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ADP: adenine diphosphate. The low-energy form of ATP. Contains only two
phosphates.
Amino acid an organic acid characterized by having an amino (nitrogen) group
Anabolism using cellular energy to synthesize higher-energy compounds (e.g.,
proteins, carbohydrates, fats) from lower-energy compounds.
Anaerobic metabolism metabolic processes that occur without the utilization of
oxygen (e.g., glycolysis).
ATP: adenine triphosphate. A high-energy stable compound used to transfer chemical
energy from one region of a cell to other regions.
Bases (in DNA and RNA):
Purines (Adenine and Guanine in both DNA, and
RNA) and Pyrimidines (Thymine and Cytosine in DNA, Uracil and Cytosine in
RNA).
Bilayer membrane (semipermeable membrane):
a membrane made up of
phospholipids. In an aqueous environment the nonpolar (hydrophobic) tails will
be on the interior and the polar (hydrophilic) heads on the outside.
Catabolism breaking down of higher-energy compounds (e.g., proteins,
carbohydrates, fats) to lower-energy ones for the production of useful energy
(e.g., ATP).
Catalysis A process by which some substance lowers the energy of activation of a
reaction, greatly speeding it up. While participating in the reaction, catalysts are
not consumed by the reaction.
Central Dogma
First formulated by Francis Crick in 1956. It refers to the information
flow in biological systems from the DNA in the nucleus to proteins synthesized in
the cytoplasm. Also described as "DNA makes RNA and RNA makes protein."
Chloroplast:
an organelle found in plant cells which contains all the proteins
needed to produce sugar from sunlight.
Chromosome:
A sequence of DNA containing genes and non-coding DNA.
Become visible during cell division when it coils and re-coils.
Citric Acid Cycle: see Krebs Cycle.
Cristae:
infoldings of the inner membrane of mitochondria. The site of oxidative
phosphorylation.
Chromatin: Stands of DNA found in the resting (G1) nucleus.
DNA: deoxyribonucleic acid. A double-helical structure made of two chains, crosslinked by pairs of bases (adenine, thymine, guanine and cytosine). The
backbones of the chains consist of alternating sugar (deoxyribose, to which the
bases are bonded) and phosphate.
Electron carrier: a substance which can be reduced (gain electrons) in one part of
the cell and carry those electrons to another part where it donates those
electrons to another molecule in a redox reaction. Example: NAD (Nicotine
Adenine Diphosphate).
Electron transport chain:
a series of molecules that participate in redox
reactions in that electrons enter at the first molecule, are transferred to the next,
and so on to a final electron acceptor.
Endocytosis:
water.
a process similar to phagocytosis but for small particles or even
Endoplasmic reticulum: a network of tubules that permeates the cytoplasm of a cell.
It has two forms: rough endoplasmic reticulum which is studded with bound
ribosomes, and smooth endoplasmic reticulum, which is not.
Endosymbiont hypothesis:
Lynn Margulis' idea that organelles enclosed in two
layers of membrane and with their own DNA were originally free-living
prokaryotes which became engulphed by and later symbiotic with other cells.
The two are mitochondria and chloroplasts.
Energy of Activation:
The energy needed to be supplied to a reaction before it can
proceed. Often supplied by the energy of collision of the molecules involved.
Enzyme:
A molecule (or complex of molecules, usually proteins, but sometimes
RNA) which catalyzes a reaction. See catalysis.
Eucaryotes:
single- and multicellular organisms whose cells contain organelles
and a nucleus.
Exocytosis:
the reverse of endocytosis. Used to expel particles such as export
proteins and/or insoluble waste products from the cell.
Exon: A section of a coding sequence of DNA or of the messenger RNA transcipt from
it that carries information that will be expressed in the cell.
Gene: Refers to a sequence of DNA that contains a code for some product, usually a
protein.
Genome: All of the genetic information in the nucleus (or mitochondrion or
chloroplast) in a cell (prokaryote or eukaryote).
Glycolysis: a series of reactions beginning with either glucose or glycogen, ending
with the production of pyruvate and energy in the form of ATP and a reduced
electron carrier (NADH+H)
Golgi complex: a specialized region of the endoplasmic reticulum. Processes
proteins synthesized in the endoplasmic reticulum.
Histone (complex):
A complex of 9 protein subunits (H1, H2A (x2), H2B (x2), H3
(x2), H4 (x2)). H1 links DNA to the remaining octomer.
Hydrophilic:
a substance that readily dissolves in or combines with water
Hydrophobic:
a substance that readily dissolves in nonpolar solvents such as oil.
Intermediary metabolism:
the processes within a cell whereby chemical energy
is transformed into compounds useful to the cell. Can be catabolic or anabolic.
Intron:
A section of a coding sequence of DNA or of the messenger RNA
transcript from it that will not leave the nucleus but instead will be cut out.
Krebbs Cycle:
the series of chemical reactions that occurs within the matrix of the
mitochondrion that begins with the incorporation of acetyl CoA with oxaloacetic
acid (to produce a three-carbon organic acid, citrate, and ends again with
oxaloacetic acid, having produced two CO2 molecules, a GTP and several
reduced electron carriers. Also known as the TCA or Citric Acid Cycle.
Lagging Strand (DNA): Because DNA polymerase works only on one direction (3'
towards 5'), one strand of the DNA can be read without interruption. The other
strand (the lagging strand) must be read in reverse, leading to the production of
Okazaki fragments.
Lysosomes:
organelles with in the cell whose function it is to digest substances.
They may be formed from the cell membrane during endocytosis or
phagocytosis, or they may be formed by the Golgi apparatus in packaging
proteins destined for exocytosis or incorporation in the cell membrane.
Matrix (of mitochondria): fluid filling the inner space of the mitochondrion. Site of the
Krebs cycle.
Messenger RNA: A sequence of RNA transcribed from a gene. After modification
(see Intron, Exon, SNRP) it carries information from the nucleus to the
cytoplasm (ribosome).
Mitochondrion: an organelle which is specialized for the production of ATP using
oxidative phosphorylation. Consists of an outer membrane, an inner membrane
which is thrown into a series of folds (cristae) and a fluid matrix.
Nucleoid: the term used for the DNA found in prokaryotes, whose DNA is not found
in a nucleus (they don't have one) and is circular rather that linear as in
eucaryotes.
Okazaki fragments:
Short sections of DNA formed from the lagging strand during
replication. Come about because of the need for repeated production and
subsequent deletion of primer RNA.
Operon:
A functioning unit of genomic DNA containing a cluster of genes under the
control of a single promoter. Found in procaryotes.
Organelle: a structure within a cell which is separated from the rest of the cell by a
membrane.
Oxidative phosphorylation:
the process of adding phosphates to ADP to create
the high-energy form, ATP. Occurs on the cristae of the mitochondrion.
Phagocytosis:
the process whereby a substance is engulphed by the cell
membrane and thus taken into the cell. It differs from endocytosis only in the
size of particles engulphed.
Phospholipids: compounds derived from the three-carbon molecule glycerol, with
two long-chain fatty acids and one polar phosphate group.
Primer RNA:
Because DNA polymerase will bind only to double-stranded nucleic
acid it is necessary to produce a hybrid DNA-RNA strand on the single-stranded
template strand of DNA before replication of that sequence can begin. The RNA
is referred to as primer RNA
Procaryotes:
single-celled organisms lacking organelles and a nucleus.
Promoter: the region of DNA preceding a transcribable gene. It provides a site for the
binding of the transcription initiation complex.
Protein:
a molecule made up of a chain of amino acids bound together
Redox reaction: a chemical reaction in which electrons (often with an associated
hydrogen atom) are transferred from one molecule (which is thus oxidized) to
another molecule (which is thus reduced).
Ribosomal RNA: The component of the Ribosome made of RNA
Ribosome: a complex found in cells, made up of several subunits, each composed of
proteins and RNA. Ribosomes are the site of manufacture of proteins.
Ribozyme: An enzyme made exclusively or predominantly of RNA
RNA: ribonucleic acid. A single stranded molecule whose backbone is made of
alternating molecules of sugar (ribose) and phosphate. Each ribose has one of
four bases (adenine, uracil, guanine and cytosine) bonded to it. See also
Messenger RNA, Ribosomal RNA, and Transfer RNA.
RNA World Hypothesis: A hypothesis of the origin of life which assumes that the first
life forms used RNA for both information storage and enzymes.
SNRP:
Small Nuclear Ribonucleic Particle (sometimes snRNP). Pronounced
"snurp". A ribozyme used to process messenger RNA transcripts by cutting out
introns and splicing exons together.
TCA cycle: Tricarboxylic Acid Cycle. See Krebs cycle.
Telomere: A non-coding sequence of bases (TTAGGG) repeated at the ends of the
linear chromosomes in eucaryotes. Sacrificed during replication of the lagging
strand of DNA.
Transfer RNA:
An RNA molecule which at one end mates with a specific amino
acid and at the other end matches a specific 3-base sequence in messenger
RNA. Thus the messenger RNA sequence is turned into a sequence of amino
acids.
Triplet code:
The information encoded in DNA for the synthesis of proteins is
read in groups of three base-pairs. Each triplet specifies an amino acid or a
"stop" or "start" codon. Four possible bases (A,T,G, or C) read in groups of three
yields 64 possible "words" for only 21 amino acids, yielding redundancy.
SUPPLEMENT
Acetylation (of histones): addition of the acetyl group (CH3-COO-) to one or more of
the protein chains that project from the histone proteins in the histone complex.
Generally leads to increased expression of downstream genes (although there
is some evidence that certain acetylations may lead to inhibition of expression).
Barr body: the form taken by one of the X chromosomes in each cell of females (XX).
The chromosome appears as a clump in the nucleus. In this form it is inactive,
thus providing dose compensation.
CpG groups: portions of the DNA rich in the sequence Cytosine-Guanosine (as read
from the 5’ end of the DNA). These areas are targets of methylation by an
enzyme of the DNMT (DNA Methyl Transferase) family.
Dose compensation: mechanism in diploid cells to prevent excessive expression of a
gene found on both chromosomes in some but not all cells. For example, males
have only one X chromosome while females have two. Normally, then, in males,
only one allele of a gene that is found on the X chromosome (but not the Y) is
expressed. In females, though, both alleles could be expressed, leading to a
double dose. To prevent this one X chromosome is condensed into a Barr body.
DNA fingerprint: an image of a gel through which fragments of DNA have been run to
sort them out by size. The pattern can be used to identify and individual or
relations between individuals
Epigenetics: The study of factors that control the expression of genes; specifically,
factors which have moderate to long-term, even transgenerational control of
genes by modifying the DNA using methylation and acetylation.
Gel Electrophoresis (of DNA): process of separating fragments of DNA based on
their length. Fragments are loaded at one end of a gel which is then placed in an
electrical field. DNA is very negative and thus moves from the negative end to
the positive end of the gel; small fragments can move through the gel faster than
large ones, so in time fragments are sorted and can then be visualized.
Imprinting: parent-specific silencing of genes, usually by methylation. Thus only the
gene expressed from the maternal or the paternal parent is expressed
(monoallelism) in the diploid cell. Found in placental mammals.
MeCP2 (Methyl CpG Binding Protein 2): binds to areas of methylation and catalyzes
the formation of a set of proteins which in turn blocks the transcription of
downstream genes. Thus it “reads” the methylation code.
Methylation (of DNA): addition of methyl (-CH3 groups to guanosine at specific
locations (see CpG groups) on the DNA. Methylation normally inhibits
expression of downstream genes.
PCR: Polymerase Chain Reaction: process of repetitively duplicating and thus greatly
increasing the DNA in a sample. Also used to selectively duplicate and thus
increase the amount of a specific sequence in a DNA molecule. Involves the
alternate heating to melt the DNA followed by duplication of the single strands
produced in melting and then cooling to restore the double stranded DNA.
Probe (in DNA fingerprinting): a fragment of DNA, complimentary to a sequence of
single-stranded DNA which might be on a fragment of DNA on a gel. The probe,
which has been labelled in some way (radioactive, fluorescent, etc.) to make it
visible, pairs with the sequence on the fragment and makes it visible.
Reprogramming: during gametogenesis the genome is globally demethylated and
deacetylated, i.e., all epigenetic markers are removed. After that some imprints
are restored. A second reprogramming takes place immediately after
fertilization.
Restriction Enzyme: enzymes derived from bacteria which cut the DNA molecule at
specific sequences.
RFLP: Restriction Fragment Length Polymorphism. Individual variation in the length of
a DNA fragment between two points cut by the same or different restriction
enzymes.
VNTR: variable number tandem repeats. Long stretches of DNA that are non-coding,
but whose length can be used in DNA fingerprinting.
Xist: a gene on the XIC (X-inactivation center) of the X chromosome in placental
mammals. Expression on one of the two X chromosomes in females causes that
chromosome to condense into a Barr body and become inactive. Involved in
dose compensation.
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