Biology

Lecture 1 – Introduction to Biology

Glossary words
A recognisable structure originating from an organism, or any
Fossil impression from such a structure, that has been preserved over
geological time.
The development or course of development especially of an
Ontogeny individual organism. In biology this is paired with phylogeny.
(Web)
The evolutionary history of a kind of organism. The evolution of
Phylogeny a genetically related group of organisms as distinguished from
the development of the individual organism. (Web)
Biological structure and especially fine structure (as of a cell) not
Ultrastructure visible through an ordinary microscope. (Web)
Fundamental hereditary material of all living organisms. In
DNA eukaryotes, stored primarily in the cell nucleus. A nucleic acid
(deoxyribo using deoxyribose rather than ribose.
nucleic
acid)
Long-chain polymer of amino acids with twenty different
Protein common side chains. Occurs with its polymer chain extended in
fibrous proteins, or coiled into a compact macromolecule in
enzymes and other globular proteins.
A similarity between two or more features that is due to
Homology inheritance from a common ancestor. The structures are said to
be homologous, and each is a homolog of the others.
Type of homology in which the divergence of homologous genes
Paralogy can be traced to gene duplication events.
Simplest structure unit of a living organism. In multicellular
Cell organisms, the building blocks of tissues and organs.
Phylogeny. The Archaea are a group of single-celled
Domain Archaea microorganisms. They have no cell nucleus nor any other
membrane-bound organelles within their cells. (Web) Are
Prokayotes.
Phylogeny. Bacteria are a large domain of single-celled,
Domain Bacteria prokaryote microorganisms. Typically a few micrometres in
length, bacteria have a wide range of shapes, ranging from
spheres to rods and spirals. (Web)

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 Phylogeny.
Domain Eukarya - Eukaryote: organisms whose cells contain their genetic
material inside a nucleus. Includes all life other than the viruses,
archaea, and bacteria. Can be large and multicellular.
- Is an organism whose cells contain complex structures enclosed
within membranes. All species of large complex organisms are
eukaryotes, including animals, plants and fungi, although most
species of eukaryotic protists* are microorganisms. (Web)
- Cell division in eukaryotes is different from that in organisms
without a nucleus (prokaryotes). It involves separating the
duplicated chromosomes, through movements directed by
microtubules. There are two types of division processes. In
mitosis, one cell divides to produce two genetically identical
cells. In meiosis, which is required in sexual reproduction, one
diploid cell (having two instances of each chromosome, one from
each parent) undergoes recombination of each pair of parental
chromosomes, and then two stages of cell division, resulting in
four haploid cells (gametes). Each gamete has just one
complement of chromosomes, each a unique mix of the
corresponding pair of parental chromosomes. (Web)
*The protists do not have much in common besides a relatively
simple organization—either they are unicellular, or they are
multicellular without specialized tissues. This simple cellular
organization distinguishes the protists from other eukaryotes,
such as fungi, animals and plants. (Web)
- Features of the eukaryotic nucleus:
• Surrounded by a double membrane or nuclear envelope
• Presence of nuclear (annular) pores (75nm in diameter)
• DNA in long, linear strands covered with histones =
chromatin
• Different organisms have different numbers of
chromosomes
• Nucleolus = subregion of nucleus where ribosomal genes
are transcribed
• RNA transcribed from DNA leaves nucleus via pores and
goes into the cell to be translated.
The bacteria are a major group of prokaryotic living organisms.
Bacteria (Web)
- Group of organisms that lack a cell nucleus, or any other
Prokaryotic membrane-bound organelles. (Web)
- Divide by binary fission (constricting ring pinches parent cell
into two)
- Microscopic
The cell wall material of many bacteria, consisting of a single
Peptidoglycan enormous molecule that surrounds the entire cell. (Web)
Circular bacterial chromosome are the bacterial chromosomes
Circular contained in a circular DNA molecule. Unlike the linear DNA of
chromoso vertebrates, typical bacterial chromosomes contain circular DNA.
me (Web)
Chromosome: In bacteria and viruses, the DNA molecule that
contains most or all of the genetic information of the cell or virus.
In eukaryotes, a structure composed of DNA and proteins that
bears part of the genetic information of the cell.
The region that harbours the chromosomes of a prokaryotic cell.
Nucleoid Unlike the eukaryotic nucleus, it is not bounded by a membrane.

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 - A small particle in the cell that is the site of protein synthesis.
Ribosome - A ribosome is the component of a biological cell that creates
proteins from all amino acids and RNA representing the protein.
DNA is used to make RNA, which is used to make protein. The
DNA sequence in genes is copied into a messenger RNA (mRNA).
Ribosomes then read the information in this RNA and use it to
create proteins. This process is known as translation; the
ribosome translates the genetic information from RNA
into proteins. Ribosomes do this by binding to an mRNA and
using it as a template for the correct sequence of amino acids in
a particular protein. The amino acids are attached to transfer
RNA (tRNA) molecules, which enter one part of the ribosome and
bind to the messenger RNA sequence. The attached amino acids
are then joined together by another part of the ribosome. The
ribosome moves along the mRNA, "reading" its sequence and
producing a chain of amino acids.
Ribosomes are made from complexes of RNAs and proteins.
Ribosomes are divided into two subunits. The smaller subunit
binds to the mRNA, while the larger subunit binds to the tRNA
and the amino acids. When a ribosome finishes reading a mRNA,
these two subunits split apart. Ribosomes have been classified as
ribozymes, because the ribosomal RNA seems to be most
important for the peptidyl transferase activity that links amino
acids together. (Web)
- Bacterial ribosomes are small (17-23 nm); eukaryotic ribosomes
are larger (25-30 nm).
- Long, whip like appendage that propels cells. Prokaryotic
Flagella flagella differ sharply from those found in eukaryotes.
- Bacterial flagellum: motility appendage; long thin filament;
corkscrew action, one of only two rotating shaft designs in
biology; composed of flagellin protein extracellular (not inside
cell membrane); 100 rpm
- Pulsing motion.

Lecture 2–Prokaryotic vs Eukaryotic cells

Glossary words

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 In cells, the centrally located compartment of eukaryotic cells
Nucleus that is bounded by a double membrane and contains
chromosomes.
Any of the membrane enclosed structures within a eukaryotic
Organelles cells.
-Network of microtubules and microfilaments that gives a
Cytoskeleton eukaryotic cell its shape and its capacity to arrange its organelles
and to move.
- Components of cytoskeleton are not composed of membrane
- Act as a form of scaffolding or as structural elements within the
cytoplasm of cells.
- Cytoskeletal components are associated with maintaining cell
shape.
- Involved in certain cell movements.
Actin filaments: (actin protein) gelsolin controls filament
assembly, 7nm; interact with myosin motors; can assemble and
disassemble; responsible for muscle contractions and cytoplasmic
streaming. In summary, myosin drives muscle contraction,
cytoplasmic streaming, microvilli.
Microtubules (tubulin protein), 13 protofilaments form cylinder,
25nm diameter; interact with kinesin motors; can assemble and
disassemble; dynein can slide one microtubule against another;
kinesin can move vesicles along microtubules (dragging motion).
In summary, kinesin moves vesciles and dynein drives cilia
beating.
Intermediate filaments (vimentin protein) 10nm filament
diameter; predominantly static. In summary intra- and inter-
cellular stabilisation.
- Tubular structures found in centrioles, spindle apparatus, cilia,
Microtubules flagella and cytoskeleton of eukaryotic cells. These tubules play
roles in the motion and maintenance of shape of eukaryotic cells.
- Microtubules are conveyer belts inside the cells. They move
vesicles, granules, organelles like mitochondria, and
chromosomes via special attachment proteins. They also serve a
cytoskeletal role. Structurally, they are linear polymers of tubulin
which is a globular protein. These linear polymers are called
protofilaments. Microtubules may work alone, or join with other
proteins to form more complex structures called cilia, flagella or
centrioles . (Web)
Actin: A protein that makes up the cytoskeletal microfilaments in
Actin eukaryotic cells and is one of the two contractile proteins in
muscle. See Microfilaments below.
In bacteria and viruses, the DNA molecule that contains most or
Chromosomes all of the genetic information of the cell or virus. In eukaryotes, a
structure composed of DNA and proteins that bears part of the
genetic information of the cell.
- Any group of proteins forming the core of a nucleosome, the
Histone structural unit of a eukaryotic chromosome.
- In biology, histones are highly alkaline proteins found in
eukaryotic cell nuclei, which package and order the DNA into
structural units called nucleosomes. They are the chief protein
components of chromatin, acting as spools around which DNA
winds, and play a role in gene regulation. Without histones, the
unwound DNA in chromosomes would be very long. (Web)
The nucleic acid-protein complex that makes up eukaryotic
Chromatin chromosomes.
Chromatin is the combination of DNA, histone, and other proteins
that make up chromosomes. It is found inside the nuclear
envelope of eukaryotic cells. (Web)
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 A system of membranous tubes and flattened sacs found in the
Endoplasmic cytoplasm of eukaryotes. Exists in two forms: rough ER studded
reticulum with ribosomes; and smooth ER, lacking ribosomes.
The endoplasmic reticulum (ER) is a eukaryotic organelle that
forms an interconnected network of tubules, vesicles, and
cisternae* within cells. Rough endoplasmic reticula synthesize
proteins, while smooth endoplasmic reticula synthesize lipids
and steroids, metabolize carbohydrates and steroids, and
regulate calcium concentration, drug detoxification, and
attachment of receptors on cell membrane proteins. (Web)
*A cisterna comprises a flattened membrane disk that makes up
the Golgi apparatus.
A system of concentrically folded membranes found in the
Golgi apparatus cytoplasm of eukaryotic cells; functions in secretion from cell by
exocytosis.
It processes and packages macromolecules, such as proteins and
lipids, after their synthesis and before they make their way to
their destination; it is particularly important in the processing of
proteins for secretion. The Golgi apparatus forms a part of the
cellular endomembrane system. (Web)
A membrane-enclosed organelle originating from the Golgi
Lysosomes apparatus and containing hydrolytic enzymes (contra secondary
lysosome).
Lysosomes are cellular organelles that contain acid hydrolase
enzymes to break up waste materials and cellular debris. They
are found in animal cells, while in yeast and plants the same roles
are performed by lytic vacuoles. Lysosomes digest excess or
worn-out organelles, food particles, and engulfed viruses or
bacteria. The membrane around a lysosome allows the digestive
enzymes to work at the 4.5 pH they require. Lysosomes fuse with
vacuoles and dispense their enzymes into the vacuoles, digesting
their contents. They are created by the addition of hydrolytic
enzymes to early endosomes from the Golgi apparatus. (Web)
In cell biology, a phagosome is a vacuole formed around a
Phagosomes particle absorbed by phagocytosis. The vacuole is formed by the
fusion of the cell membrane around the particle. A phagosome is
a cellular compartment in which pathogenic microorganisms can
be killed and digested. Phagosomes fuse with lysosomes in their
maturation process, forming phagolysosomes. This vacuole is
only found in animal cells. (Web)
Phagocyte: One of two major classis of white blood cells; one of
the nonspecific defences of animals; ingests invading
microorganisms by phagocytosis.
Phagocytosis: Endocytosis by a cell of another cell or large
particle.
Organelle that houses reactions in which toxic peroxides are
Peroxisomes formed and then converted to water.

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 - Membrane-enclosed organelle in plant cells that can function for
Vacuoles storage, water concentration for turgor, or hydrolysis of stored
macromolecules.
- A vacuole is a membrane-bound organelle which is present in all
plant and fungal cells and some protist, animal and bacterial
cells. Vacuoles are essentially enclosed compartments which are
filled with water containing inorganic and organic molecules
including enzymes in solution, though in certain cases they may
contain solids which have been engulfed.
In general, the functions of the vacuole include:
• Isolating materials that might be harmful or a threat to the
cell
• Containing waste products
• Containing water in plant cells
• Maintaining internal hydrostatic pressure or turgor within
the cell
• Maintaining an acidic internal pH
• Containing small molecules
• Exporting unwanted substances from the cell
• Allows plants to support structures such as leaves and
flowers due to the pressure of the central vacuole
• In seeds, stored proteins needed for germination are kept
in 'protein bodies', which are modified vacuoles. (Web)
The addition of carbohydrates to another type of molecule, such
Glycosylation as protein.
Glycosylation is the enzymatic process that attaches glycans (a
polysaccharide or oligosaccharide = carbohydrate) to proteins,
lipids, or other organic molecules. (Web)
A cisterna (plural cisternae) comprises a flattened membrane disk
Cisternae that makes up the Golgi apparatus. A typical Golgi has anywhere
from 3 to 7 cisternae stacked upon each other like a stack of
dinner plates, but there are usually around 6. The cisternae carry
Golgi enzymes to help or to modify cargo proteins traveling
through them destined for other parts of the cell. (Web)
Within the cytoplasm, a membrane-enclosed compartment that is
Vesicles associated with other organelles; the Golgi complex is one
example.
- A protein to which sugars are attached.
Glycoproteins - Glycoproteins are proteins that contain oligosaccharide chains
(glycans) covalently attached to polypeptide side-chains. The
carbohydrate is attached to the protein in a cotranslational or
posttranslational modification. This process is known as
glycosylation. In proteins that have segments extending
extracellularly, the extracellular segments are often glycosylated.
Glycoproteins are often important integral membrane proteins,
where they play a role in cell-cell interactions. Glycoproteins also
occur in the cytosol, but their functions and the pathways
producing these modifications in this compartment are less well-
understood. (Web)
- The membrane of the plant central vacuole.
Tonoplast - The cytoplasmic membrane surrounding the vacuole, separating
the vacuolar contents from the cytoplasm in a cell. As a
membrane, it is mainly involved in regulating the movements of
ions around the cell, and isolating materials that might be
harmful or a threat to the cell.

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 Microfilaments: Common to all eukaryotic cells, these filaments
Microfilaments are primarily structural in function and are an important
component of the cytoskeleton, along with microtubules and
often the intermediate filaments. Microfilaments range from 5 to
9 nanometers in diameter and are designed to bear large
amounts of tension. In association with myosin, microfilaments
help to generate the forces used in cellular contraction and basic
cell movements. The filaments also enable a dividing cell to pinch
off into two cells and are involved in amoeboid movements of
certain types of cells. Microfilaments are solid rods made of a
protein known as actin. (Web)
- Components of the cytoskeleton whose diameters fall between
Intermediate those of the larger microtubules and those of the smaller
filaments microfilaments.
- Intermediate filaments are one of three types of cytoskeletal
elements. The other two are thin filaments (actin) and
microtubules. Frequently the three components work together to
enhance both structural integrity, cell shape, and cell and
organelle motility. Intermediate filaments are stable, durable.
They range in diameter from 8-10 nm (intermediate in size
compared with thin filaments and microtubules). They are
prominent in cells that withstand mechanical stress and are the
most insoluble part of the cell. The intermediate filaments can be
dissociated by urea. (Web).

1. Major functions of intracellular membranes:

o Provide a surface for biochemical reactions

o Establish a number of compartments to prevent missing

o Provide for transport of materials within the cell, from the cell to its
exterior, or from the cell to an adjacent cell.

2. Plant cell walls composed principally of cellulose; polysaccharide; most

abundant molecule, rigid box.

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Lecture 3–Lipids and Membranes
Glossary words

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 - Nonpolar, hydrophobic molecules that include fats, oils, waxes,
Lipids steroids, and the phospholipids that make up biological
membranes.
- Lipids are a broad group of naturally occurring molecules which
includes fats, waxes, sterols, fat-soluble vitamins (such as
vitamins A, D, E and K), monoglycerides, diglycerides,
phospholipids, and others. The main biological functions of
lipids include energy storage, as structural components of
cell membranes, and as important signaling molecules.
(Web)
- Fats and oils for energy storage and insulation; waxes for
protective coatings; chemical messengers; structural components
of membranes.
Sterols are a subgroup of the steroids and an important class of
Sterols organic molecules. They occur naturally in plants, animals, and
fungi, with the most familiar type of animal sterol being
cholesterol. Cholesterol is vital to cellular function, and a
precursor to fat-soluble vitamins and steroid hormones. (Web)
- A molecule made up of a long non-polar hydrocarbon chain and
Fatty acids a polar carboxyl group. Found in many lipids.
- In chemistry, especially biochemistry, a fatty acid is a carboxylic
acid with a long unbranched aliphatic tail (chain), which is either
saturated or unsaturated. Most naturally occurring fatty acids
have a chain of an even number of carbon atoms, from 4 to 28.
Fatty acids are usually derived from triglycerides or
phospholipids. When they are not attached to other molecules,
they are known as "free" fatty acids. Fatty acids are important
sources of fuel because their metabolism yield large
quantities of ATP. Many cell types can use either glucose or
fatty acids for this purpose. In particular, heart and skeletal
muscle prefer fatty acids. The brain cannot use fatty acids as a
source of fuel; it relies on glucose or on ketone bodies. (Web)
A simple lipid in which three fatty acids are combined with one
Triglycerides molecule of glycerol.
A lipid containing a phosphate group; an important constituent of
Phospholipids cellular membranes.
Phospholipid bilayer: The basic structural unit of biological
membranes; a sheet of phospholipids with two molecules thick in
which the phospholipids are lined up with their hydrophobic
“tails” packed tightly together and their hydrophilic, phosphate-
containing “heads” facing outward.

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 - A biological membrane or biomembrane is an enclosing or
Membranes separating membrane that acts as a selective barrier, within or
around a cell. It consist of a lipid bilayer with embedded proteins
that may constitute close to 50% of membrane content. (Web).
- All membranes composed of Phospholipids bilayer. Contains
other components: Protein, Glycoproteins, Sterols. Different
membranes have different ancillary components.
- Cell membrane is a biological membrane that separates the
interior of all cells from the outside environment. The cell
membrane is selectively-permeable to ions and organic
molecules and controls the movement of substances in and out of
cells. It consists of the phospholipid bilayer with embedded
proteins. Cell membranes are involved in a variety of cellular
processes such as cell adhesion, ion conductivity and cell
signaling and serve as the attachment surface for the
extracellular glycocalyx and cell wall and intracellular
cytoskeleton. (Web)
A molecular model for the structure of biological membranes
Fluid mosaic consisting of a fluid phospholipid bilayer in which suspended
model proteins are free to move in the plane of the bilayer.

A semipermeable membrane, also termed a selectively-

Differentially permeable membrane, a partially-permeable membrane or a
permeable differentially-permeable membrane, is a membrane that will allow
certain molecules or ions to pass through it by diffusion and
occasionally specialised "facilitated diffusion". (Web)

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 Random movement of molecules or other particles, resulting in
Diffusion even distribution of the particles when no barriers are present.
- Movement of water across a differentially permeable
Osmosis membrane, from one region to another region where the water
potential is more negative.
- Greater solute concentration – more negative the potential
- Water moves from higher to lower (more negative) potential.
Passive movement through a membrane involving a specific
Facilitated carrier protein; does not proceed against a concentration
diffusion gradient (contra active transport and diffusion).
The energy-dependent transport of a substance across a
Active transport biological membrane against a concentration gradient–that
is, from a region of low concentration (of that substance)
to one of high concentration.
Primary active transport: Active transport in which ATP is
hydrolysed*, yielding the energy required to transport an ion or
molecule against its concentration gradient.
Secondary active transport: A form of active transport that
does not use ATP as an energy source; rather, transport is
coupled to ion diffusion down a concentration gradient
established by primary active transport.
*Hydrolysis reaction: Chemical reaction that breaks a bond by
inserting the components of water.
- A process by which liquids or solid particles are taken up by a
Endocytosis cell through invagination (to fold inward or to sheath) of the
plasma membrane.
- Endocytosis is the process by which cells absorb molecules
(such as proteins) by engulfing them. It is used by all cells of the
body because most substances important to them are large polar
molecules that cannot pass through the hydrophobic plasma or
cell membrane. The process opposite to endocytosis is
exocytosis. (Web)
- A process by which a vesicle within a cell fuses with the plasma
Exocytosis membrane and release its contents to the outside. Expelling.
- The durable process by which a cell directs the contents of
secretory vesicles out of the cell membrane. These membrane-
bound vesicles contain soluble proteins to be secreted to the
extracellular environment, as well as membrane proteins and
lipids that are sent to become components of the cell membrane.
(Web)
Having the same solute concentration said of two solutions
Isotonic
Having a greater solute concentration compared with another.
Hypertonic
Having a lesser solute concentration compared with another.
Hypotonic
An adhering junction between animal cells.
Desmosomes
A cytoplasmic strand connecting two adjacent plant cells. The
Plasmodesmata cytoplasm of adjacent cells is continuous through
plasmodesmata.

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 A 2.7 nanometer gap between plasma membranes of two animal
Gap junctions cells, spanned by protein channels. Gap junctions allow chemical
substances or electrical signals to pass from cell to cell.
In cellular biology, pinocytosis ("cell-drinking") a form of
Pinocytosis Endocytosis in which small particles are brought into the cell
suspended within small vesicles that subsequently fuse with
Lysosomes to hydrolyze, or to break down, the particles. This
process requires a lot of energy in the form of adenosine
triphosphate, the chemical compound used as energy in the
majority of cells. Pinocytosis is used primarily for the
absorption of extracellular fluids (ECF), and, in contrast to
phagocytosis, generates very small vesicles. Unlike receptor-
mediated endocytosis, pinocytosis is nonspecific in the
substances that it transports. The cell takes in surrounding
fluids, including all solutes present. Pinocytosis also works as
phagocytosis, the only difference being that Phagosomes is
specific in the substances it transports. Phagocystosis
actually engulfs whole particles, which are later broken down by
enzymes and absorbed into the cells. Pinocytosis, on the other
hand, is when the cell engulfs already-dissolved or broken-down
food. In contrast, molecule-specific endocytosis is called
receptor-mediated endocytosis.

3. Role of membrane proteins and glycoproteins

o Some are enzymatically active

o A structural role – they can restrict to a limited space a set of

interdependent reactions.

o Determinants of individuality.

o Surface receptors for stimuli.

o Transport mechanism.

o Role as selective barrier.

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Lecture 4–Proteins and Enzymes
Glossary words

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 - Long-chain polymer of amino acids with twenty different
Protein common side chains. Occurs with its polymer chain extended in
fibrous proteins, or coiled into a compact macromolecule in
enzymes and other globular proteins.
- Formed by condensation of amino acids.
- Can be described at FOUR levels.
1. Primary structure – the amino acid sequence
2. Secondary structure – the conformation changes in
primary structures due to the formation of electrostatic
and hydrogen bonds between nearby amino acids.
3. Tertiary structure – the ultimate configuration that a
polypeptide chain takes in
4. Quaternary structure – association of the individual
polypeptide chains in proteins composed of multiple
polypeptides.
- Denaturation disrupts the tertiary and secondary structure of
a protein and destroys the protein’s biological functions.
- Renaturation (reassembly into a functional protein) is
sometimes possible but denaturation is usually irreversible.
An organic compound containing both NH2 and COOH groups.
Amino acid Proteins are polymers of amino acids.
The bond between amino acids in a protein formed between a
Peptide bond carboxyl group and amino group (CO-NH-).
A catalytic protein that speeds up a biochemical reaction.
Enzymes Increase reaction rate, does not alter final equilibrium, does not
alter free energy, recyclable, decrease activation energy. See
Catalyst below.

A chemical substance that accelerates a reaction without itself

Catalyst being consumed in the overall course of the reaction. Catalysts
lower the activation energy of a reaction. Enzymes are
biological catalysts.
A chemical reaction in which the products of the reaction have
Exergonic lower free energy than the reactants, resulting in a release of
reactions free energy. Release energy.
A chemical reaction in which the products have higher free
Endergonic energy than the reactants, thereby requiring free energy input to
reactions occur. Consume energy.
The energy barrier that blocks the tendency for a chemical
Activation energy reaction to occur.
(Ea)

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 - Regulation of the activity of a protein (usually an enzyme) by
Allosteric the binding of an effector molecule to a site other than the active
inhibition/r site.
egulation - In biochemistry, allosteric regulation is the regulation of an
enzyme or other protein by binding an effector molecule at the
protein's allosteric site (that is, a site other than the protein's
active site). Effectors that enhance the protein's activity are
referred to as allosteric activators, whereas those that
decrease the protein's activity are called allosteric inhibitors.
The regulatory site of an allosteric protein is physically distinct
from its active site. Allosteric regulations are a natural example
of control loops, such as feedback from downstream products or
feedforward from upstream substrates.
- Competitive inhibition (not allosteric): inhibitor and substrate
compete – only one can bind to the active site
- Noncompetitive inhibition: An inhibitor may bind to a site
away from the active site, changing the enzyme’s shape so that
the substrate no longer fits.
In biochemistry, a macromolecule exhibits cooperative binding if
Allosteric its affinity for its ligand changes with the amount of ligand
cooperative already bound.
ly/cooperati Cooperative binding is a special case of allostery. Cooperative
ve bonding binding requires that the macromolecule have more than one
binding site, since cooperativity results from the interactions
between binding sites. If the binding of ligand at one site
increases the affinity for ligand at another site, the
macromolecule exhibits positive cooperativity. Conversely, if
the binding of ligand at one site lowers the affinity for ligand at
another site, the protein exhibits negative cooperativity. If the
ligand binds at each site independently, the binding is non-
cooperative. (Web)
An inorganic ion that is weakly bound to an enzyme and required
Cofactors for its activity.

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Lecture 5–Energy harvesting pathways
Glossary words

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 (1) Cellular respiration: The catabolic pathways by which
Respiration electrons are removed from various molecules and passed
through intermediate electron carriers to O2, generating H2O and
releasing energy.
An energy-storage compound containing adenine, ribose and
ATP (adenosine three phosphate groups. When it is formed from ADP, useful
triphospha energy is stored when it is broken down (to ADP or AMP), energy
te) is released to drive endergonic reactions.

ADP
In the presence of oxygen; requiring oxygen.
Aerobic
Occurring without the use of molecular oxygen.
Anaerobic
The anaerobic degradation of a substance such as glucose to
Fermentation smaller molecules such as lactic acid or alcohol with the
extraction of energy.

NAD+

NADH

FAD

FADH
Gains of electron by a chemical reactant; any reduction is
Reduction accompanied by an oxidation.
Relative loss of electrons in a chemical reaction; either outright
Oxidation removal to form an ion, or the sharing of electrons with
substances having a greater affinity for them, such as oxygen.
Most oxidations, including biological ones, are associated with the
liberation of energy.
The enzymatic breakdown of glucose to pyruvic acid.
Glycolysis
The anaerobic degradation of a substance such as glucose to
Fermentation smaller molecules such as lactic acid or alcohol with the
extraction of energy.
In cellular respiration, a set of chemical reactions whereby acetyl
Kreb’s cycle CoA is oxidised to carbon dioxide and hydrogen atoms are stored
as NADH and FADH2.
ATP formation in the mitochondrion, associated with flow of
Oxidative electrons through the respiratory chain.
phosphoryl Phosphorylation: Phosphorylation is the addition of a phosphate
ation (PO4) group to a protein or other organic molecule.
Phosphorylation activates or deactivates many protein enzymes.
(Web)
The passage of electrons through a series of proteins with the
Electron transport release of energy which may be captured in a concentration
gradient or chemical form such as NADH or ATP.

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Lecture 6–Mitochondria, chloroplast, endosymbiosis
Glossary words
An organelle in eukaryotic cells that contains the enzymes of the
Mitochondria citric acid cycle, the respiration chian and oxidative
phosphorylation.
The internal compartments formed by the inner membrane of a
Cristae mitochondrion. They are studded with proteins, including ATP
synthase and a variety of cytochromes. The maximum surface for
chemical reactions to occur is within the mitochondria. This
allows cellular respiration (aerobic respiration since the
mitochondrion requires oxygen) to occur.
Inner compartment of mitochondria.
Matrix In the mitochondrion, the matrix contains soluble enzymes that
catalyze the oxidation of pyruvate and other small organic
molecules.
The mitochondrial matrix also contains the mitochondria's DNA
and ribosomes. The word "matrix" stems from the fact that this
space is viscous, compared to the relatively aqueous cytoplasm.
(Web)
Any of the plant cell organelles that house biochemical pathways
Plastids for photosynthesis.
An organelle bounded by a double membrane containing the
Chloroplasts enzymes and pigments that perform photosynthesis.
Chloroplasts occur only in eukaryotes.
A flattened sac within a chloroplast. Thylakoid membranes
Thylakoids contain all of the chlorophyll in a plant, in addition to the electron
carriers of photophosphorylation. Thylakoids stack to form grana.
The fluid contents of an organelle such as a chloroplast or
Stroma mitochondrion.
The theory that the eukaryotic cell evolved via the engulfing of
Endosymbiosis one prokaryotic cell [bacteria that becomes mitochondrion] by
theory another.

Lecture 7–Cell division, mitosis and meiosis

Glossary words
Mitosis

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 Region where sister Chromatids join.
Centromere
The major microtubule organising centre of an animal cell.
Centrosome
A paired organelle that helps organise the microtubules in animal
Centriole and protist cells during nuclear division.
Specialised structure on a centromere to which microtubules
Kinetochore attach.
The nucleic acid-protein complex that makes up eukaryotic
Chromatin chromosomes.
A newly replicated chromosome from the time molecular
Chromatid duplication occurs until the time the centromeres separate
(during anaphase of mitosis or of meiosis II).
In bacteria and viruses, the DNA molecule that contains most or
Chromosome all of the genetic information of the cell or virus. In eukaryotes, a
structure composed of DNA and proteins that bears part of the
genetic information of the cell.
An array or microtubules emanating from both poles of a diving
Spindle cell during mitosis and playing a role in the movement of
microtubul chromosomes at nuclear division. Named for its shape.
es

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Lecture 8–Carbohydrate and Nucleic Acids
Glossary words

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 - A giant polymeric molecule. The macromolecules are the
Macromolecule proteins, polysaccharides, and nucleic acids. Molecular weight >
1000.
- Major macromolecules: lipids, proteins, carbohydrates, nucleic
acids (DNA and RNA)
A large molecule made up of similar subunits called monomers.
Polymer
Condensation reaction: Chemical reaction in which two
Condensation molecules becomes connected by a covalent bond and a
molecule of water is released (contra Active transport: chemical
reaction that breaks bond by inserting the components of water.
- Polysaccharides or sugars.
Carbohydrates - Source of chemical energy; form structural components; most
abundant organic compounds in nature.
- Have general formula (CH2O)n (where n is the number of carbon
atoms; generally n is between 3 and 8).
- Basic unit is sugar molecule or saccharide.
- Three main groups of carbohydrates: monosaccharaides,
disaccharides and polysaccharides.
A macromolecule composed of many monosaccharaides (simple
Polysaccharides sugars). Common examples are cellulose and starch.
A simple sugar. Oligosaccharides and polysaccharides are made
Monosaccharide up of monosaccharaides.
A polymer made up of nucleotides, specialised for the storage,
Nucleic Acids transmission, and expression of genetic information. DNA
[double strand] and RNA [always single strand] are nucleic acids.
A base.
The basic chemical unit in nucleic acids, consisting of a pentose
Nucleotide sugar, a phosphate group, and a nitrogen-containing base.
The connection in a nucleic acid strand, formed by linking two
Phosphodiester nucleotides.
bond
Purine: One of the two types of nitrogenous bases in nucleic
Purines/Pyrimidine acids. Each of the purines (adenine and guanine) pairs with a
s specific pyrimidine.
Pyrimidine: One of the two types of nitrogenous bases in nucleic
acids. Each of the pyrimidines – cytosine, thymine, and uracil
(RNA only, replaces thymine) – pairs with a specific purine.
A-G
C-T

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 A nitrogenous (nitrogen-containing) base is a nitrogen-containing
Nitrogenous base molecule having the chemical properties of a base. It is an
organic compound that owes its property as a base to the lone
pair of electrons of a nitrogen atom. In biological sciences,
nitrogenous bases are typically classified as the derivatives of
two parent compounds, pyrimidine and purine.[1] They are non-
polar and due to their aromaticity, planar. Both pyrimidines and
purines resemble pyridine and are thus weak bases and relatively
unreactive towards electrophilic aromatic substitution.[2] Their
flat shape is particularly important when considering their roles in
nucleic acids as nucleobases (building blocks of DNA and RNA):
adenine, guanine, thymine, cytosine, and uracil. These
nitrogenous bases hydrogen bond between opposing DNA strands
to form the rungs of the "twisted ladder" or double helix of DNA
or a biological catalyst that is found in the nucleotides. Adenine is
always paired with Thymine, and Guanine is always paired with
Cytosine. (Web)
In double-stranded DNA, a pair of nucleotides formed by the
Base pairs complementary base pairing of a purine or pyrimidine that is
attached to each sugar in the sugar-phosphate backbone.
- Set of instructions, in the form of nucleotide triplets, that
Genetic Code translate a linear sequence of nucleotides in mRNA into a linear
sequence of amino acids in a protein.
- A gene for each protein
• Order of amino acids is prescribed by the nucleotide
sequence of the gene.
• Order of amino acids determines the shape of the protein.
• Shape of the protein determines the function.

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Lecture 9–Homeostasis
Glossary words

Internal
environme
nt

Interstitial fluid

Homeostasis

Epithelial tissue

Muscle tissue
(skeletal,
cardiac,
smooth)

Connective tissue

Nervous tissue

Thermoneutral
zone

Ectotherm

Endotherm

Hypothermia

Torpor

Hibernation

Basal metabolic
rate

What types of tissues

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Lecture 10 & 11–Endocrine Systems & Hormones
Glossary words

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Endocrine gland

Exocrine gland

Target cells

Hormone

Hormone action
via
endocrine

Paracrine and
autocrine
signalling

Signaling

Hormone types:
peptide,
steroid,
amine,

Fight-or-flight
response

Hypothalamus-
pituitary-
endocrine
glad
systems

Anterior and
posterior
pituitary

Negative and
positive
feedback

Major endocrine
glands

Hormones,
hormones
act via
receptors

Homeostasis -

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Lecture 12–Cell Signalling
Glossary words

Lecture 13 to 15–Nervous System

L13 & 14 Nervous System & The Eye 2011.pdf (4.945 Mb)

L15 Long term potentiation.pdf (855.582 Kb)

Glossary words

Lecture 16 & 17–Immune System

Glossary words

Lecture 18–Stem Cells

Glossary words

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