteins to get through the membrane

• This is called facilitated diffusion

Active transport

• Movement of molecules that takes energy and moves them against their concentration gradient

• An example of this is the sodium potassium pump

• In this, the cell pumps sodium out and potassium in, both against their concentration gradients

• Doing so, the cell gets energy from the difference in charge

Endocytosis and exocytosis

• Endocytosis is used by the cells to take in water and molecules by folding them in vesicles from the plasma membrane

• Exocytosis is when vesicles fuse with the plasma membrane to discharge molecules

• Both of these require energy

Water potential

• Hypertonic has a higher concentration of solute than the other thing

• Hypotonic has a lower concentration of solute compared to another solution

• Isotonic has the same amount of solute

• Water potential is the amount of energy water has to flow between things; water flows from a place with high water potential to a place with low water potential

• Because hypertonic has more solute, it has less water and has a lower water potential

• Hypotonic therefore has a higher water potential despite lower solute

Water potential equation

• Water potential=pressure potential + solute potential

• You will be given the pressure potential or if not then it is 0

• To find the solute potential, you need to plug in -iCRT formula

• To find i: i is the ionization constant; if it is a compound ending in “ose” then it equals 1; if it is salt, then it equals 2

• C is the concentration of solute; will be given

• R is the pressure constant: 0.0831(liters-bars)/(mole-K); formula will be provided

• T is the temperature IN KELVIN

Osmolarity

• The concentration of solutes in something

• This is regulated in organisms

Enzymes

• The active site binds to the substrate, or the thing that is reacting

• Denaturation is when the enzyme stops working; it happens when the enzyme is exposed to the wrong temp or pH

• Denaturation is sometimes reversible

• Enzymes have active sites, where the actual substrate goes, and allosteric sites, where activators go

• Cofactors and coenzymes speed up the efficiency of enzymes

• Ribozymes do the same thing as enzymes but are made of RNA

Enzyme inhibitors

• Competitive inhibitors cover up the active site of the enzyme, or the site where the substrate goes

• Allosteric/noncompetitive inhibitors bind to the allosteric site of the enzyme, or the site where the substrate doesn’t go

Chemical reactions

• Exergonic reactions release energy

• Endergonic reactions store energy

• Chemical reactions need activation energy; the higher the activation energy, the slower the reaction

• Enzymes lower the activation energy

Photosynthesis

• Broken down into the light-dependent reactions and the Calvin Cycle

• Turns 6 C02+ 6 H20 into C6 H12 O6 + 6 O2

• Light-dependent happens in the stroma, which is like the plant cytoplasm; you can remember this because if it requires light, it is obviously on the outside

• The Calvin Cycle is in the thylakoids, which is the ones that look like pancakes and produce energy

• While NADPH is used to carry electrons in photosynthesis, NADH is used to carry electrons in cellular respiration

Light dependent reactions

• Chlorophyll absorbs light and passes these electrons on

• Light is collected in both Photosystem I and II; the light from Photosystem II is passed via electrons to Photosystem I

• Photosystem II gets these electrons from water at the beginning

• As these electrons are transferred, protons are actively transported through the thylakoid membrane, making a concentration gradient

• The ATP synthase uses this concentration gradient to make ATP

• The electrons, after leaving photosystem I, are used to turn NADP+ into NADPH

• This ATP and NADPH are used to energize the Calvin Cycle

Photophosphorlyation

The process where ATP is made from sunlight in the light dependent reactions

The Calvin Cycle

• In step 1, 3 CO2 combines with a five carbon molecule to make two three carbon molecules

• In step 2, these molecules are changed into different three carbon molecules that can eventually make glucose in a process that uses ATP and NADPH; however, some are needed to make the five carbon molecule from step 1

• In step 3, ATP is used to turn the molecules from step two that are needed into the five carbon molecule to do the cycle again

Cellular respiration

• Converts glucose into energy

• The formula is C6 H12 O6 + 6 O2 = 6 CO2 + 6 H2O + ATP

• While aerobic organisms can use oxygen, anaerobic organisms can’t and they can only do glycolysis and fermentation

• While NADPH is used to carry electrons in photosynthesis, NADH is used to carry electrons in cellular respiration

Glycolosis

• Step 1 of cellular respiration

• Happens in the cytosol

• 6-carbon glucose, 2 NAD+, and 2 ATP go in

• 2 3-carbon pyruvate, 2 NADH, and 4 ATP are produced (gain of 2 ATP)

Pyruvate Oxidation

• Step 2 of cellular respiration; occurs after glycolysis

• Occurs in the mitochondria

• 1 pyruvate and 1 NAD+ go in

• 1 2-carbon acetyl group, 1 1-carbon carbon dioxide, and one NADH are produced

• This process is facilitated by Coenzyme A, which binds to the acetyl group as it is brought into the Krebs Cycle

Krebs Cycle

• Step 3 in cellular respiration; after pyruvate oxidation

• Occurs in the matrix, or the innermost part of the mitochondria

• Coenzyme A brings in the 2-carbon acetyl group

• This is first attached to a 4-carbon molecule

• In the cycle, both of the 2 carbons from the acetyl are released into 2 1-carbon carbon dioxides

• In addition, 3 NADH, 1 FADH2, and 1 ATP are produced

• Because 2 carbons go in and 2 carbons go out, the 4 carbon group doesn’t need to be replaced

Oxidative phosphorylation

• Step 4 and final step of cellular respiration; comes after the Krebs Cycle

• Occurs on the inner membrane of the mitochondria

• The first part of this is the electron transport chain, in which the electrons from all the NADH and FADH2 produced earlier are put into the electron transport chain

• These electrons are pumped through proteins on the inner membrane, giving them energy to make a concentration gradient of H+

• Once they leave, these electrons are used to make water

• The second part of this is chemiosmosis, where ATP synthase uses the concentration gradient to produce ATP

• This produces around 30 ATP and exactly 6 water with an input of only NADH and FADH2

Fermentation

• Produces energy without using oxygen

• Glycolysis happens and produces pyruvate whether or not there is oxygen

• However, from there, in alcohol fermentation, pyruvate and NADH are used to make ethanol

• In lactic acid fermentation, pyruvate and NADH make lactic acid

• The purpose of fermentation is to generate NAD+, because if the cell ran out of NAD+, it would die

Autocrine signaling

• When a cell signals something to get a response within that same cell

• Can remember because the cell automatically signals itslef

Juxtacrine signaling

Cell signaling through direct contact

Paracrine signaling

A cell activates a ligand to signal other cells close to it

Endocrine signaling

Signaling over very long distances, for example hormones

Signal transduction

• A ligand is released that goes to target cells

• Some ligands are hydrophilic, so they need to bind to a receptor protein on the cell because they can’t cross the membrane

• Some ligands are hydrophobic and go through the membrane, but they are only used for DNA

• The first step is reception

• The second step is transduction, where signal amplification happens and kinases are used to put phosphate onto molecules, activating them

• The third step is response

• While negative feedback keeps the cell the same, positive feedback does the opposite

Interphase of cell cycle

• The first step is G1, in which the cell prepares for replication and checks to make sure it has enough resources

• The second step if S, in which the chromatids are duplicated but the chromosomes are not separated yet

• The third step is G2, where the cell finishes its centrosomes and checks for damaged DNA

• During this, the cell chromosome is not in any shape

Mitosis in cell cycle

• Comes after G2 in the interphase

• In the prophase, the chromosomes are pulled into the actual chromosome shape

• In the metaphase, the chromosomes align on the edges and the centromeres are fully attached

• In the anaphase, the chromosomes are split at the centromere and pulled to each side of the cell

• In the telophase, the cells form different nucleuses

• Although this is not a part of mitosis, in cytokinesis, the cells are separated with different membranes

• Plants have to do it differently because of their cell wall so they build a cell plate in between the cells

Cell cycle regulation

• Cyclin-dependent kinases activate cyclins; however, the cell controls how many cylins there are to regulate the cell cycle

• There are always the same number of cyclin-dependent kinases but there are varied numbers of cyclins

• The more cyclins, the faster the cell cycle

• Proto-oncogenes are like the accelerator of a car

• However, if they mutate and turn into oncogenes, they drive the cell cycle too fast and can cause cancer

• Apoptosis is when a cell kills itself because it knows it has cancer

Meiosis

• Cell division used to make reproducive gametes

• Turns a diploid cell (normal chromosomes) into haploid cells (half chromosome), or gametes

• Divided into meiosis I and II

Meiosis I

• First round of meiosis

• During prophase I, crossing over happens, where the genes from the mom and dad previously are mixed, and they condense into normal shape

• During metaphase I, chromosomes line up in pairs along the middle of the cell

• During anaphase 1, the position of the chromosomes are mixed, but the number of chromosomes remains the same

• During telophase 1, two nuclei are formed and after cytokinesis, two haploid cells with half DNA, although the DNA is in the sister chromatid shape, so it is really normal DNA

Meiosis II

• Second stage of meiosis

• In prophase II, the chromosomes line up into normal shapes

• In metaphase II, the chromosomes line up in a line in the center of each cell

• In anaphase II, the chromatids are split and the now single chromatid chromosomes are moved to each side of the cell

• In telophase II, the cells are prepared for division and in cytokinesis they are divided

• The resulting cells are fully haploid and contain one half of the chromosomes needed

Crossing over

• Happens during prophase I of meiosis I

• DNA from a chromosome from each parent is mixed

• Genes that are close together in the DNA sequence are inherited together often

• Because this process is random, different children can have different traits

Mendel’s laws

• An organism has 2 alleles for every trait

• One alleles for every trait ends up in each gamete

• Most genes are inherited and expressed together

• Genes that are close together on the chromosome are inherited together more often

Dihybrid cross

• A cross containing four different traits; like PpHh + PPHH

• To find the odds of having two separate traits, find the odds of getting each trait in a normal cross and multiply them

Non Mendelian Genetics

• Linked genes are inherited together more often because they are on the same chromosome

• Map units are how likely genes are to be separated; one map unit is one percent likelihood of separation, or low

• The lower the map units, the closer the genes are together

• Autosomal traits are unrelated to sex

• However, some traits are sex related, and many of these apply to men only because each man only gets one x chromosome

• Because females contribute more mitochondrial and chloroplast DNA, some traits can be inherited from them

• Remember that the phenotype is influenced by environment

Comondinance

Both traits are expressed, for example a rose with red and white patches

Incomplete dominance

When the traits are blended, like a pink rose

DNA structure

• DNA has AGCT, but RNA has AGCU, meaning they switch a T for a U

• AG are purines, TCU are pyrimidines, you can remember this with PureasGold for purines and CUtthePy for pyrimidines

• A pairs with T or U and G pairs with C

• Purines have two rings; pyrimidines have one ring

• While DNA has a deoxyribose sugar at the end, RNA has a ribose sugar at the end, which makes DNA better at long term

• You can remember this because DEENA has DEEEoxyribose sugar

DNA replication

• DNA is replicated in the 5 to 3 direction, but is there was an empty DNA strand and you had to fill in on top of it, that top DNA strand would be going in the 3 to 5 of the bottom one because DNA is antiparallel

• First, helicase enzyme unwinds the two DNA strands

• Topoisomerase takes stress off the split

• DNA polymerase adds new nucleotides in the 5 to 3 direction

• The RNA polymerase goes into the lagging strand and sets up RNA primers for the DNA polymerase

• At the end, the ligase fixes up holes and connects the lagging strand together

Topoisomerase enzyme

Enzyme that relieves stress in uncoiling DNA during replication

Helicase enzyme

Enzyme that unzips DNA during DNA replication

RNA polymerase (DNA replication version)

Sets up primers on the lagging strand in DNA replication

DNA polymerase

Replicates DNA in DNA replication in the 5 to 3 direction

Ligase

Links the DNA on the lagging strand that is separated

Transcription

• Process where DNA is converted into RNA

• RNA polymerase turns the DNA into RNA

• The RNA polymerase first binds to a part of the DNA called the promoter

• Proteins called transcription factors help the RNA polymerase do this

• RNA is added in the 5 to 3 direction, but don’t forget that the DNA on top of it would be running 3 to 5 because antiparallel

• This RNA that has been duplicated is called pre-mRNA and is still in the nucleus

• This has introns, which are segments of RNA that need to be removed, and exons, which are segments that need to stay

• Spliceosomes then remove the introns, and they can join the leftover exons in different ways than the order they were in

• A 5’ GTP cap is added to the front of the RNA, which allows it to get through the nucleus, and it eventually helps start translation

• A 3’ poly-A tail is added to the end to prevent degradation

Types of RNA in transcription and translation

• mRNA is the RNA that carries info from DNA to ribosome

• A nucleotide of DNA = a codon of mRNA

• tRNA brings the amino acids to the ribosome; it has 3D structure

• rRNA makes up half of ribosomes; the other half is from protein; also has 3D structure

Spliceosomes

Molecule that takes out introns during transcription; it can join the leftover exons in a different way than they were in for more variety

5’ GTP cap

Molecule that is added to the front of mRNA in transcription that lets it get through the nucleus and starts translation when the RNA gets to the ribosome

Poly-A tail

Is added to the end of mRNA to prevent degradation

Translation

• Process where mRNA is turned into protein

• Prokaryotes don’t do all of the steps of transcription and they instead to transcription and translation at the same time

• The first step is when the ribosome hits the start codon (AUG)

• The tRNA then brings in one amino acid for every three nucelotides

• New amino acids are added onto each other with peptide bonds until it hits the stop codon

• These amino acids then make a protein

• Viruses have RNA that they put into a host cell to replicate what that virus is made of

Operon

• A group of DNA with a common goal controlled by one promoter

• The promoters are where the RNA polymerase attaches to

• Operators are where repressor proteins bind

• Operons can be inducible or repressible

• In some cases, activator or repressor proteins bind to a regulatory switch protein instead of doing it themselves

Inducible operon

• Off until turned on

• Usually for digesting specific molecules

• The repressor protein is usually bound to the operator

• However, if a certain molecule comes and activates the repressor protein, it changes shape and moves off the operator, which then allows the RNA polymerase to transcribe

Repressible operon

• On until turned off

• Usually for producing needed molecules

• The repressor protein cannot bind to the operator by default

• Instead, it needs corepressor need to bind to it in order to be able to stop the RNA polymerase

Mediators

Connect regulatory proteins and allow them to communicate (operons)

Transcription factors

Help the RNA polymerase bind to the promoter and start transcription

Enhancers

Regulatory switches that activator proteins bind to

Silencers

Regulatory switches that repressor proteins bind to

Epigenetic changes

Changes to the DNA sequence or histones being covered up as a result of environment

Mutations

• A point mutation alters only one nucleotide

• A silent mutation results in no change to the amino acid sequence

• A mutation that leads to a stop codon to early is a nonsense mutation

• A frameshift mutation is when a nucleotide is added or deleted, which changes the entire line of nucleotides