atoms and cells

ATOMS AND CELLS

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Four organic elements

H Hydrogen (H)

O Oxygen (O)

N Nitrogen (N)

C Carbon (C)

Atomic weight (Mass) Total number of protons and neutrons in nucleus

Atomic Number Number of protons OR electrons = always the same and equal Electron shells First layer – max 2 electrons

Second layer – max 8 electrons Third layer - max 8 electrons Only need to know first three layers

Isotope Variation of standard element with different number of neutrons and different atomic weight to normal

Ions Losing or gaining an electron to change charge creates an ion Cation Losing an electron creates a positively charged ion

(Losing weight is always good) Anion Gaining an electron creates a negatively charger ion

(Gaining weight is bad) Acid Becomes ionized when placed in solution – produces positively charged

hydrogen ions (H+). Considered a proton donor

Base Produces negatively charged hydroxide ions (OH)-. More alkaline than acids Known as proton acceptors

pH (potential of Hydrogen)

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

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BONDS Ionic Bond

This chemical bond involves a transfer of an electron, so one atom gains an electron while one atom loses an electron. 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

Covalent Bond

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

Polar Bond Two atoms connected by a covalent bond may exert different attractions for the electrons in the bond, producing an unevenly distributed charge. 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.

Hydrogen Bond

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.




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Reactants Substances that go through changes in number or types of arrangements of

atoms within the molecule Product Substances produced by reaction

Compounds Elements combined through chemical reaction

Organic compound

Also contains carbon Four families of organic compounds important to biological function

Carbohydrates Lipids Proteins Nucleic acids

Carbohydrates 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

Disaccharides sugars formed by the bonding of two monosaccharides, including sucrose (table sugar), lactose, and maltose

Polysaccharides 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.




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Lipids 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

Proteins 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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Nucleic Acids 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

Metabolism 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

Adenosine Triphosphate (ATP)

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




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Oxidation-Reduction Important pair of reactions that occur in carbohydrates, lipid and protein metabolism Oxidised Loses electrons and hydrogen ions removing

hydrogen atom from each molecule

Reduced Gains electron and hydrogen ions adds a hydrogen atom to each molecule

Oxidation and reduction occur together one oxidised, the other reduced

Electron transport chain

This chemical reaction pairing to transport energy is a process known as the respiratory chain or, electron transport chain

Carbohydrate metabolism

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 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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The Krebs Cycle

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.

Electron Transport chain

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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Lipid Metabolism

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

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

Lactic Acid 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.




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The Cell Cytology “Cyto” = cell, the study of cells

Eukaryotic cells Found in all living animals except viruses and

bacteria 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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Diffusion

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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Isotonic Solution

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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Nucleus 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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ORGANELLES AND THEIR FUNCTIONS (Part 1)

Cytoskeleton Network of fibrous proteins changes shifting according to activity of cell maintains cell shape, enables movement, anchors organelles, directs flow of cytoplasm

Microfilaments 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

Intermediate filaments 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

Hollow microtubules 25 nanometres in diameter protein tubelin grow with one end embedded in centrosome near nucleus.

Cilia, flagella and centrioles Provide structural support and have a role in cell and organelle movement as well as division

Organelles Little organs

Cilia and flagellum 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

Endoplasmic reticulum (ER) 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

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




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ORGANELLES AND THEIR FUNCTIONS (Part 2) Lysosomes 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

Mitochondrion 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

Ribosomes Found on the ER or floating in cytoplasm

60% RNA, 40% protein Translate genetic material on RNA

molecule to synthesise protein molecule Vacuoles 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

Endocytosis “Within the cell” (Greek) – requires energy New proteins 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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Cell Cycle – known also as CDC or cell division cycle.

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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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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