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AP Biology vocabulary- Know AND understand these!! R Group: a group where different chains of atoms are substituted in to make 20 different kinds of amino acids. Non-polar covalent bonds: A bond between 2 nonmetal atoms that have the same electronegativity and therefore have equal sharing of the bonding electron pair. Functional Group: A functional group is a portion of a molecule that is a recognizable/classified group of atoms. They give the molecule its properties, regardless of what molecule contains it; they are centers of chemical reactivity. Density Dependent: Describes a factor that influences individuals in a population to a degree that varies in response to how crowded the population is. (Food) Density Independent: A factor that influences individuals in a population in a manner that does not vary with the extent of crowding present in the population. (Weather) Coenzymes: are organic molecules that are required by certain enzymes to carry out catalysis. Cofactor: inorganic substances that are required for or increase the rate of catalysis. pH: (Potential Hydrogen) is a measure of how acidic or basic a solution is. Hardy Weinberg: (Genetic Equilibrium) when the allele frequencies in a population remain constant from generation to generation. Factors that normally change gene frequencies don’t occur. There must be no natural selection, no mutations, no gene flow, no genetic drift, and mating must be random. MHC Proteins: a family of genes that code for a huge variety of cell surface proteins. When cells become infected they display them on their surface. Platelet-derived growth factor- one of many proteins that regulate cellular growth and division. Specifically blood vessel formation (angiogenesis). Five different isoforms. Cyclin- Group of proteins that control the development of cells through the cell cycle by activating cyclin-dependent kinase. Cyclin-dependent kinases- Group of proteins that regulate the cell cycle. Involved in transcription, mRNA processing, and the differentiation of the nerve cells. Homologous chromosomes- are pairs of chromosomes of about the same length, centromere position, staining patterns, and also have gene with the same characteristics at corresponding loci. Crossing over- exchange of genetic material between homologous chromosomes that result in recombinant chromosomes. This occurs in Prophase 1 of meiosis during synapsis. Law of independent assortment- Mendel’s law that states alleles of a gene will separate independently from alleles of another gene. Law of segregation- Mendel’s law that states that a pair of alleles separate from its corresponding allele into each of the gametes randomly. Sex-linked traits- Traits that are controlled by an allele on one of the sex chromosomes Autosomal- Traits that are controlled by an allele on a non-sex chromosome (autosomes) Somatic cells- any biological cell that is produced in a multi-cellular organism other than gametes, gametocytes, germ cells, or undifferentiated stem cells. Inducible operon- Is a section of DNA that’s transcription can be turned on or off. An example is the lac Operon. Repressible operon- A section of DNA that’s transcription can be turned off but is usually on. An example would be the trp Operon. HOX genes- group of related genes that determine the basic structure and orientation of an organism. Cytokines- are small cell-signaling protein molecules that are secreted by numerous cells and are a category of signaling molecules used extensively in intercellular. Cytokines can be classified as proteins, peptides, or glycoproteins; the term "cytokine" encompasses a large and diverse family of regulators produced throughout the body by cells of diverse embryological origin. Important in the immune system. cAMP- (cyclic adenosine monophosphate) is a second messenger important in many biological processes. SRY gene- (Sex-determining Region Y) is a sex-determining gene on the Y chromosome. Giberrilins- Are plant hormones that regulate growth and influence various developmental processes, including stem elongation, germination, dormancy, flowering, sex expression, enzyme induction, and leaf and fruit senescence. P53- is a tumor suppressor protein that in humans is encoded by the TP53 gene. Transposons- are segments of DNA that can move around to different positions in the genome of a single cell. In the process, they may cause mutations or affect the amount of DNA in the genome. Retrovirus- is an RNA virus that is duplicated in a host cell using the reverse transcriptase enzyme to produce DNA from its RNA genome. Lytic cycle- is one of the two cycles of viral reproduction, the other being the lysogenic cycle. The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell Lysogenic cycle- integration of the bacteriophage nucleic acid into the host bacterium's genome. Glycogen- is a molecule that serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue. Glycogen is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach. Epinephrine- (adrenaline) is a hormone and a neurotransmitter. Epinephrine has many functions in the body, regulating heart rate, blood vessel and air passage diameters, and metabolic shifts; epinephrine release is a crucial component of the fight-or-flight response of the sympathetic nervous system. Killer T cells- (Cytotoxic T Cells) belongs to a sub-group of T lymphocytes (a type of white blood cell) that are capable of inducing the death of infected somatic or tumor cells; they kill cells that are infected with viruses (or other pathogens), or are otherwise damaged or dysfunctional. Helper T cells- are a sub-group of lymphocytes, a type of white blood cell, that play an important role in the immune system, particularly in the adaptive immune system. These cells have no cytotoxic or phagocytic activity; they cannot kill infected host cells or pathogens. Rather, they help other immune cells; they activate and direct other immune cells. Neurotransmitters- are endogenous chemicals that transmit signals from a neuron to a target cell across a synapse. Neurotransmitters are packaged into synaptic vesicles clustered beneath the membrane in the axon terminal, on the presynaptic side of a synapse. They are released into and diffuse across the synaptic cleft, where they bind to specific receptors in the membrane on the postsynaptic side of the synapse. Release of neurotransmitters usually follows arrival of an action potential at the synapse, but may also follow graded electrical potentials. Plasmodesmata- are microscopic channels which traverse the cell walls of plant cells and some algal cells, enabling transport and communication between them. Insulin- is a hormone, produced by the pancreas, which is central to regulating carbohydrate and fat metabolism in the body. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen inside these tissues. Human growth hormone- is a peptide hormone that stimulates growth, cell reproduction and regeneration in humans. Testosterone- is a steroid hormone from the androgen group and is found in mammals, reptiles, birds, and other vertebrates. In mammals, testosterone is primarily secreted in the testicles of males and the ovaries of females, although small amounts are also secreted by the adrenal glands. It is the principal male sex hormone and an anabolic steroid. Estrogen- Estrogen is a hormone that comprises a group of compounds, including estrone, estradiol and estriol. It is the main sex hormone in women and is essential to the menstrual cycle. Although estrogen exists in men as well as women, it is found in higher amounts in women, especially those capable of reproducing. Thyroid hormone- hormones produced by the thyroid gland primarily responsible for regulation of metabolism. Ligand- Any substance (e.g. hormone, drug, functional group, etc.) that binds specifically and reversibly to another chemical entity to form a larger complex. Receptor tyrosine kinase- Are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. G-receptor protein receptors- comprise a large protein family of trans membrane receptors that sense molecules outside the cell and activate inside signal transduction pathways and, ultimately, cellular responses. Only in Eukaryotic cells. Second messengers- are molecules that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus. They relay the signals of hormones like epinephrine (adrenalin), growth factors, and others, and cause some kind of change in the activity of the cell. They greatly amplify the strength of the signal. Neuron- is an electrically excitable cell that processes and transmits information by electrical and chemical signaling. Chemical signaling occurs via synapses, specialized connections with other cells. Neurons connect to each other to form neural. Neurons are the core components of the nervous system, which includes the brain, spinal cord, and peripheral ganglia. Schwann cells- (neurolemmocytes) are the principal glia of the peripheral nervous system (PNS). Glial cells function to support neurons and in the PNS, also include satellite cells, olfactory unsheathing cells, enteric glia and glia that reside at sensory nerve endings, such as the Pacinian corpuscle. Action potential- is a short-lasting event in which the electrical membrane potential of a cell rapidly rises and falls, following a consistent trajectory. Action potentials occur in several types of animal cells, called excitable cells, which include neurons, muscle cells, and endocrine cells, as well as in some plant cells. In neurons, they play a central role in cell-tocell communication. In other types of cells, their main function is to activate intracellular processes. In muscle cells, for example, an action potential is the first step in the chain of events leading to contraction. Action potentials in neurons are also known as "nerve impulses" or "spikes". Depolarize- is a change in a cell's membrane potential, making it more positive, or less negative. In neurons and some other cells, a large enough depolarization may result in an action potential. Membrane potential- is the difference in electrical potential between the interior and the exterior of a biological cell. All animal cells are surrounded by a plasma membrane composed of a lipid bilayer with a variety of types of proteins embedded in it. The membrane potential arises primarily from the interaction between the membrane and the actions of two types of membrane proteins embedded in the plasma membrane. The two main proteins are ion channels and pumps. Acetylcholine- is an organic, polyatomic ion that acts as a neurotransmitter in both the peripheral nervous system (PNS) and central nervous system (CNS) in many organisms including humans. Acetylcholine is one of many neurotransmitters in the autonomic nervous system (ANS) and the only neurotransmitter used in the motor division of the somatic nervous system (sensory neurons use glutamate and various peptides at their synapses). Norepinephrine- is a catecholamine with multiple roles including as a hormone and a neurotransmitter. Areas of the body that produce or are affected by norepinephrine are described as noradrenergic. Dopamine- a simple organic chemical in the catecholamine family, plays a number of important physiological roles in the bodies of animals. In the brain, dopamine functions as a neurotransmitter. Serotonin- Approximately 90% of the human body's total serotonin is located in the enterochromaffin cells in the gut, where it is used to regulate intestinal movements. The remainder is synthesized in serotonergic neurons of the CNS, where it has various functions. These include the regulation of mood, appetite, and sleep. Serotonin also has some cognitive functions, including memory and learning. GABAA - is an inotropic receptor and ligand-gated ion channel. Its endogenous ligand is γ-amino butyric acid (GABA), a major neurotransmitter in the central nervous system. Although GABA ends up producing an inhibitory effect on neurotransmitter release, GABA is not an inhibitory neurotransmitter itself as it stimulates the GABA receptor; therefore, directly it is a stimulatory neurotransmitter. Upon activation, the GABAA receptor selectively conducts Cl- through its pore, resulting in hyperpolarization of the neuron. Phylogenetic tree- is a branching diagram or showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics Protobionts- are systems that are considered to have possibly been the precursors to prokaryotic cells Prokaryotes- are a group of organisms that lack a cell nucleus or any other membrane-bound organelles. Eukaryote- is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota Fitness- the ability to both survive and reproduce, and is equal to the average contribution to the gene pool of the next generation that is made by an average individual of the specified genotype or phenotype. Genotype- the genetic makeup of a cell, an organism, or an individual (i.e. the specific allele makeup of the individual) usually with reference to a specific character under consideration Phenotype- is the composite of an organism's observable characteristics or traits Natural selection- the gradual, non-random, process by which biological traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution. Adaptation- an alteration in the structure or function of an organism or any of its parts that results from natural selection and by which the organism becomes better fitted to survive and multiply in its environment. Genetic drift- or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling Radioactive Isotope- An isotopic form of an element with an unstable nucleus that stabilizes itself by emitting ionizing radiation. Nuclear Decay- is the process by which an unstable atomic nucleus losses energy by emitting ionizing particles or radiation. Carbon Dating- a method of establishing the approximate age of carbonaceous materials, such as fossil remains or archaeological specimens, by measuring the amount of radioactive carbon-14 remaining in them Vestigial Structures- structures that are now useless to the organism, example would be ostrich wings. Chromosomes- Usually in the form of chromatin, Contains genetic information, Composed of DNA, Thicken for cellular division, Set number per species (i.e. 23 pairs for human) Nuclear membrane- Surrounds nucleus, Composed of two layers, Numerous openings for nuclear traffic Nucleolus- Spherical shape, Visible when cell is not dividing, Contains RNA for protein manufacture Centrioles- Paired cylindrical organelles near nucleus, Composed of nine tubes, each with three tubules, Involved in cellular division, Lie at right angles to each other Chloroplasts- A plastid usually found in plant cells, Contain green chlorophyll where photosynthesis takes place Cytoskeleton- Composed of microtubules, Supports cell and provides shape, Aids movement of materials in and out of cells Endoplasmic reticulum- Tubular network fused to nuclear membrane, Goes through cytoplasm onto cell membrane, Stores, separates, and serves as cell's transport system, Smooth type: lacks ribosomes, Rough type: ribosomes embedded in surface Golgi apparatus- Protein 'packaging plant', A membrane structure found near nucleus, Composed of numerous layers forming a sac Lysosome- Digestive 'plant' for proteins, lipids, and carbohydrates, Transports undigested material to cell membrane for removal, Vary in shape depending on process being carried out, Cell breaks down if lysosome explodes Mitochondria- Second largest organelle with unique genetic structure, Double-layered outer membrane with inner folds called cristae, Energy-producing chemical reactions take place on cristae, Controls level of water and other materials in cell, Recycles and decomposes proteins, fats, and carbohydrates, and forms urea Ribosomes- Each cell contains thousands, Miniature 'protein factories', Composes 25% of cell's mass, Stationary type: embedded in rough endoplasmic reticulum, Mobile type: injects proteins directly into cytoplasm Vacuoles- Membrane-bound sacs for storage, digestion, and waste removal, Contains water solution, Contractile vacuoles for water removal (in unicellular organisms) Cell wall- Most commonly found in plant cells, Controls turgity, Extracellular structure surrounding plasma membrane, Primary cell wall: extremely elastic, Secondary cell wall: forms around primary cell wall after growth is complete Plasma membrane- Outer membrane of cell that controls cellular traffic, Contains proteins (left, gray) that span through the membrane and allow passage of materials, Proteins are surrounded by a phospholipid bi-layer. Endomembrane system- In eukaryotes, the functional continuum of membranous cell components consisting of the nuclear envelope, endoplasmic reticulum, and Golgi apparatus as well as vesicles and other structures derived from these major components. Speciation- The process in which new genetically distinct species evolve usually as a result of genetic isolation from the main population. Adaptive radiation- evolution of a number of divergent species from a common ancestor, each species becoming adapted to occupy a different environment Viable- capable of living. Pre-zygotic reproductive isolation- factors causing two species not to make before reproduction is attempted Post- zygotic reproductive isolation- factors either causing to the zygote to die or to not be able to reproduce Stanley Miller- he did an experiment that simulated hypothetical conditions thought at the time to be present on the early Earth, and tested for the occurrence of chemical origins of life. Photosynthesis- the complex process by which carbon dioxide, water, and certain inorganic salts are converted into carbohydrates by green plants, algae, and certain bacteria, using energy from the sun and chlorophyll Light reactions in photosynthesis- The light-independent reactions of photosynthesis are chemical reactions that convert carbon dioxide and other compounds intoglucose. These reactions occur in the stroma, the fluid-filled area of a chloroplast outside of the thylakoid membranes. These reactions take the light-dependent reactions and perform further chemical processes on them. There are three phases to the light-independent reactions, collectively called the Calvin cycle: carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration. Ectothermy- the ability of an organism maintain their body temperature by absorbing heat from their environment. Hydrolysis- The chemical breakdown of a compound due to reaction with water. NADPH- Nicotinamide adenine dinucleotide phosphate chlorophyll- A green pigment, present in all green plants and in cyanobacteria, responsible for the absorption of light to provide energy for photosynthesis. Its molecule contains a magnesium atom held in a porphyrin ring Photosystem I- One of two reaction sequences of the light phase of photosynthesis in green plants that involves a pigment system which is excited by wavelengths shorter than 700 nanometers and which transfers this energy to energy carriers such as NADPH that are subsequently utilized in carbon dioxide fixation. Photosystem II- is the first protein complex in the Light-dependent reactions. It is located in the thylakoid membrane of plants, algae, and cyanobacteria. The enzyme uses photons of light to energize electrons that are then transferred through a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions and molecular oxygen Electrochemical gradient- is a gradient of electrochemical potential, usually for an ion that can move across membrane. The gradient consist of two parts, the electrical potential and a difference in the chemical concentration across a membrane. ATP synthase- is an important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate (ATP). Enzyme- A substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction Pyruvate- (CH3COCOOH) is an organic acid, a ketone, as well as the simplest of the alpha-keto acids. The carboxylate (COO−) anion of pyruvic acid, its Brønsted–Lowry conjugate base, CH3COCOO−, is known as pyruvate, and is a key intersection in several metabolic pathways. Pyruvate can be made from glucose through glycolysis, converted back to carbohydrates (such as glucose) via gluconeogenesis, or to fatty acids through acetyl-CoA. It can also be used to construct the amino acid alanine and be converted into ethanol Oxidation reactions- reaction where a substance loses electrons Reduction reactions- reaction where a substance gains electrons FADH2- is to carry high-energy electrons used for oxidative phosphorylation. Proton gradient- The product of the electron transport chain. A higher concentration of protons outside the inner membrane of the mitochondria than inside the membrane is the driving force behind ATP synthesis. Oxidative phosphorylation- an enzymatic process in cell metabolism that synthesizes ATP from ADP. Substrate level phosphorylation- Synthesis of high-energy phosphate bonds through reaction of inorganic phosphate with an activated (usually) organic substrate Photophosphorylation- The production of ATP using the energy of sunlight Properties of water- adhesive, cohesive, high specific heat, universal solvent, ice floats Fluid mosaic model- biological membrane separating the interior of a cell from the outside environment. Passive transport- moving biochemicals and atomic or molecular substances across the cell membrane Osmosis- A process by which molecules of a solvent tend to pass through a semipermeable membrane from a less concentrated solution into a more concentrated one, thus equalizing the concentrations on each side of the membrane Facilitated diffusion- is a process of passive transport, aided by integral membrane proteins. Active transport- The movement of ions or molecules across a cell membrane into a region of higher concentration, assisted by enzymes and requiring energy. Diffusion- the act of a substance going from high concentration to an area of lower concentration. Conserved processes- processes that are continues in the environment, such as DNA replication in animals. Concentration Gradient – A region along which the density of a chemical substance increases or decreases. Sodium/Potassium Pump (PumpKin) – A transport protein in the plasma membrane of animal cells that actively transports sodium out of the cell and potassium into the cell. Endocytosis – the capture of a substance outside the cell when the plasma membrane merges to engulf it, it enters the cell in this new vesicle. (3 types: Phagocytosis, Pinocytosis, receptormediated). Exocytosis – the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cells. Glycoprotein – A protein with one or more carbohydrates covalently attached to it. Glycolipid – A lipid with covalently attached carbohydrate(s). Phospholipid – A lipid made up of glycerol joined to two fatty acids and a phosphate group. The hydrocarbon chains of the fatty acids act as nonpolar, hydrophobic tails while the rest of the molecules acts as a polar, hydrophilic head. Phospholipids form bilayers that function as biological membranes. Polar molecules – A molecule with opposite charges on different ends of the molecule. Ex: water Nonpolar molecules – Molecule where atoms share electrons equally so that no end is polar. Cellulose – A structural polysaccharide of plant cell walls, consisting of glucose monomers joined by B glycosidiclinkages. Hypotonic – A solution that, when surrounding a cell, will cause the cell to take up water. Hypertonic – A solution that, when surrounding a cell, will cause the cell to lose water. Isotonic – A solution that, when surrounding a cell, has no effect on the passage of water into or out of the cell. Photoperiodism - A physiological response to photoperiod, the relative lengths of night and day. Diabetes mellitus – An endocrine disorder marked by inability to maintain glucose homeostasis. The type 1 form results from autoimmune destruction of insulin-secreting cells; treatment usually requires daily insulin injections. The type 2 form most commonly results from reduced responsiveness of target cells to insulin; obesity and lack of exercise are risk factors. ADH (Antidiuretic hormone) – Increases the reabsorption of water by the body and increases the concentrations of salts in the urine by increasing the permeability of the collecting duct to water Produced by the hypothalamus and released from the posterior pituitary. Graves Disease – Autoimmune disorder where the immune system produces antibodies that bind to the receptor for TSH and activate sustained thyroid hormone production. The most common hyperthyroidism. Operon – A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway. -Lac – Operon that produces Inducable Enzymes (lactase) that breakdown lactose. -Trp – Operon that produces repressible enzymes (tryptophan) when around the cell, tryptophan serves as a corepressor to stop the production of tryptophan by the E. coli. Phototropism – growth of a plant shoot toward or away from light. Taxis – an oriented movement toward or away from a stimulus. Kinesis – A change in activity or turning rate in response to a stimulus. Osmoregulation – Regulation of solute concentrations and water balance by a cell or organism. Monosaccharides- A simple sugar (ex. Fructose, Glucose and Ribose.). Biotechnology- The exploitation of biological processes for industrial and other purposes Cytokinesis- the division of a cell’s cytoplasm at the end of mitosis or meiosis. It brings about the separation into 2 daughter cells Mitosis- a type of cell division that results in 2 daughter cells that are identical to the parent cell (nucleus) Interphase- the period of the cell cycle during which the nucleus is not undergoing division. Typically occurring between mitotic or meiotic divisions. Contains G1 phase, G2 phase, and S phase. Daughter cell- A cell formed by the division of another cell. Can be haploid or diploid, depending on the type of division: Mitosis/meiosis Progeny- a descendant(s) of a person, animal, or plant. AKA offspring Asexual reproduction- reproduction without the fusion of gametes Sexual reproduction- the production of new living organisms by combining genetic information from 2 individual of different sexes. Gregor Mendel- A 19th century monk/Botanist whose experiments in breeding peas led to his eventual recognition of genetics Gene expression- a conversion of the information encoded in a gene first into messenger RNA and then to a protein. Zygotes- a diploid cell resulting from the fusion of 2 haploid gametes; a fertilized ovum. Spores- a reproductive unit capable of giving rise to a new individual without sexual fusion. A haploid sex cell that gives rise to a gametophyte (in a plant exhibiting alternation of generations) Signal transduction pathway- a mechanism that converts a mechanical/chemical stimulus to a cell into a specific cellular response. Gametes-A mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote. Circular chromosomes- usually found in prokaryotes, containing DNA Watson- along with Crick, proposed a model for the structure of a DNA in the form of a double helix. Crick- along with Watson, he proposed a model for the structure of a DNA molecule. Their model is still accepted today. Franklin- the true founder of Watson and Crick’s DNA molecule model… they stole it from her. Avery- MacLeod-McCarthy experiment –first proved that DNA contains hereditary information Hershey-Chase experiment- confirmed that DNA was genetic material. Conducted in 1952 DNA replication- The use of existing DNA as a template for the synthesis of new DNA strands. In humans and other eukaryotes, replication occurs in the cell nucleus. Transcription- the process of creating an equivalent RNA copy of a DNA sequence. Translation-Translation is the process in which the genetic information on an mRNA molecule is used to make proteins. DNA polymerase- the enzyme responsible for DNA Replication Ligase- An enzyme which is capable of binding two smaller components into one single structure. RNA polymerase- the enzyme responsible for RNA replication Helicase- the enzyme responsible for “unzipping” the DNA molecule in preparation for replication. Topisomerase- zips the DNA back up 3’ end of DNA- the end of a DNA strand. Contains several A’s in a row (5-250) that signal the end for RNA to copy. 5’ end of DNA- the beginning of a DNA strand Purines- A double-ringed, crystalline organic base, C5 H4 N 4 , not known to occur naturally, from which is derived the nitrogen bases adenine and guanine Pyrimidines-A single-ringed, crystalline organic base, C4H4N2, that forms uracil, cytosine, or thymine. mRNA- RNA, synthesized from a DNA template during transcription, that mediates the transfer of genetic information from the cell nucleus to ribosomes in the cytoplasm, where it serves as a template for protein synthesis. Also called messenger RNA tRNA- One of a class of RNA molecules that transports amino acids to ribosomes for incorporation into a polypeptide undergoing synthesis. Also called transfer RNA rRNA-any of a class of single-stranded molecules transcribed from DNA in the cell nucleus or in the mitochondrion or chloroplast, containing along the strand a linear sequence of nucleotide bases that is complementary to the DNA strand from which it is transcribed: the composition of the RNA molecule is identical with that of DNA except for the substitution of the sugar ribose for deoxyribose and the substitution of the nucleotide base uracil for thymine. cAMP-A cyclic form of adenosine monophosphate (adenylic acid) that helps control many enzyme-catalyzed processes in living cells RNA processing- the splicing, 5-capping, and 3-polyadenylation by which eukaryotic pre-mRNA is converted into mature mRNA Intron- A segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes. Exon- A segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence. Codon-A sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule. Anticodon- a sequence of the complements of the 3 nucleotides that make up the codon, found on the ribosome. Gel electrophoresis-Gel electrophoresis is a technique used for the separation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA by using restriction enzymes to cut the DNA, in which the smaller DNA fragments move to the farthest end of the gel. Plasmid-based transformation- introducing bacteria to a plasmid which alters their DNA. Giving the specimen the genetic quality found in the plasmid. Restriction enzyme- enzymes that are specifically designed to cut DNA after certain sequences Polymerase chain reaction- heating and cooling DNA to amplify the DNA strand’s qualities. Checkpoints of the cell cycle- are control mechanisms that ensure the fidelity of cell division in eukaryotic cells. Mitosis-promoting factor- factors that initiate mitosis, ex: nuclear envelope breakdown. Organic- Of, relating to, or derived from living organisms. An organic compound; or any substance containing carbon-based compounds, especially produced by or derived from living organisms. Inorganic- Of or pertaining to substances that are not of organic origin. Relating to a substance that does not contain carbon. Free energy- the energy in a physical system that can be converted to do work Monomers- is a molecule that may bind chemically to other molecules to form a polymer [ polymers- A polymer is a large molecule (macromolecule) composed of repeating structural units(monomers). Amino acids- contain an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. Nucleotides- An organic molecule consisting of joined phosphate, five-carbon sugar (deoxyribose or ribose), and a purine or a pyrimidine (adenine, guanine, uracil, thymine, or cytosine) Monosaccharide- A simple sugar; a five- or six- carbon sugar(e.g., ribose or glucose) Lipids- Fat or oil (e.g., Fatty acids, Glycerolipids, Glycerophospholipids, etc) Carbohydrate- An organic compound to which hydrogen and oxygen are attached; the hydrogen and oxygen are in a 2:1 ratio; examples include sugars, staches, and cellulose. Protein (polypeptide)- One of class of organic compounds that is composed of many amino acids; contains C, H, O, and N. DNA- Deoxyribonucleic acid; found in the cell nucleus, its basic unit is the nucletide; contains coded genetic information can replicate on the basis of heredity. RNA- Ribonucleic acid, a nucleic acid in which the sugar is ribose; a product of DNA transcription that serves to control certain cell activities; acts as a template for protein translation; types include mRNA (messenger), tRNA (transfer), and rRNA(ribosomal) Gene pool- is the complete set of unique alleles in a species or population. Recombination- breaking and rejoining of DNA strands to form new molecules of DNA encoding a novel set of genetic information. Recombination can occur between similar molecules of DNA, as in the homologous recombination of chromosomal crossover, or dissimilar molecules, as in non-homologous end joining. Meiosis- special type of cell division necessary for sexual reproduction in eukaryotes. The cells produced by meiosis are gametes or spores. In many organisms, including all animals and land plants (but not some other groups such as fungi), gametes are called sperm and egg cells. Diploid- describes cells that have a double set of chromosomes in homologous pairs(2n) Haploid- Describe cells(gametes) that have half the chromosome number typical of the species(n chromosome number) Triploid- rare lethal chromosome abnormality caused by the presence of an entire extra set of chromosomes. Polyploidy- A condition in which an organism may have a multiple of the normal number of chromosomes (4n, 6n, etc.). Mitosis- A type of nuclear division that is characterized by complex chromosomal movement and the exact duplication of chromosomes; occurs in somatic cells. Metabolic (metabolism) - A group of life-maintaining processes that includes nutrition, respiration (the production of usable energy), and the synthesis and degradation of biochemical substances. Calvin cycle- Cycle in photosynthesis that reduces fixed carbon to carbohydrates through the addition of electrons (also known as the “dark cycle”) Chemosynthesis- biological conversion of one or more carbon molecules (usually carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules(e.g. hydrogen gas, hydrogen sulfide) or methane as a source of energy, rather than sunlight, as in photosynthesis. Cellular respiration- the set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. Glycolysis- The anaerobic respiration of carbohydrates Kreb’s cycle- Process of aerobic respiration that fully harvests the energy of glucose; also known as the citric acid cycle. Electron transport chain- A complex carrier mechanism located on the inside of the inner mitochondrial membrane of the cell; releases energy, and is used to form ATP Chemiosmosis- The coupling of enzyme catalyzed reactions. Fermentation- metabolic process whereby electrons released from nutrients are ultimately transferred to molecules obtained from the breakdown of those same nutrients ATP- Adenosine-5'-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells as a coenzyme. ADP- Energy-storage molecules Surface-to-volume ratio- amount of surface area per unit volume of an object or collection of objects. The surface-area-to-volume ratio is measured in units of inverse distance. Apoptosis- process of programmed cell death (PCD) that may occur in multicellular organisms. Biochemical events lead to characteristic cell changes (morphology) and death. Differentiation- A progressive change from which a permanently more mature or advanced state results; for example, a relatively unspecialized cell’s development into a more specialized one. Morphogenesis- Biological process that causes an organism to develop its shape. It is one of three fundamental aspects of developmental biology along with the control of cell growth and cellular differentiation. Negative feedback- serves to stabilize a system, e.g., maintain temperature, concentration, direction, etc. Positive feedback- Process in which the effects of a small disturbance on a system include an increase in the magnitude of the perturbation. 1st law of thermodynamics- Heat and work are forms of energy transfer. 2nd law of thermodynamics- The entropy of any isolated system not in thermal equilibrium almost always increases. Entropy- thermodynamic property that can be used to determine the energy not available for work in a thermodynamic process, such as in energy conversion devices, engines, or machines. Endothermy- Pertaining to organisms which are capable of maintaining their bodily temperature above the temperature of the external environment Ground tissues of plants include the following three types of cells: -parenchyma cell- the most common component of ground tissue, have thin walls and serve various functions including storage, photosynthesis and secretion -collenchyma cell-thick but flexible cell walls, serve as mechanical support functions -sclerenchyma cell-thickest cell wall, serve as mechanical support Dermal tissues of plants- consists of epidermis cells that cover the outside of plant parts, guard cells that surround stomata, and various specialized surface cells such as hair cells, stinging cells, and glandular cells- these cells secrete cuticle. Vascular tissues of plants (usually occur together to form vascular bundles): - Xylem- functions in the conduction of water and minerals and also mechanical supporttwo cell walls, primary and secondary-dead at maturity (completely lacking cellular components) o Two types: tracheids (long and tapered) and vessel elements (shorter and thicker)- - Pits- places in xylem where secondary wall is absent - Phloem-functions in the conduction of sugar o sieve-tube members- form fluid conducting tubes called sieve tubes- no nuclei or ribosomes- pores form sieve plates o Companion cells- associated with sieve tubes- connected by plasmodesmata to help the sieve tubes that lack nuclei -apical meristem- contains actively dividing cells that increase length -primary structure of roots: Epidermis of roots (lines the outside surface of the root), root hairs (produced by epidermal cells), cortex (makes up bulk of roots), endodermis (ring of tightly packed cells at the innermost portion of the cortex), Casparian strip (creates a water-impenetrable barrier between the cells), vascular cylinder/stele (tissues inside endodermis), pericycle (lateral roots arise) -primary structure of stems: Epidermis of stems (cells contain cutin, which forms cuticle), cortex (consists of ground tissue types that lie between the epidermis and the vascular cylinder), vascular cylinder (contains various arrangements of xylem, phloem, pith) -lateral meristem- contains actively dividing cells that increase girth -Cork cambium (produces new cells on its outside and sometimes on its inside) -palisade mesophyll- consists of parenchyma cells equipped with numerous chloroplasts and large surface areas, specializations for photosynthesis -spongy mesophyll-consists of parenchyma cells loosely arranged below the palisade mesophyllnumerous spaces provide air chambers that provide carbon dioxide to photosynthesizing cells -guard cells- specialized epidermal cells that control opening and closing of stomata-put pic on card with definition -mechanisms that control opening and closing stomata: high temperatures close them, low CO2 open them -stomatal opening is accompanied by diffusion of potassium ions into the guard cells which is followed by water, which causes guard cell expansion -osmosis- water enters roots through this process -two pathways the water move towards center of root -apoplast- water moves through cell walls -symplast-water moves through cells - root pressure- an osmotic force that can be seen as guttation (formation of small droplets - of sap [water and minerals]- occurs because of the continuous movement of water out of the root by xylem and by the higher mineral concentration inside the stele maintaining by the selective passage of ions throughout the endodermis capillary action- rise of liquids in narrow tubes because of adhesion and cohesion cohesion-tension theory-transpiration (evaporation of water from plants, removes water from leaves, causing a negative pressure), cohesion (produces a single, polymerlike column of water from roots to leaves), bulk flow (water through xylem cells occurs as water molecules evaporate from the leaf surface), sun- the driving force for the ascent of sap through plants- use pic as reference -translocation- movement of carbohydrates through phloem from a source (leaves) to a sink (site of carb utilization)- described by the pressure-flow hypothesis -pressure-flow hypothesis- sugar enters sieve tube members by active transport, which develops a concentration gradient of solutes in source versus sink, then water enter sieve tube members (water potential) moving down water concentration gradient, pressure builds up and water and sugars move by bulk flow through sieve tubes, pressure is reduced in sieve-tube members at the sink as sugars are Hypocotyl-below the epicotyl and attached to the cotyledons- becomes the young shoot Radicle-below the hypocotyl and develops into the root Epicotyl-top portion of the embryo and it becomes the shoot tip Plumule-attached to the epicotyl-these are the young leaves Coleoptile- a sheath that surrounds and protects the epicotyl- these emerge first and appears as leaves, but the first true leaves emerge from the plumule within the coleoptile seed- consists of an embryo and a seed coast and storage material endosperm-storage material-formed in double fertilization cotyledons- formed by using the storage material in the endosperm Flower- reproductive shoot; bears structures that function in sexual reproduction Sepal-modified leaf that helps enclose and protect a flower bud before it opens Petal-attract pollinators Stamen-male reproductive structure that consists of a pollen-bearing anther and its filament (stalk) Pistil- female reproductive structure and consists of three parts: an egg-bearing ovary, a style and a stigma fruit-fosters dispersal of seeds-developed from the ovary pollen grains-matured from microspores- male gametophyte in conifers embryo sac-the plasma membrane that forms from six nuclei undergoing cytokinesis double fertilization-the fertilization of the egg and the polar nuclei each by a separate sperm nucleus Auxin-plant hormone that promotes plant growth by facilitating the elongation of developing cells- produced at tips of roots and shoots, where, in concert with other hormones it influences plant responses to light (phototropism) and gravity (geotropism/ gravitropism) Cytokinins- plant hormones that stimulat cytokinesis- produced in roots and transported to other parts of the plant-variety of effects depending on the target- could weaken apical dominance (the dominant growth of the apical meristem) and delay senescence (aging) of leaves Gibberellins- plant hormones promote cell growth- made in young leaves, roots and seeds then transported to other parts-promote fruit development, inhibits aging, and can cause bolting (rapid elongation of stem) abscisic acid ( ABA) plant hormone-growth inhibitor-maintains dormancy in seeds ethylene plant hormone-gaseous hormone that promotes the ripening of fruit tropism- growth pattern in response to an environmental stimulus -phototropism- response to light is achieved by the action of the hormone auxin- auxin is produced in the apical meristem, moves downward by active transport into the zone of elongation and generates growth by stimulating elongation- concentrates on shady side -gravitropism (geotropism)-the response to gravity by stems and roots- auxin and gibberllins are involve, but their action depends on concentration and the target (i.e. root/stem) statoliths-specialized starch-storing plastids that settle at the lower ends of cells, somehow influence the direction of auxin movement circadian rhythm-a clock that measures the length of daylight and night in plants photoperiodism- response of plants to changes in the photoperiod (relative length of daylight and night) mechanism for maintaining circadian rhythmn: - Phytochrome ( a protein modified with a light-absorbing chromophore) is involved- there - are two forms: Pfr (far red light- P730) and Pr (red light- P600)- the two forms are photoreversible (when Pr is exposed to red light it is converted to Pfr- and visa versa)Label picture below Pfr resets the circadian rhythmn clock Pr is made naturally in the plants leaves During the daylight both forms are in equilibrium because Pr is made naturally than converted by sunlight to Pfr then Pfr is converted by to Pr because the sun also has far red light At night Pr accumulates because there is no sunlight to convert it to Pfr Night length is responsible for resetting the circadian-rhythm clock short-day plant-these flower when daylight length is shortened long-day plant-these flower in the spring when the daylight length is increasing day-neutral plant-do not flower in response to daylight length- other stimuli cause them to bloom Florigen-a flowering hormone that is produced in the leaves and travels to shoot tips Taproot- a large single root fibrous root (adventitious)- a cluster of many fine roots annuals, mineral nutrients, essential nutrient, macronutrients, micronutrients, nitrogen-fixing bacteria, nitrogen fixation energy transfer-the transfer of energy from one material to another abiotic - non-living components of an ecosystem ex. Wind, rain, sun, rocks biotic- living components of an ecosystem ex. Plants and animals habitat-The area or environment where an organism or ecological community normally lives or occurs population- a group of individuals of the same species that can interbreed community- a group of populations that live close enough for interaction biogeography- study of past and present distribution of species biome- terrestrial or aquatic life zones characterized by vegetation type in terrestrial biomes or physical environment in aquatic biomes Ex. Lakes (freshwater biome- may have seasonal thermocline), Wetlands (a habitat that is inundated by water at least some of the time and that supports plants adapted to water-saturated soil), Streams and Rivers (fresh water biome with current), Estuaries (transition area between river and sea ex. Sounds, bays, inlets), Intertidal zone (periodically submerged and exposed by the tides), Oceanic Pelagic zone (open ocean), Coral reef (formed largely from the calcium carbonate skeletons of corals), Marine benthic zone [neritic] (seafloor- generally does not receive light), tropical rain forest (high temperature and heavy rain- epiphytes and vines are commonusually nothing grows on floor), desert (hot and dry), savanna (grasslands with scattered treesthey are tropical with high temperatures, but little rainfall), Chaparral (midlatitude regions of continents- rainfall is seasonal with moderate temperature- far-flung distribution), temperate grassland (less water and subject to lower temperatures than savannas- ex American prairie), northern coniferous forest [taiga] (winters are cold and precipitation is in the form of snow- ex. pine forests), temperature broadleaf/deciduous forest (occupy regions that have warm summers, cold winters and moderate precipitation- trees that shed their leaves during the winter ), tundra (temperatures during winter are so cold that ground freezes (permafrost)- during summer melted topsoil supports a grassland type of community) Zonation in aquatic environments: Draw and label -photic zone, aphotic zone, benthic zone, littoral zone, limnetic zone, profundal zone oligotrophic- type of lake that is usually nutrient poor and oxygen rich. Eutrophic- type of lake that is usually nutrient rich and oxygen poor. Canopy-the uppermost layer of vegetation in a terrestrial biome Permafrost- a permanently frozen soil layer Regulator- an animal for which mechanisms of homeostasis moderate internal changes in the face of external fluctuations Conformer- an animal for which an internal condition conforms with a change in an environmental variable Size of a population (N)- the number of individuals living within specific boundaries Density- number of individuals per unit area (or volume) Ex. The number of oak tress per square kilometer in the Minnesota Co. Dispersion- pattern of spacing among individuals within the boundaries of the population Examples: Uniform, Clumped, Random age structure- relative number of individuals of each age in the population Ex. Human growth fecundity- The power of reproducing abundantly; fruitfulness or fertility life table- used to estimate how long individuals (on average) can be expected to live; agespecific summaries of the survival pattern of a population survivorship curves- a graphic method of representing the data in a life table; a plot of proportions in a cohort still alive at each age; 3 types- I, II, III zero population growth (ZPG)- death rate and birth rate are equal Ex. Two mice reproduce, but usually only two of their offspring survive to reproductive age reproductive rate- r= (births-deaths)/N [N- population size at beginning of interval] Biotic potential (intrinsic rate of growth)- when reproductive rate is at maximum exponential (geometric) population growth- assumes resources are unlimited, size of a population grows exponentially (growth rate is at max); J-shaped curve Example African elephants carrying capacity (K)- maximum population size that a particular environment can sustain logistic population growth- growth rate nears zero as the carrying capacity is reached; S-shaped curve Example Paramecium and Daphnia K-selected populations- a.k.a density dependent selection- type of selection that operates in populations that are living near the limit imposed by resources (its carrying capacity); competition for resources is strong Example- mature trees growing in a old-growth forest r-selected populations- a.k.a density independent selection- maximizes growth rate and occurs in environments in which population densities are well below carrying capacity; characterized by opportunistic species (grasses, insects) that quickly invade a habitat, quickly reproduce and then die intraspecific competition- competition for resources between individuals of the same specie interspecific competition- competition for resources between different species limiting factor- elements that prevent a population from attaining its biotic potential Ex. densitydependent factor (agents wholse limiting effect becomes more intense as the population density increases- ex disease and competition), density-independent factor (occur independently of the density of the population- ex natural disasters) species diversity- the variety of different kinds of organisms that make up the community Ex. species richness ( number of different species), relative abundance (the proportion each species represents of all individuals) predation- +/- interaction between species in which one kills and eats the other defensive adaptations of prey- cryptic coloration (camouflage), aposematic coloration (warning coloration), Batesian mimicry (harmless/unpalatable mimics harmful/palatable), Mullerian mimicry (two or more unpalatable/harmless species resemble each other- if there are more predator will adapt and avoid those characteristics) Ecological succession- the process of a disturbed area possibly being colonized by a variety of species, which are gradually replaced by other species, which are in turn replaced by still other species Examples- primary succession (begins on a virtually lifeless area, such as a new volcanic island), secondary succession (occurs when an existing community has been cleared by a disturbance that leaves the soil intact, such as the 1988 fire in Yellowstone) Coevolution (predator/prey evolution)- the evolution of one species in response to new adaptations that appear in another species Symbiosis- when two or more species live in direct and intimate contact with each other (sometimes synonymous with mutualism) Commensalism- +/0 relationship; Ex barnacles attached to whales Mutualism- +/+ relationship; Ex. Nitrogen fixing bacteria on root nodules of legumes Parasitism- +/- relationship; Ex. Ectoparasite= ticks; endoparasite= tapeworm Parasitoid- a parasite that kills Competitive exclusion principle (Gause’s)- no two species can sustain coexistence if they occupy the same niche; when two species compete for the same resource only one will be successful ex. Paramecium ecological niche- describes all the biotic and abiotic resources in the environment used by an organism Ex. fundamental niche (the niche that an organism occupies in the absence of competing species), Realized niche (when predators are present both by be able to survive by occupying their realized niche that part of their existence where niche overlap is absent) character displacement (niche shift)- result of resource portioning, certain characteristics may enable individuals to obtain resources more successfully resource partitioning- in an effort to minimize competition and maximize success species will coexist and occupy slightly different niches keystone species- a species that has a pivotal ecological role; not necessarily the most abundant trophic structure- the different feeding relationships in an ecosystem which determine the route of energy flow and the pattern of chemical cycling trophic level- organization of animal and plants that reflect their main energy source; primary producers (autotrophs that convert sun energy into chemical energy- ex plants and photosynthetic protists), primary consumers (eat primary producers- ex herbivores), secondary consumers (primary carnivores- eat primary consumers), tertiary consumers (secondary carnivores- eat the secondary consumers) Detritivores- consumers that obtain their energy by bonsuming dead plants and animals (detritus)- decomposers are very small detritivores (ie bacteria) food chain- the pathway along which food energy is transferred from trophic level to trophic level (starts with producers) food web- interconnected feeding relationships in an ecosystem production/comsumption- in ecology it refers to the synthesis/degradation of organic compounds by an organism ecological (trophic) efficiency- the proportion of energy represented at one trophic level that is transferred to the next level; the sizes of the tiers in an energy pyramid indicate the efficiency; average efficiency is 10%, so 10% of energy is passed to next level ecological pyramids- used to show relationships between trophic levels primary productivity- the amount of light energy converted to chemical energy by autotrophs in a given time period; gross primary productivity [GPP] (total primary production in an ecosystem), net primary productivity [NPP] (is equal to GPP minus the energy used by the primary producers for respiration [R]- the formula:NPP = GPP -R) biomass- the total mass of organic matter of a group of organisms in a particular habitat standing crop biomass- the total biomass of photosynthetic autotrophs present at a given time biogeochemical cycles- describe the flow of essential elements from the environment to living things and back to the environment; hydrologic (Reservior-oceans, groundwater, glaciers; Assimilation-plants absorb water from soil, animals drink; Release- plants transpire, animals/plants decompose), Carbon (Reservior- atomosphere as CO2, fossil fuels; Assimilationplants use in photosynthesis, animals consume plants; Release- plants/animals release through cell respiration, burning of fossil fuels), Nitrogen (Reservior- atmosphere as N2, soil as ammonium, ammonia, nitrite or nitrate; Assimilation- plants absorb, animals eat plants; nitrogen fixation[N2 to ammonia or nitrate], nitrification [ammonium to nitrite and nitrite to nitrate OR ammonium to nitrate Release-denitrification [nitrate back to nitrogen gas], ammonification [organic molecules back to ammonium), Phosphorus (Reservior- rocks and ocean sediment; Assimilation- plants absorb phosphate from soil and animals eat plants; Release- plants/animals decompose and animals excrete in wastes) biological magnification- toxin accumulation in tissues; toxins become more concentrated in successive levels of a food web (i.e. humans and top consumers are affected most by toxic compounds in environment) conservation biology- integrates ecology physiology molecular biology genetics and evolutionary biology to conserve diversity at all levels bioremediation- the use of organisms to detoxify and restore polluted and degraded ecosystems (i.e. oil spill) Pictures came from: Campbell, AP Biology http://scienceaid.co.uk/biology/ecology/food.html