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Atoms and Cells

Atoms and Cells

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ATOMS AND CELLS

Four organic elements H O N C Hydrogen (H) Oxygen (O) Nitrogen (N) Carbon (C)

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Atomic weight (Mass) Atomic Number Electron shells

Isotope Ions Cation Anion Acid

Total number of protons and neutrons in nucleus Number of protons OR electrons = always the same and equal First layer – max 2 electrons Second layer – max 8 electrons Third layer - max 8 electrons Only need to know first three layers Variation of standard element with different number of neutrons and different atomic weight to normal Losing or gaining an electron to change charge creates an ion Losing an electron creates a positively charged ion (Losing weight is always good) Gaining an electron creates a negatively charger ion (Gaining weight is bad) Becomes ionized when placed in solution – produces positively charged hydrogen ions (H+). Considered a proton donor Produces negatively charged hydroxide ions (OH)-. More alkaline than acids Known as proton acceptors Scale 0 -14 – acid to alkaline Neutral pH = 7 Basic substance pH  7 Acid substance  7 Skin pH about 5 Blood pH about 7.4

Base

pH (potential of Hydrogen)

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ATOMS AND CELLS
BONDS Ionic Bond
This chemical bond involves a transfer of an electron, so one atom gains an electron while one atom loses an electron.

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One of the resulting ions carries a negative charge, and the other ion carries a positive charge. Because opposite charges attract, the atoms bond together to form a molecule The most common bond in organic molecules, a covalent bond involves the sharing of electrons between two atoms. The pair of shared electrons forms a new orbit that extends around the nuclei of both atoms, producing a molecule. There are two secondary types of covalent bonds that are relevant to biology: Polar Hydrogen Two atoms connected by a covalent bond may exert different attractions for the electrons in the bond, producing an unevenly distributed charge.
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Covalent Bond

Polar Bond

 an intermediate case between ionic and covalent bonding, with one end of the molecule slightly Negatively charged and the other end slightly positively charged.
 Resulting molecule is neutral; at close distances the uneven charge distribution can be important. Water is an example of a polar molecule; the oxygen end has a slight positive charge whereas the hydrogen ends are slightly negative. Polarity explains why some substances dissolve readily in water and others do not. Because they’re polarized, two adjacent H2O (water) molecules can form a linkage, where a (electronegative) hydrogen atom of one H2O molecule is electro statically attracted to the (electropositive) oxygen atom of an adjacent water molecule. molecules of water join together transiently in a hydrogen-bonded lattice. Hydrogen bonds have only about 1⁄20 the strength of a covalent bond, yet even this force is sufficient to affect the structure of water, producing many of its unique properties, such as high surface tension, specific heat, and heat of vaporization.
Hydrogen bonds are important in many life processes, such as in replication and defining the shape of DNA molecules.

Hydrogen Bond

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ATOMS AND CELLS
Reactants Product Compounds Organic compound Substances that go through changes in number or types of arrangements of atoms within the molecule Substances produced by reaction Elements combined through chemical reaction Also contains carbon Four families of organic compounds important to biological function  Carbohydrates  Lipids  Proteins  Nucleic acids Carbohydrates

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Formed by chemical reaction process of concentration, or dehydration synthesis and broken apart by hydrolysis (Addition of water). Several sub-categories  Monosaccharides  Disaccharides  Polysaccharides

Monosaccharides

Monosaccharides, also called monomers or simple sugars, are the building blocks of larger carbohydrate molecules and are a source of stored energy Key monomers include glucose (also known as blood sugar), fructose, and galactose. These three have the same numbers of carbon (6), hydrogen (12), and oxygen (6) atoms in each molecule — C6H12O6 — but the bonding arrangements are different. Molecules with this kind of relationship are called isomers sugars formed by the bonding of two monosaccharides, including sucrose (table sugar), lactose, and maltose are formed when many monomers bond into long, chain-like molecules. Glycogen is the primary polymer in the body; it breaks down to form glucose, an immediate source of energy for cells.

Disaccharides Polysaccharides

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ATOMS AND CELLS
Lipids            Proteins

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Known as fats Contain oxygen, carbon and hydrogen - sometimes phosphorous and nitrogen Mainly nonpolar bonds  insoluble in water Six times more stored energy than carb molecules Hydrolysis  form glycerol and fatty acids Fatty acid – long chain of carbon atoms with hydrogen attached Carbon chain – full number of hydrogen atoms  saturated fat (eg butter, lard) Carbon chain less than full number of hydrogen atoms  unsaturated (eg margarine, vegetable oils) All fatty acids contain carboxyl or acid group –COOH at the end of each carbon chain Phospholipids contain phosphorous and often nitrogen to form and layer in the cell membrane Steroids are fat soluble compounds such as vitamin A or D and hormones to regulate metabolic processes Among the largest molecules  up to 40 million atomic units Always contain hydrogen, oxygen, nitrogen and carbon (HONC)  sometimes sulphur and phosphorous Human body builds up protein molecules using 20 different kinds of smaller molecules called amino acids Amino acids  each is comprised of an amino group –NH2, a carboxyl group -COOH, with a carbon atom between them. Amino acids link together by peptide bonds to form long molecules called polypeptides  then become or assemble to become proteins. Examples of proteins in the body include antibodies, haemoglobin and enzymes (catalysts that accelerate reactions in the body.

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ATOMS AND CELLS

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Nucleic Acids

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Found mainly in cell’s nucleus  body’s genetic blueprint Composed of nucleotides – made up of five carbon sugar (deoxyribose or ribose), a phosphate group and nitrogenous base DNA (deoxyribonucleic acid) - nitrogenous base made up of adenine, thymine, cytosine and guanine  always pair off A-T, C-G RNA (ribonucleic acid)  occurs in a single strand – thymine is replaced by uracil – nucleotides pair off A-U, C-G DNA – double stranded helix – three dimensional structure From Greek “metable”  change Refers to the chemical reactions that occur in the body Either catabolic or anabolic reactions Catabolic – break down food into energy Anabolic – use of energy to build up compounds the body needs Cellular metabolism – chemical alteration of molecules of the cell Enzymes – accelerate chemical reactions without being changed Substrates – molecules that chemicals react with Stores energy until the cell needs it Three phosphate groups attached to a nitrogenous base of adenine ATP’s energy is stored in high energy bonds that attach to second and third phosphate groups. Energy is produced when one or two of the phosphate groups are removed, releasing energy and converting ATP into either the two phosphate molecule adenosine diphosphate (ADP) or single phosphate molecule adenosine monophosphate Metabolic reactions later reattach phosphates to reform ATP molecule until energy is needed again

Metabolism

Adenosine Triphosphate (ATP)

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ATOMS AND CELLS
Oxidation-Reduction Important pair of reactions that occur in carbohydrates, lipid and protein metabolism Oxidised

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Loses electrons and hydrogen ions  removing hydrogen atom from each molecule Gains electron and hydrogen ions  adds a hydrogen atom to each molecule Oxidation and reduction occur together  one oxidised, the other reduced

Reduced

Electron transport chain Carbohydrate metabolism

This chemical reaction pairing to transport energy is a process known as the respiratory chain or, electron transport chain      Cellular respiration activities  really glucose metabolism  provides energy that is stored in ATP molecules. Oxidation process  energy released from molecules and transferred to other molecules Cellular respiration  occurs in every cell in the body and is cells source of energy Complete oxidation of glucose will produce 38 molecules of ATP Occurs in three stages – glycolysis, the Krebs cycle and the electron transport chain

Glycolysis

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From the Greek glyco (sugar) and lysis (breakdown), this is the first stage of both aerobic (with oxygen) and anaerobic (without oxygen) respiration. Using energy from two molecules of ATP and two molecules of NAD+ (nicotinamide adenine di-nucleotide), glycolysis uses a process called phosphorylation to convert a molecule of six-carbon glucose — the smallest molecule that the digestive system can produce during the breakdown of a carbohydrate — into two molecules of three-carbon pyruvic acid or pyruvate, as well as four ATP molecules and two molecules of NADH (nicotinamide adenine dinucleotide). Taking place in the cell’s cytoplasm, glycolysis doesn’t require oxygen to occur. The pyruvate and NADH move into the cell’s mitochondria, where an aerobic (with oxygen) process converts them into ATP.

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ATOMS AND CELLS
The Krebs Cycle

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Electron Transport chain

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Also known as the tricarboxylic acid cycle or citric acid cycle This series of energy producing chemical reactions begins in the mitochondria after pyruvate arrives from glycolysis. Before the Krebs cycle can begin, the pyruvate loses a carbon dioxide group to form acetyl coenzyme A (acetyl CoA). Acetyl CoA combines with a four-carbon molecule (oxaloacetic acid, or OAA) to form a six carbon citric acid molecule that then enters the Krebs cycle. The CoA is released intact to bind with another acetyl group. During the conversion, two carbon atoms are lost as carbon dioxide and energy is released. One ATP molecule is produced each time an acetyl CoA molecule is split. The cycle goes through eight steps, rearranging the atoms of citric acid to produce different intermediate molecules called keto acids. The acetic acid is broken apart by carbon (or decarboxylated) and oxidized, generating three molecules of NADH, one molecule of FADH2 (flavin adenine dinucleotide), and one molecule of ATP. The energy can be transported to the electron transport chain and used to produce more molecules of ATP. OAA is regenerated to get the next cycle going, and carbon dioxide produced during this cycle is exhaled from the lungs. Series of energy compounds attached to the inner mitochondrial membrane Molecules in the chain are called cytochromes Electron transferring proteins contain a heme (iron group) Hydrogen from oxidised food sources attach to coenzymes  combine with molecular oxygen Energy produced is used to reattach inorganic phosphate groups to ADP or ATP molecules Pairs of electrons transferred to NAD  produce three molecules of ATP by oxidative phosphorylation  after first phosphorylation  yield is only two ATP Oxidative phosphorylation is important because it makes energy available in a form cells can use End of chain – two + charged hydrogen molecules combine with to electrons and an atom of oxygen to form water Final molecule to which electrons are passed is oxygen Electrons are transferred from one molecule to the next, producing ATP molecules.

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ATOMS AND CELLS
Lipid Metabolism    

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Only portions of process involved in carbohydrate metabolism Lipids contain 99% of bodies stored energy More inclined to be stored in adipose tissue When ready to metabolise lipids  catabolic reactions break apart two carbons from the end of the fatty acid chain to form Acetyl CoA  enters Krebs cycle to produce ATP Reactions continue to strip two carbon atoms at a time until the entire fatty acid chain is converted to CoA.

Protein Metabolism

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Focuses on the production of amino acids used for synthesis Apart from energy released into the electron transport chain during protein metabolism, by products such as ammonia and keto acid are also produced The liver converts ammonia to urea, which is carried to the kidneys for elimination Keto acid enters the Krebs cycle and is converted to pyruvic acid to produce ATP Severe soreness and fatigue in muscles after strenuous exercise is the result of lactic acid build up during anaerobic respiration. Glycolysis continues because it doesn’t need oxygen to take place. Glycolysis does need a steady supply of NAD+, which usually comes from the oxygen -dependent electron transport chain converting NADH back into NAD+. In its absence, the body begins a process called lactic acid fermentation, in which one molecule of pyruvate combines with one molecule of NADH to produce a molecule of NAD+ plus a molecule of the toxic by product lactic acid.

Lactic Acid

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ATOMS AND CELLS
Cytology Eukaryotic cells The Cell “Cyto” = cell, the study of cells Found in all living animals except viruses and bacteria

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Have a semi-permeable membrane known as the plasma membrane Gel filled sac with nuclei and organelles inside Nucleus Controls and directs the activity in the cell

Cytosol

Fluid material found in the gel like cytoplasm that fills the cell

The cell membrane              Selective permeability Bilayer of phospholipids interspersed with protein molecules Outer surface hydrophilic heads Inside, between two layers, hydrophobic, non polar tails made up of fatty chains Cholesterol molecules between phosphate layers add stability and make less permeable to water soluble substances Cytoplasm and the matrix where cells live are mainly water Polar heads attract polarised water while non-polar tails lie between the layers, shielded from water and creating dry middle layer Membrane interior is made up of oily fatty acid molecules that are electro statically symmetric or non polarised Lipid soluble molecules can pass through oily fatty layer, but not water Phospholipids also known as amphipathic molecules due to their polar and non-polar regions Cell membrane is designed to hold the cell together  distinct functional unit of protoplasm. Can fix minor tears, but major damage will cause the cell to disintegrate Allows some movement across cell membrane by diffusion, osmosis or active transport.

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ATOMS AND CELLS
Diffusion

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Spontaneous migration of molecules or other particles from areas of higher concentration to lower concentration

High  Low  Equilibrium  (both directions)    Rate of movement depends on temperature, size of molecule (smaller = faster) Is a form of passive transport – no expenditure of cell energy Molecule can diffuse through cell membrane if it is (this is known as simple diffusion);  Lipid soluble  Uncharged  Very small  Assisted by carrier molecule Facilitated diffusion – the cell membrane allows non polar molecules (don’t readily bond with water) to flow from high to low concentration areas via channel proteins that create diffusion friendly openings for molecules to diffuse through

Osmosis    Passive transport similar to diffusion  solvent moving through semi permeable membrane from higher lower concentration Water is called universal solvent Solvents are two parts Solvent (liquid) and solute (substance dissolved in solvent)   Water is a polar molecule  small enough to pass through pores of most cell membranes, but will not pass through lipid bilayer Osmosis occurs where there is a different molecular concentration of water on the two sides of the membrane  solvent (water) is allowed to pass through but keeps out the particles (solute) dissolved in the water Osmolarity is the term used to describe concentration of solute particles per litre. As water diffuses into a cell, hydrostatic pressure builds  pressure becomes equal to and balanced by the osmotic pressure outside.

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ATOMS AND CELLS
Isotonic Solution

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Same concentration of solvent and solute as found inside cell  equilibrium  equal flow in and out of the cell

Hypotonic Solution

Less solute and higher water potential than inside the cell. Eg. If human cell placed in solution of distilled water  diffusion would occur until cell bursts

Hypertonic Solution

Opposite to hypotonic  water flows out and cell would shrink

Active Transport.  Movement across semi-permeable membrane against normal concentration gradient i.e. opposite of diffusion and osmosis – moves from LOW  HIGH concentration gradient Requires expenditure of energy released from ATP molecule Protein molecules in the hydrophilic heads of the outer layer detect and move compounds through the membrane Carrier or transport proteins interact with passenger molecules and use ATP supplied energy to move them against the gradient Carrier molecules – usually amino acids and ions – combine with transport molecules to pump them against the gradient Active transport lets cells obtain nutrients that can’t pass through the membrane by other means Secondary active transport and processes that are similar to diffusion but instead use imbalances in electrostatic forces to move molecules across the membrane.

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ATOMS AND CELLS
Nucleus

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Largest cellular organelle  the first to be discovered by scientists  accounts for about 10% of the volume of the cell and holds a complete set of genes

Outermost part is the nuclear envelope  phospholipid bilayer  selectively permeable barrier

Inside phospholipid bilayer is the fluid filled space called the perinuclear cistema

Large pores in the barrier allow free movement in molecules and ions  large protein molecules included

Nuclear lamina  intermediate filaments lining the surface of the envelope  functions in the disassembly and reassembly of the nuclear membrane during mitosis and bins the membrane in the endoplasmic reticulum.

Nucleoplasm  clear viscous material that forms the matrix in which the organelles of the nucleus are imbedded. Nucleus contains DNA in structures called chromatin or chromatin structures Chromatin contract during cell division making chromosomes Chromosomes contain DNA  encoded with genetic information needed to direct cells activities Nucleolus  main subnuclear body  sores RNA molecules  ribosomes  messenger RNA (mRNA).

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ATOMS AND CELLS
ORGANELLES AND THEIR FUNCTIONS (Part 1) Cytoskeleton

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Network of fibrous proteins  changes  shifting according to activity of cell  maintains cell shape, enables movement, anchors organelles, directs flow of cytoplasm Rod like structures 5-8 nanometres wide that consist of a stacked protein called actin  provide structural support and have a role in organelle movement and cell division Strongest and most stable part of the cytoskeleton  10 nanometres wide  interlocking proteins  including keratin  maintain cell integrity and resist pulling forces of the cell 25 nanometres in diameter  protein tubelin  grow with one end embedded in centrosome near nucleus.  Cilia, flagella and centrioles

Microfilaments

Intermediate filaments

Hollow microtubules

Organelles Cilia and flagellum

Provide structural support and have a role in cell and organelle movement as well as division Little organs Found on cells exterior – organelles that help with movement Flagellum – whip like projection use for movement eg sperm.

Centrosome

Located next to the nucleus  two centrioles  sprouts microtubules that function in separating genetic material during dell division Direct contact with cell nucleus  transports proteins and RNA  membrane bound canals and cavities that extend from nuclear membrane to cell membrane  site of lipid and protein synthesis Rough ER – dotted with ribosomes on surface Smooth ER – no ribosomes on surface

Endoplasmic reticulum (ER)

Golgi apparatus

Flattened sacs or membranes connect to ER  located near nucleus  used for storing, packing and modification of proteins for secretion to various destinations in the cell Page 13 of 16

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ATOMS AND CELLS
ORGANELLES AND THEIR FUNCTIONS (Part 2) Lysosomes

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Tiny membranous sac containing acids and digestive enzymes  breaks down large food molecules eg proteins, nucleic acids, carbs, into material the cell can use  destroy foreign particles  removes non-functioning structures   powerhouse of the cell rod like structure with two membranes  smooth outer and invaginated (folded) inner  divides cell into compartments Inward folding devices are called christae Critical functions – respirating and breaking down food Releases energy stored in ATP ,olecules in the mitochondrion to accelerate chemical reactions

Mitochondrion

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Ribosomes

Vacuoles

Endocytosis New proteins

Found on the ER or floating in cytoplasm 60% RNA, 40% protein Translate genetic material on RNA molecule to synthesise protein molecule  more common in plant cells  open spaces in cytoplasm sometimes carry materials to cell membranes for discharge  membranous sacs formed when food masses are pinched off from cell membrane and pass into the cytoplasm of the cell – ENDOCYTOSIS  vacuum cleaners – help to remove structural debris, harmful materials and export unwanted materials “Within the cell” (Greek) – requires energy  Building blocks of all living systems.  “proteios” – holding first place (Greek)  New proteins are synthesised by the cell, beginning in the nucleus where the gene code is transcribed to message RNA (mRNA).  mRNA nuclear pores to rough ER  ribosomes translate message one base pair at a time  Ribosomes use tRNA (transfer RNA) to get required amino acid and link it together through peptide bods to form proteins   

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ATOMS AND CELLS
Cell Cycle – known also as CDC or cell division cycle.

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Extends from the beginning of one cell division to the beginning of the next cell division Two distinct phases o Interphase – “resting phase”  Actively growing and carrying out normal metabolic function and preparing for cell division. o Mitosis  Period of cell division  Cell life cycle varies from short to long, or no replication  Continuiung process Interphase divided into subphases  G1 – Growth  creating organelles, begins metabolism synthesis protein  S – Synthesis – DNA replication occurs – single double helix DNA molecule in nucleus become two sister chromatids  centrosome duplicated  G2 – gap = enzymes and proteins needed for cell division produced during this subphase.

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ATOMS AND CELLS

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Prophase o First active phase of mitosis o Nucleus, nuclear membrane, nucleoplasm and nucleoli begin to disappear o Centrioles push apart to opposite ends of the nucleus o Form poles and mitotic spindle between them and asters  radiate from the poles into the cytoplasm o Chromatin shorten and coil  form chromosomes o Chromosomes divide into chromatids and remain attached to centromere o Tubules called kinetochre interact with spindle to ensure each daughter has full set of chromosomes o Start to migrate towards equatorial line, imaginary line between the poles Metaphase o Nucleus is gone o Chromatids have lined up on equatorial line and attached to the mitotic spindle by the centromere Anaphase o Centrosomes split  separating duplicate chromatids and forming chromosomes o Spindles shorten pulling chromosomes towards opposite poles o Cell elongates o Late anaphase  cleavage furrow forms  this is the site of cytokenisis.

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