Patterns of Inheritance

Who was Gregor Mendel?
Gregor Mendel was the first "geneticist" to figure out a concrete law on inheritance. He was a monk in what was then Austria, working with the inheritance of pea plants. 

Are there diseases that are genetically transmittable?
Yes, many in fact. Thankfully most are recessive, due to evolution, ones that are dominant have mostly killed off their hosts.

What is incomplete dominance? 
A condition in genetics that causes both, blended or some traits of the parents to appear in the offspring.

The Facts: 
-The Law of Segregation is: A sperm or egg carriers only one allele for each inherited character because allele pairs separate from each other during the production of gametes
-The Law of Independent Assortment is: Each pair of alleles segregates independently of other pairs of alleles during gamete formation.
-The Rule of Multiplication is: 1/2*1/2 = 1/4, which is true for genetics when it comes to recessive traits
-The Rule of Addition is used to figure out the probability of certain phenotypes (Aa and AA produce the same phenotype)
-"Carriers" refers to those who carry a recessive gene for a disorder, but do not show signs of said disorder
-Cystic fibrosis is one of said diseases, which causes mucus to be produced in excess in many places in the body, including the lungs
-Chromosome Theory of Inheritance: Genes occupy specific loci on chromosomes and chromosomes that undergo segregation and independent assortment during meiosis.
-Recombination frequency is when the offspring have the phenotype of the parent.
-Sex-linked genes are ones that are specifically on the sex chromosomes, usually on the X
-Red-Green Color blindness is attached to the X, and is much more common in males, since they only have one. Females, having two, have the chance of having a non-affected X, which allows them full color vision.

Some Helpful Terms:
-Character: A heritable feature that varies among individuals
-Trait: A variant of a character
-Homozygous: Two of the same allele
-Heterozygous:  Two different alleles
-Phenotype: The physical traits
-Genotype: The genetic make-up
-Testcross: Mating between an individual of unknown genotype and homozygous recessive to figure out the genetic make up of the other
-Inbreeding: Mating of closely related organisms
-Codominant: Both alleles are expressed in a heterozygous individual
-Pleiotropy: Genes that affect more than one character

Diagram:

This is an example of a Punnett square, for the shape and color of peas. It is apparent that green and wrinkled are the recessive traits, while smooth and yellow are dominant. About 1/4 will be green, and 1/4 will be wrinkled- this being an example of the rule of addition. On that note, only 1/16 will be green AND wrinkled (rule of multiplication).








Summary:
This chapter discusses one of the coolest facets of biology- genetics and inheritance. GO GENETICS! But it starts off talking about Gregor Mendel, and how he came to study genetics. He was very meticulous in controlling which plants bred with which, giving some very concrete data. The punnett square was crucial in the field of genetics, giving us a good way of seeing how genetic variation operates.
Not only that, but it goes on to talk about the things that Mendel didn't know, such as incomplete dominance, co-dominance and sex linked genes.

A Cool Video:
http://www.youtube.com/watch?v=oVl8OH_7QSc

Photosynthesis: Using Light to Make Food

What is the equation for photosynthesis?

6CO2 + 6H2O --> (Light Energy) --> C6H12O6 + 6O2

What is the difference between photosynthesis and the Calvin cycle?

The Calvin cycle doesn't require sunlight.

What does the Calvin cycle produce?

Sugars: Cellulose, Starch and other organic compounds.

The Facts:

-The Calvin cycle doesn't require sunlight
-Plants are known as producers because they create their own energy
-Another word for producers is autotrophs
-Photosynthesis is similar to cell respiration in that it's how the cell produces energy
-Without photosynthesis, cell respiration couldn't occur, as photosynthesis creates oxygen for it
-Similarly, without cell respiration, photosynthesis couldn't occur, as it requires the carbon dioxide that cell respiration gives off
-The energy released by electrons is conserved as it is passed from one molecule to another.
-Cellular respiration uses redox reactions to harvest the chemical energy stored in a glucose molecule.
-Chemiosmosis is the mechanism that not only is involved in oxidative phosphorylation in mitochondria but also generates ATP in chloroplasts
-ATP synthase couples the flow of H+ to the phosphorylation of ADP.

Some Helpful Terms:

-Autotrophs: Organisms that make their own food, sustaining themselves
-Producers: Organisms that make up the food supply
-Photoautotrophs: Organisms that produce organic materials from inorganic molecules using light energy
-Chlorophyll: Light-absorbing pigment in chloroplasts that converts solar energy into chemical energy
-Mesophyll: The green tissue in the interior of the leaf where chloroplasts are concentrated
-Stomata: Pores in the lead in which CO2 enters
-Stroma: Thick fluid inside the chloroplasts
-Thylakoids: Sacks suspended in in the stroma
-Grana: Stacks of thylakoids
-Photosystem: A light-center complex consisting of light-harvesting complexes.

Diagram:

The plant that contains chlorophyll is absorbing the light energy from the sun. Not only that, but it also takes in the CO2. Within the plant, photosynthesis occurs, releasing oxygen and creating glucose.














Summary:
This chapter was about photosynthesis, which is another way that cells harvest energy, but this is exclusively to plants and other organisms that contain chloroplasts and chlorophyll. Plants are known as the producers, as they create their own food, and consumers eat them for their energy.
Photosynthesis consumes sunlight and water and produces O2 and carbohydrates for the plant. There are two types of energy cycles for plants- one is the light cycle (photosynthesis) and the dark cycle (the calvin cycle).


A Cool Video:
http://www.youtube.com/watch?v=C1_uez5WX1o

The Cellular Basis of Reproduction and Inheritance

What are the stages of cell reproduction?

1) Interphase
2) Prophase
3) Metaphase
4) Anaphase
5) Telophase
6) Cytokinesis

What is Mitosis? 

Cell reproduction consisting of one cell dividing it's genetic information into two identical cells, barring mutation.

What are the differences between animal and plant mitosis?


Animal cells, since they don't have a cell wall, have a cleavage furrow right as they're about to split, that will become part of the new cell membranes. In plants, since they have a cell wall, they develop a cell plate in between them that will become the new part of the cell wall. Not only that, but plants also have to split up their chloroplasts, something animals do not have.

The Facts:

-Sexual reproduction allows for quick adaptation and evolution
-Asexual reproduction usually creates identical offspring to the parent, but cannot adapt very fast
-Prokaryotes reproduce mostly by binary fission
-Because of anchorage dependence, if you left some animal cells in a dish, they'd grow along the bottom
-A tumor is uncontrolled growth of cells
-A benign tumor is one that stays on it's origin
-A malignant tumor is one that spreads to other tissues
-Haploid gametes are created by splitting sex cells into halves, each with half the genetic information
-Meiosis consists of two cycles of splitting, ending in four cells as opposed to two
-There are many genetic disorders caused by failures in chromosome development.

Some Helpful Terms:

-Asexual Reproduction: The creation of genetically identical offspring by a single parent without the presence of sperm or an egg
-Chromosomes: Structures that contain most of the organism's DNA
-Binary Fission: Prokaryotes use this type of reproduction, essentially just splitting themselves in half.
-Chromatin: A combination of DNA and protein molecules
-Sister Chromatids: Identical copies of a DNA molecule
-Centromere: What joins the chromatids together
-Interphase: Takes up most of the cell's life, this is while it is performing it's normal functions
-Density-Dependent Inhibition: A phenomenon in which crowded cells don't divide.
-Anchorage Dependence: When cells have to be in contact with a solid surface to divide.
-Metastasis: The spread of cancer cells beyond their origin

Diagram: 

(Going clockwise)
Interphase cell: Performing intended functions
Prophase: Nuclear envelope dissolved, chromosomes free
Metaphase: Chromosomes lining up, spindles attaching
Anaphase: Cell is beginning to split, chromosomes split apart, going to different sides
Telophase: Cells almost completely divided, nuclear envelope reforms on both sides










Summary:
This chapter covers cell reproduction, both mitosis and meiosis. Mitosis is the asexual reproduction of cells, whereas meiosis is specifically for the sex cells. Asexual reproduction requires no mate, and produces genetically similar offspring. In animals, sexual reproduction requires a mate, but produces genetically varied offspring, and is very susceptible to adaptation.
This also gives some good real-life examples of when things go wrong- tumors are uncontrolled cell growth. While from a perspective of cell reproduction, interphase seems rather useless, in fact that's a very good thing, seeing as that is when the cell is doing its job.


A Cool Video:

(warning, contains profanity)
http://www.youtube.com/watch?v=cxNNOcVOwaU

How Cells Harvest Chemical Energy

What is the equation for cellular respiration?

C6H12O6 + 6O2 --> 6CO2 + 6H2O + ATPs (Energy)

What are the three stages of Cellular Respiration?

Stage 1: Glycolysis
Stage 2: The citric acid cycle
Stage 3: Oxidative phosphorylation

Where do the three stages take place?

Glycolysis: Cytoplasm
Citric Acid Cycle: Inside the Mitochondria
Oxidative Phosphorylation: Inner mitochondrial membrane

The Facts:

- Slow-twitch muscles are better for endurance running; they can sustain repeated use, but don't provide lots of speed
- Fast-twich muscles are better for sprinting; they fatigue quickly, but provide lots of speed
- Almost all eukaryotic cells go through cellular respiration
- Glycolysis breaks down glucose into two pyruvate
- Pyruvate is a three-carbon compound used in cellular respiration
- The Citric Acid Cycle breaks down the pyruvate and creates Carbon Dioxide, the main purpose is to supply oxidative phosphorylation with electrons
- Oxidative Phosphorylation deals with the electron chain and chemiosmosis
- Chemiosmosis uses the concentration gradient's potential energy to create ATP
- Fermentation is a type of respiration that doesn't require oxygen
- Certain poisons block the electron transport chain, others inhibit ATP synthase

Some Helpful Terms:

-Redox reaction: The movement from one molecule to another
-Oxidation: Loss of electrons from one substance
-Reduction: Gaining electrons to one substance
-Electron Transport Chain: Serious of redox reactions in which electrons pass in steps to oxygen
-Substrate-Level Phosporylation: An enzyme transfer from a phosphate group, forming ADP to ATP
-Chemiosmosis: Chemical osmosis through the concentration gradient, energy produced used to make ATP
-Lactic Acid Fermentation: Used to regenerate NAD+, converted into pyruvate
-Alcohol Fermentation: Yeast in anaerobic enviroments converts pyruvate to CO2 and ethanol
-Obligate Anaerobes: Organisms that are poisoned by oxygen
-Facultative Anaerobes: Can make ATP with either fermentation or oxidative phosphorylation

Diagram:

Glucose starts off as the energy source. It goes through glycolysis to prepare to become pyruvate, generating 2 ATP molecules just by itself. Then the pyruvate becomes the energy source for either aerobic or anaerobic respiration, the latter going through fermentation, producing Lactic acid or Ethanol. The former that uses oxygen, the pyruvate goes through the Krebs (Citric Acid) cycle, producing CO2 and sent to the electron transport chain, taking in oxygen, producing H2O and some ATP










Summary:
This chapter was very specifically about cell respiration and how the cells make energy (ATP). Basically it goes through the steps of cell respiration- Glycolysis, which prepares the glucose for the citric acid cycle, by making most of it into pyruvate and producing 2 ATP. During the citric acid cycle, oxygen is used to finish creating pyruvate and sending it to the electron transport chain.
Then during oxidative phosphorylation, water is produced, as well as 34-36 ATPs. This produces the most energy. Then fermentation is the cycle of respiration that requires no oxygen, and produces lactic acid and ehtanol.

Cool Video:
 http://www.youtube.com/watch?v=vlZZUtpyCgQ

The Working Cell

AUTOMATICALLY AN AWESOME CHAPTER BECAUSE IT STARTS WITH MARINE BIOLOGY!
(I love Marine Biology. Just throwing that out there.)

The Facts:
-Photophores are organs that produce light usually found on deep-sea creatures. That's an awesome adaptation and I mean "awesome" in the sense that it literally fills me with awe.
-Selective permeability describes something that allows certain substances to pass through it, and not others
-Osmosis is the movement of water through a selectively permeable membrane
-The first law of Thermodynamics states that all energy in the universe is constant
-The second law of Thermodynamics states that energy isn't always recycled due to entropy, or "randomness" of energy becoming unusable

Key Terms: 
-Diffusion: The tendency for particles to spread out evenly in an open space
-Concentration Gradient: the concentration of particles or a substance
-Tonicity: The ability of solution to cause a cell to gain or lose water
-Aquaporins: transport proteins that help with the rapid diffusion of water
-Endocytosis: the process of which a cell takes in substances
-Exocytosis: the process of which a cell expels substances
-Phagocytosis: the process of which a cell "eats"
-Pinocytosis: the process of which a cell takes in liquids
-Kinetic Energy: Energy of motion
-Potential Energy: Stored energy

A basic example of kinetic vs potential energy. And possibly entropy, if you account for the loss of energy in this situation













Summary:

This chapter was all about the actual functions of cells as a whole, rather than the individual that we read about in the previous chapter. The kinetic energy of a person on a bike, or the potential energy of a ball we're about to punt across a field  both qualify for scientific marvel. That is, the laws of thermodynamics.
Not only does it cover energy on a macro scale, it also looks at diffusion, active transport and passive transport. Cells are very busy little beings, always finding their place, and trying to equal out concentrations.

http://www.youtube.com/watch?v=sdiJtDRJQEc
This guy has a cool voice

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1.02.28

The Chemical Basis of Life

What are ionic bonds?
Ionic bonds are formed when some electrons the valence shell of an atom connects with gaps in another atom's valence shell to make the desired 8. 


What are covalent bonds?
When two atoms share one or more pairs of valence shell electrons.


What is the pH scale?
The pH scale is a measuring scale for acidic/basic levels in certain substances. It goes from 0 to 14, 7 being neutral. High acids are closer to 0 and high bases are closer to 14. For a point of reference, human blood is neutral. 

The Facts: 

-The four most abundant elements in the human body are oxygen, carbon, hydrogen and nitrogen
-Hydrogen bonds are weak, but contribute to many of the emergent properties of water
-Acids have high concentrations of H+ (hydrogen ions)
-Bases have high OH- (hydroxide ions)
-Blood is considered and aqueous solution

Some Key Terms:

-Matter: Anything that occupies space and has mass
-Element: A substance that cannot be broken down into another
-Compound: a substance consisting of two or more different elements combined in a fixed ratio
-Proton: A subatomic particle with a positive charge
-Electron: A subatomic particle with a negative charge that orbits the proton
-Neutron: A subatomic particle that makes up the nucleus of an atom with a neutral charge
-Atomic Number: The number of protons in an atom
-Mass Number: The sum of the neutrons and protons in an atom
-Isotopes: An atom with a different number of neutrons
-Radioactive Isotope: An isotope in which the nucleus decays, giving off energy

This is a drawing of the pH scale, the word "base" being interchangeable with "alkaline"
















Summary:
This chapter was but a mere introduction into the chemistry-based side of biology. It incorporated the chemical basis in basic functions throughout life, and how chemistry directly affects our world. It segues into this by introducing the acid that certain ants produce to effectively do "gardening" by killing off any intruding plant life.
It goes on to describe molecular structure, how atoms and elements bond, focusing on the emergent properties of water. Water has many interesting qualities due to the weak hydrogen bonds, including cohesion and adhesion. Then it ends with my favorite part- the ecological practices! From dying coral reefs to finding life on Mars, ecological biology rocks my world.

http://www.youtube.com/watch?v=qmgE0w6E6ZI

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1.02.28

The Molecules of Cells

What is a Dehydration Reaction?
A reaction which involves removing water.


What is Hydrolysis?
Breaking the bonds made with the dehydration reaction by adding water once more.


What's a Monosaccharide?
Monomers, essentially the simplest carbohydrates. 

The Facts:
-Lipids have a kink in them when they double-bond
-The Primary structure of a protein is the structure of its amino acids
-A secondary structure is when the parts of a polypeptide coil fold into an alpha helix
-A tertiary structure is the overall three-dimensional structure of the protein
-A quaternary structure is two polypeptide chains link together

Key Terms:
-Hydrocarbons: Compounds that are made up of only hydrogen and carbon
-Isomers: Compounds with the same formula but a different shape
-Hydrophilic: Likes water
-Hydrophobic: Dislikes water
-Hydroxyl Group: Hydrogen atom bonded to an oxygen atom, bonded to a carbon skeleton
-Carbonyl Group: Carbon double bonded to an oxygen atom
-Carboxyl Group: Carbon double bonded to an oxygen atom and bonded to the Hydroxyl group
-Amino Group: Nitrogen bonded to two hydrogen atoms and then to a carbon skeleton
-Phosphate Group: Phosphorus bonded to four oxygen atoms
-Methyl Group: Carbon bonded to three hydrogens

An example of a lipid molecule that has a double-bonded CH molecule, thus creating a "kink."












Summary: 
This chapter was about the molecular structure of the different groups, both on a micro and macro scale.

http://www.youtube.com/watch?v=7k2KAfRsZ4Q

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1.02.28

A Tour of the Cell

What are the different types of microscopes? 
-Light Microscope (LM)
-Electron Microscope (EM)
-Scanning Electron Microscope (SEM)
-Transmission Electron Microscope (TEM) 

What's the difference between prokaryotic cells and eukaryotic?
Prokayrotes have no nucleus, and are essentially "simpler" than eukaryotic cells. They are also generally smaller than eukaryotes.

What are the different cell junctions and what are their purposes?
-Tight Junctions: prevent leakage
-Anchoring Junctions: fastens cells together into sheets. They are common in tissues that are subject to stress
-Gap Junctions: small gaps that allow molecules to flow through pores into other cells

The Facts:
-Only prokaryotes have capsules
-Cells were discovered in 1665 by Robert Hooke
-Chloroplasts consist of several different internal structures including the stroma, thylakoids and granum
-Flagellum and cilia have very similar structure and movement
-Animal cells do not have cell walls, plants do. While this means we have more motion, it also takes away any chance at photosynthesizing
 
Key Terms:
-Organelles: "Little Organs"
-Cellular Metabolism: Chemical activities that occur across the cell
-Nucleus: The "brain" of the cell, contains the DNA
-Nucleolus: A structure in the nucleus where the ribosomal RNA is synthesized
-Golgi Apparatus: Receives and modifies and ships out what's given by the ER
-Mitochondria: Carries out cellular respiration and converts things into chemical energy
-Lysosome: Digesting enzymes enclosed in a membranous sac
-Peroxisome: An organelle involved in metabolic functions
-Chloroplasts: Photosynthesizing organelles
-Endosymbiosis: A theory that mitochondria were formerly small prokaryotes that started living in larger cells

This is a cut-section diagram of an animal cell. As you can see, the organelles have a very set placement.

















Summary: 

This chapter was made to aquaint us with the structure of a cell, its funtions and the functions of its many organelles. First it establishes how we go about seeing cells: several different types of ultra-powerful microscopes that all serve to see different things.
Then it moves on to functions of the cells, which is primarily to exist and reproduce. Then the junctions exist to keep the cell alive and working properly. The organelles are extensive, and I have listed a few and their functions above. 

http://www.youtube.com/watch?v=Mszlckmc4Hw

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1.02.28

Biology: The Study of Life

What are the characteristics of life?
There are seven agreed upon characteristics of life, which can be summed up in the following:
1) Order: All living things demonstrate complex organization, structure, and complexity.
2) Regulation: The environment in which the living thing inhabits may change, but homeostasis still allows the organism to keep a constant inner state.
3) Growth and Development: The ability to pass on DNA and to use that DNA to grow into another organism from birth
4) Energy Processing: Organisms take in some form of energy, and can be processed to fuel the organism's functions
5) Response to the Environment: An organism's ability to react to a change in the environment.
6) Reproduction: Organisms are able to reproduce their own kind
7) Evolutionary Adaptation: An organism's ability to pass on it's genes and utilize them in a way that allows for the greatest evolutionary advantage.


What are the three accepted Domains in Classifying life?
In the art of classifying life, the broadest category we can place an organism in would be a domain, which recently made the cross from two to three.
1) Eukarya: Most of what we see is in this domain. Classified by having a nucleus, as well as other cellular structures.
2) Bacteria: Microscopic, prokaryotic and mostly unicellular.
3) Archaea: Recently discovered, also prokaryotic and for the most part, unicellular.


What is Natural Selection?
Natural selection as a concept isn't too difficult, the basic idea being is a given organism with a desireable trait, perhaps acquired through mutation or breeding, this trait will allot the creature with a greater chance of living, and thus allowing it to have offspring with the same traits. Those offspring then have a better chance of living, thus will reproduce themselves (see where this is going?).


The Facts:
-Science is a part of everyday life, such as in problem solving or testing out a new idea.
-While some organisms may not have all the characteristics of life, that doesn't necessarily mean they're not alive.
-Eukaryotic cells are divided into compartments and consist of many internal organelles and structures such as nuclei.
-DNA is crucial to life, as it not only ensures evolution, but also that lifeforms have a universal genetic structure.
-Earth itself is one giant structure, known as the biosphere, which supports all known life.

Some Key Terms:

-Biology: The scientific study of life
-Biosphere: Consists of all the environments on Earth
-Producers: Provide food for the typical ecosystem
-Consumers: Eats the plants and other animals
-Cell: Basic unit of life
-Genes: Units of inheritance
-Evolution: An explanation for the unity and diversity in life, that all things changed over time
-Natural Selection: A key mechanism for evolution, stating that the organisms with the more desirable traits will pass them on
-Hypothesis: a proposed explanation for a set of observations
-Theory: Supported by a large and growing body of evidence
  

Diagram:
This is a clear demonstration of the cycle of life from a biological system and the concept of energy transfer.










Summary: 

This chapter was very brief, but was a basic overview of systems of life, as well as classification. It touched on the layers of biological study, from the ecosystems to structures on a microscopic level- the study of life is a very broad topic. From there it talks about the classification of life which has three domains (see above) and further sub-branches (Kingdoms, Phylum, Class, Order, Family, Genus and Species).
It then moves on to talk about my personal hero, Charles Darwin, a man of great intelligence who originally came up with the theory of Natural Selection. The idea of Natural Selection is that the ones with the desirable traits will continue to live and have children, thus having offspring with the same traits, and eventually this leads to a change of the species as a whole. Or perhaps creating a new one.

Here is a sped-up version of evolution, courtesy of the Simpsons:

http://www.youtube.com/watch?v=faRlFsYmkeY

P.S. Darwin is my homeboy

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1.02.28