Lecture 8

Activation energy- The amount of energy that reactants must absorb

before a chemical reaction will start.
Active site-The part of the enzyme molecule where a substrate
molecule attaches (by means of weak chemical bonds); typically, a
pocket or groove on the enzymes surface.
Allosteric site- allosteric regulation (or allosteric control) is the
regulation of a protein by binding an effector molecule at a site other
than the protein's active site. The site to which the effector binds is
termed the allosteric site.
ATP- A molecule composed of adenosine and three phosphate groups;
the main energy source for cells. A molecule of ATP can be broken
down to a molecule of ADP and a free phosphate; this reaction releases
energy that can be used for cellular work.
Catabolic pathway- metabolic pathways that breaks down molecules
into smaller units that are either oxidized to release energy, or used in
other anabolic reactions.
Catalyst- a substance that increases the rate of a chemical reaction
without itself undergoing any permanent chemical change
Competitive inhibitor- a form of enzyme inhibition where binding of
the inhibitor to the active site on the enzyme prevents binding of the
substrate and vice versa. Most competitive inhibitors function by
binding reversibly to the active site of the enzyme.
Endergonic reactionEnergy- The capacity to cause change, or to move matter in a direction
it would not move if left alone.
Entropy-A measure of disorder, or randomness. One form of disorder is
heat, which is a random molecular motion.
Exergonic reaction- is a chemical reaction in which the standard
change in free energy is positive, and energy is absorbed.
Feedback inhibition- A cellular control mechanism in which an enzyme
that catalyzes the production of a particular substance in the cell is

inhibited when that substance has accumulated to a certain level,

thereby balancing the amount provided with the amount needed.
First law of Thermodynamics-The total energy of an isolated system is
constant; energy can be transformed from one form to another, but
cannot be created or destroyed.
Kinetic Energy-Energy of motion. Moving matter preforms work by
transferring its motion to other matter, such as leg muscles pushing
bicycle pedals.
Metabolism- The total of all the chemical reactions in an organism.
Noncompetitive inhibitorPhosphorylation- turn many protein enzymes on and off, thereby
altering their function and activity. Protein phosphorylation is one type
of post-translational modification.
Potential Energy- Stored energy; The energy that an object has due to
its location and/or arrangement. Water behind a dam and a chemical
bond both possess potential energy.
Second law of Thermodynamics- In any cyclic process the entropy will
either increase or remain the same. Entropy: a state variable whose
change is defined for a reversible process at T where Q is the heat
absorbed. Entropy: a measure of the amount of energy which is
unavailable to do work.
Substrate-A specific substance on which an enzyme acts. Each enzyme
recognizes only the specific substrate of the reaction it catalyzes. A
surface in or on which an organism lives.
Thermodynamics- the branch of physical science that deals with the
relations between heat and other forms of energy (such as mechanical,
electrical, or chemical energy), and, by extension, of the relationships
between all forms of energy.

Lecture 9
Acetyl CoA- an important molecule in metabolism, used in many
biochemical reactions. Its main function is to convey the carbon atoms
within the acetyl group to the citric acid cycle to be oxidized for energy
production.

Aerobic- Containing or requiring molecular oxygen.

Anaerobic- Lacking or not requiring molecular oxygen.
ATP synthase- A protein cluster, found in cellular membrane (including
the inner membrane of mitochondria, the thylakoid membrane of
chloroplasts, and the plasma membrane of prokaryotes), that uses the
energy of a hydrogen ion concentration gradient to make ATP from
ADP. An ATP synthase provides a port through which hydrogen ions
diffuse.
Cellular respiration- The aerobic harvesting of energy from food
molecules; the energy-releasing chemical breakdown of food
molecules, such as glucose, and the storage of potential energy in a
form that cells can use to preform work; involves glycolysis, the citric
acid cycle, the electronic transport chain, and chemiosmosis.
Chemiosmosis- the movement of ions across a selectively permeable
membrane, down their electrochemical gradient. More specifically, it
relates to the generation of ATP by the movement of hydrogen ions
across a membrane during cellular respiration or photosynthesis.
Cristae- a fold in the inner membrane of a mitochondrion. The name is
from the Latin for crest or plume, and it gives the inner membrane its
characteristic wrinkled shape, providing a large amount of surface area
for chemical reactions to occur on.
Electron transport chain- A series of electron carrier molecules that
shuttle electrons during redox reactions that release energy used to
make ATP; located in the inner membrane of mitochondria, the
thylakoid membrane of chloroplasts, and the plasma membrane of
prokaryotes.
Fermentation- the anaerobic harvest of food by come cells.
Glycolysis- the multistep chemical breakdown of a molecule of glucose
into two molecules of pyruvic acid; the first stage of cellular respiration
in all organisms, occurs in the cytoplasmic fluid.
Krebs cycle- the central metabolic pathway in all aerobic organisms.
The cycle is a series of eight reactions that occur in the mitochondrion.
These reactions take a two-carbon molecule (acetate) and completely
oxidize it to carbon dioxide.

Mitochondrial matrix- The mitochondrion consists of an outer

membrane, an inner membrane and a gel-like material called
the matrix. This matrixis more viscous than the cell's cytoplasm as it
contains less water. The mitochondrial matrix has several functions: It
is where the citric acid cycle takes place.
NAD+ Nicotinamide adenine dinucleotide is a coenzyme found in all
living cells. The compound is a dinucleotide, because it consists of two
nucleotides joined through their phosphate groups.
Oxidation- The loss of electrons from a substance involved in a redox
reaction always accompanies reduction.
Oxidative phosphorylation- he metabolic pathway in which the
mitochondria in cells use their structure, enzymes, and energy
released by the oxidation of nutrients to reform ATP.
Redox reaction- Short for reduction-oxidation reactions; a chemical
reaction in which electrons are lost from one substance (oxidation) and
added to another (reduction). Oxidation and reduction always occur
together.
Substrate-level phosphorylation- a type of metabolic reaction that
results in the formation of adenosine triphosphate (ATP) or guanosine
triphosphate (GTP) by the direct transfer and donation of a phosphoryl
(PO3) group to adenosine diphosphate (ADP) or guanosine diphosphate
(GDP) from a phosphorylated reactive ...

Lecture 10
Autotroph- an organism that makes its own food from inorganic
ingredients, thereby sustaining itself without eating other organisms or
their molecules. Plants, algae, and photosynthesis bacteria are
autotrophs.
Calvin cycle- The second of two stages of photosynthesis; a cyclic
series of chemical reactions that occur in the stroma of a chloroplast,
using the carbon in CO2 and the ATP and NADPH produced by the light
reactions to make the energy-rich sugar molecule G3P, which is later
used to produce glucose.
Carbon fixation- the initial incorporation of carbon CO2 into organic
compounds by autotrophic organisms such as photosynthetic plants,
algae, or bacteria.

Carotenoids- a class of more than 600 naturally occurring pigments

synthesized by plants, algae, and photosynthetic bacteria. These richly
colored molecules are the sources of the yellow, orange, and red colors
of many plants (1). Fruit and vegetables provide most of
the carotenoids in the human diet.
Chlorophyll a- A green pigment in chloroplasts that participates directly
in the light reactions.
Chlorophyll- A light absorbing pigment in chloroplasts that plays a
central role in converting solar energy to chemical reactions.
Cyclic electron flow- A route of electron flow during the light
reactions of photosynthesis that involves only photosystem I and
produces ATP but not NADPH or oxygen.
Electromagnetic spectrum- the full range of radiation, from the very
short wavelengths of gamma rays to the very long wavelengths of
radio signals.
Glyceraldehyde-3-phosphate- a chemical compound that occurs as an
intermediate in several central metabolic of all organisms. It is a phosphate
ester of the 3-carbon sugar glyceraldehyde and has chemical formula C3H7O6P.

Heterotroph- An organism that cannot make its own organic food

molecules from inorganic ingredients and must obtain them by
consuming other organisms or their organic products; a consumer or
decomposer in a food chain.
Light reactions- The first of two stages in photosynthesis, the step in
which solar energy is absorbed and concerted to chemical energy in
the form of ATP an NADPH. The light reactions power the sugarproducing Calvin cycle but produce no sugar themselves.
NADP+ An electron carrier (a molecule that carries electrons) involved
in photosynthesis. Light drives electrons from chlorophyll to NADP+
forming NADPH, which provides the high-energy electrons for the
reduction of carbon dioxide to sugar in the Calvin cycle.
Noncyclic electron flow- The combined action of photosystem II and
photosystem I in which electrons flow in a linear manner to produce
NADPH.

Photon- A fixed quantity of light energy. The shorter the wavelength of

light, the greater the energy of a photon.
Photosynthesis- The process by which plants, algae, and some bacteria
transform light energy into chemical energy stored in the bonds of
sugars. This process requires the input of carbon dioxide and water and
produces oxygen gas as a waste product.
Photosystem- A light harvesting unit of a chloroplasts thylakoid
membrane; consists of several hundred molecules, a reaction-center
chlorophyll, and a primary electron acceptor.
Reaction center- In a photosystem in a chloroplast, the chlorophyll a
molecule and primary electron acceptor that triggers the light
reactions of photosynthesis. The chlorophyll donates an electron
excited by light energy to the primary electron acceptor, which passes
an electron to an electron transport chain.
Stoma- A pore surrounded by guard cells in the epidermis of a leaf.
When stomata are open, CO2 enters the leaf and water and O2 exit. A
plant conserves water when its stomata are closed.
Stroma- A thick fluid enclosed by the inner membrane of a chloroplast.
Sugars are made by in the stroma by the enzymes of the Calvin cycle.
Visible light- a form of electromagnetic (EM) radiation, as are radio
waves, infrared radiation, ultraviolet radiation, X-rays and microwaves.
Generally, visible light is defined as the wavelengths that are visible to
most human eyes.
Wavelength- The distance between crests of adjacent waves, such as
those of the electromagnetic spectrum.

Lecture 11
Adenylyl cyclase- an enzyme with key regulatory roles in essentially
all cells. It is the most polyphyletic known enzyme: six distinct classes
have been described, all catalyzing the same reaction but representing
unrelated gene families with no known sequence or
structural homology.
Cyclic AMP- a second messenger important in many biological
processes. cAMP is a derivative of adenosine triphosphate (ATP) and
used for intracellular signal transduction in many different organisms,
conveying the cAMP-dependent pathway.

G-protein-linked receptor- also known as seven-trans membrane

domain receptors, 7TM receptors, heptahelicalreceptors,
serpentine receptor, and G proteinlinked receptors (GPLR), constitute
a large protein family of receptors that sense molecules outside the
cell and activate inside signal transduction
Hormone- is any member of a class of signaling molecules produced by
glands in multicellular organisms that are transported by the
circulatory system to target distant organs to regulate physiology and
behavior.
Ligand-gated ion channel- a group of trans membrane ion
channel proteins which open to allow ions such as Na+, K+, Ca2+, or
Cl to pass through the membrane in response to the binding of a
chemical messenger (i.e. a ligand), such as a neurotransmitter.
Ligand- an ion or molecule (functional group) that binds to a central
metal atom to form a coordination complex. The bonding between
metal and ligand generally involves formal donation of one or more of
the ligand's electron pairs.
Local regulatorProtein kinase- a kinase enzyme that modifies other proteins by
chemically adding phosphate groups to them (phosphorylation).
Phosphorylation usually results in a functional change of the
target protein (substrate) by changing enzyme activity, cellular
location, or association with other proteins.
Scaffolding protein- are crucial regulators of many key signaling
pathways. Although scaffolds are not strictly defined in function, they
are known to interact and/or bind with multiple members of a signaling
pathway, tethering them into complexes.
Second messenger signal-transduction pathwayTyrosine-kinase receptor- are the high-affinity cell surface receptors for
many polypeptide growth factors, cytokines, and hormones. Of the 90
unique tyrosine kinase genes identified in the human genome, 58
encode receptor tyrosine kinase proteins.

Lecture 12
Anaphase- The third stage of mitosis, beginning when sister
chromatids separate from each other and ending when a complete set

of daughter chromosomes has arrived at each of the two poles of the

cell.
Anchorage dependence- an increase in proliferation which is seen
when cells are allowed to attach to a solid surface.
Benign tumor- an abnormal mass of cells that remains at its original
site in the body.
Binary fission- a means of asexual reproduction in which a parent
organism, often a single cell, divides into two individuals of about equal
size.
Cell cycle- an ordered sequence of events (including interphase and
mitotic phase) that extends from the time a eukaryotic cell is first
formed from a dividing parent cell until its own division into two cells.
Cell division- The reproduction of a cell
Cell plate- a plate that develops at the midpoint between the two
groups of chromosomes in a dividing cell and that then forms the wall
between the two daughter cells.
Centromere- The region of a chromosome where two sister chromatids
are joined and where spindle microtubules attach during mitosis and
meiosis. The centromere divides at the onset of anaphase during
mitosis and anaphase II of meiosis.
Centrosome- material in the cytoplasm of a eukaryotic cell that gives
rise to microtubules; important in mitosis and meiosis; functions as a
microtubule-organizing center
Chromatin- The combined DNA and proteins that constitutes
chromosomes; often used to refer to the diffuse, very extended form
taken by the chromosomes when a eukaryotic cell is not dividing.
Cleavage- A division or separation of form
Cytokinesis- The division of the cytoplasm to form two separate
daughter cells. Cytokinesis usually occurs during telophase of mitosis,
and two processes make up the mitotic phase of the cell cycle.
Density-dependent inhibition- where other factors such as weather or
environmental conditions and disturbances may affect a population's
carrying capacity. An example of a density-dependent variable is
crowding and competition.

G1 phase- the first of four phases of the cell cycle that takes place in
eukaryotic cell division. In this part of interphase, the cell synthesizes
mRNA and proteins in preparation for subsequent steps leading to
mitosis.
G2 phase- the third and final subphase of Interphase in the cell cycle
directly preceding Mitosis. It follows the successful completion of
S phase, during which the cell's DNA is replicated.
Gamete- A sex cell; a haploid egg or sperm. The union of two gametes
of opposite sex produces a zygote.
Genome- an organism's complete set of DNA, including all of its genes.
Each genomecontains all of the information needed to build and
maintain that organism. In humans, a copy of the entire genome
more than 3 billion DNA base pairsis contained in all cells that have a
nucleus.
Interphase- The phase in the eukaryotic cell cycle when the cell is not
actually dividing. During interphase, cellular metabolic activity is high,
chromosomes and organelles are duplicated, and cell size may
increase. Interphase accounts for 90% of the cell cycle.
Kinetochore- the protein structure on chromatids where the spindle
fibers attach during cell division to pull sister chromatids apart.
M phase- The phase of the cell cycle when mitosis divides the nucleus
and distributes its chromosomes to the daughter nuclei and cytokinesis
divides the cytoplasm, producing two daughter cells.
Malignant tumor- an abnormal tissue mass that spreads into
neighboring tissue and to other parts of the body; a cancerous tumor.
Meiosis- in a sexually reproducing organism, the process of cell division
that produces haploid gametes from diploid cells within the
reproductive organs.
Metaphase plate- the centromeres of the chromosomes convene
themselves on themetaphase plate (or equatorial plate), an imaginary
line that is equidistant from the two centrosome poles.
Metaphase- The second stage of mitosis. During metaphase, the
centromeres of all the cells duplicated chromosomes are lined up on an
imaginary plate equidistant between poles of the mitotic spindle.

Mitosis- The division of a single nucleus into two genetically identical

daughter nuclei. Mitosis and cytokinesis make up the M phase of the
cell cycle.
Mitotic phase- The phase of the cell cycle when mitosis divides the
nucleus and distributes its chromosomes to the daughter nuclei and
cytokinesis divides the cytoplasm, producing two daughter cells.
Mitotic spindle- A spindle-shaped structure formed of microtubules and
associated proteins that is involved in the movement of chromosomes
during mitosis and meiosis.
Prometaphase- the second phase of mitosis, the process that separates
the duplicated genetic material carried in the nucleus of a parent cell
into two identical daughter cells. During prometaphase, the physical
barrier that encloses the nucleus, called the nuclear envelope, breaks
down.
Prophase- The first stage of mitosis. During the prophase, duplicated
chromosomes condense to form structures visible with a light
microscope, and the mitotic spindle forms and begins moving the
chromosomes toward the center of the cell.
S phase- the part of the cell cycle in which DNA is replicated, occurring
between G1 phase and G2 phase. Precise and accurate DNA replication
is necessary to prevent genetic abnormalities which often lead to cell
death or disease.
Sister chromatids- one of the two identical parts of a duplicated
chromosome. While joined, two sister chromatids make up one
chromosome; chromatids are eventually separated during mitosis or
meiosis II
Somatic cell- any cell in a multicellular organism except a sperm or egg
cell or a cell that develops into a sperm or egg; a body cell.
Telophase- The fourth and final stage of mitosis, during which daughter
nuclei form at the two poles of a cell. Telophase usually occurs together
with cytokinesis.
Transformation- the genetic alteration of a cell resulting from the direct
uptake and incorporation of exogenous genetic material (exogenous
DNA) from its surroundings and taken up through the cell
membrane(s).

Tumor-an abnormal mass of cells that forms within an otherwise normal

mass of cells.

Lecture 13
Asexual reproduction- The creation of genetically identical offspring by
a single parent, without the participation of gametes.
Autosome- A chromosome not directly involved in determine the sex of
an organism; in mammals, for example any chromosome other than X
or Y.
Chiasmata- The X-shaped, microscopically visible region representing
homologues chromatids that have exchange genetic material through
crossing over during meiosis.
Crossing over-the receptacle exchange of genetic material between
nonsister chromatids during prophase I of meiosis
Diploid cell- A cell containing two sets of chromosomes, one set
inherited from each parent.
Fertilization- The union of haploid gametes to put is a diploid zygote.
Gamete- A haploid cell, such as and egg or sperm. Gametes unite
during sexual reproduction to reduce diploid zygote.
Gene- discrete unit of hereditary information consisting of a specific
nucleotide sequence.
Haploid cell- A cell containing only one set of chromosomes.
Heredity- The transmission of traits from one generation to the next
Homologous chromosome- Chromosome pairs of the same length,
centromere position, and staining pattern that possess alleles of the
same genes at corresponding loci.
Karyotype- Display of the chromosome pairs of a cell arranged by size
and shape.
Life cycle- The generation to generation sequence of stages in the
reproductive history of an organism.

Locus- a specific place along the length of a chromosome where a

given gene is located
Meiosis- two-stage type of cell division in sexually reproducing
organisms that result in cells with half the chromosome number of the
original cell.
Meiosis I- The first division of a two-stage process of cell division in
sexually reproducing organisms that result in cells that are half the
chromosome number of the original cell.
Meiosis II- The second division of a two-stage process of cell division in
sexually reproducing organisms that result in cells with half the
chromosome number of the original cell.
Recombinant chromosomes-A chromosome created when crossing over
combines the DNA from two parents into a single chromosome.
Sex chromosomes- one of the pair of chromosome are responsible for
determining the sex of an individual.
Sexual reproduction- A type of reproduction in which two parents give
rise to offspring that have unique combinations of genes and inherited
from the gametes of the two parents.
Somatic cell- any cell in a multicellular organism except a sperm or egg
cell.
Tetrad- a set of homologues chromosomes, each composed of two
sister chromatids. Tetrads form during prophase I of meiosis.
Variation- Differences between members of the same species.
Zygote- The diploid product of the union of haploid gametes in
conception; a fertilized egg.