Biology Notes - Organised from week 1 to week 11, colour coded by each week\'s learning objectives. PDF

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WEEK READING MOODLE REVIEWSEMINARLEARNINCURVEQUIZESWEEK 1 Shapes of valence shells in an atom and their hierarchy DONE DONE DONE 12WEEK 2 DONE DONE Nada 1 2 WEEK 2B Halfway DONE DONE 1 2 WEEK 3 Halfway None DONE 1WEEK 4 DONE DONE DONE 1WEEK 5 Halfway DONE DONE 1WEEK 6 Halfway Except last moodle vide...

Description

WEEK

WEEK 1 - Shapes of

READING

MOODLE

REVIEW SEMINAR

LEARNIN CURVE QUIZES

DONE

DONE

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1 2

WEEK 2

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Nada

WEEK 2B

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WEEK 4

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1

WEEK 5

Halfway

DONE

DONE

1

WEEK 6

Halfway

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WEEK 7

DONE

Except last moodle video DONE

DONE

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None

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WEEK 9

None

DONE

DONE

WEEK 10

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WEEK 11

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1 2 1 2 1 2 1 2 3 1 2 Study Notes

valence shells in an atom and their hierarchy

PROGRESS TRACKER

WEEK 1 Life's Basics: What Is (Not) Life? 1. Recognise the unifying characteristics of life on Earth. 4 Key Characteristics of Living Organisms 1. Complexity - Precise special organisation or cellular structure - Minimum unit of complexity - the cell o Containing the features of  storing and transferring genetic information to grow, develop, replicate  is enclosed in a membrane  undergoes metabolism. 2. Ability to respond to the environment 3. Ability to reproduce - Sexual reproduction - Mitosis 4. Capacity to evolve - Change over generation in response to environmental pressure due to advantage of a particular trait.

More characteristics that are debatable 5. Metabolism - Living things use energy and consume nutrients to carry out chemical reactions to sustain life. 6. Homeostasis - Maintenance of stable internal environment in face of changing external environment 7. Growth and development - Regulated growth that is precise at particular times.

Ecology: the study of how organisms interact with one another and their natural environment. - No living organism is in isolation - Determined through evolution

Prion -

No genetic material Can reproduce by having misfolded protein infect other prions to be misfolded as well

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Infectious genetic material Not able to metabolise or reproduce

Viruses

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Can respond to environment such as in host cell Multiplies

Giruses (giant viruses) - More genetic material that other viruses - Invades host to reproduce Bacteria -

Cell structure Divide and replicate

Protozoan parasites - Cell structure with defined regimes - Lives on or in a host to reproduce

Parasitoids - insects that reproduce by laying eggs in another living organism

What Fuels Life: - energy o all living organisms must be able to generate energy to survive o mostly from chemical bonds

2. Employ the scientific method to study the natural world around us. The Scientific Method Biology uses inductive logic. Observational Study ~ Step 1: Observation Step 2: Hypothesis Step 3: Prediction Step 4: Experiment/ New observations Step 5: Reject or revise hypothesis/ hypothesis supported Experimental Study ~ Test 2+ groups of controlled conditions, manipulating the IV and the DV.

Presenting and Graphing Data ~

3. Describe how atoms combine to form molecules linked by chemical bonds. Atoms (+) protons (-) electron (neutral) neutron Atomic mass is determined by the number of protons and neutrons. - Each proton and electron have a mass of 1. - Electron has negligible mass. - The number of neutrons in each element can vary. Isotopes: atoms of the same element that have different number of neutrons. Ions: eclectically charged atoms. (Ionisation) - An atom that lost an electron is positively charged. - An atom that gained an electron is negatively charged. - Atom loses an election  Cation (+) - Atom gains an electron  Anion (-)

Orbital: where an electron is present most of the time. (2, 8, 8) o 1st shell: spherical with 1 orbital. o 2nd shell: dumbbell shaped 3 orbitals. - Electrons in orbit closer to the nucleus have less energy compared to electrons further from the nucleus. Periodic Table - Arranged in increasing atomic number. - Horizontal: row - Vertical: group - First 3 horizontal rows’ elements in the same row have the same number of shells - Members of the same group (vertical) all have the same number of electrons in their outer shell - Left of PT: low electronegativity - Right of PT: high electronegativity *Atoms can combine with other atoms to form Molecules through chemical bonds. Valence electrons: electrons farthest from the nucleus with the highest energy level which determines an atom’s ability to combine with other atoms. When atoms combine with each other atoms form a molecule and shares valence electrons with each other.

Furthest shell from the nucleus is called the Valence Shell. Molecular Orbital: the merged orbital where valence electrons are shared to form one single orbital containing a full complement of two electrons.

Double Bond: when 2 adjacent atoms share 2 pairs of electrons, resulting in 4 orbitals occupying a single electron merge to form two molecular orbitals. Octet Rule: the rule for forming stable molecules (2 8 8)

Polarity

TYPES OF MOLECULAR BONDING: A) (Nonpolar) Covalent bond: when 2 atoms EQUALLY share electrons. Eg: H + H  H2 a. Single bond b. Double bond - Covalent bonds tend to be non-polar - Molecules are more likely to form when they have similar electronegativity Example of Covalent Bond: Glucose (C6H12C6) o Atoms are connected via covalent bonds o Glucose formed by the carbon backbone o Most important source of energy in all organisms o Cells harvest energy by the breaking of glucose bonds

Electronegativity: a difference in the ability of atoms to attract electrons, which increases across a row in the periodic table. As number of protons increase, electrons are held more tightly to the nucleus. Eg: O is more electronegative than H and attracts electrons more readily than H. Each column on the PT has a 0.5 electronegativity between them

B) Polar covalent bond: ENQAUAL sharing of electrons. a. Polar covalent bond (+)  Larger the electronegativity charge, stronger the polar covalent bond b. Non-polar covalent bond (-) = a covalent bond between atoms that

C) -

Ionic Bond: bond between oppositely charged ions. Usually bonds between metals and non-metals Large difference in electronegativity Relatively strong bonds, unless in water as water is polar when an atom of very high electronegativity is paired with an atom of very low electronegativity, the difference in electronegativity is so great that the electronegative atom “steals” the electron from its less electronegative partner. In this case, the atom with the extra electron has a negative charge and is a negative ion. The atom that has lost an electron has a positive charge and is a positive ion.

D) Hydrogen Bond: interaction between hydrogen atom and an electronegative atom. Weakest molecular bond. Influences the structure of liquid water and ice. Ice – water molecules becomes hydrogen bonded to 4 water molecules, forming an open crystalline structure. Melting – hydrogen bonds destabilize and break, making water denser than ice. Chemical Reactions - When reactants transform into different molecules, into products. - During a chemical reaction, atoms keep their identity but change which atoms they are bonded to. - The closer the atom is to a full valence shell (more towards to left or right of the PT), the more reactive they become

Solubility

What determines solubility?  Intermolecular forces between the solute and the solvent o Inter= between molecules o Intra= within molecules  Formation of hydrogen bonds o Polarity

4. Describe the properties of water as the medium of life. Water is polar - Contains polar covalent bonds, with uneven distribution of electrons. Hydrophilic: water loving. - Hydrophilic compounds are polar and dissolves in water. - Acts as a good solvent Hydrophobic: water hating. - Hydrophobic compounds are nonpolar Cohesion: tend to stick to one another - Resulted from water being made up of hydrogen bonds - Cohesion leading to high surface tension - Ice molecules are formed in lattice patterns, which is less dense than water molecules. Water’s response to being heated - When water is being heated, energy is added by heating to break hydrogen bonds - The abundant hydrogen bonds make water more resistant to temperature changes than other substances

WEEK 2 – MACROMOLECULES 1. Determine how organic macromolecules which include proteins, nucleic acids, carbohydrates and lipids, are built from simpler units. -

Organic Molecules: carbon-containing molecules.

Carbon Carbon-Based Molecules are Structurally and Functionally Diverse  Carbon atoms can link with each other by covalent bonds to form long chains o Chains can be branched, 2 carbons at the ends of the chain, or within the chain can link to form a ring. o Eg: C2H6 + C2H6  C4H12 (ethane)  Carbon atoms can link through single covalent bonds, or double covalent bonds.  Carbon-containing molecules can adopt a wide range of arrangements (isotopic)  Carbon atoms form 4 covalent bonds. o A carbon atom behaves as if it has 4 unpaired electrons, due to the fact that one of the electrons in the outermost spherical orbital moves into the empty dumb shell-shaped orbital. In this process, the single large spherical orbital and three dumb bell-shaped orbitals change shape, becoming four equivalent hybrid orbitals, each with one electron o Eg: C + H4  CH4 (methane). The bonds between the carbon and hydrogen can rotate freely about their axis.  The carbon atom lies at the centre of the 3D structure, this structure is called a tetrahedron.

Carbon-Based Molecules - All are large molecules that consists of polymers (complex molecules made up of repeating simpler units connected by covalent bonds.).  Proteins o provide structural support and acts as a catalyst that facilitates chemical reactions. o Polymer for: amino acids.  Nucleic Acid o Encodes and transmits genetic information. o Polymer for: nucleotides.  Carbohydrates o Provides a source of energy and make up the cell wall in bacteria, plants, algae. o Polymer for: sugars  Lipids o Make up cell membranes, store energy, and act as signalling molecules. o Mad up of fatty acids and organic molecules.

Functional Groups add Chemical Character to Carbon Chains Functional Groups = groups of one or more atoms that have particular chemical properties on their own, regardless of what they are attached to. Eg: - Amine (=NH) - Amino (-NH2) - Carboxyl (-COOH) - Hydroxyl (-OH) - Ketone (=O) - Phosphate (-O-PO3H2) - Sulfhydryl (-SH) - Methyl (-CH3)

*The nitrogen, oxygen, phosphorus, sulfur atoms in functional groups are: - more electronegative than the carbon atoms. - Functional groups containing these atoms are polar, hence many functional groups, as well as atoms attaching to the functional groups become polar. o With the exception of methyl group (-CH3) which is nonpolar. o Molecule must be polar in order to become soluble in the cell’s aqueous environment o The polar nature of functional groups gives them the ability to become reactive.

Proteins - Made up of amino acids linked covalently to form a chain.  -

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Amino Acids Contains a central carbon atom – a (alpha) carbon. The alpha carbon is linked to 4 groups o Amino group (-NH2) o Carboxyl group (-COOH) o Hydrogen atom (H) o R Group / side chain (varies for each amino acid)

Charges of an amino acid Amino and carboxyl group are ionised, charged. o Amino group gains a proton  -NH+3 o Carboxyl group loses a proton  -COOHence the pH commonly found in a cell is 7.4.

Bonds in Protein (peptide bonds) - The carbon atom in the carboxyl group -------covalently joins with……..the nitrogen atom in the amino group with the next amino acid by covalent bonds. - These covalent bonds are called peptide bond. - The formation of peptide bonds involves the loss of a water molecule o Carbon atom from carboxyl group releases 1 Oxygen atom o Nitrogen atom of the amino group releases 2 H atoms

Nucleic Acid - They are large molecules that carries information in the sequence of nucleotides that make them up. - Nucleotides bonded covalently

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Nucleotides Composition 5 – carbon sugar o Sugar in DNA: deoxyribose  Has a H atom on the second carbon. o Sugar in RNA: ribose  Has a -OH group on the second carbon. Nitrogen containing group (Base) o Pyrimidine base – single ring structure (smaller).  Cytosine (C)  Thymine (T)  Uracil (U) o Purine base – double ring structure.  Guanine (G)  Adenine (A) Phosphate group

*DNA: A, T, C, G. *RNA:A, U, C, G. Bonds in Nucleic Acid - Each adjacent pair of nucleotides are connected by a phosphodiester bond. o Formed when a phosphate group is covalently bonded to the sugar unit in another nucleotide. o The bond releases 1 water molecule

DNA -

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Consists of 2 strands of nucleotides twisted around to form a double helix. o With the sugar-phosphate backbone facing outwards around the double helix, and the bases pointing inwards. The baes forms specific purine-pyrimidine pairs that are complementary. o A–T o C–G  Formed from hydrogen bonds.

Carbohydrates - Made up of C, H, O atoms in a 1:2:1 ratio –CH2O. - Made up of saccharides (sugars). - Water soluble. Types of Carbohydrates  Monosaccharide – C6H12O6. o Bonded through glycosidic bonds through the loss of a water molecule. o Unbranched carbon chains with  aldehyde (HC=O) group  aldoses  ketone (C=O) group  ketoses o other carbons each carry one hydroxyl group (-OH), and one hydrogen atom (H) o linear in structure,  with aldehyde and aldehyde group is at the top o if linear in structure,  structured in ring form  the carbon in aldehyde or ketone groups forms a covalent bond with the O of OH group, carried by another carbon in the same molecule. o Eg: glucose.  Disaccharide o 2 monosaccharides s linked together through covalent bonds. o Eg: (monosaccharide) glucose + fructose  (Disaccharide) sucrose - table sugar.  Oligosaccharides o 3-10 monosaccharide molecules.  Polysaccharide o Polymers that provides long-term energy storage, and structural support to cells such as cellulose in plant cell walls. o Eg: starch, glycogen  Complex Carbohydrates o Long branched chains of monosaccharides.

Basic Monosaccharides

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All C6H12O6, but in different configurations. Glucose o Product of photosynthesis. Galactose o Found in dairy. Fructose o Commercial sweetener.

Bonds of Carbohydrates - Carbohydrates are made of chains of monosaccharides Types of Monosaccharides  Aldose o Contains Aldehyde (HC=O) group 

Ketoses o Contains Ketone (C=O) group

Breaking down of Carbohydrates through HYDROLYSIS - Add one water molecule to break covalent bond between 2 monosaccharides and get 2 individual monosaccharides. Dehydration - Lose a water to covalently bond 2 monosaccharides to form a disaccharide.

Lipids = chemically diverse group of molecules that shares a property instead of a structure. - Hydrophobic molecules - Can group together to function as storage compounds - Can be found in cellular membranes - Nonpolar A) Triacylglycerol Structure~ - A glycerol head group. - Bonded through ester links to 3 hydrophobic fatty acid tails. o Uncharged. Bonding: the carboxyl end of each fatty acid chain attaches to glycerol at one of the OH groups, releasing a molecule of water. - The hydrocarbon chains of fatty acids do not contain polar covalent bonds. Examples~ - Vegetable oil

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Animal fat

Types of Fatty Acid - Triacylglycerol can contain different types of fatty acids attached to the glycerol backbone. - fatty acids differ in their hydrocarbon chain lengths. - Most fatty acid contains an even number of carbon atoms o Due to the synthesised by stepwise addition of 2-carbon units. 

Saturated o No double bonds o Linear o Tightly packed o Eg: butter (solid in room temp as can be tightly packed)

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Non-saturated o Additional double bonds  In either cis or trans configuration  Cis: contains hydrogen atoms on the same side of the carbon chain, leading to bent carbon chain.  Trans: contains hydrogen atoms on the opposite side of the carbo chains, leading to linear shape, makes it harder to metabolise and break down trans fats. o Bent and kinks in carbon chains o Eg: olive oil (liquid in room temp)

B) -

Steroids Composed of 20 carbon atoms Bonded to form fused rings Hydrophobic Serves as a precursor for the synthesis of steroid hormones (estrogen, testosterone) Eg: cholesterol

C) Phospholipid - Charge phosphocholine group (hydrophilic, negatively charged) to 2 fatty acid tails (hydrophobic) - The combination of hydrophilic and hydrophobic molecules makes it an amphipathic molecule. - Found in cellular membrane as a bilayer.

Van der Waales force - When uncharged molecules are in constant motion leading to regions of slight positive and slight negative charge. - Leading for the molecule to be temporarily polarized molecules.

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The molecules then weakly bind to one another due to attraction of opposite charges. The force acts together to help stabilise molecules.

Fatty Acid’s Melting Point  Fatty acid length increase  Van der waales force increases  MP increases - It is due to the van der waales forces, which make the melting point of fatty acids depending on their length, and level of saturation. - Length of hydrocarbon chain increase  number of van der waals interaction between the chain increases  melting point increases (as more energy is needed to break the number of van der waales force).  Double bonds decrease MP - The kinds created by double bonds increases the tightness of packing of molecules - Reduce number of intermolecular interactions - Melting point decreased

2. Identify biologically important macromolecules and their functions within a cell or organism. Functions of Macromolecules in the cell: Function of Protein:  Protein acts as a catalyst (enzyme) the accelerates the rates of chemical reactions.  Protein acts as structural components necessary for cell shape and environment. Function of Nucleic Acid  DNA (deoxyribonucleic acid) a. Genetic material in all organisms that is transmitted from parent to offspring. b. Contains information needed to specify the amino acid sequence of all the protein synthesized in an organism.  RNA (ribonucleic acid) c. Helps with protein synthesis d. Regulates gene expression. Function of Carbohydrates  Primary source of energy for metabolism.  Structural support to cells such as cellulose in plant cell walls.

Lipids  Storage compounds  Used in cellular membranes to act as barriers

3. Describe the chemical composition and structure of DNA and explain how this structure facilitates its biological role.

4. Apply theoretical knowledge of chemical bonding to the form and function of proteins.

Energy = the capacity to do work - Energy is neither created nor destroyed, but stored. - Systems will always increase towards anentropy

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o Energy involved in transformation, some energy will be lost in heat and hence reduces available energy. Kinetic – energy in motion. Eg: movement in muscles Potential – c...