Biology (Semester I)

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Biology (Semester I) by Mind Map: Biology (Semester I)

1. Changing the above molecule by replacing one of the fatty acids with a phosphate group will create a phospholipid

2. Macromolecules

2.1. Monomers and Polymers

2.1.1. Monomers bind together to form polymers

2.1.2. These bind together using hydrogen bonds

2.1.3. Bonds can be formed through "dehydration synthesis", the act of removing water in order to enable a hydrogen bond

2.1.4. This act can be reversed through "hydrolysis", rendering no need for a hydrogen bond, thus breaking it apart

2.2. Carbohydrates

2.2.1. Monosaccharides Monosaccharides have one monomer Can be detected by Benedict's solution or a glucose test strip Glycogen stores energy for short bursts in muscle tissue Common monosaccharides are glucose and fructose (basically the same thing but still)

2.2.2. Disaccharides Disaccharides have two monomers A common disaccharide is sucrose, lactose, and maltose

2.2.3. Polysaccharides Polysaccharides can have thousands of monomers Commonly referred to as "starches" Can be detected by iodine

2.3. Nucleic Acids

2.3.1. DNA and RNA are composed of nucleic acids RNA is a single helix DNA is a double helix that creates proteins These two form our genetic makeup A virus contains one DNA or RNA strand with a protein shell

2.3.2. Nucleic acids are composed of nucleotides Aside from composing our DNA and RNA, nucleotides help with signaling cells and help with enzymatic reactions They are generally made up of a varying number of phosphates, sugars, and have a nitrogen base

2.4. Proteins

2.4.1. Amino acids are the essential building blocks of everything biological Different amino acids form different proteins, which are the main pieces of building things There are twenty different amino acids An amino acids carbon base allows it to bond with many other molecules, this variable is called the R-group This R-group determines what type of amino acid it will be

2.4.2. Enzymes are proteins that catalyze a substrate so it can change into a number of products An enzyme can only act when the substrate reaches the activation site The enzyme is unique to the chemical reaction. Depending on the chemical reaction you can have numerous enzymes that will only work with that substrate Sort of like a lock and key, once you have the "lock", the substrate at the activation site, the "key", the enzyme, can unlock the products These products do everything from produce essential things for the body to diffusing toxins You can denature an enzyme with "denaturation", which changes the shape of an enzyme, rendering it useless. This can can be done in a variety of methods. Enough heat (boiling is suffice) Chemical changes High concentration of other substance, low concentration of enzyme Salt

2.5. Lipids

2.5.1. Four types of lipids Steroids Any hormone created by a living thing fall under this category. Cholesterol Cholesterol has been classified as a waxy steroid of fat, however, it acts differently in some respects Although essential to our health, cholesterol is a terrible thing to have in access as it directly relates to cardiovascular disease Fatty Acids These make up triglyceride, one fatty acid attached to each of the three molecules in glycerol Phospholipids Phospholipids are extremely useful as they make up the membranes of our cells A pool of phospholipids will ALWAYS end up forming a lipid bilayer, because of the polar head and nonpolar tail

2.5.2. Stores energy Fats are packets of energy that are being stored for later use Energy from complex carbohydrates is broken down here and stored, also Unlike glycogen, this is only released when needed, while glycogen releases it for an extra boost

2.5.3. Saturated and unsaturated fats When a fat is plentiful with hydrogen, we call that saturated, and when it lacks hydrogen, it is unsaturated. Trans fat doesn't have anything to do with these A saturated fat is a solid, and an unsaturated fat is a liquid

3. Anatomy of a Cell

3.1. Common to most eukaryotes

3.1.1. Nucleus Nucleolus in the nucleus creates ribosomes that are sent to rough endoplasmic reticulum Contains DNA

3.1.2. Ribosomes Created in the nucleolus and sent to the rough endoplasmic reticulum

3.1.3. Endoplasmic Reticulum Rough ER Rough ER are dotted with ribosomes, and proteins synthesized on the ribosomes are sent through the ER Smooth ER These ER synthesize lipids, phospholipids, and steroids, making them a very essential part of a cell, especially in cells meant for hormone development. These lack ribosomes

3.1.4. Golgi Apparatus The Golgi apparatus puts the finishing touches on the macromolecules produced, then organizes then sends them out of the cell out to where they should go.

3.1.5. Mitochondria The mitochondria are the power sources of cells. They give them power to move, divide, and basically make it function. A mitochondrion combines sugars from carbohydrates and mixes it with oxygen to create ATP, the main energy source for a cell to power.

3.1.6. Cytoskeleton Pushes cell membrane and makes it secure

3.2. Plant Cell

3.2.1. Chloroplasts Turn solar energy, carbon dioxide, and water into glucose Main parts of cells that deal with photosynthesis in the plant

3.2.2. Cell Wall The cell wall is very rigid and is the main thing in keeping a plant cell together Found in prokaryotes as well

3.2.3. Vacuole Central vacuole takes up at least half of the cell and serves the purpose as basically a large lysosome The vacuole helps with intracelluar digestion Found in animal cells too, but smaller

3.3. Bacteria Cell

3.3.1. Flagellum Can also be found in animal cells, helps the cell move around

3.3.2. Pili They help attach bacteria to surfaces so they don't fall and can spread faster

3.3.3. Nucleoid Where the DNA is held

3.3.4. Plasma Membrane What holds the nucleoid together

3.3.5. Capsule The outer wall that holds together the cell and connects the pili to the cell

3.4. Animal Cell

3.4.1. Lysosomes These are transfer vesicles much like vacuoles to plant cells and carry certain things from the ER to the Golgi apparatus

4. Operating a Microscope

4.1. The Microscope

4.1.1. A light microscope uses a beam of light to project the image

4.1.2. An electron microscope utilizes a beam of electrons to project an image A scanning electron microscope is used to study cell surfaces A transmission electron microscope is used to study the inside of cells

4.1.3. A "micrograph" is a photograph taken via microscope

4.1.4. "Magnification" is the zoom setting, and "resolving power" measures clarity

4.2. How to operate the light microscope (similar microscopes that work with this method as a guideline include microscopes such as the dissecting microscope)

4.2.1. Step 1: Turn on light

4.2.2. Step 2: Place slide on stage

4.2.3. Step 3: Adjust to least magnification

4.2.4. Step 4: Adjust height of stage (coarse focus)

4.2.5. Step 5: Adjust resolving power of microscope (fine focus)

5. Nobel Prizes of 2012

5.1. Medicine and Physiology

5.1.1. The award was given jointly to Sir John B. Gordon and Shinya Yamanaka

5.1.2. They were awarded this for the discovery that there is a cell with the ability to reprogram mature cells back to the point to where they were pluripotent.

5.1.3. This advances stem cell research immensely and leaves behind the controversy from Embryonic Stem Cells

5.2. Physics

5.2.1. Was awarded to Serge Haroche and David J. Wineland.

5.2.2. They were awarded for "ground-breaking experimental methods that enable measuring and manipulation of individual quantum systems"

5.2.3. There were two different methods, one of them including trapping a photon in a box of mirrors and sending in things to manipulate it.

5.3. Chemistry

5.3.1. Robert J. Lefkowitz and Brian K Kobilka were awarded for their work on G-couple-protein receptors, which is a receptor that works with sensing light, flavour, and odour.

5.4. Literature

5.4.1. Novelist Mo Yan won the prize for his writing, including one of his best novels "Life and Death Are Wearing Me Out".

5.4.2. His writings have been described as being hallucinatory, historic, and other things.

5.5. World Peace

5.5.1. European Union is the receiver of this prize.

5.5.2. This means 500,000,000 million people actually win this prize and split a $1,200,000 prize.

5.5.3. Many think of trade and such when the Union is brought up, but since the Union was created, war as been at bay for a majority, which was its essential use.

5.6. Economics

6. Mitosis

6.1. Cell Cycle

6.1.1. Interphase Longest period a cell is in The cell can be developing in this stage, making new DNA molecules, or just working Phases G1 and G2 are used for growing while phase S synthesizes DNA

6.1.2. Mitosis A small amount of the time, after interphase, a cell will enter mitosis, which has five main phases. Prophase Metaphase Anaphase Telophase Cytokenesis

7. Meiosis

7.1. There are two different types of cells, diploid cells and haploid cells.

7.1.1. Diploid cells tell to be body cells. Body cells are also called somatic cells. Diploid cells hold 46 chromosomes (IN HUMANS) and generally go through mitosis.

7.1.2. Haploid cells are normally sex cells, and have 23 chromosomes (again, HUMANS), which is the same amount of PAIRS of chromosomes that diploid cells have, making diploid cells have twice as many as haploid cells

7.2. Seperated into two steps, with the same exact names.

7.3. One is labeled I and the other II

7.3.1. Homologous pairs are formed from chromatids that match their parents' traits. For example, the chromosome that has the trait for hair colour in your mother matches with the chromosome in your father. These pairs are ripped apart, leaving the end sex cell with hall the chromosome that came from the father and half from the mother. Sex chromosomes are different, depending on the sex chromosome the first sex cell has, you can be XX or XY. XX is a girl, and this pair is happy, however in XY, the X hates the stumpy little Y and they don't for a pair, changing DNA depending on whether the child would be a girl or a boy. Sometimes, DNA replication will mess up and create an extra or forget to make a certain chromosome. We get strange effects from this.

7.3.2. II is exactly like mitosis

8. The Cell Membrane and Transport

8.1. The Cell Membrane

8.1.1. The cell membrane is made of a bunch of phospholipids lined up to create a membrane The lipid molecules have a polar head and a non-polar tail. There are two layers of this with the heads pointing in opposite directions. This the the phospholipid bilayer. The bilayer is set up like this for "selective permeability", making sure only stuff the cell wants gets in. In between these two layers in floating cholesterol.

8.1.2. The membrane is littered with random channel proteins. Channel proteins use passive transport to allow water and oxygen in They are basically gaps where water can get in, and water knows to do it because the insides are hydrophilic.

8.2. Transport

8.2.1. Active Transport Most chemicals get into the cell using active transport. Active transport is normally used to battle diffusion and combat the concentration gradient. Almost any movement your cells do when transporting needs a handy little molecule of ATP to power it. Many channel proteins are more like gateways. You fill the inside of the protein up with your chemical, you then pay a small fee of ATP, and your chemical is allowed in, picking up stuff that needs to go out and then letting it out when the next customer comes. Cytosis Using vesicles (also made of phospholipids) helps gets things in and out of the cell.

8.2.2. Passive Transport Using passive transport does not require any energy! This is useful so water and oxygen can get in. This happens through nature wanting everything to be in equilibrium. When you drop a drop of water, most of the time it is going to spread as far out as possible because of diffusion. Osmosis is the diffusion of water, even if the water is a solution with something else.

9. Photosyntesis, Glycolysis, and Cellular Respiration

9.1. Photosynthesis

9.1.1. The first thing that happens is a photon hits the plant In the chlorophyll, the photon excites an electron through photoexcitation, causing the electron to break off, thus starting the process. Because of this, two things happen. The electron is taken around by the electron transport chain. The chlorophyll freaks out over the fact it lost an electron.

9.1.2. Photosynthesis utilizes three things and transforms it The three things are glucose, sunlight, and water Plants really dig the colours red and blue They make oxygen (which we breath) as a byproduct of this

9.2. Glycolysis

9.2.1. The general breaking down of sugars and is anaerobic, while the rest of cellular respiration is aerobic and requires oxygen Fermentation Fermentation takes different forms. There are mainly two types of fermentation, alcoholic fermentation, and lactic acid fermentation.

9.2.2. The process breaks up the glucose into two pieces of pyruvic acids

9.2.3. Glycolysis uses 2 ATP and some glucose to yield 4ATP, 2 pyruvates, and 2 NADH

9.3. Cellular Respiration

9.3.1. Cellular respiration is the set of metabolic reactions responsible for turning biochemical energy from nutrients into adenosine triphosphate. (ATP is REALLY IMPORTANT.)

9.3.2. Kreb's Cycle The Kreb's cycle takes the pyruvate molecules and reworks them into 2 more ATP molecules (per glucose molecule) It works by, first, oxygen binds with one of the carbons from the pyruvate moleclue, leaving behind something called acetyl coenzyme A with a by-product of carbon dioxide Some NAD+ is floating around, so it might as well be turned into two more molecules of NADH 1 glucose molecule can yield six NADH molecules and two FADH2 molecules Some energy is also created Citric acid is a by-product of this process, so it is also called the "Citric Acid Cycle"

9.3.3. Electron Transport Chain In the membrane of the mitochondria, electrons from the NADH are sent to power electron pumps. Protons from within the mitochondria are sent through the chain into an area with very little room to move around. The electrons diffuse through an enzyme called ATP synthase, where the electrons' energies are used to squish ATP together.

10. Genetics (DNA Coding)

10.1. DNA

10.1.1. DNA Structure The DNA helix is like a spiraled ladder. The sturdy backbone is made of sugars and phosphate groups. Linking across the bases are four different types of nucleiotides. Adenine, Thymine, Cytosine, and Guanine Adenine will ONLY link with Thymine, vice versa, and Cytosine with ONLY link with Guanine, vice versa.

10.1.2. DNA Replication DNA repliction occurs in the middle of interphase, during a part of it called the S phase. Enzymes unzip DNA like a zipper and nucleotides come in, binding with the now available RNA and they have to be identical because of how nucleotides bond.

10.1.3. Transcription When a cell is working, it generates protiens to make up more cells and do other functions, etc. In order to make proteins, a code has to be given. This code is the DNA. However, DNA cannot fit through nuclear pores, so a different process must occur. Enzymes unzip the section of DNA where proteins will need to be coded for. Then the strand of RNA is sent out of the nucleus and the DNA is repaired. Before the RNA is sent out, it is matched by a set of nucleotides, however anything that will be thymine is replaced with Uracil. This will happen twice to the strand.

10.1.4. Translation Once the RNA is out, it floats around until it finds one of the many ribosomes litered throughout the rough endoplasmic reticulum. Once it goes through a ribosome, groups of three nucleotides called "codons" are matched with an anticodon that has the nucleotides that match it on one end and an amino acid on the other. These amino acids link together with peptide bonds and form the protein that the DNA codes for.

11. Molecular Biology and DNA Manipulating Equipment

11.1. Micropipettes

11.1.1. Micropipettes are used to to take a small amount of fluid and get exact measurements with various substances

11.1.2. There are four different types of micropipettes, each with a different range of how much liquid they can hold. This is measured in microliters (μ)

11.2. Centrifuge

11.2.1. Mixtures are stored in microtubes when they need to be stored in small amounts.

11.2.2. These microtubes, if the substances they hold want to be seperated, are loaded into a centrifuge which spins them at high velocties and sperates the chemicals

11.2.3. This is a device often used in seperating blood cells from other things in blood like plasma, etc.

11.2.4. A centrifuge must be balanced, or it will destroy the motor and not work.

11.3. Gel Electrophorisis

11.3.1. If you need to identify the components of a substance using suspected chemicals, you can use gel electrophorisis.

11.3.2. Loading substances into small wells formed in gel and running electricity through it seperates the substances by polarity, size, and charge.

11.3.3. Is generally used for substance identification and DNA matching, seeing if DNA on a person matches someone else DNA or if parental DNA matches the child.

12. Inheritance of Genotypes and Phenotypes and Genetic Disorders

12.1. Traits

12.1.1. There are many traits that can be passed down from your parents. Depending on the trait, there will be traits that are either dominant or recessive. For example, brown eyes are a dominant eye colour while blue eyes are a recessive eye colour.

12.1.2. The phenotype, which is the technical name for a trait

12.1.3. Phenotypes are defined by your genotype.

12.2. Determining a Trait

12.2.1. Your parents will carry the trait themselves, and depending on where they stand on it you can take on that trait or an entirely different one.

12.2.2. If the genotype for your trait is homozygous, then it is either completely dominant or completely recessive.

12.2.3. If it is heterozygous, you have both a dominant and a recessive showing and thus the dominant trait will show.

12.2.4. To determine the probability of what trait a child could have, we use Punnet Squares. A Punnet Square is a visual method that helps us determine trait possibilities. Generally, you make a column and a row for each gene that affects the trait, and then put every possible combination in each column and row, then combine them in the squares to show if you are homozygous or heterozygous.

12.3. Mendelian Genetics

12.3.1. Gregor Mendel Ended up using pea plants, pea plants are good because they have a number of characteristics that are easily definable and can breed quickly. Mendel's Laws Law of Segregation Law of Independent Assortment

12.3.2. The name of the first generation is always called the P generation for the parents. They're children are the F1 generation and the grandparents are the F2 generation. Mendel noticed that sometimes when the P had a purple and a white flower, the F1 is also purple.

12.3.3. Mendel observed many different traits in the pea plants including pea colour, pod colour, rounded vs. wrinkled pod, etc. He observed that some traits, such as a rounded pea, would show up more than a different trait, such as a wrinkled pea. This is because some traits show dominance over other traits, which would be recessive. However, sometimes two traits will show codominance where the two traits both show up, such as in blood type when a type A and a type B give a type AB child. Incomplete dominance is where both traits are "there" such as a red and white flower making a pink flower. Contrasted with codominance, codominance would show red and white spolches of colour on the flower in the same situation.

12.4. Genetic Disorders

12.4.1. Sex-Linked Some disorders are located on certain sexes because they are located on the 23rd chromosome, also called the sex chromosome. These disorders are harder to predict, but males are very susceptable to these diseases. This is because women have two X chromsomes, allowing for any disorders to be easily corrected. Men do not have the second X, so they are more susceptable to the diasease not being corrected. In other words, Girls 1 Boys 0 You can still use a Punnet Square to determine the likelihood, however it isn't perfect. Sex-Linked Disorders Colour blindness is sex-linked and more susceptable with males. Others include hemophilia, Duchenne muscular dystrophy, and Turners syndrome. Lupus has been linked to mostly females, and while we don't have much information on how disorders are linked with certain genes, research in this is helping advance all areas of disorder research.

12.4.2. Dominant As long as there is there is one copy of the mutated gene, it will show up in the genotype as dominant. Huntington's Disease is a very infamous one because you do not show symptoms till you are at least 40 years of age, allowing you to pass it on easily. Anthropomorphism, or dwarfism, is a dominant condition as well.

12.4.3. Recessive In order for a recessive disorder to be passed, it must show two copies of the mutated gene or it will not be passed down. Sickle cell anemia, which is a one letter mistake in genetic code, is recessive and will only show up if it is a homozygous recessive. Other recessive disorders include cystic fibrosis Tay-Sachs disorder, and PKU. Nonharmful phenotypes are determined the same way, such as wet vs. dry earwax.

13. Evolution

13.1. Selection

13.1.1. Natural Selection Natural selection is the process of which an individual with a trait that favours its environment will be more suited to live in it and thus those who don't have said trait will perish. A simple example would be how if a mutation occured on an insect who lived in a grassy environment and was normally brown that made it green, it would be less susceptable to predators finding it and thus that trait will survive while others don't. When a species is divided and put in different environments, the environment will greatly differ the species from one another.

13.1.2. Sexual Selection

13.2. Evidence for Evolution

13.3. Primate and Human Evolution