ATOMS AND CELLS

HUBS1401

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 Scale 0 -14 – acid to alkaline
Hydrogen)
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 This chemical bond involves a transfer of an electron,
Bond 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 The most common bond in organic molecules, a covalent bond involves the sharing of
Bond 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 Because they’re polarized, two adjacent H2O (water) molecules can form a linkage, where a
Bond (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 Also contains carbon

compound
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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 ATOMS AND 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  Stores energy until the cell needs it
Triphosphate  Three phosphate groups attached to a nitrogenous base of adenine
(ATP)  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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 ATOMS AND CELLS
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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 This chemical reaction pairing to transport energy is a process known as the
transport chain respiratory chain or, electron transport chain

Carbohydrate  Cellular respiration activities  really glucose metabolism  provides

metabolism 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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 ATOMS AND CELLS
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The Krebs  Also known as the tricarboxylic acid cycle or citric acid cycle
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  Series of energy compounds attached to the inner mitochondrial
Transport membrane
chain  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
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Lipid  Only portions of process involved in carbohydrate metabolism

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  Focuses on the production of amino acids used for synthesis

Metabolism  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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 ATOMS AND CELLS
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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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 ATOMS AND CELLS
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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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 ATOMS AND CELLS
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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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 ATOMS AND CELLS
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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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