ADP: adenine diphosphate. The low-energy form of ATP. Contains only two phosphates. Amino acid an organic acid characterized by having an amino

Transcription

1 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 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

2 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)

3 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: Hydrophobic: a substance that readily dissolves in or combines with water 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.

4 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.

5 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

6 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.

7 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..