Unit 0

GRAPHS need to have:

1. Meaningful title

2. Include independent and dependent variables

3. The units for each variable should be clearly indicated

4. Data for each repeated trial

TYPES OF GRAPHS

In a line graph, each data point is connected to the next point in the data set with a straight line.

Scatter point is used when the data for all variables are numerical and continuous. Each piece of data is represented by a point.

A bar graph is kind of a graph in which the independent variable represents groups or nonnumerical categories and the values of the dependent variables are shown by bars.

A variant of a bar graph called a histogram can be made for numeric data by first grouping or binning, the variable plotted in the x-axis

Box (whisker plots) is used to show the location and variability of a data set.

Pie chart is a circular statistical graphic, which is divided into slices to illustrate numerical proportion.

Graphs with logarithmic scales are used to visualize data with large numbers plotted against small numbers.

Independent = x axis

Dependent = y axis

Independent variable = cause

Dependent variable = effect

EXPERIMENTAL DESING & STATISTICAL ANALYSIS

A controlled experiment is a scientific test done under controlled conditions:meaning that just one or a few factors are changed at a time, while all others are kept constant.

Most experiments originate from an observation, which leads to a scientific question. A hypothesis is then created, which is a tentative, yet specific and testable explanation for one or more observations. It describes in concrete terms what you expect will happen in a certain circumstance.

A null hypothesis is a form of hypothesis that is deemed “true” until problem wrong based on experimental data. Reflects that there will be no observed effect in our experiment. It is denoted by H0.

While an alternative hypothesis reflects that there will be an observed effect for our experiment. While this one is denoted by HA.

Constant/control: these are all the other variables that are kept identical between all the groups being tested.

Experimental group is the one that receives treatment. There can be more than one experimental group.

Control groups is the one that does not receive the independent variable. this group provides a baseline that lets the experimenter see if the independent variable has an effect.

1. Negative control groups do not receive any additional treatment that is expected to have an effect. They are identical to the experimental groups, except they do not receive the independent variable.

2. Positive control groups do receive an additional treatment that is known to produce the effect expected in the experimental groups. They are identical to the experimental groups, except they (1) do not receiving the independent variable and (2) receive some other…

Creating a strong hypothesis needs to be testable, include the independent and dependent variables, and make a specific prediction about the outcome of an experiment. A strong one needs to be specific if not it is weak.

ORGANIZING AND DISPLAYING DATA

Data tables are constructed to record and organize important data collected during an experiment.

The standard error of the mean in statistics are used in science to analyze experimental data and to measure how strongly the data supports or does not support a scientist’s hypothesis. SEM or SE is a common form of statistical analysis used in biology experiments. It is sued to measure how much the data taken from a sample group deviates from the actual population.

If the standard error is high it means that the data taken from the sample group does not very accurately represent the entire population. It also means that there is a lot of variation in the data collected from the same group.

Data only supports a hypothesis if it is statistically significant. To determine if two groups are significantly different from one another, the averages of two groups, with plus or minus two standard errors (+-2SEM) should not overlap. This is easiest to see when the means and error bars are graphed.

Error bars for each average are created using +-2SEM which gives you 95% certainty that the difference between two groups is real and not due to chance (if error bars do not overlap)

CHI - SQUARED TEST

Often written as x^2 test, is another common form of statistical analysis used in biology. It is also called a “goodness of fit.” It is used to determine if the observed distribution of a given phenomenon is significantly different from an expected distribution.

A null hypothesis (H0) states that the data will be consistent with a specific, expected distribution (usually the distribution that results from random chance or some other predetermined expectation), and it typically specifies the proportion to be found in each category.

An alternative hypothesis (HA) predicts an outcome that does not match the expected distribution.

(Of the p value, just use the column of 0.05 since it means you are about 95%. Besides, everyone mostly uses that but it CAN be asked for you to use 0.01 which would mean you are 99% of your hypothesis.)

If the chi-squared value exceeds the critical value then you can reject your null hypothesis. But if it is lower, then you can accept it.

Unit 1 - Chemistry of Life

Water

1. Polar Molecule

2. Intramolecular covalent bonding

   1. Intermolecular bonding is a hydrogen bond.

3. In a water molecule, the oxygen atom is negative and the hydrogen atoms are positive

   1. This creates a dipole moment: a measure of the polarity of a molecule, indicating how much positive and negative charge is separated within the molecule

4. Water's properties:

   1. Cohesion is the attraction of water molecules in which strong cohesive forces are present because they form hydrogen bonds with each other

   2. Adhesion is when one substance is attracted to another. Meaning that water adheres to different molecules/surfaces

   3. Surface tension refers to the difficulty to break the surface of the water because of, mentioned previously, cohesive forces

   4. Specific heat is the amount of heat energy it takes to raise or lower the temperature. And water has a high specific heat (it can absorb o release a large amount of heat with only a slight change in its own temp).

   5. Evaporative cooling is when water has a high heat of vaporization, so the water can absorb a lot of heat and leave the surface cooler

   6. Dissociation of water happens when hydrogen shifts from one water molecule to another

CHNOPS

Proteins ALWAYS have Carbon, Hydrogen, Nitrogen, and Oxygen. They SOMETIMES have Sulfure. And they NEVER have phosphorus

Carbohydrates ALWAYS have Carbon, Hydrogen, and Oxygen. They NEVER have Nitrogen, Phosphorus, and Sulfur

Nucleic Acids ALWAYS have Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus. They NEVER have Sulfur

Lipids ALWAYS have Carbon, Hydrogen, Oxygen, and Sulfure. They SOMETIMES have Phosphorus. And they NEVER have Nitrogen

All four macromolecules contain carbon.

They have four valence electrons.

Isotopes are two atoms of an element that have different number of neutrons

Energy level AKA Electron shell is an electron’s potential energy (location/structure).

Main functional groups:

1. Carboxyl

2. Carbonyl

3. Hydroxyl

4. Amino

5. Phosphate

6. Sulfhydryl

Bonds

1. Ionic bonds: It is the transfer of electrons between a positive and a negative ion (so that both can have complete valence shells).

2. Covalent bonds: It is the sharing of electrons (a molecule is created by two or more atoms in a covalent bond).

   1. Nonpolar covalent bond: the equal sharing of electrons and distribution of charge.

   2. Polar covalent bond: unequal sharing of electrons and distribution of charge causes partial positive/negative for each atom.

3. Hydrogen bonds are responsible for molecular properties (shape and function of protein). They are usually weaker than covalent bonds.

4. Metallic bonds are formed by the attraction between metal ions and free electrons

Dehydration: To form a polymer, water is removed (H20). It is a condensation reaction, requires energy and enzymes, and builds complexity.

Hydrolysis: occurs when polymers are broken down into monomers through the addition of water (H20). It releases energy (Exergonic) and requires enzymes.

There are 4 types of macromolecules:

1. Proteins

2. Carbohydrates

3. Lipids

4. Nucleic Acids

Proteins

They can catalyze chemical reactions, transport molecules, provide structural support, hormonal or response, and immune regulation.

Their function can include, but are not limited to:

1. Structural

2. Catalytic

3. Signaling

4. Defense

5. Transport

6. Hormones

The monomer of Proteins are amino acids. While its polymer are polypeptides.

Its structures are:

1. Primary structure (peptide bonding of amino acids)

2. Secondary structure (alpha-helix and beta-pleated sheets)

3. Tertiary structure (R-group bonding / disulfide bridges)

4. Quaternary structure (Multiple chains bonded together).

Depending of the structure of the amino acid, they will have different chemical and physical properties that determine their function.

They consist of an amino group, carboxyl group, and R group (either hydrophobic, hydrophilic, or ionic).

Denaturation: Loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals.

Carbohydrates

Its main purpose is to serve as short-term energy. They also contribute to the structure of organisms (e.g. cellulose and exoskeletons).

1. They can provide energy or the brain, muscles, and other organs.

2. They can also help in cell communication.

Its monomer are monosaccharides. While its polymer is a polysaccharide.

Monosaccharides have the formula of 1:2:1 (CHO).

However, there are also disaccharides; which are two monosaccharides joined by dehydration. The most common ones are:

1. Maltose

2. Sucrose

3. Lactose

While the most common polysaccharides are:

1. Sucrose

2. Lactose

3. Starch

4. Glycogen

5. Cellulose

6. Chitin

They include sugar and starch.

They are made of multiple hydroxyl and carbonyl groups. If the carbonyl group has an aldehyde it is aldose sugar. But if it has a carbonyl group in the middle, it is ketose sugar.

Lipids

They work as a long-term energy storage. They also make up the phospholipid bilayer that can be found in cells.

The monomer of Lipids is Glycerol and Fatty Acids. While they don't have a polymer.

Lipids can be saturated and unsaturated

1. Saturated don’t have a double carbon bond and solids at room temp.

2. While unsaturated have a double-carbon bond and liquid at room temp.).

Phospholipids are formed by 1 glycerol, 2 fatty acids, and 1 phosphate group.

1. The heads are hydrophilic and are found on the outside part

2. While the tails are hydrophobic and are found on the inside of the bilayer

Steroids are carbon skeleton of 4 fused rings. They are hydrophobic and insoluble in water. Cholesterol is a type of steroids with a short tail and a hydroxide group.

Nucleic Acids

They make up DNA and RNA; which means they store and share genetic information.

Its monomer is a nucleotide. While its polymer is DNA/RNA.

The structure of nucleotides is: a phosphate group, a sugar base, and a nitrogenous base (A,T,C,G,U).

1. Purines have a double-ring structure (Adenine and Guanine)

2. Pyrimidines have a single-ring structure (Cytosine, Thymine, and Uracil)

The pairing of a purine and pyrimidine allows stability and accuracy of DNA replication and the transmission of genes.

The sequence of the nucleotides are read from the 5’ end to the 3’ end.

The strands in DNA are positioned in opposite directions (while one goes from 5’ to 3’, the other one goes from 3’ to 5’)

DNA is double-stranded with antiparallel strands held together by hydrogen bonds

DNA

1. It contains deoxyribose

2. It uses Thymine

3. It is double-stranded (two complementary strands)

Both

1. Are made up of nucleotides

2. Sugar molecule, phosphate group, & nitrogenous base

3. They have A, C, and G

4. They transmit genetic information

5. Important for synthesis and regulation of proteins

RNA

1. It contains ribose (it has one more oxygen atom).

2. It uses Uracil

3. It is single-stranded

Unit 2 - Cell Structure and Function

Organelles:

Plasma Membrane

1. It is made up of a phospholipid bilayer (two lipid layers)

2. The heads (outside) are hydrophilic and the tails (inside) are hydrophobic.

3. Selectively permeable

4. Think of it as the border and toll that exists among each country

5. It has different types of proteins:

   1. Peripheral proteins that are located on the inner or outer surface of the membrane

   2. Amphipathic proteins firmly bound to the plasma membrane (integral proteins)

   3. Transmembrane proteins extend all the way through the membrane

   4. Receptor proteins, such as hormones, serve as docking for arrivals at the cell

   5. Transport proteins form pumps that use ATP to actively transport solutes across the membrane

   6. Channel proteins from channels that selectively allow the passage of certain ions or molecules

   7. Glycoproteins and some lipids, such as glycolipids, are exposed on the extracellular surface and play a role in cell recognition and adhesion

Ribosomes

1. They help synthesize proteins. They are made of rRNA and protein. They show common ancestry.

2. Think of it as little factories all throughout the city that produces proteins.

Lysosome

1. They contain hydrolytic enzymes (digestive enzymes) that break down excess or worn-out cell parts. They also help with apoptosis.

2. Think of it as the dumps were things get burned and destroyed

Mitochondria

1. It is the power house of the cell. It generates ATP with its high surface area to volume ratio

2. It has a phospholipid bilayer in its outer membrane

3. This is where Glycolysis and the Kreb's Cycle take place.

4. Think of it as the power plants providing energy for all the city

Endoplasmic Reticulum (ER)

1. They provide mechanical support and work in intracellular transport.

2. The Rough ER compartmentalizes the cell and helps the ribosomes to synthesize proteins.

3. The Smooth ER it performs synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons, and stores calcium ions.

4. Think of it like a messenger company that prepares everything to send it where it needs to be

Golgi Complex

1. It is composed of membrane sacs called cisternae. They carry out the final steps of preparing a protein. They help in packaging proteins and sorting them before transporting.

2. Vesicles enter it via cis face and depart via trans face.

3. Think of it like the airport with the security part; checking everything and then sending it.

Vacuole

1. They can store and release macromolecules/waste. Plants have a specialized one that, mainly works, as water retention.

2. Think of them as storage units that keep things you might use later

Chloroplasts

1. They capture, store, and use solar energy for photosynthesis. They have a double membrane and thylakoids.

2. Think of them as big solar panels that are used for big neigborhoods, companies, etc.

3. The pancakes and the honey (for you to remember easily)

Cytoplasm

1. Gelatinous liquid that fills the inside of the sell. It is made of water, salts, and various organic molecules.

2. Think of it as the roads; the ground where everything is organized.

Cytoskeleton

1. A collection of fibers that will provide support for the cell and its organelles. it can help with intracellular transport.

2. Think of them as the pillars and concrete that support each building and hose

Nucleus

1. It contains chromosomes (genes) and controls/regulates the activities of the cell.

2. Think of it as the government; where everything is overseen and important things are kept

Centrosomes

1. Main microtubule-organizing centres in distinct eukaryotic lineages. It's responsible for pulling apart sister chromatids during cell division.

2. Think of them as the foreman in a construction site telling everyone where things are supposed to go

Endospores

1. Allows the bacterium to produce a dormant and highly resistant cell to preserve the cell's genetic material in times of extreme stress.

Flagellum

1. Bacterial locomotion.

2. They extend from the cytoplasm to the cell exterior. They are composed of major structural elements, basal body, and the hook and filament.

Vesicle

1. Vesicles are small membrane-bound sacs that function in moving materials within a cell as well as interactions between cells.

2. Think of them as trucks or airplanes that can take packages either to other organelles or to other cells.

Cell envelope

1. A combination of the cell membrane, cell wall, and outer membrane if it is present.

Nucleolus

1. the largest nuclear organelle and is the primary site of ribosome subunit biogenesis in eukaryotic cells.

2. Think of it as the mayor’s office within the government.

Prokaryotes

Archaea and Bacteria

It has no nucleus, no membrane-bound organelles and it is unicellular

Eukaryotes

Fungi, Animals, Protists, and Plants

Only animal cells have centrioles

Cell size

Surface area - to - volume ratio affects the way a biological system obtains resources, eliminates wastes, pull/remove heat energy, and exchange materials with the environment.

The greater SA/V ratio, the more efficient the cell becomes.

If the cell reaches a point where the surface are doesn’t allow enough nutrients to pass, then the cell divides.

Tissues and membranes have folds to increase SA.

Plasma Membrane

The movements of molecules across the plasma membrane is regulated by the hydrophobic and hydrophilic properties of the phospholipids. Small, non polar molecules (nitrogen, oxygen, carbon dioxide) can pass freely.

1. For example, water is a small, polar molecule that can pass the membrane in small quantities with the help of aquaporins.

It has selective permeablity. This allows for certain molecules to enter or exit the cell.

Aquaporins are proteins embedded in cell membranes that facilitate the transport of water molecules in and out of cells.

There are proteins embedded into the plasma membrane.

1. The proteins can be hydrophobic, hydrophilic, charged, uncharged, polar, or nonpolar.

2. All depending of the amino acids in them. These proteins have five categories:

   1. Adhesion proteins: form junction between cells

   2. Receptor proteins: receive messages such as hormones

   3. Transport proteins: pumps that actively transport stuff using ATP

   4. Channel proteins: form channel that passively transport stuff

   5. Cell surface markers: act as ID card for the cell

Fluid mosaic model describes the structure of cell membranes. It suggests that proteins float within a flexible layer made up mostly of phospholipids.

Membrane Transport

1. Passive Transport: It means that molecules can go from a high to low concentration area without using energy.

   1. Simple diffusion includes small non-polar molecules, with the concentration gradient

   2. Facilitated diffusion include small polar molecules with the concentration gradient

      1. When water utilizes this diffusion method, it is called osmosis.

      2. This process is aided by transport proteins, channel proteins, and carrier proteins.

2. Active Transport: Same as passive but it needs energy to work. One example of this transport is the sodium-potassium pump

   1. Exocytosis means removing bulk material out of the cell.

      1. A transport vesicle from the Golgi moves along the microtubules in the cell and reaches the plasma membrane. Then the vesicle fuses with the plasma membrane and releases the stuff out of the cell.

   2. Endocytosis meas taking bulk material into the cell ( a type of active transport).

      1. Phagocytosis (cell-eating): cellular process for ingesting and eliminating particles larger than 0.5 μm in diameter

      2. Pinocytosis (cell-drinking): A process by which with the cell takes in the fluids along with dissolved small molecules.

      3. Receptor-mediated endocytosis: involves receptor proteins on the cell surface that bind to a specific susbtance and triggers their uptake into the cell in vesicles.

   3. Primary active transport involves the direct transfer of molecules across the membrane using energy from ATP

   4. Secondary active transport involves the transfer of molecules across the membrane using the energy stored in the concentration gradient of another substance

      1. It is accomplished using cotransporters / exchangers

      2. One example of this is the glucose transporter (GLUT) protein

Tonicity and Osmoregulation

Water moves by osmosis from high water potential (low solute concentration) to low water potential (high solute concentration). It is all based on equilibrium.

Types of osmoregulation:

1. Hypertonic: high solute concentration and low water concentration (raisin)

2. Isotonic: balanced between water and solute concentration (normal)

3. Hypotonic: low solute concentration and high water concentration (bloated)

Plant cells are more able to exist in a hypotonic environment due to their cell wall.

Water potential: Ψ = ΨS + ΨP

Solute potential is the solute concentration in consideration of the water flow.

If you add more solute, the water potential of the solution will be lowered

Ѱs = -iCRT

A concentration gradient occurs when there is a difference in concentration of a particular substance between two regions. Substances will naturally move from areas of high concentration to areas of low concentration until equilibrium is reached.

Endosymbiotic Theory

It is a theory of how eukaryotic membrane-bound organelles existed in eukaryotic cells.

It states that an early ancestor of the eukaryotic engulfed a prokaryotic cell, and the prokaryotic became an endosymbiont.

Evidence:

1. In 1883, a botanist named Andreas Schimper discovered that plastids divided just like bacteria did.

2. During the 1950s and 1960s, biologists discovered that the mitochondria and plastids have their own DNA

3. They even found that the DNA was more like those of prokaryotes rather than eukaryotes.

Modern Cell theory

The cell is the smallest living unit in all organisms

All living things are made of cells.

Unicellular or multicellular

All cells some come from other pre-existing cells

Unit 3 - Cellular Energetics

Enzymes

They help by facilitating chemical reactions and lowering the activation energy required for these reactions to occur.

They are composed of one or more polypeptide chains (amino acid long chains)

The specific arrangement of the amino acid residues in space determines the 3D structure that it will have

Induced fit mechanism is a process that occurs when an enzyme changes its shape slightly to accommodate the binding of a specific substrate.

Active site: a specific region of the enzyme that interacts with a substrate. Their shape must be compatible.

1. This site is usually a depression or cleft on the surface of the enzyme

2. Enzymes are highly specific and only catalyze specific reactions

3. A tighter fit allows for more efficient formation of the transition state

   1. The transition state refers to the highest-energ state of a reacion, where old bonds are breaking and new ones are forming.

Allosteric site: where a molecule binds to a specific site on the enzyme and changes the shape of the active site.

1. Causing the enzyme to become more or less active.

Enzyme catalysis helps to organize living things by allowing the cell to perform its functions more efficiently and faster

1. For example, they catalyze the breakdown of nutrients to generate energy. They can synthesize macromolecules and can transfer information between molecules

2. Catalysts work by providing an alternative reaction pathway with a lower activation energy. They do this by:

   1. Changing the relative positions of atoms in the reactants, making it easier for them to form the products

   2. Stabilizing the intermediate products or transition states, making the reaction proceed more smoothly

   3. Providing an alternative and more favorable transition state or the reaction to proceed

Enzyme-substrate recognition is their unique 3D shape that allows substrates to bind in a specific way.

Types of inhibitors

1. Competitive inhibitors

   1. Blocks the active site from the substrate, slowing down catalysis.

   2. They bind in the enzyme active site

2. Noncompetitive inhibitors

   1. Alters the active site in a war that does not allow the substrate to bind, slowing down catalysis.

   2. It binds in the allosteric site

3. Activator

   1. It allow the enzyme to more successfully bind to the substrate enhancing catalysis

   2. It can bind in various locations

4. Cofactors and coenzymes

   1. Cofactors

      1. Inorganic and small

      2. Bound to enzyme molecule (temporarily)

      3. Mg, Fe, K, Ca, Zn, Cu

   2. Coenzymes

      1. Organic, non-protein molecules

      2. Bind temporarily or permanently to active site

      3. Many vitamins.

5. Feedback

   1. They prevent cells from wasting energy and substrates on chemical reactions that are not necessary at the time

Environmental effects on enzymes

1. Temperature

   1. It is able to either speed up or slow down reactions.

   2. Usually, at colder temperatures, the enzyme and substrate will “bump” less because molecules move slower.

   3. And vice versa, in hotter temperatures there are more collisions between enzymes and substrates because they are able to move quicker.

      1. Although, if the temp. becomes too high, the enzyme might began to denature

   4. Most enzymes have an optimal temperature range. Most enzymes in the human body work best around 97 - 99 degrees Fahrenheit (37 degrees Celsius)

2. pH

   1. pH is a measurement referring to the number of hydrogen ions present in a solution

   2. If there are a lot of hydrogen ions, then it has a low pH

   3. An increase or decrease in the pH of the optimal conditions will cause the enzyme to slow down and possible denature.

   4. Most enzymes work best at a pH of 7. Although some work better in an acidic environment

3. Concentration

   1. If the concentration of either the substrate or the enzyme is increased, then the rate of the reaction will also increase

   2. Since there is more opportunity for the two to meet

   3. Ideally, both concentrations increase if one does. However, if only one increases, then the other works as a limiting reagent

   4. The limiting reagent in a chemical reaction is the reactant that gets completely used up first and thus limits how much product can be formed.

4. Inhibitors

   1. They don’t denature the enzyme but can still affect it

   2. As mentioned previously, there are different types of inhibitors and they both make the substrate to no longer bind to the enzyme

Entropy: the measure of system's thermal energy per unit temperature that is unavailable for doing useful work. Low entropy means tidy; high entropy means messy.

Law of Thermodynamics

1. First Law of Thermodynamics: Energy cannot be created or destroyed; it just changes form. It is also called conservation of energy.

2. Second Law of Thermodynamics: Energy cannot be changed from one form into another without a low of usable energy.

Metabolism

One of the most important factors is the energy stored in molecules and that it can be converted to different types of energy through chemical reactions

Metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly.

It is the sum of all chemical reactions occurring is a cell or organisms.

1. Catabolic pathways releases energy by breaking down a complex molecule into simpler components

2. Anabolic pathways consume energy to build complex molecules from simpler ones.

   1. It requires energy.

3. Anabolism is the synthesis of complex molecules from simpler ones

   1. It releases energy.

4. Endergonic reactions require input of energy

   1. Building polymers (with dehydration)

5. Exergonic reactions releases energy

   1. Digests polymer (with hydrolysis)

Phosphorylation: it is the addition of a phosphoryl group to a molecule. It builds polymers from monomers. It also includes hydrolysis.

Photosynthesis

COWs → GO

1. Carbon Dioxide + Water + Sunlight → Glucose + Oxygen

2. H2O + CO2 → C6H12O6 + O2

Steps

Light-dependent reactions

1. Light is captured by the chloroplasts and then an electron from a molecule of chlorophyll travels through the ETC

   1. Light hits first Photosystem II, which is embedded in the internal membrane of the chloroplasts

   2. H+ ions to move into the thylakoid space and to replenish electrons

      1. Then the light splits water (photolysis) into two H+ ions and 0.5 O2 and electrons

   3. This replaces the missing electrons in PSII, that jump into PSI

      1. The only way for these electrons to leave is through ATP

      2. ADP is phosphorylated when H+ goes through it

   4. Electron carriers (NADH, FADH2, NADPH)

Calvin Cycle

1. This happens in the stroma with the help of ATP and NADPH

   1. CO2 is turned into sugar

2. The first step requires Rubisco

   1. It is responsible for carbon fixation, taking carbon dioxide from the air and converting it into a organic, usable form.

3. After carbon has been fixed, this form is converted to glucose.

   1. A lot of bonds are created

      1. This bonds are created with electrons and energy. This is where the electron carriers and ATP from the L.D.R come into play

4. With ATP and electrons, many organic carbon into glyceraldehyde-3-phosphate or G3P.

   1. G3P is a precursor of starch, cellulose, and glucose

5. ATP is used to broke down ADP and a phosphate group which can be recycled and rebonded.

   1. Similarly, NADPH becomes NADP+

Summary

1. Light-dependent

   1. Location: thylakoid membrane, PSII, and PSI

   2. Input: Excited electrons and H2O

   3. Output: NADPH, ATP, and O2

2. Light-independent

   1. Location: stroma

   2. Input: 3 CO2, 9 ATPs, 6 NADPH

   3. Output: Sugar

Cellular Respiration

GO → COW!

1. Glucose + Oxygen → Carbon Dioxide + Water + ATP

2. C6H12O6 + O2 → H2O + CO2

Steps

Glycolysis

1. This step involves breaking down glucose

   1. It has 6 carbons, two 3-carbon molecules of pyruvate

2. A small amount of energy is released when breaking the bonds.

   1. This is captured as 2 molecules of ATP

3. The breaking of bonds also creates a few electrons that are picked up by electron carriers (NADH)

   1. These same electrons will be dropped of in the ETC later on

4. First, a phosphate group is transferred from ATP to glucose, making glucose-6-phosphate

5. Second, glucose-6-phosphate is converted into fructose-6-phosphate

6. Third, a phosphate group is transferred from ATP to fructose-6-phosphate producing fructose-1,6-biphosphate

7. Fourth, ructose-1,6-biphosphate splits into two three-carbon sugars:

   1. Dihydroxyacetone phosphate (DHAP)

   2. Glyceraldehyde-3-phosphate (only this continues)

8. Fifth, DHAP is converted into glyceraldehyde-3-phosphate and it is used up

Krebs Cycle

1. It takes place in the mitochondria

2. First, acetyl CoA joins with a four-carbon molecule

   1. Releasing CoA group and forming a six-carbon molecule AKA citrate

3. Second, citrate becomes isocitrate with the removal and addition of a water molecule

4. Third, isocitrate is oxidized and releases a molecule of carbon dioxide.

   1. NAD+ is reduced to form NADH

5. Fourth, reducing NAD+ to NADH and releasing a molecule of carbon dioxide in the process.

   1. The remaining four-carbon molecule forms the unstable compound succinyl CoA

6. Fifth, CoA of succinyl CoA is replaced by a phosphate group, which is then transferred to ADP to make ATP

   1. It forms GTP and four-carbon molecule as a product (succinate)

7. Sixth, succinate is oxidized forming another four-carbon molecule called fumarate

8. Seventh, water is added to the four-carbon molecule fumarate, converting it into another four-carbon molecule called malate

9. Eigth, oxaloacetate is regenerated by oxidation of malate. Another molecule of NAD+ is reduced to NADH in the process

ETC

1. This is where the most of the ATP is generated

2. A concentration gradient is formed, and ATP synthase is responsible for creating ATP.

3. As the electrons travel through the chain, they go from a higher to a lower energy level, moving from less electron-hungry to more electron-hungry molecules. Energy is released in these “downhill.”

4. When oxygen accepts the electron, it forms a bond with hydrogen ions and water is created.

Fermentation

1. If the organism doesn’t have oxygen available, anaerobic respiration starts

2. And without oxygen, the Krebs Cycle and the ETC can’t happen. This is where fermentation begins

3. Cells MUST recycle their electron carriers in order to continue to reuse them to produce ATP

   1. They will find another molecule to drop their electrons off on

   2. Secondly, during anaerobic respiration, glycolysis, alone, is producing ATP

   3. This means that ATP production is MUCH lower than in aerobic respiration.

Fitness

Fitness refers to an organism's ability to survive and reproduce in a particular environment.

Variation allow organisms to respond differently to environmental stimuli. They can most likely survive and reproduce better.

Adaptations AKA beneficial traits make it better for them to survive and reproduce in their environment’

Any sort of differences will create selective pressure that allows some organisms to survive and reproduce more than others.

Selective pressure is an environmental factor that causes certain traits to be more or less advantageous, leading to changes in the frequency of those traits over generations.

Unit 4 - Cell Communication and Cell Cycle

Cell Communication

1. Paracrine

   1. It means to communicate over short distances. The cells sends out signals to nearby cells to change a behavior in them.

   2. An example of this is muscles contracting and synaptic signaling

   3. Think of it as walking to the other side of the street

2. Juxtacrine

   1. It is direct contact that occurs when the 2 cells are adjacent to another.

   2. In plant cells, the signals are passed through the plasmodesmata

   3. In animal cells, the signals are passed through gap junctions that directly connect the cytoplasm of two cells

   4. Think of it as a handshake

3. Autocrine

   1. It involves the cell releasing a chemical and then having a receptor that receives this message

   2. An examples of this are cancer cells that release their own growth hormones to expand

   3. Think of it as sending a message to yourself

4. Endocrine

   1. It involves sending a ligand through the bloodstream to another cell or to another organ cell

   2. An example of this is when the pancreas cells release insulin when the blood sugar levels are too high

   3. A ligand is a molecule that binds to another (usually larger) molecule. In cell communication, it's often the signal molecule that binds to a receptor.

   4. It travels great distances, so the ligand has a longer lifespan

   5. Think of it as sending a package to another country

5. Direct signaling across gap junctions

   1. Similar to endocrine signaling. However, it involves signaling molecules moving directly between adjacent cells

Types of receptors

1. Internal receptors

   1. Cytoplasmic receptors

2. Cell-surface receptors AKA transmembrane receptors

   1. External ligand-binding domain

   2. Hydrophobic membrane-sprinting regimes

   3. Intracellular domain inside the cell.

   4. Ion channel-linked receptors

   5. G-protein linked receptors

   6. Enzyme-linked receptors

3. Signaling molecules

   1. Small hydrophobic ligands

   2. Water soluble ligands

   3. Other ligands (e.g. Nitric oxide)

Transduction is the process by which a cell converts one kind of signal or stimulus into another.

Signal Transduction stages

1. Reception

   1. This happens when the signal is detected when the ligand binds to the receptor protein in the target cell

   2. This causes a change in the shape of the cytoplasm of the inside of the receptor

   3. Cell surface receptors are proteins that bind to external signaling molecules such as hormones or neurotransmitters. They trigger changes inside the cell when activated

      1. They cover the entire membrane. They are important because most singaling molecules are too big to cross the plasma membrane

      2. Examples of this are ion channel receptors, G-protein-couple receptors, cyclic-AMP, etc.

2. Transduction

   1. The signals is transmitted and amplified through the cell

   2. Proteins are activated in phosphorylation. When the phosphate group is added, the protein will be “activated” to do its job (while ATP becomes ADP)

   3. Then amplification happens in which a sequence of steps of turning on communication pathways happen

      1. An example of this is cAMP or G-protein

3. Response

   1. It is when the signal is carried out.

      1. The response can vary; it can be turning on an enzyme, transporting a molecule, etc.

Lipid hormones are hormones derived from lipids such as sterols and fatty acids. They are typically non-polar and can pass through cell membranes easily.

Secondary messengers are molecules that relay signals received at receptors on the cell surface — such as the arrival of protein hormones, growth factors, etc. — to target molecules in the cytosol and/or nucleus.

Insulin

It is a ligand that tells the liver that the blood sugar level is too high. Without it, there would be difficulties in regulating blood levels.

Changes in Signal Transduction

1. Mutations

   1. They have the ability to greatly impat the cell cycle

   2. They can disturb the production of proteins

   3. Mutations in the signal transfuction pathway can prevent the cell from regulating its cycle

2. Chemicals

   1. They can also alter signal transduction pathway

   2. They can activate or hamper the pathway’s response

      1. e.g. lead, PCBs, and ethanol can have neurotoxic effects with specific signal transduction pathways

   3. Temperature and pH also affect in this because they can get damaged or denatured

   4. Inhibitors may block the sites of the receptor proteins and will disrupt the transduction

3. Feedback

   1. A negative feedback loop is a process in which the body senses a change and activates mechanisms to reverse that change.

      1. An example of this is blood sugar regulation.

      2. When you eat, blood glucose rises and the pancreas detects it. Then it releases insulin, which travels through the bloodstream and signals the liver about the increase of glucose. So that then the liver can take it and store it as glycogen

   2. A positive feedback loop amplifies or increases changes; this tends to move a system away from its equilibrium state and make it more unstable.

      1. An example of this is childbirth

      2. During labor, oxytocin is releases because it is a response to contractions intensifying. Oxytocin is released into the bloodstreams to stimulate these contractions

Cell Cycle

1. G1 - Cell grows

   1. Checkpoint: the integrity of the DNA is assessed

2. S - DNA replication

3. G2 - Cell continues to grow

   1. Checkpoint: proper chromosome duplication is assessed

4. Mitosis - cell divides

   1. In Prophase, the nuclear membrane begins to desintegrate, chromosomes condense, and the spindle begins to form. DNA is wrapped into equal amount of chromosomes

   2. In Metaphase, the chromosomes begin to line up in the middle of the cell and the centrosomes move to the ends of the cell

      1. Checkpoint: attachment of each kinetochore to a spindle fiber assessed.

   3. In Anaphase, the centromeres separate and the spindle fibers pull apart taking the sister chromosomes

   4. In Telophase begins when the chromosomes move to opposite ends of the cell

   5. In Cytokinesis two new daughter cells and there are 2 separate nucleoli

5. G0 - resting states where cells that aren’t ready go to

The Cdk-Cyclin complex is a key regulator of cell cycle progression, formed by cyclin-dependent kinases (Cdks) binding with cyclins.

Key genes that regulate the division process:

1. Tumor Supressor Gene (p53) OFF - is a protein that helps to properly check and repair damages in DNA.

2. Growth Promoter Genes ON - Unlimited growth

3. Apoptosis Genes OFF - cells don’t go through apoptosis

   1. Apoptosis is a process of programmed cell death that occurs in multicellular organisms. It's a way for the body to get rid of old, unnecessary, or damaged cells.

4. Chromosome Maintenance Genes (telomerase) ON - unlimited divisions

5. Touch-Sensor Gene OFF - overcome density dependence

Unit 5 - Heredity

Meiosis

Gametes AKA sex cells are created in meiosis. Diploid (2n) organisms carry two copies of every gene (one from the father and one from the mother).

A normal human being has 46 chromosomes. The sex cells have 23 chromosomes, so that the gamete has 46 in total.

Steps:

1. Prophase I: Each chromosome carefully aligns with its homologue partner so that the two match up at corresponding positions along their full length.

2. Metaphase I: Homologue pairs line up at the metaphase plate for separation.

3. Anaphase I: the homologues are pulled apart and move apart to opposite ends of the cell. The sister chromatids remain attached to one another and don't come apart.

4. Telophase I: the chromosomes arrive at opposite poles of the cell

5. Prophase II: chromosomes condense and the nuclear envelope breaks down, if needed.

6. Metaphase II: The chromosomes line up individually along the metaphase plate. I

7. Anaphase II: The sister chromatids separate and are pulled towards opposite poles of the cell.

8. Telophase II: nuclear membranes form around each set of chromosomes, and the chromosomes decondense.

Genetic Diversity

1. Crossing over

   1. Occurs during Prophase I

   2. The points where homologues cross over and exchange genetic material. They exchange parts of their chromosome that are at their corresponding location

   3. So it is not adding or removing genes, just changing them

2. Independent assortment

   1. The way chromosomes line up can vary the outcomes.

   2. It refers to the way chromosomes line up in the first and second round of division in meiosis.

3. Random fertilization

   1. You can't choose the sperm and egg that will join together, so no outcome will be the same.

   2. There are potentially thousands of spen that can fertilize the one mature egg

   3. Meaning that the genetics in each of them are going to be different

4. Nondisjunction

   1. Meiotic error creates cells with too many or too little chromosomes

   2. This often happens if chromosomes can’t be properly divided in apahase I or II.

   3. An example of this is Down syndome, since there is an extra copy of the 21st chromosome (n+1).

Gregor Mendel came up with certain laws of modern genetics:

1. Law of Segregation

   1. It states that the two alles from each parent are segregated during gamete formation

   2. All so that each gamete gets only one fo the two copies of the gene

2. Law of Independent Assortment

   1. It states that the two alleles get split up without regard to how the other alleles get split up

   2. This means that you can get your father’s copy of genes for eye color but you won’t necessarily get your father’s hair color.

3. Law of Dominance

   1. It states that when parents with pure, contrasting traits are crossed together, only one form of the trait appears in the next generation

Punnet squares

Normal Punnet Squares are monohybrid since they show only one trait with two parents. If an inheritance pattern is dihybrid, then two different traits are analyzed.

Key terms:

1. Phenotype is the physical appearance of an organism or the actual depiction of a trait

2. Genotype is the alleles that make up an individual trait

3. Alele is a version of a gene that can be either dominant or recessive

4. Dominant refers to a trait that produces enough protein/product to have more power over another trait

5. Recessive refers to a trait that does not produce enough protein/product so it is overpowered

6. Homozygous Dominant is an organism with two dominant alleles

7. Homozygous Recessive is an organism with two recessive alleles

8. Heterozygous is an organism with one dominant and one recessive allele

9. Sex-linked genes are genes that are located on the sex chromosomes (X and Y in humans). Their expression can result in traits that differ between sexes.

   1. Traits that are sex-linged are color blindness and hemophilia.

   2. These effects will only happen if both or your sole X chromosome has it.

   3. Men are more likely to have sex-linked genes because men only have one X chromosome

Non-Mendelian Genetics

1. Multiple alleles

   1. As opposed to having a dominant or recessive allele, there might be more than two versions of a gene that contribute to the overall phenotype.

   2. Blood type and fur color inheritance is a good example for this

2. Sex-linked traits

   1. EXPLAINED ABOVE

3. Incomplete dominance

   1. It refers to the traits that neither allele is dominant over the other. Instead they both sort of combine

   2. They can be homozygous dominant and homozygous recessive but if they have an incomplete dominance, the homozygous dominant trait won’t be highlighted

   3. An examples of this are flower colors. If a red flower and a white flower are crossed and their offsprings are pink, then they are incomplete dominant.

4. Co-dominance

   1. It refers to the traits that are both equally dominant (co-captains)

   2. An example are the different color spots in animals. Like cows with spots.

Non-Nuclear Inheritance

There are inheritances from organelles

Chloroplasts and mitochondria are randomly assorted, so the traits determined by them do not follow Mendelian rules

Mitochondria are inherited from the maternal side so it doesn’t follow those rules either

Chloroplasts are inherited from the maternal side (ovule) so they are maternally inherited traits

Environmental effects on Phenotype

1. Environmental conditions AKA natural selection determines which traits are more fit to a species in a given environment.

   1. This refers to selective pressure

   2. One common example of this effect’s on phenoty is the coloration of mice. Certain color makes them either more vulnerable or more fit to predators

   3. Global warming trends also affects the habitat of many animals which pressures them to adapt or die

2. Phenotypic plasticity occurs when individuals with the same genotype have different phenotypes because they are in different environments

   1. Meaning that organisms can change their physical traits as a response in change in their environment

   2. These changes include, but are not limited to, appearance, behavior, and physiology

   3. An example of this are arctic foxes that create a thick, white coat during winter.

   4. This is environmental camouflage that helps them during different seasons.

Unit 6 - Gene Expression and Regulation

DNA Replication

It is semiconservative since one strand is kept (as template) and a new one is generated.

1. It all starts on the origin of replication.

2. Helicase unwinds the double helix so that it can get replicated by breaking hydrogen bonds between bases

3. Then, DNA polymerase III extends these primers by adding complementary nucleotides.

   1. Although it needs RNA primase

4. Next, with RNA primase adds short RNA primers to the template strands.

   1. Primase makes an RNA primer, or short stretch of nucleic acid complementary to the template

5. And that is when DNA polymerase III can start replicating once RNA primer is added

6. Afterwards, DNA polymerase I goes through the replicated DNA done by DNA polymerase III to fix any mistakes.

   1. It also goes through RNA primer and changes it out with appropriate DNA nucleotides

7. Finally, ligase "pastes" everything together and creates the new strands.

8. The topoisomerase prevents that after the fork, DNA doesn't wind too tight. It makes temporary nicks to the helix to release tension.

9. Also, telomeres puts “protective caps” at the ends of chromosomes so they don’t deteriorate or fuse with other chromosomes.

10. Throughout this whole process, the lagging and leading strand are created.

    1. Leading strand: goes in a 5' to 3' direction away from the fork.

    2. Lagging strand: goes in a 5' to 3' in direction to the fork.

       1. Okazaki fragments happen in the lagging strand and then they are filled in.

Definitions:

Helicase opens up the DNA at the replication fork.

Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.

Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.

Primase synthesizes RNA primers complementary to the DNA strand.

DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the new DNA.

RNA primers are removed and replaced with DNA by DNA polymerase I.

The gaps between DNA fragments are sealed by DNA ligase.

Replication fork is a point in a DNA molecule where the two strands separate during replication

Types of RNA

1. Messenger RNA AKA mRNA

   1. It serves as a temporary copy of the DNA to travel from the nucleus to the cytoplasm for transcription

2. Ribosomal RNA AKA rRNA

   1. The structural component of the ribosome in which transcription takes place

3. Transfer RNA AKA tRNA

   1. Brings the correct amino acid to each of the mRNA’s codons

DNA Transcription

The central dogma of molecular biology describes the process in which DNA is converted into a protein. It involves two main stages: transcription (DNA to RNA) and translation (RNA to protein).

There are 3 steps in Transcription:

1. Initiation occurs when the rRNA in the ribosome interacts with the mRNA at the start codon

2. Elongation occurs when tRNA brings the amino acid as specified by the mRNA codons

3. Termination occurs when the polypeptide is released from the ribosome

This process begins with the DNA transcription into mRNA

1. It occurs in the nucleus and is carried out by RNA polymerase.

2. It binds to the promoter area and adds complementary RNA nucleotides based on the template strand

3. Unwinds the double helix

4. Synthesizes a complementary RNA strand.

The sequence of bases in the mRNA molecule is known as a codon

Series of enzyme-regulated modifications:

1. When the RNA strand is being transported to the ribosome, a 5' cap and 3' poly(A) tail joins the strand.

2. Introns (non-coding regions) and exons (coding regions) form a RNA strand with the correct codon sequence.

   1. This is done by a enzyme called spliceosome

Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. Certain exons of a gene may be included within or excluded from the final processed messenger RNA (mRNA) produced from that gene.

DNA translation

1. mRNA is used to synthesize a polypeptide in the ribosomes / cytoplasm

2. The ribosome then reads the sequence of nucleotides and matches it to the sequence of amino acid in a protein.

3. First, mRNA is bound to the ribosomes and the nucleotides are read in groups of three

   1. Each codon specifies which amino acid is corresponding to it

4. That way, the polypeptide chain will be growing

5. The ribosome consists of three sites:

   1. Aminoacyl site (A site): it holds tRNA to carry amino acids that will be added to the chain

   2. Peptidyl-tRNA site (P site): it holds tRNA so that it can grow

   3. Exit site (E site): binds a tRNA without an attached amino acid before the tRNA exits the ribosome.

6. When the stop codon is read, the synthesize of the polypeptide will be stopped

   1. The stop codons are UAG, UGA, or UAA

1. In prokaryotes, Transcription and translation happen simultaneously

   1. This is because they allow them to adapt better to changes in their environment and reproduce quicker if needed

   2. This is known as co-transcriptional translation

   3. While it goes through the same process of transcription, the ribosomes bind to the mRNA and begin translation

Special cases

Retro viruses have the unique ability to reverse the flow of genetic information

They use RNA as the genetic material and replicate through reverse transcription

Regulatory sequences

They and proteins work together to ensure that genes are expressed at the appropriate time and level in different cells and tissues

These regulatory proteins bind to specific sequences within the regulatory regions and can either enhance or repress the activity of the promoter.

If these sequences are not regulated, it can lead to several diseases such as cancer

1. Enhancers are sequences that can increase the level of transcription of a gene

2. Silencers can decrease this same level

3. Promoters can provide the binding site for the RNA polymerase and other initiation factors

   1. They usually contain a TATA box which is recognized by the TATA-binding protein (TBP)

   2. The TATA box is a DNA sequence found in the promoter regions of genes. It is crucial for the initiation of transcription, as it helps position RNA Polymerase II

4. Terminators are sequences that signal the end of the transcription

There are also negative regulatory molecules that can inhibit gene expression by binding to DNA and blocking transcription:

1. Repressors are proteins that bind to DNA sequences and prevent RNA polymerase from initiating transcription

2. Transcriptional corepressors are proteins that bind to transcription factors rather than directly binding to DNA.

Epigenetics refers to the study of heritable changes in gene function that occur without changes to the underlying DNA sequence.

1. One of the most common epigenetic modification sis methylation of cystosine bases in DNA (gene repression)

2. Epigenetic modifications can lead to epigenetic changes which affect gene expression and increases the risk of certain diseases later in life

In Prokaryotes, operons transcribe a single mRNA molecule.

1. They are controlled by a single promoter

2. An example of this is the lac operon: a set of genes in bacteria that are responsible for the breakdown of lactose into glucose and galactose. It consists of three parts: the promoter, operator, and structural genes.

3. Operons are regulated by a lac repressor and a catabolic activator protein (CAP)

   1. It detects glucose and activates transcription when glucose is low

   2. They are also found in E. coli but they are repressible operons

4. In Eukaryotes, genes are influences by transcription factors that bind to regulatory sequences

There are different ways to regulate gene expression

Differential gene expression is the process by which genes are turned on or off in different cell types, at different stages of development, or in response to environmental changes.

This differences make different products and have different influences on the function of the cell; they are:

1. Small RNA molecules

   1. Non-coding RNAs that are about 20-25 nucleotides in length

   2. microRNAs (miRNAs) which are small non-coding RNAs that bind to the 3’ untranslated regions of specific mRNAs

   3. Small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) are processed by RNA-induced silencing complex (RISC) to generate single-strandede siRNAs to target mRNAS for degradation

2. Mutations:

   1. Point mutations change a single nucleotide in the DNA sequence

      1. It all depends on the location o the mutation and the specific nucleotide change

   2. Insertions and Deletions (Indels) can either add or substract a nucleotide from the DNA sequence

      1. This can cause a Frameshift mutations which changes the reading frame of the gene

   3. Errors in mitosis and meiosis may also create genetic variation as they wouldn’t be the same

      1. One way that genetic variation can increase is through the horizontal acquisition of genetic information (in prokaryotes) is:

         1. Transformation (uptake of naked DNA)

         2. Transduction (viral transmission of genetic information)

         3. Conjugation (cell-to-cell transfer of DNA)

         4. Transposition (movement of DNA segments within and between DNA molecules)

   4. Whether a mutation is detrimental, beneficial, or neutral, it depends on how it is going to be received in the environment

      1. They are the primary source of genetic variation because it creates different DNA sequences

      2. Genetic variation is the raw material for evolution as it allows natural selection to act on different variations

      3. Examples of this are antibiotic resistance mutations, pesticide resistance mutations, and sickle cell disorder

Biotechnology is the use of living systems and organisms to develop or make products, or any technological application that uses biological systems, living organisms, or derivatives thereof.

It has a wide range of applications and it is used:

1. Medicine: used to develop new drugs, diagnostic tools, vaccines, and therapies

2. Agriculture: used to improve crop yields and resistance to pests and diseases

3. Environmental management: used to clean up contaminated soil and water, and to create new methods of waste management

4. Industrial production: used to produce useful products (biofuels, bioplastics, and enzymes for industrial use)

5. Research: used to study genetics and biology of living organisms

6. Forensics: used to identify individuals based on DNA analysis and to solve crimes

7. Food production: used to improve the nutritional content of food, extend the shelf life, and increase resistance to pests and diseases

8. Others: it can also be used in wildlife, cosmetics, and conservation

9. Technology:

   1. Recombinant DNA

   2. Gene cloning

   3. Polymerase Chain Reaction

   4. Gel Electrophoresis

   5. Genetically modified organisms

   6. Human safety concerns

   7. Environmental concerns

   8. GMOs

Pros

1. More crop yields

2. More resistance to pests and diseases

3. Less us of pesticides

4. Better nutritional content

5. More tolerance to environmental stress

Cons

1. Potential health risks for humans

2. Potential harm to beneficial insects and other non-target organisms

3. Lack of long-term research

4. Potential for crossbreeding with wild relatives and creating “superweeds”

5. Economic and ethical concerns about the control of the food supply by a few large companies

Issues regarding biotechnology

1. Ethical

   1. There are concerns about genetic engineering, human cloning, and the use of stem cells

   2. It raises the question of manipulating of life and the creation of “designer babies”

2. Legal

   1. They include intellectual property rights, regulation of GMOs, and patenting genetic material

3. Social

   1. They include issues around healthcare, bioprospecting and bio-piracry, and the potential for biotechnology to exacerbate social inequalities

Unit 7 - Natural Selection

Natural Selection: a process by which certain traits become more or less common in a population over time. Its basic idea is that there is variation among individuals in a specific population.

Contributing effects to it:

1. Overproduction

2. Variation

3. Adaptation

4. Competition

5. Differential reproductive success

Types of Natural Selection:

1. Directional selection: one end of the phenotypic spectrum is selected for

2. Disruptive selection: both ends of the phenotypic spectrum are selected for

3. Stabilizing selection: both ends of the phenotypic spectrum are selected against

Fitness is what will determine how certain organisms will survive and reproduce in a given environment.

The surrounding environment plays into natural selection. In any biome, the population will be affected by both biotic (living) and abiotic (nonliving) factors

1. Biotic factors: vegetation, predators, prey, etc.

   1. A biotoic environment refers to the living components of an ecosystem; organisms and their interactions

   2. If it is stable, it will have a lower rate of evolution since the selective pressure on the population are constant

   3. If they have fluctuating conditions within the environment will change competitors’ behaviors; predators or prey

      1. Increasing natural selection

2. Abiotic factors: soil, temperature, and other non-living environmental components

   1. An abiotic environment refers to the non-living components of an ecosystem; such as climate, geology, and physical features

   2. if it is stable, it will have a lower rate of evolution but if not, temperature, precipitation, and resource availability might change.

Theory of Darwin

Charles Darwin provided the theory of evolution after studying natural selection in the Galapagos Islands. This theory is based on three major propositions:

1. Species change over time

2. Divergent species share a common ancestor

3. Natural selection is the mechanism that produces these changes in species/populations

His theory of natural selection was based on the idea there is more variation among individuals in a population that can be sustained by the resources available in their environment

1. This then clarifies the idea of the struggle for survival among individuals

2. Meaning that not every species or individual is going to survive and reproduce

He also made the observation that different traits tend to be inherited in different ways

1. Some traits are determined b a single gene, while other are determined by several genes

2. Some traits are more able to be passed down generations than others

Phenotypic Variation: Phenotypic variation refers to the differences in physical traits among individuals of the same species due to genetic and environmental factors.

1. A good example of this are peppered moths that were initially white with some black speckles on their wings.

2. However, after the Industrial Revolution, the darkened trees made moths more visible for predators

3. That forces the moths to increase their fitness once a mutation made them have darker wings

In contrast to natural selection, artificial selection manipulates the phenotypic frequencies of a population or species through selective breeding

1. It the process of intentionally breeding organisms for specific traits. Usually, humans choose which traits they want to preserve and which ones no

2. Artificial selection can be used to study the genetic basis of traits in organisms

   1. It refers to how genes determine physical characteristics or behaviors of an organism

   2. By breeding individuals with specific traits and tracking the inheritance of those traits over multiple generations, they can learn about the genes that control those traits

3. Convergent evolution is the process by which unrelated or distantly related organisms evolve similar traits due to similar selective pressures in their environments

   1. This is not artificial because it is manipulation of environmental pressure

4. It can increase/decrease the variation in a population of organisms.

5. It can also lead to the development of new species.

Genetic Drift it occurs due to random fluctuations in the frequency of alleles in a population

1. The effect of genetic drift affects more small populations because the fluctuations might be large relative to the overall size population.

2. Bottleneck effect: occurs when population size is rapidly and dramatically reduced due to an environmental disturbance

3. Founder effect: occurs when a few individuals become isolated from their original population, forming a new gene pool

Gene flow is the movement of genes from one population to another

1. it can occur when individuals migrate from one population to another because they are bringing their genes along with them

2. It can also act to homogenize the genetic makeup of populations that are geographically close to each other, by reducing the frequency of rare alleles in a population

Speciation is when populations are separated and can no longer interbreed, they will evolve independently, and over time, the genetic differences between the populations will become so great that they won’t be able to have a successful offspring

Hardy-Weinberg Equilibrium

For you to check the allele frequency, it needs to follow a certain criteria:

1. No mutations

2. No artificial/natural selection

3. No gene flow

4. Infinite population size

5. Random mating

Equations:

1. p + q = 1

2. p^2 + 2pq + q^2 = 1

Common Ancestry

1. Endosymbiont theory

   1. In eukaryotic cells

   2. Membrane-bound organelles

   3. Linear chromosomes

   4. Genes containing introns

   5. Evidence of Evolution:

      1. Fossils: Provides evidence of how extinct organisms once appeared on Earth and increases understanding of ancestral species

         1. The fossil record refers to all fossils discovered and the information derived from them about past life forms on Earth over millions of years.

      2. Homology: Structural similarities between organisms, indicating common ancestry

         1. Anatomical homology

            1. Homologous structures

            2. vestigial structure

            3. Comparative embryology

         2. Molecular homology

      3. Analogy: Distantly related organisms with similar structural features, caused by convergent evolution, indicate the significance of natural selection

      4. Transitional Species: These species, often in the form of fossil evidence, possess features of more than one major taxonomic group, illustrating a literal transition in biological forms

      5. Artificial Selection: Humans controlling the mating of organisms that have desirable traits

Population evolution

Genomic changes refers to alterations in the structure or number of genes in an organism’s genome. They include:

1. Mutation

2. Recombination

3. Genetic Drift

Pathogens are microorganisms - such as bacteria, viruses, and fungi - that cause disease in their host.

Taxonomy: it is the ordered division and naming of organisms Evolutionary relatedness is illustrated in evolutionary trees of which there are two types:

Phylogenetic trees

1. A phylogenetic tree is a diagram that shows the evolutionary relationships between different groups of organisms

   1. They offer a timeline of evolution and shows evolutionary relationships through distance (how close or far related are certain species)

   2. They are a fundamental tool in evolutionary biology to understand

2. Cladograms focus more on the morphological similarities between species like beak types

   1. They can be hypothesized with reasonable differences

   2. They also show relationships between lineages.

3. Speciation refers to the origin of new species, is at the focal point of evolutionary theory

   1. It evolves a population into different species over time with:

      1. Geographical isolation

      2. Reproductive isolation

      3. Ecological isolation

   2. Microevolution: it is a change in allele frequencies in a population over generations

   3. Macroevolution: it refers to large-scale evolutionary changes that occur over long periods of time, resulting in the formation of new species or higher taxonomic groups.

   4. Types of Speciation:

      1. Allopatric

         1. Occurs with geographic isolation and two populations become reproductively isolated

      2. Sympatric

         1. Individuals within the same geographic area are influenced by either disruptive selection or mating preferences

         2. They can be categorized as:

            1. Postzygotic isolation refers to mechanisms that prevent successful development and reproduction after fertilization has occurred between members of different species.

            2. Prezygotic isolation is a mechanism that prevents different species from interbreeding and producing hybrid offspring. This occurs before the fertilization of eggs.

4. The points where two species diverge, are called nodes

   1. They help to point out the common ancestor and show a trait that is shared, gained or lost

   2. It can also show the out-group of the species

5. The rate of speciation and evolution may also differ under different ecological conditions

   1. Punctuated equilibrium and gradualism are two different known methods

      1. Punctuated equilibrium claims that most species will exhibit little net evolutionary change for most of their geological history, remaining in an extended state called stasis.

      2. Gradualism proposes that evolution is a slow and steady process that occurs over hundreds of thousands or millions of years

   2. Divergent evolution occurs when different populations of a species adapt to different habitats, leading to the development of new forms

   3. Adaptive radiation happens when a lineage diversifies into many new forms as it adapts to different habitats and ecological niches

Extinction

Extinction can be caused by changes to a species’ environment

Ecological stress refers to pressure on an organism's ability to survive due to changes in its environment such as temperature shifts, food scarcity or increased competition for resources.

At times, the rate of extinction has increased dramatically and caused a mass extinction

Mass extinction is the result of disruptive global environmental changes

A high rate of extinction, the effect on diversity may be neutral or negative (if the number of species last outweighs the number of species that evolved)

A high rate of speciation, where new species are evolving, will increase the amout of diversity in an ecosystem

Variations in population

Populations with high genetic variation are more likely to persist through environmental disturbances

Ecological disturbance created by humans:

1. Habitat loss

2. Associated loss of prey

Early life on Earth

1. The origin of life on Earth refers to the process and timeline by which life first emerged on our planet, a subject of ongoing scientific research. It is generally accepted that this occurred around 3.9 billion years ago. This can be explained by:

   1. Abiogenesis is the process by which life arises naturally from non-living matter, such as simple organic compounds

   2. Panspermia proposes that organic molecules were transported to Earth by a meteorite or other celestial events

2. Inorganic precursors are simple compounds (with CHNOPS) which participate in chemical reactions to form complex molecules

3. Abiotic synthesis of small organic molecules

4. Joining of these small molecules into macromolecules

5. Packaging of molecules into protocells

6. Origin of self-replicating molecules

7. The first genetic material was probably RNA, not DNA

Abiogenesis is the process by which life arises naturally from non-living matter, such as simple organic compounds.

Unit 8 - Ecology

Environmental sensing is the ability of organisms to detect and respond to changes in their environment

1. Organisms use a variety of behavioral and physiological mechanisms to sense if there has been a change in environment

   1. Organisms respond to changes in their environment through behavioral mechanisms.

      1. These changes may be environmental cues (temp., light, and food availability)

   2. The physiological mechanisms that they use is change genes, enzymes, and hormones in response to environmental cues

2. Many organisms are dependent on the seasons, hibernating, or migrating in winter

   1. All due to changes in temp., weather, patterns, resources, and shelter

   2. Examples of all this are:

      1. Photoperiodism: plant’s change of growth and development based on daylight

      2. Phototropism: plant’s change of direction based on light direction

      3. Taxis: animal’s change to move towards or away from stimulus

      4. Kinesis: animal’s change of direction based on stimulus

      5. Fight-or-flight response: physiological response when perceiving a threat or danger

      6. Predator warnings: communicating danger one organism to another

         1. Different species have their own highly evolved mechanisms of communication.

         2. This can involve the release of hormones, behavioral patterns, mating dances, warning calls, etc.

Cooperative behavior refers to actions taken by organisms that benefit others in their group, often at a cost to themselves.

A mutualistic relationship is one where both organisms involved benefit from their interaction with each other.

Trophic levels is the energy level in which organisms exist and based on what it eats

1. Autotrophs produce their own energy while Heterotrophs get their energy from other organisms

2. Maintaining energy:

   1. Endotherms maintain an even temperature in their bodies (humans)

   2. Ectotherms do not maintain an even temperature in their bodies (snakes and fish)

   3. Different organisms use different reproductive strategies in response to the amount of enery available

   4. There is a relationship between metabolic rate per unit body mass and the size of multicellular organisms

      1. Metabolic rate is the speed at which an organism's body uses energy or burns calories.

Populations can vary in size, density, and distribution; they can affect specie interactions and resource availability

In population ecology, the focus is on understanding the dynamics of the population and how a population is affected by various factors, such as:

1. Competition

2. Predation

3. Habitat availability

A number of factors are important for a population to survive. They are divided in biotic and abiotic factors. Some of them are:

1. Resources

2. Habitat

3. Competition

4. Predation

5. Diseases

6. Climate

   1. The relative importance of these factors varies depending on the species and the specific environment in which it lives

Population growth equation

1. dN / dt = B - D

   1. dN is the change in population

   2. dt is the change in time

   3. B is the birth rate

   4. D is the death rate

Exponential growth is the number of individuals in a population increases geometrically at a constant rate over time

1. There are no limiting factors

2. The population has a high reproductive rate

3. The population has a low mortality rate

Exponential growth equation

1. dN /. dt = (r max) (N)

   1. dN is the change in population size

   2. dt is the change in time

   3. r max is the maximum per capita growth rate of the population

   4. N is the population size

Logistic growth refers to the growth pattern where expansion is rapid initially due to abundant resources, but slows down as resources become limited leading to stabilization around carrying capacity.

Populations are often affected by factors that inhibit their ability to continue to survive and reproduce; they are:

Logistic growth model describes how population growth may start slowly, then increase rapidly until reaching carrying capacity due to environmental resistance such as limited resources.

1. Density-dependent factors: factors in the environment that affects populations differently depending on the size of the population

   1. As the population size increases, the effects of this would increase as well

   2. Examples of this are access to food, amount of predators, diseases, and migrations

2. Density-independent factors: factors in the environment that can afect a population regardless of the size

   1. These are weather and climate

   2. They lead to a limit in the number of organisms that can survive in an environment

   3. This limit is the carrying capacity. The equation for this is:

      1. dN/dt = rmaxN (K-N / K)

         1. N = population size

         2. dT = chnage over time

         3. K = carrying capacity

         4. rmax = maximum per capita growth rate of a population

In a community, several species interact with one another through different processes, that can have positive, neutral, or negative effects:

1. Competition for resources

2. Predation

3. Mutualism

Species diversity refers to the number of unique species living in the area and the percentage of the population represented by each species

Simpson’s Diversity Index can measure the biodiversity in an area:

1. D = 1 - Σ(n / N)^2

   1. n = total number of organisms of a particular species

   2. N = total number of organisms of all species

Predation is an interaction where one organism (the predator) kills another (the prey) for food.

Interspecies competition is a form of competition in which individuals of different species compete for the same resources in an ecosystem, such as food or living space.

Commensalism is a type of symbiotic relationship where one organism benefits without affecting the other organism positively or negatively.

Parasitism is a type of relationship where one organism (the parasite) benefits at the expense of the other (the host).

Keystone species are species that have a disproportionate effect on the ecosystem

1. If this are disrupted, it can have catastrophic effects within the ecosystem

2. An example of them are sea otters

   1. By preying on sea urchins, which consume kelp, otters help protect kelp forests. Because kelp forests are an ecological niche for a variety of other organisms living in the marine ecosystem, otters provide an ecosystem service.

Invasive species are non-native organisms that causes harm to the ecosystem into which it has been introduced

1. They are able to outcompete other organisms for resources and disrupt existing ecosystem interactions

Anthropogenic impacts are environmental changes caused by human influence that ends up

1. Destroying habitats

2. Extinction

3. Pollution

4. Spread of invasive species

5. Climate change

Levels of Ecology:

1. Each level of organization has emergent properties, new properties that are not present in the level's component parts but emerge from from these parts' interactions and relationships.

2. The levels of ecological study offer different insights into how organisms interact with each other and the environment.

   1. Organism

   2. Population

   3. Community

   4. Ecosystem

   5. Biosphere