BIO 12 Week in Review...

This week in Biology...

• MON-Review of Transcription, Part II of Protein Synthesis: Translation (Notes), completed our posters, DNA/mRNA/tRNA codon worksheet
• TUE-Questions about Protein Synthesis, Protein Synthesis in-class demonstration (this was funny but also helpful for understanding the concept), Mutations worksheets (H.W.)
• THU-Assessment/Quiz on Protein Synthesis (demonstrating our learning in unique and innovative ways, now that is cool), I did 2 Show-Me videos to illustrate the required components of our quiz (I enjoyed trying something new). However, technical difficulties were slightly frustrating (1 video did not work).
• FRI-Sorting out technical difficulties from previous class, Play-doh/technical model of Fluid Mosaic Cell Membrane Model (I chose the new school method of technology for this one and used Whiteboard)

P.S. Very happy with my mark of 99 right now :)

Protein Synthesis was the theme of the week... here is a video to outline the process:

http://www.youtube.com/watch?v=41_Ne5mS2ls&feature=related

BIO 12 Reference Fluid Mosaic

Bio 12 Mosaic Cell Membrane

Green heads and blue tail: Phospholipids
Yellow dots: Cholesterol
Red blobs: Glycolipids
Purple blobs on phospholipid head: Glycoproteins
Transport Proteins: Purple blob nearby
bottom of photo with hole on top (not
Displayed)
Receptor Protein: Indentation on top of purple blob near bottom of photo (not
Displayed)

Protein Synthesis Show Me Assignment

http://www.showme.com/sh/?h=IBZ6ssq

BIO 12 UNIT 1: STUDY NOTES

• ORGANIC MOLECULES CONTAIN CARBON --> carbohydrates, proteins, lipids, nucleic acids, ATP
• monomer = one unit of a molecule and polymer = multiple monomers which form a larger molecule

2 MAIN TYPES OF REACTIONS:

1. DEHYDRATION SYNTHESIS --> Monomers are joined to create polymer(s) with the production of water molecule(s) [water comes from an -H and -OH group taken from the monomers, each monomer can give either an H or OH but NOT BOTH
2. HYDROLYSIS --> Polymer(s) are broken down into smaller monomers and water is given away (i.e. the H and OH link up to separate monomers) [OPPOSITE OF DS]

• Here is a helpful link to elaborate on these processes in the form of animations:

          http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html

BIO 12 UNIT 1: STUDY NOTES

Proteins: Amino acid monomers with an amine (NH2) group and an acid (COOH) group and an interchangeable "R" group [20], Dipeptides contain a PEPTIDE bond, 4 levels of POLYMERS: primary, secondary, tertiary, quaternary (each more complex and distinct than the last), PROTEINS (bigger polymer) have at least 50 a.a.

•  Carbohydrates: Composed of MONOSACCHARIDE monomers such as glucose (C6H12O6), contain ester linkages, distinct hexagonal shaped POLYMERS (POLYSACCHARIDES) [Starch, glycogen, cellulose)
• Lipids: Primarily composed of FATTY ACID CHAIN monomers (saturated or unsaturated fats) [HYDRO-CARBON CHAINS THAT END WITH A -COOH ACID GROUP], polymers include TRIGLYCERIDES [3 Fatty acid chains and glycerol], PHOSPHOLIPIDS [2 Fatty acid chains, glycerol, phosphate group/ head-tail structure], STEROIDS [Sterol Ring composition]  
• Nucleic Acids: Nucleotides are the monomers here composed of PHOSPHATE, SUGAR, and NITROGEN BASE, Polymers: DNA, RNA, etc. ~ATP (special nucleotide with 3 P groups) DISTINCT STRUCTURES (i.e. double-helix of DNA)

                                                                                                     ATP 

BIO 12 UNIT 1: STUDY NOTES

CARBOHYDRATES:

• Empirical formula: CH2O (simplified from C6H12O6)

BIO 12 UNIT 1: STUDY NOTES

CARBOHYDRATES

1. Monosaccharides => Simple sugars (monomers of carbohydrates) (single units of GLUCOSE and its isomers)
2. Disaccharides => Fairly simple sugars, 2 monosaccharides linked with an ester linkage and also has a separate water molecule
3. Polysaccharides => Polymers of carbohydrates comprised of more than 2 monosaccharides, complex

--- 3 TYPES OF POLYSACCHARIDES: Starch, Glycogen, Cellulose

• The link to the below video is great in expanding on the above concepts and linking them to real world biological applications:

http://www.youtube.com/watch?v=_qf_r5EVP6U

BIO 12 UNIT 1: STUDY NOTES

CARBOHYDRATES

1. Starch --> We attain energy from starch from plants by ingesting their nutrients, FAIRLY STRAIGHT-SLIGHTLY BRANCHED CHAINS OF SUGAR MONOMERS
2. Glycogen --> The energy from glycogen is stored within our body (long term), HIGHLY COMPLEX, ABUNDANTLY BRANCHED CHAINS OF SUGAR MOLECULES
3. Cellulose --> SIMILAR TO STARCH, FAIRLY STRAIGHT BUT HAS ALTERNATING LINKAGE PATTERNS UNLIKE STARCH OR GLYCOGEN, fibre (cannot be digested)

BIO 12 UNIT 1: STUDY NOTES

CARBOHYDRATES

Main Fuctions:

• MONOMERS = Chemical energy in Cellular Respiration AND Building blocks for polymers
• DIMERS = Short term energy stores, source of food (plants)
• POLYMERS:

1. Starch - Source of energy from ingesting foods such as plants [GLUCOSE]
2. Glycogen - Stored energy in body (liver and muscles) [excess glucose --> long term energy]
3. Cellulose - Structure for plants (cell wall), FIBRE (cannot be digested BUT helps keep us full and aids in making us excrete wastes)

Below is a link to an awesome video which shows our body and how we use fat and carbohydrates to function, specifically, athletes/sports, this was really interesting and thought provoking:

http://www.youtube.com/watch?v=wHM4X0I4iq0

BIO 12 UNIT 1: STUDY NOTES

LIPIDS

Fatty Acids:

• Saturated Fats and Unsaturated Fats:
• Similarities in molecular structure = Long chains of C attached to H with an ending acidic (COOH) group 
• Differences in molecular structure = Saturated contains NO double bonds between C but Unsaturated do contain double bonds between C

BIO 12 UNIT 1: STUDY NOTES

LIPIDS

• Phospholipids are primarily found on the cell membrane, in fact they compose the cell membrane (Lipid bilayer). This makes them significant in playing a role in one of the most important cellular organelles of the body: membrane which is important because of its ability in SELECTIVE PERMEABILITY 
• Neutral Fats or Triglycerides are often find in the thigh or torso area of the human body. Their significance is providing insulation to keep us warm and also storing reserves of fuel to keep us alive and functioning properly.
• Steroids such as cholesterol are found in brain, nerve tissue, and the blood stream. Cholesterol is important because of its presence at the cell membrane (selective permeability). As well, certain steroids act as chemical messengers in the body and play vital roles in many physiological processes.  Adrenocorticoid Hormones are important as anti-inflammatory agents, helps in retaining ionic compounds in the body, found in the liver. Finally, steroids found in reproductive systems are sexual hormones.Testosterone, estrogen, and progesterone all aid in the sexual and physical development of males and females and aid in the menstrual cycle a female undergoes when bearing a child.  

BIO 12 UNIT 1: STUDY NOTES

BIO 12 UNIT 1: STUDY NOTES

PROTEINS

• Primary Structure: A linear sequence of amino acids, peptide bonding occurs between 2 amino acids. The peptide bond is polar resulting in attractive forces with a slightly negative and positive portion. This leads to our second structure. 
• Secondary Structure: Spiral/Alpha-Helix or pleated sheet shape forms due to the aforementioned -H bonding from the primary structure. 
• Tertiary Structure: The Alpha-Helix than twists and forms into an irregular shape due to ionic, covalent, and H bonding occuring between the R groups of the secondary structure. The shape is very specific to the original sequence or order of the amino acid chains.
• Quaternary Structure: The organization of 2 or more polypeptide chains (tertiary). Similar bonding causes these shapes to form it is just a more complex version of a tertiary structure (i.e. multiple polypeptide). 

Here below is a video to briefly overview these concept:

http://www.youtube.com/watch?v=lijQ3a8yUYQ

BIO 12 UNIT 1: STUDY NOTES

PROTEINS

Functions:

• Structure (present in many forms such as the material of our nail)
• Enzymes (vital to many biological processes/chemical reactions of the body)
• Transport (ex. hemoglobin transporting oxygen of blood in body)
• Hormones (chemical messengers)
• Immunity (protection against foreign bodily invaders)

BIO 12 UNIT 1: STUDY NOTES

Nucleic Acids: ATP

• ATP- Adenosine Triphosphate
• Provides most of the energy to cells and body: chemical (reactions), transport (ions), mechanical (muscle contractions)
• Is a nucleotide similar to that of RNA as both are comprised of ribose sugar, a nitrogen base (adenine) BUT unlike RNA which only has 1 Phosphate group like the name suggests ATP has 3 Phosphate Groups:

• Due to this structural difference ATP is a high energy molecule because its last 2 P groups are easily broken during Hydrolysis. Enzymes break down an ATP molecule when energy is needed and this breakdown provides it with ENERGY. Many processes including Dehydration Synthesis can occur with the attained energy. 
• After an ATP molecule is manipulated for its energy it can be reused after DS when the Phosphate groups reattach (this is in a sense why ATP is sort of the currency $$$ of energy in our body)

BIO 12 UNIT 1: STUDY NOTES

CELL ORGANELLES:

• Cell Membrane- (Plasma) Membrane, phospholipid bi-layer with proteins that determine what enters and exits the cell (SELECTIVE PERMEABILITY)
•  Ribosomes- Create proteins, often bound to ER, small structures, many found in a cell, cell's "workbenches"
• Vesicles- To transport materials throughout and out of a cell, membrane-bound sacs that act as "taxis", come from pinching off of ER, or Golgi body, cell membrane
• Lysosomes- Specialized vesicle like structures that contain digestive enzymes, play role in digestion within a cell
• Nucleus- The "control centre of the cell", contains RNA and DNA, controls cellular activities and protein production in the cell (i.e. DNA), contains chromosomes (hereditary information), double membrane
• Chromosomes- Hereditary information containing organelles found in the nucleus, long DNA threads
• Smooth Endoplasmic Reticulum- Does not have ribosomes attached, tubules that extend from nucleus, controls lipid synthesis, detoxification of drugs, package proteins
• Mitochondria- The energy producers of the cell, create ATP through cellular respiration by using glucose and oxygen to create usable energy (ATP), double membrane
• Golgi Body- Series of flattened vesicles that modify, package, and help secrete proteins (PROTEIN SYNTHESIS and EXOCYTOSIS)
• Vacuoles- Storage of food, water, ions, etc. membrane-bound sacs that are larger in plant cells but more abundant in animal cells
• Nuclear Envelope- Surrounds the nucleus and contains pores, double membrane, protects nucleus, RNA transport of material and information throughout cell via nuclear pores
• Nucleolus- Found within the nucleus, creates ribosomes, synthesizes RNA
• Rough Endoplasmic Reticulum- Has many ribosomes attached, tubules extending from the nucleus, where ribosomes create many proteins

BIO 12: UNIT 1 STUDY NOTES

Cellular Interrelationships

• Photosynthesis and Cellular Respiration: A Vice-versa style relationship
• Photosynthesis uses energy to create glucose but Cellular Respiration uses glucose to create ATP energy: PHOTOSYNTHESIS works as such that the products of cellular respiration (CO2, energy, H2O) are the reactants and its products (C6H12O6, O2) are the reactants of CELLULAR RESPIRATION
• Endocytosis/Intracellular Digestion: Phagocytosis or Pinocytosis occurs with the cell membrane ingesting a molecule, digestive vacuoles store/engulf the molecule and fuse with a lysosome coming from the golgi complex, special digestive enzymes within the lysosome, created from a ribosome, attached to the rough ER and transformed into a lysosome at the golgi complex help break down the molecule leaving residual material to be stored in the vacuole or reaching the cytoplasm. The cell can now use the broken down molecule for several processes and the residual material in the vacuole will eventually undergo exocytosis and secretion.
• Protein Synthesis and Exocytosis: 

1. DNA found within the nucleus controls what protein and enzyme will be made (controls what happens)
2. mRNA copies the DNA code and acts as a "messenger" to tell the ribosome to make the desired protein  
3. After reading the amino acid codons from the mRNA, the ribosome creates the protein
4. A vesicle forms from the smooth ER and transports the protein to the golgi complex
5. The vesicle fuses with the golgi complex, where modification and packaging of the protein occurs
6. A secretory vesicle forms from the golgi complex and transports the protein to the cellular membrane where the contents are released out of the cell (EXOCYTOSIS)

Here is a strong video over viewing some of the major interrelationship between cell organelles:

http://www.youtube.com/watch?v=LP7xAr2FDFU&feature=related

BIO 12 UNIT 1: STUDY NOTES

CELL DIAGRAMS & ELECTRON MICROGRAPHS

• Labeling an Animal Cell:

1. Vacuole
2. Microtubules
3. Nuclear Membrane
4. Nuclear Pore/Nucleoplasm
5. Nucleolus
6. Nucleus
7. Centrioles
8. Cytoskeleton
9. Mitochondria
10. Smooth ER
11. Cell Plasma Membrane
12. Ribosomes
13. Golgi Complex
14. Cytoplasm
15. Lysosome
16. Rough ER

• Labeling a Plant Cell: 

A. Nucleus

B. Nucleoplasm

C. Nucleolus

D. Nuclear Envelope/Membrane

E. Endoplasmic Reticulum

F. Ribosome

G. Vacuole

H. Cytoplasm

I. Chloroplast

J. Cell Wall

K. Cell Membrane

L. Mitochondria

M. Lysosome

N. Golgi Complex

• Electron Micrographs of Plant & Animal Cells:

1. Lysosome
2. Rough ER
3. Chromosome
4. Golgi Body
5. Vacuole
6. Mitochondria
7. Ribosome
8. Nucleolus
9. Nucleus/Nuclear Membrane
10. Centrioles
11. Cell Membrane
12. Cytoplasm

1. Nucleus
2. Nucleolus
3. Cell Membrane
4. Cytoplasm
5. Cell Wall
6. Vacuole
7. Chloroplast

BIO 12: UNIT 1 STUDY NOTES

• The 4 Nitrogenous Bases of DNA:
• Adenine bonding with Thymine
• Guanine bonding with Cytosine 
• DNA Structure:
• DNA is a polymer composed of many simple units (monomers) of nucleotides which are composed of a sugar called deoxyribose, a phosphate group, and one of the four nitrogenous bases
• Complimentary base pairing for DNA means that A bonds with T and C bonds with G (this rule cannot be broken and AT/CG are thus considered "complimentary" pairs)
• DNA often takes the shape of a two-stranded double helix where anti-parallesim occurs in such that one side is different than the other (ex. one side starts with sugar and ends with phosphate but the other starts with phosphate and ends with sugar)
• Due to attractive forces, weak Hydrogen bonds (bonding) form the rungs or connectors of the nitrogenous base pairs

BIO 12: UNIT 1 STUDY NOTES

DNA Replication

--> STEP I: 

• Enzyme DNA Helicase unzips and unwinds the DNA double helix (i.e. H bonds are broken resulting in two separate strands of DNA), these two individual strands are known as DNA templates

--> STEP II:

• Enzyme DNA Polymerase forms covalent bonds between the sugar and phosphate molecule (DS) and helps create the nucleotides of DNA by aiding with complimentary base pairing: free-floating nucleotides attract to their base pairs (leading strand = continuous, lagging strand = okagasaki fragments, shorter portions are joined)

--> STEP III:

• Enzyme DNA Ligase acts as the glue to adhere the base pairs together with H Bonds, this is the last step in creating the finished DNA double-helix

****THE END RESULT IS TWO IDENTICAL COPIES OF DNA THAT ARE CONSIDERED SEMI-CONSERVATIVE BECAUSE ONE STRAND IS FROM THE ORIGINAL PARENT DNA AND THE OTHER IS THE NEW DAUGHTER STRAND FROM DNA REPLICATION (THE FREE FLOATING NUCLEOTIDES WHICH ATTRACTED TO THE PARENT STRANDS)****

* DNA Replication MUST occur for Cell Division to occur in providing each daughter with a copy of the DNA molecule and many copies of DNA must continuously be created for the vitality and functionality of a cell

• HERE IS A VIDEO DESCRIBING DNA REPLICATION:

http://www.youtube.com/watch?v=Luw5_z8mIrI&feature=BFa&list=PL38E7B903667B4498&lf=results_video

BIO 12 UNIT 1: STUDY NOTES

Recombinant DNA

--> DEFINITION: a type of DNA that is artificially created by inserting a strand or more of DNA into a different set of DNA

• Here is a video describing a process of recombinant DNA:

http://www.youtube.com/watch?v=8rXizmLjegI

BIO 12 UNIT 1: STUDY NOTES

The Uses of Recombinant DNA

3 Uses for Recombinant DNA:

1. Agricultural uses such as creating disease or climate resistant crops (genetically modified foods)
2. Develop and produce products such as human hormones (i.e. insulin for diabetics)
3. Gene Therapy (diagnose and treat and research for genetic disorders and diseases)\

• Here is a video highlighting some of the major uses of this technology:

http://www.youtube.com/watch?v=TpmNfv1jKuA

BIO 12 UNIT 1: STUDY NOTES

DNA VS RNA

• Structure:

Similarities:

• Nucleic Acids
• Polymers of nucleotide monomers
• Macromolecules

Differences:

• DNA is double-stranded and larger
• RNA is single-stranded and smaller
• DNA: Deoxyribonucleic acid
• Deocyribose sugar
• RNA: Ribonucleic acid
• Ribose sugar
• DNA has the nitrogenous base of THYMINE which bonds with Adenine
• RNA has the nitrogenous base of URACIL which bonds with Adenine
• Differences in function:
• DNA:
• Located in nucleus
• Contains genetic information
• Template for RNA
• Vital for functionality of cell (controls what happens, what proteins should be made [enzymes])
• RNA:
• Formed in nucleus
• Copies DNA genetic code and delivers material around cell and to specific organelles where the specific processes such as PROTEIN SYNTHESIS may occur (here also is where RNA holds the code to make a specific sequence of amino acids --> POLYPEPTIDE)
• Here is a great video explaining the major similarities and differences of RNA and DNA: http://www.youtube.com/watch?v=MxFNLvl1JOo

BIO 12 Week in Review...

A Glance at the Week of Feb 27, 2012-March 2, 2012:

• Monday: Reviewed our Cells topic with a few worksheets and discussed our quiz (Thursday)
• Tuesday: Began our DNA topic and did a few activities relating to structure: Colouring and Qs, recreating a DNA double helix on paper (cut and paste), and we did notes on DNA Replication
• Thursday: Cells Quiz (I did really well, 10/10), DNA Replication review/colouring and qs, introduced to Recombinant DNA: watched videos, completed an activity modelling the process of incorporating insulin genes into a bacterial plasmid in order to produce insulin (did not go so well for me), started colouring and qs for this topic
• Friday: Did some really interesting stuff with Stitch on our I PADS to recreate DNA and RNA structure (on blog) and also briefly looked at a comparison between DNA and RNA, discussed Unit Test and Study Notes-->THURSDAY 

-A Short week coming up: :) Monday-Wednesday no school, [Thursday is our Unit Test]

BIO 12 RNA Structure

BIO 12 DNA Structure