Biology

Alkaliphiles

Base Addict (pH 9+)

Scientific Method

A series of steps followed to solve problems including observing, asking a question, doing background research, constructing a hypothesis, testing the hypothesis by doing an experiment, analyzing data and drawing conclusion and reporting results (whether the hypothesis was correct).

Golgi Apparatus (GA)

A set of flattened, membrane-bound sacs that serves as the packaging and distribution center of the cell

Duplication Mutation

Consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.

Antibodies

Proteins that make up the Immune System that fights off specific infection Specific targets (lock and key model) Found on the surface of WBCs

base

supports the microscope has the switch for light carry it in palm of hand while walking

Eukaryotic

"Eu"- New "Karyotic"- Nucleus Has a nuclei, mitochondria and other membrane bond organelles (large variety) Example: plant cells (square-like)- cell wall animal cells (circular-like)- no cell wall

Eubacteria

"Eu"- new Current forms of bacteria Constantly evolving due to reproduction rate Can be found everywhere

Lysosomes

"Lyso"- Break apart -Only in animal cells -Small spherical organelles that contain the cell's digestive enzymes -breakdown organic compounds

Animal Cells vs. Plant Cells

Animal Cells: Lysosomes and Centrioles Plant Cells: Cell Wall, Chloroplast, Central Vacuoles

Study of Cancer

Oncology "Onkos"- G. bulk, mass, or tumor "-logy"- G. study of Oncology is a branch of medicine that deals with tumors A medical professional who practices oncology is an oncologist

Arm

One of the places that is grasped to carry the microscope

Diaphragm

controls amount of light range from 1-5 5 being the most light

Viron

inactive form of virus (outside of host cell)

microscope

instrument used to enlarge the image of an object by using one or more lens

Virulent

extremely severe or harmful in its effects

Types of microscopes

simple, compound, stereoscopic, electron

Metabolism

the chemical process that occurs within a living organism in order to maintain life

Capsid

virus composed of a protein coat

Asking a question

Can the item I observed be of any significance to a problem (can it help cure it?)

C terminus

Carbon (loses hydroxide [OH])

Living things are primarily made up of...

Carbon- 18.5% Hydrogen- 9.5% Oxygen- 65%

Body Organization

Cells> Tissues> Organ> Organ System

Unregulated Cell Growth

Certain genes in DNA contain information to make specific proteins that control cell growth and division (p53). If there is a mutation within one of these genes, disruption of the cell cycle could occur Oncogene: a gene that when mutated can cause cancer

Nonsense Mutation

Change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.

Insertion Mutation

Changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly

Deletion Mutation

Changes the number of DNA bases in a gene by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gne, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s)

Substrate

Chemical of interest that is being modified

Psychrophiles

Cold Addict

Periodic Table

Columns have the same number of valence electrons excluding Helium which only has 2 valence electrons while the others in that column have 8, this is because the outermost ring is completer Rows have an increasing atomic number (by one) going across each period Elements differ by the number of protons their atoms contain Mass Number (Atomic Weight)- amount of all the protons and neutrons combined Atomic Number- The number of protons in an atom Electrical Charge- The charge of the nucleus Elemental Symbol- Symbol of the atom

Acid

Compound that form hydrogen ions (H+) when dissolved in water -pH < 7

Peptide Bonds

Covalent bonds the form between the C terminus and N terminus of amino acids

X-rays, CT scanning, MRI scanning, Ultrasound (and other radiological technologies)

Creates 3-D pictures of the inside of the body

Leading/ Lagging Strand DNA

DNA polymerase can only synthesis DNA in a 5' (phosphate) to 3' (hydroxyl) direction Leading strand: DNA is synthesized continuously because new strand is being made in 5' to 3' direction Lagging strand: DNA is synthesized discontinuously to form short pieces called Okazaki fragments Referring to the picture: Centro-carbon (does not count)

DNA

Deoxyribonucleic Acid -Composed of 1 deoxyribose sugar, phosphate, and a nitrogenous base -Contains hereditary material -Contains information for our genes which code for our proteins (traits) -Every cell has the same DNA and contains over 3 billion base pairs and extends over 6 feet long -Negatively charged at a neutral pH due to its phosphate backbone -Migrates towards the positively charged electrode -Double Helix (Stranded) -Bases of one strand form hydrogen bonds with its "partner" on the other strand -Complementary Base Pairing: Adenine with Thymine and Guanine with Cytosine -Formed through dehydration synthesis Organic compound-Nucleic Acid Monomers-Nucleotides Discovered by Rosalind Franklin (photo 51), Maurice Wilkins, Francis Crick, and James Watson

Cancer Treatment

Dependent on age of patient, stage of cancer, cancer/tumor type, location/ areas affected and several other variables Surgery: -Removal of affected area/ tumor -Ex: Mastectomy (surgical removal of one or both breasts to avoid spread of tumor Chemotherapy: - "Cheme": Chemicals - Most anticancer drugs interfere with the cell cycle, by attempting to slow down the uncontrolled growth (they also interfere with healthy cells Radiotherapy: -"Radio": Radiation -Used as palliative treatment (where cure is not possible and the aim is for symptom relief) or as therapeutic treatment (where therapy has survival benefit and it can be curative)

Concentration Gradient

Difference in distribution of substances across space -Substances move from high to low concentration

Dos and Don'ts (Microscope)

Do: Focus under low power first before turning to a higher power Carry the microscope with two hands (one holding the arm, the other supporting the base with the cord) Don't: Focus under high or medium power with the coarse adjustment knob

Enzymes

Ends in "ASE" (breakdown foods during digestion) -Helps get chemical reactions started by speeding them up and allows metabolisms to move at a rate that supports life (lowers activation energy to increase rate of reaction) -Substrate specific: only acts on certain substances (substrates)> Lock/Key model (as demonstrated by picture) -Requires certain pH and Temperature: acidic pH (stomach)+ normal body temperature

Lens

Enlarges the image by bending light toward your eye

Protease

Enzyme that breaks down proteins

Amylase

Enzyme that breaks down starch

Lactase

Enzyme to break down lactose

Fermentation

Fermentation: the chemical breakdown of a substance by bacteria, yeasts, or other microorganisms, typically involving effervescence (bubbles in liquid/fizzing) and the giving off of heat. -Lactic Acid Fermentation: fermentation in which lactic acid is produced from carbohydrate materials (as lactose in whey) by the action of any of various organisms but especially the lactic acid bacteria -Lactic Acid: (Mostly while working out) causes pain or a burning sensation in the part of the body that does not receive enough oxygen -Alcoholic Fermentation: a process in which some sugars (as glucose) are converted into alcohol and carbon dioxide by the action of various yeasts, molds, or bacteria on carbohydrate materials (as dough or sugar solutions) some of which do not themselves undergo fermentation but can be hydrolyzed into fermentable substances (as in the production of alcohol and alcoholic beverages)

Cell Wall

Found in Prokaryotes and Plant Cells Eukaryotes; not in Animal Cells Provides protection and support Supports and maintain the shape of the plant cell Connects the cell with adjacent cells Acts as a pressure vessel to prevent over-expansion Allows bacteria to live in various environments

Stereoscope

Gives a 3D view of an object Used for items that are too thick to allow light to pass through

Dehydration Synthesis

Goes from monomers to polymers by linking monomers through covalent bond formation -Releases Water to form peptide bonds (H+ + HO- > H2O)

Pie Chart

Graph that represents parts of data that make up a whole

Experimental Group

Group being experimented or tested on

Water and Its Properties

H2O -Makes up 70-95% of living cells -Necessary for all biochemical reactions that occur in the body -A habitat for many organisms -It is beneficial to live in because it stores heat longer and heats slower than other substances (not as much temperature fluctuation as air) -Adhesion: -An attraction between molecules of different substances -Causes capillary action -The movement of water in small tubes due to water being attracted to the walls of the tube (adhesion) -Ex: water moving up a paper towel -Surface Tension -A measure of how difficult it is to stretch or break the surface of a liquid (Ex: water molecules do not want to part and let anything through) -Cohesion -An attraction between substances of the same kind (water is attracted to water) -Causes surface tension on a body of water -Water molecules are polar (charged) and form hydrogen bonds with one another -Universal Solvent -Ionic compounds and polar molecules dissolve best in water due to the attraction between opposite charges (Like dissolves like : Polar dissolves polar)

Haploid vs. Diploid

Haploid- used to describe when a cell has one set of chromosomes - 23 chromosomes - gametes (sperm and egg) Diploid- used to describe when a cell same size, same shape, same genes has: - two full sets of chromosomes (pairs of 23 each) - somatic cells are diploids ( parents have the same genes but different versions)

How (Normal Karyotypes) Differ from HeLa karyotype

HeLa karyotype - 0-4 autosomes (should have 2) chromatids - Clonal marker (does not have any markers) Cancer cells replication is not controlled—it mutates—therefore, replication has more DNA— the more DNA—the more chromotids

HeLa Cells Vs. Normal Human Cells

HeLa: Immortal (can grow apart/outside of the body), Cancerous, 30+ additional chromosomes (76+) mutated and rearranges Normal Human Cells: Mortal (dies apart/ outside of the body), Not Cancerous, 23 pairs (46 chromosomes) not mutated or rearranged Same: Somatic

Thermophiles

Heat addict

HeLa Cells

Henrietta Lacks' cells (first two letters of her first and last name) -Human cervical cancer cells- first immortal cell line in history -Human Papiloma Virus 18 caused HeLa cells to become cancerous -This cancer is acquired because one would need to contract and have persistent HPV 18/ HPV 16 for at least ten years before getting cancer Medical Advancements Achieved with HeLa Cells -Polio Vaccine -Chemotherapy -Cloning -Gene Mapping -IVF (In Vitro Fertilization) -Studying: Salmonella, HIV (Human Immunodeficiency Virus), Tuberculosis, Nanotechnology discovered, Enzymes that prevent cells from dying

Ethical Issues Surrounding HeLa

Henrietta Lacks' cells were taken without her knowledge/consent -Used for science -Family was broke and did not know what happened (others profited)

Nose piece

Holds the high and low power objective lenses; can be rotated to change magnification

Stage Clips

Holds the slide in place

Gel Electrophoresis

How it Works: 1. Agarose gel gets submersed in a tank containing a salt solution that conducts electricity 2. DNA samples are then loaded in slots made in the agarose gel 3. Tracking die (Ethium Bromide) is then added to the DNA samples in order to track DNA migration 4. An electric current is passed through the gel that has a positive charge and the other end of the gel has a negative charge. (The movement of charged molecules through the gel is called migration [Molecules migrate towards the opposite charge]). What it is Used For: -Commonly used in labs to separate charged molecules like DNA, RNA, and protein according to their size -In paternity testing, restriction enzymes are used to cut DNA at specific sites -Samples of DNA from the mother, offspring, and possible fathers are compared

pH

Importance to Biochemistry: -Affects the structure and activity of macromolecules in the body system -Regulation is a major part of homeostasis Scale ranges from 0-14

Control Group

In an experiment, the group that is not exposed to the treatment; contrasts with the experimental group and serves as a comparison for evaluating the effect of the treatment.

"Bad" Bacteria

In human hosts, certain types of bacteria can cause many illnesses: -Tetanus -Pneumonia -Syphilis -Tuberculosis As long as the the bacteria is not antibiotic resistant, they can be treated with antibiotics Antiseptics, sterilization and disinfectants can help prevent contamination and risk of infection from bacteria

Stable Atoms

In order for an atom to be balanced/ neutral/ stable the number protons and electrons have to be the same (it would not have a charge)

Laws Regarding Informed Consent and Human Tissue Research

Informed Consent Law- individual has to be informed of and consent to a procedure/ treatment suggested by a doctor "Common Rule" Genetic Privacy Act and Commentary Human Tissue Act of 2004

Inherited vs. Acquired Mutations

Inherited: passed from antecedent to offspring through egg or sperm cells -These mutations are in every cell of the body -Only 10-15% of all cancers are inherited (i.e. breast cancer [BRCA1, BRCA2 genes] Acquired: -At some point in a person's life in one cell. Once the ancestral cell divides, it is passed on to new cells -Somatic mutations are not present in egg or sperm cells -85-90% of all cancers are acquired (i.e. lung cancer, melanoma, stomach cancer) Carcinogen: any cancer causing agent that can mutate DNA

Nucleus

Internal structure that houses the cell's DNA Controls most of the cell's functions Location in which ribosomes and RNA are made

Reasearch

Investigate if anyone has tried to use what you observed to try an help the proton you are trying to help or solve

Atomic Charge Interactions

Like charges (+,+) (-,-) repel Opposite charges (+,-) attract

Hypotonic Solution

Lowly concentrated with solute -a solution that causes water to move into the cell

Medium-Power Objective Lens

Magnifies 10 times

Lower-Power Objective Lens

Magnifies 4 times

High-Power Objective Lens

Magnifies 40 times

Eyepiece (Ocular Lens)

Magnifies the image, usually by 10 times

Pathogenic Bacteria

Make humans sick by excreting a toxin

Antibiotics

"Anti"- Against "Bio"- Life Selective poisons that seek to kill/ hamper the growth of bacteria Bacteria-specific Must be taken to completion to prevent reinfection

Archaebacteria

"Archae"- old/ ancient Oldest known organisms Beginning of life on Earth?- Chemosynthesis Live in extreme environment (Heat, extreme cold, extremely acidic, etc.) (also been called Extremophiles [extreme environment])

Prokaryotic

"Pro"- Before "Karyotic"- Nucleus -Lacks a nucleus, mitochondria and other membrane bound organelles -Example: Bacteria - Unicellular - Everything floats around inside the cell - 1 strand of floating DNA - Can live in various environments

"Good" Bacteria- Probiotics

"Pro"- for "Bio"- life Probiotics- Good bacteria Has health benefits to the host: -Aids in digestion -Produces vitamins -Keeps the organism healthy Ex: Bacteria in digestive system (lactobacillus) Converts milk to lactic acid (makes it hard for bad bacteria to survive)

Hydrolysis

(Water split) - Adding water ( H2O) to break apart polymers

CODIS site

-DNA matching system -Certain bonds within a chromosome have repeating bases -1 out of 10 people have the same codons within these parts -DNA from crimes help identify perp if they have the same codons -Need multitudes of test to insure suspect is perp

Gene

-DNA segment sequences that code for many different traits (A group of codons that code for a specific protein). -The protein determines a specific trait -DNA has thousands of genes (There are an estimated 20,000-25,000 genes in the human genome -The average gene is 10,000-15,000 base pairs long

Specialized Cells

-Differentiated: designed for a specific function -Are not sufficient to survive by themselves -Must live in conjunction with the rest of the organism -Some organelles may be present in excess and some may be missing all together

NADH and FADH2

-Electron carriers that serve as temporary forms of energy -Donate and Accept Electrons to drive the electron transport chain -Energized forms of NAD and FADH

Cytoplasm

-Fluid that contains the cell's organelles -Everything inside the cell membrane, but outside of the nucleus

Antibiotic Resistance

-Some bacteria species are able to survive after prolonged exposure to one or more antibiotics -Ex. Methicillin-Resistant Staphylococcus Aureus (MRSA) -Bacteria builds up resistance because they reproduce rapidly, therefore they evolve rapidly - Things that speed up resistance: - Not completing antibiotic prescriptions - Mutations - Over-use of antibotics

Nuclear Membrane

-Surrounds the nucleus -Contains nuclear pores that allow specific materials to pass into the cytoplasm

NAD+ & FADH

-Temporary forms of energy that are used to make ATP -Low energy forms (missing its electrons and release energy)

Interphase

-The cell appears to be "resting" -Broken into 3 parts: -First Growth Phase (G1) -The cell grows quickly in size -Organelles duplicate -Synthesis Phase (S) -DNA is copied (DNA Replication) -Each chromosome consists of two chromosotids attaches at a centramere -Second Growth Phase (G2) -Cell grows more -Cell prepares to divide

Cell Division in Eukaryotes

-The organelles most directly involved in cell division include: -Animal Cells: nucleus, centrioles, cell membrane -Plant Cells: nucleus, golgi apparatus, cell wall -The cell cycle is strictly regulated by thousands of proteins and enzymes to ensure each step is correct -Normal cells do not divide forever, they receive signals (growth factors from their surroundings that tell them when to stop dividing) Mitosis and Meiosis -Mitosis: - Used for unicellular organisms to reproduce or to produce somatic cells in multicellular organisms - Results in an exact number of original cells - Same number of chromosomes (diploid cells) -Divides for growth, development, and specialization -Meiosis: - Reproduces chromosome number by one-half in new cells (haploid cells) - Produces gametes

Cell Cylce

-The repeating set of events that make up the life cycle of the cell -Cells alternate between a division stage and a "resting" stage -The cycle can be broken down into: -Interphase -M phase (Mitotic) -Prophase -Metaphase -Anaphase -Telophase -Cytokinesis

Binary Fission

-The way bacteria reproduce -Asexual reproduction: process of making a new organism without requiring a mate -The circular strand of DNA undergoes replication and the cytoplasm divides -- dividing the cell -Produces two identical bacteria

Vaccines

-White blood cells (WBC) wake antibodies in response -Used to build your body's immune system memory by injecting a weak or dead virus ( dead bacteria, inactive virus, weakened bacteria/virus) - This triggers the body to make antibodies/ T-cells against that particular virus -Discovered by Edward Jenner in 1796 - Used cow pox virus to immunize against small pox virus (very similar) - Latin: "vacca"- cow

Stem Cell

-a class of undifferentiated cells that are able to differentiate into specialized cell types -they become the type of cell they are surrounded by Controversy -Embryonic Stem Cells: Derived from a four-or-five-day old embryo that is in the blastocyst phase of development Blastocyst: Development: -1. Male sperm fertilizes female egg to form a single cell (zygote) -2. Zygote undergoes a series of divisions -3. After 4-6 days, the mass of cells is called the blastocyst Make up: -Embryoblast -Inner cell mass -Trophoblast -Outer cell mass Research Breakthrough (IPS) -Most of adults' cells are multipotent Multipotent: Can only become type of cell from tissue it was originated -Induced-pluripotent stem cells solved the controversy -Type of pluripotent stem cells that are generated directly from adult stem cells -Pluripotent -Can make all the different types of cells in the body when placed in specific tissue

Muscles

-a consequence of contraction of these cells results in movement (subtypes: smooth ,striated, cardiac) Skeletal (Striated) Muscle: -Voluntary Striated Multinucleate -Striated: Stripped-Multinuclei -Voluntary besides for fight or flight -Voluntary: Can control -Involuntary: Cannot control Smooth Muscle -Involuntary muscle -Lacks striation -Lines blood vessel and organ walls: found in the stomach, small intestine, lungs, blood vessel walls, large intestine, bladder, uterus, eye, esophagus, liver, gallbladder, common bile duct, ascending colon, appendix, spleen, pancreas, transverse colon, descending calon, sigmoid colon, and rectum Cardiac Muscle -Heart -Involuntary muscle, found only inn the heart -Groups of cardiac muscle contract in unison -Intercalated discs (thick black lines in picture) is where one cell meets another

p53

1) DNA damage 2) Cell cycle abnormalities 3) Hypoxia Normal: 4)p53 5) Cell cycle arrest 6) DNA repair 7) Cell cycle restarts or 4) Apoptosis (programmed cell death) (When cellular damages occurs, p53 arrests the cell cycle until the damage is repaired. If damage cannot be repaired apoptosis) Mutated: 4) Cell cycle continues (Mutated p53 does not arrest the cell cycle. The damaged cell continues to divide, which may result in cancer)

Characteristics of Life

1. Made of one or more cells 2. Growth and Development 3. Reproduction 4. Obtaining and Using Energy 5. Response to Environment (homeostasis) 6. Adaptation to Environment

Macromolecules of Life

1. Needed for cells to function 2. Formed by biochemical reactions of living things Organic Compounds and their Monomers: -Must contain carbon (carbon is covalently bonded to other elements [i.e.H,O]) a. Lipids (fats) > Fatty Acid Tail and Glycerol Head (9 calories/1 gram) b. Proteins > Amino Acids (4 calories/1 gram) c. Carbohydrates > Simple sugars (4 calories/1 gram) d. Nucleic Acids > Nucleotides (Not found in foods)

Lytic Cell

1. Viral genome enters host cell 2. Viral genome is replicated and transcribed 3. Viral RNAs are transcribed and proteins processed 4. Particles assemble inside host, then burst or bud to exterior

Before steps in using a microscope

1. carry microscope to your lab table using two hands. Do not place it on the edge of table 2.Plug in microscope. Turn on light source 3. Put microscope on lowest power 4. Open diaphragm to the widest opening 5. Place a prepared slide on the stage and secure with stage clips

After steps in using a microscope

1. put the microscope on the lowest power 2. lower the stage 3. Remove the slide 4. Turn off the light

During steps of using a microscope

1. raise stage and slide close to the objective lens 2. Focus with coarse adjustment knob. Then focus with fine adjustment to obtain a clear image 3. Once clear, move to medium power. Only use fine focus on medium power 4. Once clear, move to high power. Only use fine focus on high power

Equilibrium

A condition in which the concentration of a substance is equal throughout a space How to Calculate: -Add the item percentage in the solution with the . item percentage in the solute and divide by two: -The answer is the answer for both the solvent and solute (they are the same). The same step is then repeated for any other items. In the end, the items in both should be equal and add up to 100%

Chemical Equation

A representation of a chemical reaction that uses symbols to show the relationship between the reactants and the products Must have the same number of atoms of an element before and after a reaction

Monomer

A small unit that can join together with other small units to form polymers Single, repeating subunits (building blocks)

Vesicle

A small, membrane bound sac for transporting substances

Tumors

A swelling in the body caused by abnormal proliferation (rapid increase in numbers) of tissue Types: -Benign: Harmless/Localized (ex. wart) -Malignant: Dangerous/Can Metastasize -Metastasis: spreading of cancerous cells from one organ to another

Homeostasis

A tendency to maintain a balanced or constant internal state; the regulation of any aspect of body chemistry, such as blood glucose, around a particular level (especially with temperature: no matter the weather, our body has to keep a certain temperature because it has maintain a constant environment despite changes in the external environment, therefore living organisms have to release heat) Regulation of different levels to maintain a constant balance pH, temperature, hydration, and ions (iron, sodium, and potassium) are maintained by transport across the cell membrane

Nonpolar Covalent Bonds

A type of covalent bond in which electrons are shared so they can become "full" Not charged

ATP

Adenosine Triphosphate (Diphosphate is when uncharged [ADP]) -Nucleic Acid -The molecule that can store and transport the energy needed for survival -Contains one high energy bond -Only lasts a few seconds (Immediate Energy) -ATP Hydrolysis -ATP-P=ADP -breaking down the bond between the last two phosphates is how the energy is released from ATP ADP+P=ATP -ATP Synthase -An enzyme that performs this conversion Main source of energy in all living things 1 base- adenine base 1 sugar- ribose 3 phosphates Comes from breaking down chemical energy (carbohydrates) Formed in the mitochondria- through cellular respiration -ADP returns to the mitochondria to be rebuilt into ATP (storing energy again) the process of cellular respiration

Human Tissue Act of 2004

An act of the UK parliament applying to England, Northern Ireland and Wales. It consolidated previous legislation and created the Human Tissue Authority to "regulate the removal, storage, use and disposal of human bodies, organs and tissue.

Matter

Anything that has mass and volume (takes up space)

Methods of Cancer Diagnosis

Biopsy Endoscopy X-ray, CT scanning, MRI scanning, Ultrasound (and other radiological technologies) Tumor Markers Screening

Tumor Markers Screening

Blood or urine test to screen for certain molecules which can sometimes indicate the suspicion of certain types of tumors However, elevated levels do not necessarily mean cancer is present

Covalent Bonds

Bonds created by sharing electrons with other atoms.

Conclude

Bring to an end of the experiment where the data is processed and the experiment is wrapped up

Mitochondria

Powerhouse of the cell Harvests energy from organic compounds to make ATP (energy) Cells with high energy demands (like muscles) contain more mitochondria

Apoptosis

Programmed cell death -After a certain number of divisions, body cells are naturally signaled to "commit suicide" (Triggered by telomeres that shortens with every cell division. Once telomeres reach a certain length, a signal is released to trigger apoptosis)

Bacteria

Prokaryotes -Reproduce asexually by replicating their contents and splitting in half -Microscopic, living organisms -Among the oldest living organisms on Earth -Several Types- Some are harmful and others provide benefits necessary for life -Can be killed with antibiotics

Nucleolus

Prominent structure in the nucleus Produces Ribosomes

Endotoxin

Protein toxin found on outside of the membrane

N terminus

Nitrogen (loses hydrogen [H])

Nuetron

No charge, found in nucleus

Repeat Expansion Mutation

Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. This expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.

Total Magnifaction

Objective lens times Ocular lens

Ionic Bonds

One atom completely gives up extra electrons to another so they are both "full" There is no covalent bonding

Paramecium

One-celled organism that lives in ponds and other bodies of water

Experiment

Orderly procedure carried out with the goal of verifying (establishing) the validity (logically sound) of a hypothesis A good experimental design increases the validity of results A well designed experiment should include: -Separate group of test subjects -One independent variable -One dependent variable -Controlled environment

Autotrophs

Organism capable of creating their own food Serve as the basis of the food chain 2 Types -Chemoautotrophs -An organism, typically a bacterium, that derives energy from the oxidation of inorganic compounds. -Photoautotrophs -Only about 1% of the sun's energy is captured by autotrophs to use in photosynthesis Photosynthesis: -Organisms that can accomplish this include: -Plants -Algae -Some bacteria -Occurs in the chloroplasts of plants and algae in and the cell membrane of prokaryotes -Dependent on temperature -Photosynthesis occurs at an optimal temperature -When it becomes too hot or cold: 1. Transpiration -Process by which water moves up a plant due to water being "lost" at the leaves 2. Enzyme active is affected -Dependent on water -Reactant- photosynthesis increases as water increases up to a certain point -Absorbed through roots (to carry nutrients from the soil), travels along the plant, and is evaporated from leaf surfaces -Transpiration -Dependent on Carbon dioxide concentration -Reactant- increases as concentration increases up to a certain point -Dependent on Sunlight -Photosynthesis increases as light increases until all the pigment are being used (more light = more energy = more bonds = more glucose) -Uses sunlight to make organic compounds (Glucose) from Carbon dioxide and addition carbon compounds -Rubisco is the enzyme that catalyzes the first step of photosynthesis -Consists of two Photosystems (a collection of protein complexes embedded in thylakoid membrane that consists of clusters of chlorophyll and other pigment molecules): -Light Dependent Reaction (Stage I) -Takes place in thylakoids -Requires sunlight (Composed of several colors) -Contains two main pigments (Light absorbing molecule whose main goal is to absorb light energy and use that energy to power chemical reactions. Whatever color is not absorbed are then reflected. The color that is reflected is then the color of that object) -Chlorophyll -The primary pigment involved in photosynthesis -Main source of light absorption in photoautotrophs -Absorbs mostly reds and blues and reflects greens and yellows (the optimal colors of light for photosynthesis are red and blue) -Carotenoids -Accessory pigments that absorb different wavelengths than chlorophyll -Reflects mostly reds, oranges and yellows -Chlorophyll absorbs light energy -Light energy excites electrons -High energy electrons travel down an electron transport chain that powers the conversion -Responsible for autumn leaf colors (because there are less hours of sunlight, chlorophyll has no job, and therefore breaks down) -Energy is captured from sunlight. Light energy and water is converted into temporary chemical energy (ATP & NADPH) -Water molecules changes to oxygen gas -ADP (uncharged) converts to ATP (charged) -NADP (uncharged) converts to NADPH (charged) -Light Independent Reaction (Stage II) -a.k.a: The Dark Reaction, Calvin Cycle, and Carbon Reactions -Takes place in the stroma -Does not require sunlight -Uses the chemical energy (ATP & NADPH) from Stage I to convert atmospheric Carbon Dioxide into Glucose -Enzymes catalyze the splitting of water molecule to form oxygen gas -As water is split, hydrogen ions are removed from the molecules and are sent to the stroma. A concentration gradient builds up, which eventually causes the spinning of ATP synthase -Uses Carbon dioxide, ATP and NADPH from Stage 1 to create glucose. ADP and NADP travel back to thylakoid to recharge -Chemical energy created in Stage 1 is used to create organic compounds -Photosynthesis Chemical Reaction: 6 Water + 6 Carbon Dioxide yields(Activation Energy [Sunlight Provides This]) 6 Oxygen + 2 Glucose -Importance: -Beginning of food chain on land and in shallow water -Carbon Dioxide Reduction -Greenhouse goes lead to global warming -Oxygen Production -Necessary for Aerobic Cellular Respiration Glucose: -Carbohydrate -Contains 5 high energy bonds -Can be placed together to generate polysaccharides (starch) which are capable of long term energy storgae Referring to picture: Calvin Cycle 1. Light 2. e- 3. Water 4. O2 + H+ 5. Photosystem II 6. H+ 7. Chlorophyll 8. NADP 9. NADPH 10. ADP 11. ATP 12. Sugar 13. Carbon fixation 14. Carbon Dioxide 15. ATPase 16. Thylakoid Membrane 17. Photosystem I

Chromosomes

Parts of a Chromosome: Chromotid- 1/2 of a chromosome Chromosome- 2 chromotids; DNA and proteins coiled up together -Specific proteins are called histones Centromere- attached point of sister chromotid DNA Packaging into Chromosomes 1. DNA winds around histone proteins (glue balls) 2. The chain winds around itself several times (condensing) 3. The completed structure of tightly wound DNA is called a chromosome Types of Chromosomes: Autosomes: chromosomes that are not directly involved in determining the gender of offspring human (somatic cells contain 22 pairs of autosomes) Sex chromosomes: one pair of the 23 pairs of chromosomes- determines the gender of offspring -Also called the X and Y chromosomes -Females: XX -Males: XY Chromosome Abnormalities and Ways of Detecting Genetic Abnormalities: If a person has more or less than 46 chromosomes, it can create a variety of problems. A karyotypes can detect these abnormalities because it is a photo of the chromosomes in a cell that arranges them by size in pairs -Amniocentesis: A process used by doctors to extract amniotic fluid from a pregnant mother. This technique is used to retrieve the cells used in creating a karyotype of an unborn child. An ultrasound is taken first to avoid injury to fetus. Controversial because some might abort the baby if it has a genetic disorder. It may also cause the amniotic sac to burst.

Smooth Endoplasmic Reticulum (SER)

Performs various functions including making lipids and breaking down substances Does not have attached ribosomes

Lipids

Provide long term energy storage Structural component of different parts of living things Ex: phospholipids in the cell membrane (phospholipid bilayer) Not soluble in water (Cannot mix with water evenly. Instead it forms little globules) Phospholipids: -Key role in the structure and function of the cell membrane Ex: Waxes that coat the leaves of a plant Glycerol head (hydrophilic)- polar Fatty acid tail (hydrophobic)- nonpolar Theses would be considered the monomers of most lipids Steroids: Ex: Cholesterol -Helps insulate nerve cells so they conduct impulses quickly -Too much can lead to arterial plaque or even heart disease Ex: Hormones i.e.: Testosterone is responsible for creating male characteristics i.e.: Cortisone is an anti-itch cream Fats: made of fatty acids Saturated vs. Unsaturated -Less bonds means easier for the body to break down and therefore healthier Unsaturated: -Healthy (liquid at room temperature) -Some of the carbons are double bonded (not full) Ex: olive oil, vegetable oil, fish oil Saturated: -Unhealthy (solid at room temperature) -All of the carbons are bonded to four atoms Ex: butter, lard, bacon grease

Mutations in DNA

Provides great opportunity for genetic variation in order to be better suited for the environment Types of Mutation: -Missense Mutation -Nonsense Mutation -Insertion -Deletion -Duplication -Frameshift mutation -Repeat expansion

Elements

Pure substances that are made up of one kind of atom

Buffering

Purposely adding one substance to another to adjust the pH towards neutral

Rough Endoplasmic Reticulum (RER)

RER and GB go hand in hand Has attached ribosomes Helps transport the proteins that are made by its attached ribosomes Portion of the ER that contains the protein, pinches off to form vesicles

DNA's code

Read in triplets DNA: CCC, GAT RNA: GGG, CUA Codon: a segment of DNA (3 nucleotide) that specifies an amino acid - The important information in DNA is in the bases (A,T,C,G). When a codon is read only base sequence matters

Biopsy

Removal of tissue for testing

Sexual Selection

Reproductive success, the ability to create offspring and pass on genes, means everything, even more important than survival A major struggle exists between males of a species for possession of the female. Female's choice. Fighting -Some males will fight, even to the death -Stags have antlers to defend itself Courtship -Elaborate displays/behaviors -Peacock has an elaborate tail to attract peahen Sexual Dimorphism -Males look different than females; often the physical difference is hindering to male survival -Lion has mane to protect itself during fights Cause of sexual selection occur when males or females of any species differ in color, structure, or habitat

RNA

Ribonucleic Acid -Ribonucleic Acid > Sugar -Intermediate molecules that allows for DNA to direct the synthesis of proteins DNA > RNA > Proteins -Single stranded -Complementary Base Pairing: Adenine with Uracil and Guanine with Cytosine

Isotonic Solution

Same Concentration -a solution that causes water to move in and out of the cell at the same rate

N

Symbol used to represent one set of chromosomes In humans, haploid number is N or 23; diploid number is 2N or 46 In chimps; N or 24 (telomeres and centromeres were fused for humans' N=23)proven in 2005 Walrus: N=32 Field Horsetail: N=216

Field of View

The area visible through the microscope eyepiece Highest Power-less you can see Low Power-more you can see When under microscope the image is upside down and backwards

Genetics

The branch of biology that focuses on heredity -Heredity: passing of traits from parents to offspring Gregor Mendel -The father of genetics -First to develop rules for breeding and patterns of inheritance -Austrian monk who experimented with garden pea plants for breeding(mating) -Reason for using pea plants -Cheap -Grow quickly (Can observe several generations within short time periods -Easy to mate -Can be cross-pollinated or self pollinated Possess seven, easily distinguishable, single-gene traits (there are two physical expressions of each trait) -Theory of Heredity -There are different versions of genes. These different versions account for variations in characteristics -Allele: the different versions of a gene -Flower color (purple or white) -Flower position (end or middle of branch) -Plant height (tall or short) -Pod color (green or yellow) -Seed color (green or yellow) -Pod shape (smooth or wrinkled) -Seed shape (smooth or wrinkled) -Some traits were always expressed (dominate), and others were only expressed sometimes (recessive) -For each inherited trait, an organism inherits two alleles, one from each parent -When gametes are formed, the alleles for each gene in an individual separate independently of one another. Thus, gametes carry only one allele for each inherited trait. When gametes unite during fertilization, each gamete contributes one allele Dihybrid Cross -Demonstrate the Law of Independent Assortment. During meiosis, alleles separate independently of one another. Each gamete carries one allele for each trait -Tracks the inheritance of two traits at one time -Genes are located on separate chromosomes 1. Determine the genotype for both parents 2. Determine the four possible gamete combinations for each parent -Use FOIL method (First, Outer, Inner, Last) 3. Set up a dihybrid cross (4 x 4) 4. List the possible gametes for one parent across the top and the other parent down the side 5. Cross each of the possible gametes remembering to keep the alleles for each particular trait together 6. Determine the ratios for each genotype Punnett Square -A tool used to predict inheritance -Known as a "simple cross" when only one trait is being investigated -"F1" generation- the first generation of offspring produced by crossing two parental lines Dominant: information that always shows itself when present -Represented by capital letter Incomplete Dominance: a form of intermediate inheritance in which one allele for a specific trait is not completely dominant over the other allele. This results in a combined (blended) phenotype -Use lowercase letters -Ex: snapdragon color is expressed by incomplete dominance. The two primary colors are white (w) and red (r). Therefore the genotype rr calls for the phenotype of a red flower, ww calls for white, rw calls for pink Codominance: a condition in which both alleles of a gene pair in a heterozygote are fully expressed, with neither one being dominant or recessive to the other. This results in a "patchy" (not blended) phenotype -Use capital letters -Example: rabbit fur color is expressed by codominance. Two fur colors are white (W) and black (B). Therefore, the genotype BB calls for the phenotype of black fur, WW calls for white, BW calls for black and white Human Blood Type -Determined by codominant alleles. There are three different alleles: IA, IB, and i -The IA and IB alleles are codominant, and the i -The possible human phenotype for blood group are type A (only A antigens), type AB (both A and B antigens), type B (only B antigens), and type O (no antigens) - Type A and B individuals can either be homozygous (IAIA or IBIB, respectively), or heterozygous (IAi or IBi, respectively) Recessive: information that is always hidden by dominant -Can only see recessive if dominant is missing -Represented by lowercase letter Homozygous: purebreed -two of the same alleles -can be homozygous dominant or homozygous recessive -Ex. SS, ss Heterozygous: hybrid -has two different alleles -one dominant and one recessive -Ex. Ss Genotype: gene combinations (RR, Rr, rr) -Allele combinations -Every person has two alleles for a trait Phenotype: physical characteristics (roller or non-roller, blue or brown eyes) -Description of the trait Environmental Influence on Phenotype -Although the environment cannot alter the genotype, it can influence the phenotype Environmental examples: pH, temperature, light Life style examples: hair dye, tanning, tattoo, size- depending on amount of consumption Polygenic Trait -controlled by more than one gene -each dominant allele "adds" to the expression of the next dominant allele -Allows a wide range of physical traits Ex: Skin Color, Hair Color, Eye Color, Height Multiple Alleles -Some traits have more than two alleles (or versions). These alleles (depending on which two are present in the offspring) will interact to create the phenotype. Different forms of inheritance exist within these alleles Ex. -Blood types -Eye color Hardy-Weinberg Equilibrium: -Theorem -Deals with Mendelian genetics in the context of populations of diploid, sexually reproducing individuals. Following a set of assumptions (such as an infinitely large breeding population, random mating, no migration/emigration, no natural selection, and no mutations), this theorem states that: 1. allele frequencies in a population will not change from generation to generation 2. if the allele frequencies in a population with two alleles at a locus are p and q, then the expected genotype frequencies are p^2+2pq+q^2 or (p+q)^2. This frequency distribution will not change from generation to generation once a population is in Hardy-Weinberg equilibrium. If there are only two alleles at a locus, the p+q, by mathematical necessity, equals one; p^2+2pq+q^2 also equals one. It is possible to apply the Hardy-Weinberg Theorem to loci with more than two alleles, in which case the expected genotype frequencies are given by the multinomial expansion for all k alleles segregating in the population: (p^1 + p^2 + p^3 + . . . + p^k)^2

Nucleus of an Atom

The center of the atom which contains the protons and neutrons

Chemical Bonds

When two or atoms share or transfer a pair of eletrons

What happens if you use direct sunlight to observe the specimen

You could damage your eyes

Body Tube

allows the light from the objective to pass upward to form the first magnified image

Evolution

change in species over time (not in life time)

electron microscope

microscope that forms an image by focusing beams of electrons onto a specimen

Reason for never using the course adjustment knob on high power

might crack the slide

Solvent

substance that is dissolving the solute

Activation Energy

The energy needed to start a chemical reaction

Cell Structure/ Transport

The phospholipid bilayer, also known as the cell membrane consists of two layers that are semi-permeable The lipid portion of the cell membrane acts as a barrier, while the protein portion determines specific functions including: pumps, receptors, adhesion, etc. Passive Transport -Movement across the cell membrane that does not require any ATP (energy) -Occurs due to a concentration gradient -Occurs from an area of high to low concentration Types: -Diffusion: small and nonpolar particles can diffuse through the cell membrane -Osmosis: water -Water moves out of the cell- the cell shrinks -Water moves into the cell- the cell swells and can burst -Water moves in and out at the same rate: -The cell remains the same size -There is no net movement of the water -Equilibrium is reached -Ion Channels (Facilitated Diffusion): transmitted proteins embedded in the cell membrane that offer an opening for longer and charged particles like ions Active Transport -Movement across the cell membrane that requires ATP -Substances move against concentration gradient in order to import amino acids, sugars and other substances from outside the cell -Occurs from an area of low to high concentration Types: -Uniport: moves ions/ molecules in one direction -Symport: moves two different ions/ molecules in the same direction -Antiport: moves two different ions/molecules in opposite directions -Channel Pumps: Very specific; can work into or out of the cell to maintain unequal levels -Sodium-Potassium Pump: located on the cell membrane of all animal cells -Responsible for 1/5 of cells total ATP usage -Pumps Na out of cells and K into cells -In order to maintain cell membrane potential, intracellular concentrations of sodium must be low and K must be high -Membrane Potential: an electrical charge that exists across the cell membrane -1. Three sodium ions and a molecule of ATP -2. The splitting of ATP provides energy to change the shape of the channel. Th sodium ions are driven through the channel. -3. The sodium ions are released to the outside of the membrane and new shape of the channel allows two phosphate ions to bind -4. Release of the phosphate allows its channel to revert to its original form, releasing the potassium ions on the inside of the membrane -Vesicles: membrane-bound sac and has a phospholipid bilayer just like the cell membrane; can bring substances that are too long (like amino acids) for protein transport in and out of the cell -Endocytosis: the movement of substances into the cell by means of a vesicle -Pinocytosis: "cell drinking" the process of taking up liquid from the surrounding environment (extracellular fluid). Tiny pockets form along the membrane, fill with liquid, and pinch off. -Phagocytosis: "cell eating"- extension off cell membrane surrounds a particle and package it within a vesicle and then the cell engulfs it. Ex. Amoebas and macrophages use this process -Exocytosis- the movement of substance out of a cell by means of a vesicle (this process is used by the golgi apparatus to export proteins) Dynamic Equilibrium: ceases to change ratio of concentration; substances between the two organisms move at a certain rate Hypertonic Solution: a solution highly concentrated with solute that causes water to move out of the cell Isotonic Solution: having the same osmotic pressure as some other solution, especially one in a cell or a body fluid. -Cells are isotonic, and therefore an animal cannot live in both salt and fresh water Gradients: an increase or a decrease in the magnitude of a property observed in passing from one point or moment to another Integral Proteins:Helps with the transportation of materials -Biological gradients: key component of the biological world; the potential energy from these gradients is often used to perform biological work

Chemical Reaction

The process of chemical bonds being broken and formed to produce different substances

Cancer

The uncontrolled cell division that leads to the invasion of body tissue and organs Refer to a group of over 100 diseases

20 Amino Acids Found in Nature

There are 64 possible codons and only 20 different amino acids Multiple codons specify the same amino acid Amino acids are the building blocks of proteins Every three base > codon > amino acids > proteins

Codons

There are four different bases (A, T, C, G) -Codons are combinations of three bases (ATG, GGG, CAT, etc.) -There are 64 possible codon combinations (4^3=64) -Every codon specifies an amino acid

Endoscope

Tiny video camera inserted through mouth or anus

Single Strand Binding Proteins

Topisomerose- prevents super-coiling Proteins that attach to each strand of DNA to prevent premature annealing Attach to DNA strand after it is unzipped by helicase

Central Dogma of Molecular Biology

Transcription Translation Proteins are then exported from nucleus

fine adjustment knob

this part moves the stage slightly to help you sharpen or "fine" tune your view of the specimen

Nitrogenous Bases

Two Types: Purines and Pyrimidines Purines: double ringed compounds, Adenine and Guanine Pyrimidines: single tiny compounds, Thymine (Uracil) and Cytosine Purines always bond with pyrimidines >> Keeps the rungs of the ladder even Adenine and Thymine are connected by two hydrogen bonds Thymine and Cytosine are connected by three hydrogen bonds

Spirillus

Spiral-shaped

Robert Hooke

1660 English scientist with Oxford education Improved on compound microscope -increased magnification power -increased clarity discovered "cells" -observing cork cell-recognized shape

Polymer

A chain of monomers

Missense Mutation

A change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.

Line Graph

A graph that uses line segments to show changes that occur over time

Plan

A set of actions that you think you can do to achieve the question you asked

Isotope

Alternative form of an element; same number of protons, different number of neutrons

Cell Division in Prokaryotes

Binary Fission -The process of cellular division used by bacteria -The resulting prokaryotic cells are clones; exact genetic copies of each other -The only exception is in the case of a mutation (mistake) during DNA replication

Telomeres

Caps found at the end of chromosomes that help prevent deterioration

Transcription

DNA is converted to RNA

Bar Graph

Compares quantities of data

Cellulase

Enzyme that breaks down cellulose

Molecules

Formed when 2 or more atoms join together chemically

Compounds

Formed when 2 or more different types of elements are joined together

Halaphiles

Salt addict

Radioactive

Isotopes in which the atom decays over time and emits radiation

Coccus

Sphere-shaped

Nanotechnology

Nanotechnology studies objects and phenomenas at a very small scale; roughly to 100 nm (1 billionth of a meter). It is a new, interdisciplinary science involving Physics, Chemistry, Biology, Engineering, and Computer Science. -Nano-sized particles exhibit different properties than larger particles of the same substance (properties of materials change at the nano-scale) -The more surface area, the more area of reaction -The scale at which nanotechnologies are measured helps scientists to: -Learn more about the nature of matter -Develop new theories -Discover new questions and answers in many areas including health care, energy, and technology -Figure out how to make new products and technologies that can improve people's' lives Potential Health Risks: -Health Issues -Transparticles could be inhaled, swallowed, absorbed through the skin, or deliberately injected -Scientists are unaware if they could trigger inflammation and weaken the immune system or if they could interfere with enzymes and proteins -Environmental Issues (National and International agencies are currently studying the risks to be able to develop new regulations) -Nano-particles could accumulate in soil, water, and plants -Traditional filters are too big to contain them to contain them Nano-scale science and engineering can improve lives by: -Introducing new materials such as: -Stain resistant clothes -Paint that doesn't chip -Protective nano-paint for cars -Water and dirt repellent -Resistant to chipping and scratches -Brighter colors -Enhanced glass -Enhancing health care items such as: -Chemical and biological sensors -Drugs and delivery services -Nerve Tissue Talking to Computers -Nano nuero-electronic network interface -Nerve cells with semiconductors (computer chips) -Possible application in brain research, prosthetics, and biosensors -Detecting Diseases Earlier -Quantum dots that glow in UV light -Injected in mice (it collected within tumors) -Could locate as few as 10-100 cancer cells -Growing Tissue to Repair Hearts -Nano-fibers help heart muscle grow in the lab -Filaments "instruct" muscle to grow in an organized way (before nano-technologies, the fibers grew in random directions) -Preventing Viruses from Infecting the US -Nano-coatings can cover the protein shell of viruses (this could stop viruses from binding to cells) -Making Repairs to the Body -Nano-sized delivery systems could break apart kidney stone, clear plaque from blood vessels, and carry drugs to tumor cells -Improving technologies such as: -Having better data storage and computation -Nano-media has a storage scale in nano-meters (meaning a thousand times more storage along each dimension or a million times greater storage density in total) -Bettering environmental conditions such as: -Creating clean air (by using nano-paint) -Nano-paint on buildings could reduce pollution -When exposed to UV light, titanium dioxide (TiO2) non-particle in paint break down organic and inorganic pollutants (it could decompose air pollution particles -Creating clean energy (nano-solar cells- inorganic nano-rods embedded in semiconducting polymer, sandwiched between two electrodes) -Nano-solar cells mixed in plastic could be painted on buses, roofs, and clothing

Products

Newly formed substances

"Good" Bacteria in the Environment

Plays an essential part in decomposing and recycling dead matter (nutrients) Ex. Sewage Decomposition - A large amount of bacteria is added to sewage to help break down organic waste products

Proton

Positively charged particle, found in nucleus

Ions

Positively or negatively charged atoms due to unequal amounts of protons and electrons Atoms, molecules or compounds that have gained or lost electrons

Translation

RNA is converted to proteins

Bacillus

Rod-shaped

"Common Rule"

The Federal Policy for the Protection of Human Subjects. Shared standards adopted by federal agencies for the protection of human research subjects.

Specific Heat

The amount of energy needed to raise the temperature of a substance by 1 degrees Celsius (water's specific heat is higher than any other common substance; a large amount of energy is required to increase or decrease its temperature

Ribosomes

The cellular site where proteins are made Composed of RNA and protein

Frameshift Mutation

This type of mutation occurs when the addition or loss of DNA bases changes a gene's reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. This mutation shifts the grouping of these bases and changes the code for amino acid. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations

Atoms

Tiny particles of matter that are made of three particles: protons, neutrons, and electrons

Graphs

Ways to represent data

Invention of the Microscope

Zacharias and Hans Janssen in 1597 -Dutch eyeglass maker -Created first compound microscope -Single tube with 2 lenses (one at each end) -Magnification of ~3x - ~9x

Endoctosis

a process in which a cell surrounds and takes in material from its environment

Soluble

ability of a substance to dissolve or mix into a solution uniformly

compound microscope

lets light pass through an object and then through two or more lenses

bulb/mirror

light source

Ecotoxin

Excreted outside the cell

Histones

"Glue balls" that hold the DNA tightly wound

Acidiphiles

Acid Addict (pH 3-)

Course Adjustment Knob

Moves slide up and down

Unicellular

Single-celled

Stage

Supports the slide being viewed

Lyse

To burst apart/ explode

Neutral

pH of 7 Ex: pure water

Biochemistry

Study of the chemical composition and interactions between the molecules that make up living things

Chemistry

Study of the properties and composition of matter

Catalyst

Substance that increases the rate of a chemical reaction without itself undergoing any permanent change

Solute

Substance that is being dissolved in the solvent

Culturing Cells

The taking of cells from any multicellular eukaryotes, especially animal cells

The Citric Acid Cycle (Krebs Cycle)

- A general pathway into which many metabolites feed. It consists of a number of reactions which generate NADH and FADH2, which can in turn be used by the oxidative phosphorylation pathway to generate ATP. The Citric Acid Cycle occurs in the matrix of the mitochondria. Step 1: The acetyl CoA (a two carbon compound) joins with oxaloacetate (4 carbon molecule) to form citrate (6 carbon molecule) Step 2: The citrate is then converted to isocitrate (isomer of citrate) Step 3: Isocitrate is then oxidised to alpha-ketoglutarate (a five carbon molecule) which results in the release of carbon dioxide. One NADH molecule is also formed in this step. Step 4: Here alpha-ketoglutarate is oxidised to form a 4 carbon molecule which picks up coenzyme A forming succinyl CoA. This conversion also forms a NADH molecule. Step 5: Succinyl CoA is then converted to succinate (4 carbon molecule) and one ATP molecule is produced. Step 6: Succinate is converted into fumarate (4 carbon molecule) and a molecule of FADH2 is produced. Step 7: Fumarate is converted to malate (4 carbon molecule) Step 8: Malate is then converted into oxaloacetate and NADH is also produced here. One round produces 2 molecules of carbon dioxide, three molecules of NADH, three hydrogen ions, and one molecule of FADH2. Each molecule of glucose produces double this (4 carbon dioxide, 6 NADH, 2 FADH2, and 2 ATP) -Although the primary role of the Krebs Cycle is production of NADH and FADH2, it also produces molecules that supply various biosynthetic processes, which can enter or exit the cycle at various points depending on the demand on different reactions. -For example: alpha-ketoglutarate can leave the cycle to be converted into amino acids; succinate can be converted to haem

DNA Replication and DNA Replication Errors

- The process of making an exact copy of a cell's DNA - Must happen before cellular division takes place - Happens during S-phrase of interphase Steps: 1. New DNA is formed by using old DNA as a template a. The enzyme helicase attaches to the rungs of the double helix b. Helicase unzips the DNA molecule by breaking hydrogen bonds between base pairs 2. Different enzymes (DNA polymerase) move along the exposed DNA strand and move along the strand, adding new nucleotides (at the rate of 50 nucleotides per second in mammals/ 500 nucleotides per second in bacteria) -Added nucleotides are complementary to the template strand -Bases from original DNA strand bond with base on the new nucleotides 3. Process continues until two new strands (identical) are formed from one -DNA replication is semi-conservative meaning that each double helix consists of one original DNA strand and one new strand -Constantly creating new cells > Growth/ development (Zygote>Baby>Adult) > Repair old/ damaged cells - New cells must contain a full set of genetic instruction (DNA) -DNA polymerase enzymes have a proofreading role to help prevent incorrect nucleotides from being added to the new strand of DNA - They can only add nucleotides if the previous one is correct - DNA polymerase can backtrack to remove the incorrect match and replace it - Allows for only one error per billion bases Referring to the picture: Top left card explains the semi-conservative characteristics of DNA Top right card explains how helicase unwinds duplex DNA. It also shows and describes replication forks- area where the double helix separates. It explains that many helicases perform this process forming 100 replication forks at the same time to replicate an entire human chromosome in about 8 hours (if only one was responsible it would take 33 days to replicate DNA in a single cell). Bottom center card explains that no matter what, all of the DNA in a cell must be copied before cellular division takes place

Cell Membrane

-A cell structure that controls which substances can enter or leave the cell -Found in all cells -A boundary that encloses the cell and separates it from the external environment -Regulates what enters and leaves the cell -Boundary of transport -Also known as the phospholipid bilayers (hydrophobic tails and hydrophilic heads) -Only small substances and non-polar can push through the cell membrane, others go through the proteins -Fatty acid tails of one of the phospholipids are hydrophobic, so they keep water out of the middle space Referring to the picture: 1. (2H2O) 2 water molecules 2. (O2) 1 diatomic oxygen molecule 3. (4H) 4 Hydrogen atoms 4. Water-splitting enzmye 5. Outside of thylakoid 6. Cluster of pigments 7. Thylakoid membrane 8. Thylakoid space

Cell Communication

-Cell-to-cell communication is essential for multi-cellular organisms -Prokaryotes and unicellular eukaryotes function independently of one another -Signal transduction pathways aim to convert signals into cellular responses Signaling Cells -Produce signaling molecules -All types of macromolecules and their building blocks can be signaling molecules Endocrine Signaling -Happens over a long distance -Hormones are the major signaling molecules of endocrine signaling Target Cells -Receives the signaling molecules from the signaling cells -Responds by means of a receptor protein, which specifically binds to the signal molecule and initiates a response Juxtracrine Signaling -Happens via direct cell contact Paracrine Signaling -Happens over short distances Peripheral Proteins: Help with cell communication Cell-surface Receptors -Receptors that are embedded in the membranes of cells -Interact in cell signaling by receiving extracellular molecules Intracellular Receptors -Hydrophobic signal molecules typically diffuse across the plasma membrane -Interact with intracellular receptors in the cytoplasm Extracellular signals can act slowly or rapidly to change the behavior of a target cell. These changes in cell behavior has major consequences at the level of the organism. When an extracellular signal molecule goes into the cell-surface receptor protein, it would go through one of two processes: a fast process which takes 6 seconds to minutes or a long process which would take minutes to hours. The long process, after the molecule goes into the receptor protein, entails going into the nucleus in through the RNA and DNA and causing an altered protein synthesis. The fast process, after the molecule goes into the receptor protein, entails going through an intracellular signaling pathway causing an altered protein function causing an altered cytoplasmic machinery and eventually causing altered cell behavior Referring to Picture: Top Left Picture: Three Main steps in a Signaling Pathway: Reception- Takes place when the signaling molecule, which is in the extracellular fluid, implants itself into the receptor within the plasma membrane Transduction- Takes place in the cytoplasm when the relaying molecules relay the message picked up by reception Response- Takes in the cytoplasm, the cell responds to the signaling molecule after it is transferred in the transduction step Middle Left Picture: Extracellular signal molecule activates signaling pathways Extracellular Signal Molecule-Red Dot Receptor Protein-Green Chalice Shape Intracellular Signaling Protein-Grouped Green Shapes Effector Proteins-Shapes Split Into Three Categories: Metabolic Enzyme (Alters Metabolism)-Left Blue Shape Gene Regulatory Protein (Alters Gene Expression)-Middle Blue Shape Cytoskeletal Protein (Alters Cell Shape or Movement) Bottom Left Picture: Different Forms of Intracellular Signaling: Gap Junctions- the message of transmission is transferred directly from cell to cell; it is local; and its specificity depends on anatomic location Synaptic- the message of transmission is transferred across synaptic cleft; it is local; and its specificity depends on anatomic location and receptors Paracrine and Autocrine- the message of transmission is transferred by diffusion in interstitial fluid; it is locally diffused; and its specificity depends on receptors Endocrine- the message of transmission is transferred by circulating body fluid; it is general; and its specificity depends on receptors. Top Right Picture: Secreting and Target Cell Communication Bottom Right Picture: Endocrine and Target Cell Communication: Hormones are stored in secretory vesicles; secretion stimulated by stimulating exocytosis Hormones are freely dissolved in the circulation Hormones signal via cell surface receptors

Base (Alkaline Compounds)

-Compounds that reduce the concentration of H+ in a solution -Often forms hydroxide ions (OH-) when dissolved in water -pH > 7

Nervous System

-Coordinate receipt of and response to stimuli (Subtypes: neurons, glial cells) -Peripheral Nervous System(PNS): The portion of the nervous system containing nerves and ganglia lying outside the brain and spinal cord -Central Nervous System(CNS): The part of the nervous system which, in vertebrates, consists of the brain and spinal cord, to which sensory impulses are transmitted and from which motor impulses pass out, and which coordinates the entire nervous system -Neuron -Specialized, impulse-conducting cell that is the functional unit of the nervous system, consisting of the cell body and its processes, axon, and dendrite Found in: Cranial Nerves: Vagus; CNS: Cerebrum, Cerebellum, Brain Stem, Spinal cord; Brachial Plexus: Musculocutaneous Nerve, Radial Nerve, Median Nerve, Ulnar Nerve; Thoracoabdominal Nerves: Intercostal Nerve, Subcostal Nerve, Iliohypogastric Nerve, Ilioinguinal Nerve, Lateral Cutaneous of the Thigh, Genitofemoral Nerve; Lumbar Plexus: Obturator Nerve, Femoral Nerve, Muscular Branches of Femoral Nerve, Genitofemoral Nerve, Saphenous Nerve; Sacral Plexus: Sciatic Nerve, Tibial Nerve, Common Peroneal Nerve, Deep Peroneal Nerve, Superficial Peroneal Nerve, Sural Nerve; Pudendal Nerve -Axon: the appendage of neuron that transmits impulses away from the cell body -Dendrite: the branching process of a neuron that conducts impulses toward the cell -Myelin: a soft, white, fatty material in the membrane of Schwann Cells and certain neuroglial cells: the substance of the myelin sheath -A region where nerve impulses are transmitted and received, encompassing the axon terminal of a neuron that releases neurotransmitters in response to an impulse, an extremely small gap across which the neurotransmitters travel, and the adjacent membrane of an axon, dendrite, or muscle or gland cell with the appropriate receptor molecules for picking up the neurotransmitters -Motor Neuron: A nerve found in the spinal cord that conducts impulses to a muscle, gland, or other effector -Sensory Neuron: A nerve cell found in the spinal cord, and dorsal root ganglion that conducts impulses from a sense organ to the CNS -Interneurons: any neuron having its cell body, axon, and dendrites entirely within the central nervous system (brain and spinal cord), especially one that conveys impulses between a motor neuron and a sensory neuron

Meiosis

-Form of cellular division that splits the number of chromosomes in half -Starts with one somatic cell -Males: testes cell -Females- ovary cells Gametogenesis: -The creation or formation of haploid gametes -Sperm Cell -Egg Cell -Referred to by the type of sex cell generated by the process: -Oogenesis: the creation of egg cells -Ends in 1 healthy egg cell and 3 waste (polar bodies) -Spermatogenesis: the creation of sperm cells -Ends in 4 healthy sperm cells -There are two divisions -Meiosis I: -Prophase I: The chromosomes condense, and the nuclear envelope breaks down. Crossing-over occurs. -Crossing-over: Portions of a chromatid are exchanged with the corresponding portion on the homologous pairing chromosome. Makes number of a gene combinations basically unlimited -Synapsis: the fusion of chromosome pairs at the start of meiosis -"Tetrad Forms": two homologous chromosomes will align next to each other. But, since each is made up of two sister chromatids it will look like a group of four -Metaphase I: Pairs of homologous chromosomes move to the equator of the cell -Anaphase I: Homologous chromosomes move to the opposite poles of the cell -Telophase I and Cytokinesis: Chromosomes gather at the poles of the cells. They cytoplasm divides -Meiosis II: -Prophase II: A new spindle forms around the chromosomes -Metaphase II: Metaphase II Chromosomes line up at the equator -Anaphase II: Centromeres divides. Chromatids move to the opposite poles of the cells -Telophase II and Cytokinesis: A nuclear envelope forms around each set of chromosomes. The cytoplasm divides. Cytokinesis: -Cell Membrane pinches in forming a cleavage furrow -Controlled by the action of the spindle fibers -Two identical cells are formed -Vesicles formed by the Golgi Apparatus fuse at the midline of the plant cell -Forms a membrane bound cell walls called a cell plate -Two identical cells are formed

Junk DNA

-Non-coding DNA: segments of DNA that do not serve any biological function -Separate genes from each other with long gaps, so that mutations (such as the deletion or insertion of base pairs) do not cause a frame shift across the entire chromosome Only about 2-3% of all DNA actually codes for traits- also known as genes Protection of the Genome: Exons and Introns Exons: coding region of DNA Introns: non-coding regions of DNA (junk)

Viruses

-Non-living, sub-microscopic particle (not a cell) that invades a living cell and destroys it -Consists of a nucleic acid (DNA/RNA) wrapped in a protein coat (capsid) - Primary goal is to "hijack" the cell's machinery in order to replicate -(Antibodies can not kill viruses) Ex: Ebola, Herpes, Epstein Barr (Mononucleosis), Rhinovirus (common cold), HIV, Chicken Pox

Centrioles

-Only in animal cells -Two small cylinder shaped structures is in the cytoplasm made of microtubules -Perpendicular to one another -Play a key role in cellular division (mitosis/meiosis)

Central Vacuole

-Only in plant cells -Large sac that stores water, and sometimes ions, nutrients, and waste -When its full, the cell becomes rigid to help the plants stand upright

Chloroplasts

-Only in plant cells -Organelles responsible for carrying out photosynthesis Contains: -Outer Membrane -Inner Membrane -Stroma -Space inside the chloroplast -Where dark reaction occur -Where starches (glucoses) are created -Thylakoids -Flattened disk shaped structure - Contains chlorophyll & other pigments -Sight of light reactions -Granum -Stacks of thylakoids -Pigments= light-absorbing molecules -Supplies energy to cellular activities along with the mitochondria

Carbohydrates

-Provide short term and intermediate term energy storage -Are a structural component of different living things (Ex: Cellulose is a carbohydrate in cell walls; Chitin is a carb in exoskeletons) -Sugars -The monomers are simple sugars (saccharides) -Scientific words for carbs typically ends in "ose" -Chemical formula is often found in the form CnH2nOn (therefore there are 2 Hydrogens per every 1 Carbon and 1 Oxygen [1C:2H:1O) -Ex: Glucose- C6H12O6 Ex: Breads, Candy, Leafy Foods, Grain, Oat, Wheat Monosaccharides -Single sugars: glucose, fructose,and galactose (sucrose= glucose + fructose) -Monomers of carbohydrates Disaccharides -2 sugars joined: sucrose, lactose, maltase Polysaccharides -Many sugars joined together: starch in plants, glycogen in animals cellulose -Also called "complex carbs" Oligosaccharides -2 to 10 sugars joined: Raffinane and Stachyase The bigger the molecules, the better they store energy because they need to be broken down

Connective Tissue (CT)

-Provides structure and connection; characterized by a non-cellular matrix outside the cells Subtypes: Loose, Dense, Fibrous, Cartilage, Bone, Blood, Adipose -Fibrous: types of cells in all C.T, lays down filaments density denotes types of tissue (Dense Regular CT, Dense Irregular CT, Loose CT, Reticular CT) -Dense Irregular C.T.: Dermal Layer of skin; Makes skin malleable; Connects muscle to the epidermis; formed in collagen bundles -Collagen: Gives elastic property to many body parts; Breaks down with age (causes saggy skin) -Dermal Layer: Skin below the epidermis -Dense Regular C.T.: Ligaments, Tendons, Aponeurosis; Enables movement of bone against muscle and muscle against muscle; has great tensile strength that resists pulling forces especially well in one direction; found bundled in a parallel fashion -Ligaments: Attaches bone to bone -Tendons: Attaches bone to muscle -Aponeurosis: A pearly-white fibrous tissue that takes place of a tendon in sheet like muscles having a wide area of attachment -Reticular C.T.- forms a scaffolding for other cells in several organs, such as lymph nodes and bone marrow; a network of reticular fibers -Reticulum: Net or Network -Reticular Fibers: Joins connective tissue to other tissues -Loose CT: Holds organs in place and epithelial tissue to underlying tissues -Epithelial Tissue: Lines inner and outer surfaces; Subtypes are based on shape (squamous, cuboidal, columnar) and number of different layers (simple, stratified, pseudo-stratified) -Squamous: No shape -Cuboidal: Cubes that form circles -Columnar: Columns -Simple: Single -Stratified: Layered -Pseudo-stratified: Falsely-layered -Stratified Columnar: Layered columns; found in the retina, anus, salivary glands, uterus, reproductive system, and male urethra -Stratified Cuboidal: Layered cubes that form circles; found in the lining of sweat glands, lining of the conjunctiva of the eye, and mammary glands -Simple Columnar: Single columns; found in the lining of the digestive tract, lining of the gallbladder, and lining of the uterus -Pseudo-stratified Columnar: falsely layered columns; found in the tracheal and bronchial regions of the pulmonary system, and Fallopian tubes -Stratified Squamous: layered-no shape; found in the lining of the mouth, lining of the nose, and lining of female reproductive system -Simple Squamous: single no shape; found in alveoli of the lung, capillaries of the lung, blood vessels, lines the inside of the heart, lines bowman's capsules, and kidney glomerulus -Simple Cuboidal: Single-cubes that form circles; found in kidney tubular and surface of the ovaries -Transitional: A type characteristically found lining hollow organs, that are subject to great mechanical change due to contraction and distension -Cartilage: Includes firm, whitish, flexible C.T.; subtypes include Hyaline, Fibro-cartilage, and Elastic -Hyaline: Motion; found in the embryonic skeleton, articular cartilage of a joint (shoulder), covers the end of long bones in joint cavities, forms coastal cartilage of ribs, nose, trachea, and larynx -Fibrocartilage: Cushions Bones; invertebral disc, meniscus, articular cartilage of a joint (knee) -Elastic: Extension; ear, epiglottis -Adipose: Contains large globules of fat; subtypes include white fat and brown fat -Uses: Fuel reserve (Stores Energy), Protection, Insulation/ Heart regulation -Adult Numbers are stable (adults can not increase or decrease the size of adipose cells [not get rid of them]) -White Fat: not as nutritious (bears convert all food they gorge into white fat); found in epicordial, mesenteric, amental, retroperitoneal, gonadal, subcutaneous, abdominal, gluteal, and femoral regions -Brown Fat: hibernating/ migrating species (nutritious); found in the neck, supraclavicular, para aortic, para vertebral, and suprarenal regions -Blood: Supplies oxygen to cells and tissues; provides essential nutrients to cells, such as amino acids, fatty acids, and glucose; removing waste materials such as carbon dioxide, urea, and lactic acid; protecting the body from infection and foreign bodies through the white blood cells; transporting hormones from one part of the body to another, transmitting messages, and completing important processes; regulating acidity (pH) levels and temperature; engorging parts of the body when needed -Red Blood Cells (Erythrocytes) -Hemoglobin: protein that carries oxygen on red blood cells; missing nuclei -Found in bone marrow, blood stream, and kidneys -White Blood Cells (Leukocytes) -Antibodies -Defends the body against disease and foreign substances -Found in bone marrow, lymph nodes, spleen and blood stream -Platelets (Thrombocytes) -Cell fragments of cytoplasm -Key in blood clotting -Found in bone marrow and blood stream -Skeletal System (made of the axial and appendicular skeletons) -Axial: consists of 80 bones and six major parts:the skull bones, the ossicles of the middle ear, the hyoid bone, the rib cage, sternum, and vertebral column -Spinal Process: On top of vertebrae -Transverse Process: On the sides of vertebrae -Appendicular: The portion of the skeleton of vertebrates consisting of bones that support the appendages -Bones purposes are to store minerals, create structure, protect organs, and produce blood. They are made 2/3 of Calcium and 1/3 Phosphates. Muscles cannot function properly without bones. 10% of total calcium is in the bloodstream and if there is not enough calcium, bones start to break down. The reason bones need calcium is because they are constantly being remodeled with old bone being reabsorbed and new bone being formed as well as producing blood. In order to have the bones receive minerals, as well as organs and muscles, calcium is carried in the bloodstream. It is important for heart function, helps with muscle contractions, nerve signaling, and blood clotting along with bone growth and development. Any calcium that is in blood not attached to proteins are considered Free (Ionized) Calcium. In order for a bone to be made, to grow, and heal, it has to go through three major steps. Bones are also subtyped into long, short, flat, irregular, and sesamoid. -Osteoblast: cell that secretes the matrix for bone formation -Osteocyte: a bone cell, formed when an osteoblast becomes embedded in the matrix it has secreted -Osteoclast: a large multinucleate bone cell that absorbs bone tissue during growth and healing -Long bones: hard, dense bones that provide strength, structure, and mobility; have one shaft and two ends -Short bones: provides support and stability with little to no movement; designated as those bones that are as wide as they are long -Flat Bones: bones whose principal function is either extensive protection or the provision of broad surfaces for muscular attachment -Irregular bones: bones which, from their peculiar form, cannot be grouped as long, short, flat or sesamoid bones. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment, and maintaining pharynx and trachea support, and tongue attachment -Sesamoid: a small independent bone or bony nodule developed in a tendon where it passes over an angular structure, typically in the hands and feet -Ribs: 12 pairs of ribs for both genders (Subtypes include true ribs, false ribs, and floating ribs -True: attached to thoracic vertebrae and sternum (7 pairs) -False: attached to adjacent rib by cartilage (3 pairs) -Floating: attached only to the spine (2 pairs) -Cervical Vertebrae: 7 bones in all mammals besides sloths (8-9) and sirenia (6) -C1 is called the atlas -C2 is called the axis

Electron Transport Chain

-Purpose: Use electrons provided by NADH and FADH2 to build ATP -Reactants: 10 NADH, 2 FADH2 -Products 34 ATP, 6H2O, 10 NAD+, 2 FADH -Locations: Mitochondria -1 NADH= 3 ATP - 10 NADH= 30 ATP -1 FADH2= 2 ATP - 2 FADH2= 4 ATP -Electrons are passed through a series of protein carrier complexes embedded in the mitochondrial membrane. Oxygen is the final electron acceptor. -Oxygen takes the 2 H and makes water -H2O is found at the end of the ETC

Genetic Variation

-Refers to the differences in genetic information between organisms of the same species -Allows for new, more favorable gene combinations to come about -Essential to evolution -Differences in genes occur in organisms that reproduce sexually include: crossing-over, independent assortment, and random fertilization -Sexual Reproduction: involves the joining of two parent reproductive cells to create offspring -Parents' gametes are haploid, so when they join, the zygote is diploid -The offspring have traits of both parents but not identical because both parents contribute genetic material -Random Fertilization: the zygote that becomes a new organism is created by random joining of gametes -2 separate gametes from completely genetically different parents -Each gamete had crossing-over take place somewhere while it was being formed -Then chromosomes were separated twice (independent assortment basically takes place twice) -Independent Assortment: Random distribution of homologous chromosomes -Homologous Chromosomes: chromosomes similar in shape, size and genetic content -Each pair consists of two homologous (one from the mother and one from the father -Maternal and paternal chromosomes of a homologous pair ar randomly pulled to opposite sides of the cell during Anaphase I & II -About eight million different gene combinations can be produced from one original cell based on independent assortment alone (crossing-over and random fertilization add to the variety) -Then the sperm that joins the egg during fertilization is completely random -Occurs only in eukaryotes

Migration

-Smaller molecules migrate through the gel more quickly and therefore travel further distance than large fragments -Molecules are therefore separated by size -DNA marker (stand) with fragments of known length is run on the gel at the same time to serve as a basis for comparison - Allows for figuration of approximate DNA lengths

Glycolysis

Metabolic process that serves as the foundation for both aerobic and anaerobic cellular respiration Energy Input: Two ATP molecules are needed to start glycolysis -Step 1: The conversion of D-glucose into glucose-6-phosphate (G6P). The enzyme that catalyzes this reaction is hexokinase. Mg is involved to help shield the negative charges from the phosphate groups on the ATP molecule. The glucose ring is phosphorylated. 1 molecule of ATP has been consumed. -Hexokinase: an enzyme that catalyzes the phosphorylation of many six-membered glucose-like ring structures. -Phosphorylated: process of adding a phosphate group to a molecule derived from ATP -Step 2: The rearrangement of G6P into fructose-6-phosphate (F6P). This reaction occurs with the help of the enzyme phosphoglucose isomerase (PI). The isomerization reactions involves the rearrangement of the carbon-oxygen bond to transform the six-membered ring into a five-membered ring. The six-membered ring opens and closes in such a way that the first carbon becomes external to the ring -Step 3: F6P is converted into fructose-1, 6-bisphosphate (FBP). A second molecule of ATP provides the phosphate group that is added on to the F6P molecule. The enzyme that catalyzes this reaction is phosphofructokinase (FPK). A Mg atom is involved to help shield negative charges -Step 4: The enzyme Aldolase splits FBP into two sugars that are isomers of each other. These two sugars are dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP) -Isomers: Each of two pr more compounds with the same formula but a different arrangement of atoms in the molecule and different properties -Step 5: The enzyme triophosphate isomerase (TIM) rapidly inter-converts the molecules DHAP and GAP. Gap is the only molecule that continues in the glycolytic pathway. All of the DHAP molecules produces are further acted on by the enzyme TIM, which reorganizes the DHAP into GAP so it can continue in glycolysis. At this point in the glycolytic pathway, there are two 3-carbon molecules, but glucose is not yet fully converted into pyruvate -Step 6: Glyceraldehyde-3-phosphate is oxidized by the coenzyme nicotinamide adenine dinucleotide (NAD). The molecule is phosphorylated by the addition of a free phosphate group. The enzyme that catalyzes this reaction is glyceraldehyde-3-phosphate dehydrogenase (GAPDH). -Oxidized: combine or become combined chemically with oxygen -GAPDH: contains appropriate structures and holds the molecule in a conformation such that it allows the NAD molecule to pull a hydrogen off the GAP, converting the NAD to NADH. The phosphate group then attacks the GAP, converting the NAD to NADH. The phosphate group then attacks the GAP molecule and releases it from the enzyme to yield 1, 3 biophoglycerate, NADH, and a hydrogen atom. -Step 7: 1, 3 bisphoglycerate is converted to 3-phosphoglycerate by the enzyme phosphoglycerate kinase (PGK). This reaction involves the loss of a phosphate group from the starting material. The phosphate is transferred to a molecule of ADP that yields the first molecule of ATP. Since two molecules of 1,3 bisphoglycerate are present (because there were two 3-carbon products from stage 1 of glycolysis), two molecules of ATP are synthesized at this step. Since two ATP are synthesized a net of 0 ATP molecules are left. Mg is involved to shield the negative charges on the phosphate groups of the ATP molecules -Step 8: Involves a simple rearrangement of the position of the phosphate group on the 3 phosphate molecule, making it 2 phosphoglycerate. The molecule responsible for catalyzing this reaction is called phosphoglycerate mutase (PGM). The reaction mechanism proceeds by first adding an additional phosphate group to the 2' position of the 3 phosphoglycerate. The enzyme then removes the phosphate from the 3' position leaving just the 2' phosphate, and thus yielding 2 phosphoglycerate. The enzyme is also restored to its original, phosphorylate state -Mutase: an enzyme that catalyzes the transfer of a functional group from one position on a molecule to another. -Step 9: Involves the conversion of 2 phosphoglycerate to phosphoenolpyruvate (PEP). The reaction is catalyzed by the enzyme enolase. -Enolase: enzyme that works by removing a water group, or dehydrating the 2 phosphoglycerate. The specificity of the enzyme pocket allows for the reaction to occur. into pyruvate with the help of the enzyme pyruvate kinase. This reaction involves the transfer of a phosphate group. The phosphate group attached to the 2' carbon of the PEP is transferred to a molecule of ADP, yielding ATP. Again, since there are two molecules of PEP, 2 ATP molecules are generated -Step 10: converts phosphoenolpyruvate Energy Output: 2 ATP, 2 NADH, and 2 pyruvate molecules Net Gain: 2 NADH molecules, 2 pyruviates and 2 ATP molecules

Nucleic Acids

Monomer: Nucleotides (3 parts) -Sugar (2 types) -Deoxyribose -Ribose -Phosphate -Bases (4 types) -Adenine -Thymine (Uracil in RNA) -Guanine -Cytosine 5 types: -DNA -RNA -ATP -NAD -FADH

E. coli

Most strains are harmless (lives in digestive tract) while others could make you sick Symptoms: - Severe cramps - Diarrhea (often bloody) Ways to get it: - Eatting uncooked ground beef - Drinking contaminated water/ unpasteurized milk - Working with cattle

DNA markers

Necessary when completing gel electrophoresis so to estimate the size of other fragments because the fragment sizes are known on the marker

Electron

Negatively charged particles that orbit around the nucleus Arranged in rings. The first 3 rings starting from the closet to the nucleus, when filled, their energy levels go 2-8-8 Valence Electrons- the electrons in the outermost orbit used to help create chemical bonds Energy Levels- the way electrons are arranged in orbits

Genetic Privacy Act and Commentary

Set guidelines for protecting privacy of information stored in genetic data banks

Electron Dot Diagram

Shows the valence electrons of an atom

Simple Microscope

Similar to a magnifying glass and has only one lens

Ebola

Single stranded RNA Has only 9 proteins encoded by its genome EBOV glycoprotein- expressed on virion surface and used for attachment on host cells Causes severe hemorrhagic fever

Budding

Some eukaryotes, such as hydras or sponges, emerge a daughter by cloning itself

Observe

Something that you see or find in your surroundings that you see as being significant

Contractile Vacuole

Star-shaped structure that helps the paramecium pump out excess water

Reactants

Starting materials for a chemical reaction

Hypothesis

Starting with the word "if"; an educated guess one makes before experimenting, to think of a possible outcome to the experiment

Law of Conservation of Matter

States that matter can neither be created nor destroyed

Cell Theory

States that: 1. All living things are made of one or more cells 2. Cells are the basic units of structure and function in organisms 3. All cells arise from existing cells - Must copy the mother's cells original contents (including DNA)

Cellular Respirations

The process of converting organic compounds (particularly glucose) into ATP All organisms need energy for all of life's functions in the form of ATP and therefore all preform Cellular Respiration -Plants get glucose from photosynthesis -Animals get glucose from the food they eat 1. Glucose is in the cytoplasm, O2 is in the mitochondria 2. A small amount of energy is produced along with 2 Pyruvic Acid molecules 3. The 2 Pyruvic Acids move into the mitochondria 4. Oxygen reacts with the Pyruvic Acid to produce carbon dioxide, water, and a large amount of energy Glucose (C6H12O6) + 6 Diatomic Oxygen Molecules (6O2) > 6 Carbon Dioxide (6CO2) Molecules + 6 Water Molecules (6H2O) + ATP -Oxidation is loss (of electrons) -Reduction is gain (of electrons) -Phosphorylation: Reaction that results in the addition of a phosphate group to an ADP molecule to create ATP (ADP+P yields ATP) -Substrate level phosphorylation: ATP formation from the transfer of a phosphate (Glycolysis, Krebs) -Oxidative phosphorylation: The addition of phosphate from the oxidation of NADH and FADH2 to gradient that powers ATP synthase (ETC) Aerobic (preferred energy creating pathway in humans) -Requires oxygen -Occurs in mitochondria (eukaryotic cells) & cell membrane (prokaryotic cells) -38 ATP in total -Steps: -Glycolysis -Krebs Cycle -Electron Transport Chain (ETC) Anaerobic -Does not require oxygen -Occurs in cytoplasm -2 ATP in total -Steps: -Glycolysis -Fermentation Yields 2 ATP

Fertilization

The process of joining 2 haploid gametes to result in 1 diploid zygote Two types (dependant on the organism): -Internal: (Most species of land animal use this method) -Advantages: -Increases chance that egg and sperm will meet -Offspring are protexted -Disadvantages: -Few offspring (multiple births are less likely because it puts stress on the mother) -Takes a long time (relatively) which can hinder a species' chance of survival -Longer gestation/development period for offspring -Occurs less frequently because the organism needs to produce gametes and find a mate (requires energy) -External: (Most species of aquatic animals use this method) -Advantages: -Lots of offspring -Less stress on mother -Disadvantages: -Offspring are not protected -Depends on environment (sperm is motile) Terminology: -Zygote: fertilized egg -Grows by mitosis -Haploid: 23 chromosomes an organism or cell having only one complete set of chromosomes (sex cells/gamete). -Diploid: 46 chromosomes an organism or cell having two sets of chromosomes or twice the haploid number (somatic cells) -Motile: capable of moving

Sugar Phosphate Backbone

The sugar and phosphate groups of the nucleotides make up the backbone of DNA (Vertical sidepieces of the ladder) Referring to the picture: Sugar- Pentagon with an S Phosphate- Circle with a P

Polar Covalent Bonds

Unequal sharing of electrons to make a charged end of the molecule One end usually ends up slightly positive One end usually ends up slightly negative Charged

R nought (R0)- Basic Reproduction Number

Used to measure transmission potential of a disease Refers to amount of people a sick person will infect (an average) R0<0 disease will die out R0>0 disease is capable of spreading throughout a population The higher the R0, the harder it is to control the epedemic

Bioremediaiton

Using living things to hhelp clean up dead matter

Bacteria Characteristics

Various Types of Movement - Cilla (rotational), Flagella (wave-like) Various ways of Obtaining Energy -Decomposers -Photosynthetic -Chemosynthesis

Proteins

Various functions in the body: - Builds and repairs tissues (muscle, bones, etc.) -Drive to speed up biochemical reactions -Aid in digestion -Benefits the immune system -Maintains cell structure Ex: Nuts, Meat, Beans, Dairy, Eggs -Formed through dehydration synthesis Polymer = Protein = Polypeptide -Monomer: Amino Acids -20 different amino acids -All have different chemical properties (polar/nonpolar, charged, etc.) -4 Parts: Same in all amino acids (Refer to picture) -N terminus (NH2) > Amino Group -C terminus (CO2H) > Carboxyl Group -Hydrogen -R group -Protein folding -Proteins fold to give 3D structure based on chemical properties of R-groups (polar likes polar, nonpolar likes nonpolar, nonpolar doesn't like polar)

Endoscopy

Viewing the inside of the body with an endoscope

Host Cells

Viruses take over the cells machinery to produce more virus

Bacteriophages

Viruses that infect bacteria

Bonds

What holds atoms together

Independent Variable

What is being changed (x axis)

Dependent Variable

What is being measured (y axis)