Bio Final Study Guide

Bio-105 Final Study Guide Chapter 10 – Molecular Biology •

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Structure of DNA: Watson & Crick (1953) ○ A -> T, G -> C ○ Nucleotides: Building blocks of DNA  Deoxyribose, phosphate, nitrogenous base, (purines: adenine and guanine, pyrimidines: cytosine and thymine) ○ 1 phosphate, 1 deoxyribose, 1 nitrogenous base (A,T,C,G) ○ Purine: Double ringed structures, includes Guanine and Adenine ○ Pyrimidines: One-ringed structures, includes Thymine and Cytosine ○ Sugar-Phosphate Backbone: Holds no information, is purely structural ○ Double-helix: Complimentary base pairing (A -> T, G -> C)  Via HYDROGEN BONDS ○ Deoxyribonucleic acid Structure of RNA ○ A -> U, G -> C ○ Nucleotides: Building blocks of RNA  Ribose, phosphate, nitrogenous base (purines: adenine and guanine, pyrimidines: cytosine and uracil) ○ Single-stranded ○ Purine: Double ringed structures, includes Guanine and Adenine ○ Pyrimidines: One-ringed structures, includes Thymine and Cytosine Functions of the 3 kinds of RNA ○ Messenger RNA: Carries genetic information from DNA to the ribosome ○ Transfer RNA: brings the amino acid to the ribosome during translation ○ Ribosomal RNA: Structural RNA in ribosomes (protein + RNA), doesn’t carry genetic information The Human Genome ○ Mapping of all the genes in the human body. Useful to try to isolate and identify genes that cause or predispose for cancers and other genetic disorders. ○ Chromatin: Made of DNA and histones ○ Histones: A type of protein found in chromosomes ○ Genes: Biologic units of heredity that are located at a specific position on a particular chromosome Replication (to replicate) ○ During S phase the two strands of the DNA molecule separate, each strand is used as a template to assemble a complimentary strand.

THIS REQUIRES DNA POLYMERASE: It adds the complimentary bases, covalent bonds then hold them together (covalent is the one that gives up its electrons), it then “proofreads” the order of the pairs to make sure its correct. ○ So basically during replication A  T and G  C each break up. A separates and goes off to find another T. T goes off and finds itself another A. Same thing for G and C. In this way, it creates an exact copy. ○ Occurs once per cycle ○ 1 Mistake every like, 10 billion base pairs, due to DNA’s abilities (polymerase). ○ Within 1 chromosome there are many different starting points that are called ORIGINS OF REPLICATION ○ DNA Ligase: Links together DNA fragments (pieces), doesn’t have as much of a role. Only is there when there are gaps. Transcription (think of transcribing something, passing information from one person to another) ○ Takes the genetic information for one gene and transfers it to a messenger. Similar to replication, but only 1 gene at a time is transcribed (versus all of them in replication). This can happen at virtually any time (occurs many times per cycle) ○ So basically, instead of taking both A  T and G  C sides for replication, it just grabs one of them and does that. ○ THIS REQUIRES RNA POLYMERASE WHICH IS RESPONSIBLE FOR TRANSCRIPTION Translation 3 Steps ○ 1) Initiation: Small subunit of ribosome attaches to mRNA  Initiator transfer RNA: Carries methionine • Methionine (M): Is always the first amino acid brought over • Start Codon: always AUG • Stop Codon: UAC, this is COMPLIMENTARY (A  U, etc) to AUG ○ mRNA binds to small subunit of RNA ○ Initiator transfer RNA binds to start codon AUG ○ Large subunit binds to small subunit ○ 2) Elongation: More amino acids are getting attached to methionine (M)  A) Codon recognition  B) Peptide bond formation  C) Translocation ○

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 Each cycle adds 1 amino acid to A site ○ 3) Termination: Where polypeptide reaches stop codon and is released from the ribosome. Large & small come apart.  UAA, UAG, UGA DNA  transcription  RNA  Translation  Polypeptide In summary: ○ Replication: Identical copy made TAKES PLACE IN NUCLEUS ○ Transcription: Messenger RNA is made (transcribe the shit over to the messenger) TAKES PLACE IN NUCLEUS ○ Translation: Protein synthesis (protein is made from what the messenger knows) TAKES PLACE IN CYTOPLASM ○ RNA Polymerase: Can’t proofread like DNA can, that’s why HIV can screw that shit up so bad ○ DNA is never converted, information is merely transferred (to the messenger RNA) which tells the ribosome to assemble the amino acids ○ Primary Structure of Protein: Is the order of the bases ○ Different Functions of Proteins: (?) ○ Mutations  Base substitution: Bases are A,T,G,C, so this just means A where G should be, etc.  Base deletion: Gone entirely, leads to a misalignment down the chain called a frameshift mutation  Base addition: Added base where it shouldn’t be, also causes a frameshift mutation Chapter 11 – Genetic Basis of Cancer

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Caused by mutations. 2 types: ○ Inherited mutations: Genetic pre-disposition from birth ○ Environmental factors: Environmentally-caused mutations, such as tobacco smoke or an unhealthy profession Cause by translocations, viruses and other risk factors ○ Translocations: Bit of a gene stitched on to the wrong spot of another gene ○ Viruses: HPV, HIV, etc ○ Risk factors: Tobacco, table salt, etc Types ○ Carcinoma: Skin cancer, lining of digestive system, etc ○ Sarcoma: Muscle or bone cancer ○ Leukemia: Affects blood ○ Lymphoma: Cancer of the lymph nodes 4 most common types ○ Prostate, breast, lung, colon

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Top Cancer Killer in the US: Lung ○ Because its difficult to detect until its too late Cancer prevention from early detection Chapter 15 – Evolutionary History

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Okay natural selection is essentially, you have these mutations. So you’re born with like, a little wing or some shit. That little wing winds up helping you get along a little better in the world, so before you know it, you and all the other little winged mutants are outnumbering the rest of us. You start mating with each other, and more and more, you only have little winged children. Eventually we welcome our winged overlords. ○ Natural selection: specific variations among members of a species cause changes to be made to the species as a whole  1. Individual variations: Black beetle born yellow  2. Overproduction and competition: Not enough food to go around, too many beetles  3. Differences in reproductive success: Chick beetles dig yellow beetles  4. Adaptations occur over time: More beetles are born yellow Microevolution: Remember micro = small, so microevolution is the changes in a population from one generation to another. In other words, not changing species, just making changes within the existing species. ○ Remember a population is a group of one species, interacting. So like, all of the roaches in your filthy house are a population. Not all the roaches in the world. Macroevolution: (Speciation)this is the creation of new species over long periods of time. So like, with enough natural selection and pressure, rats turn in to winged creatures of doom. That breathe fire. Evidence in support of Evolution 1. Fossil record: Carbon 14 dating of fossils and whatnot 2. Biogeography: The idea that there was once a pangea (one big continent) 3. Comparative anatomy: Homologous structures (think how we have somewhat similar bone structure to all animals, our legs look like dog legs, etc) (homology) 4. Comparative embryology: Embryos of all kinds of shit look similar initially 5. Molecular biology: DNA, determine base sequence of large portions of genetic material 6. Stupid people dying in funny ways: Eliminates stupid people from gene pool Radioisotopes and dating of fossils: Essentially, there are these things called radioisotopes. Like Carbon 14. They degrade (give off all their energy)

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at a measurable rate. So if a bone should have a pound of C14 in the beginning, and now its got 2/3 of a pound, we can measure how long it would have to have been sitting in the ground for that to happen. The Geologic Record: PPMC 1. Precambrian: (4.6 Billion years ago) Life begins, single-cell little shits, prokaryotic. Ancient algae and soft-bodied organisms. Eukaryotic organisms don’t begin for ~2.1 billion years. 2. Paleozoic: (542m – 251m yrs ago). Means “ancient animal”, Permian mass extinction ended it, when 96% of life on planet earth ceased to exist. During this time though, more stuff started to pop up around, mostly water creatures, and some little things that started to crawl their asses up on to the land. 3. Mesozoic: (251m – 65m yrs ago). Means “middle animal”. This is Jurrasic Park. Age of reptiles, mammals do emerge towards end. Cretaceous mass extinction caps off this period nicely, 50% of life ends. Woops. 4. Cenozoic: (65m – present). Means “recent animal”, smaller organisms, abundance of mammals. I mean shitloads of mammals. Mammals, birds, and flowering plants all start.

Chapter 16 – Prokaryotes and Protists •

Kingdom Monera: Bacteria and Achaea ○ Major Characteristics:  NO NUCLEUS  Cell wall made of peptidoglycan  Flagella made of flagellin  Mostly heterotrophs (bacteria need to eat!) • Those that are not cyanobacteria ○ Which means photosynthetic ○ They have pigments in their thylakoid membranes that operate like a chloroplast in a plant  Shapes of Bacteria: • Coccus: balls (streptococcus) • Cillus: rods (e coli) • Spirillus: spiral (anthrax)  Aerobic Bacteria: Requires air (you need to breathe while doing aerobics)  Disease-causing bacteria: Some bacteria causes disease, which requires you to take antibiotics, these prevent the bacteria from making their cell walls (like penicillin).

Endospores: The crap that is left behind when a bacteria “dies”, and all it needs is a little water to come back like BOOM. That’s why anthrax is such a bitch to get rid of.  Endosymbiosis: This is membrane in-folding • Ancient Prokaryote: Years ago when we were prokaryotes, our plasma membranes infolded and formed a nuclear envelope, RER, SER and golgi apparatus • Endosymbiosis: Photosynthetic prokaryote organism entered the plasma membrane. Might be why the chloroplast has 2 cell walls. Kingdom Protista  This is the “miscellaneous” category. Algae, slime molds, all that greasy shit. Mostly heterotrophic save for algae.  Protozoa: Single cell, small, but eukaryotic and heterotrophic • Flagellate- Giardia • Amoeba – Amoeboid Movement • Apicomplexan – Plasmodium (ALL PARASITIC like malayria) • Ciliate – Paramecium (shit in water)  Slime Molds: heterotrophic • Cellular slime molds: Spend most of their lives as individual unicellular protists, but when a chemical signal is secreted (WHEN THEY GET THEIR CELLULAR PHONE CALL), they assemble into a cluster that acts as one organism • Fruiting body  spores  release amoebas • (Has single cell stage) • Plasmodial slime molds: Involves numerous individual cells attached to each other, forming one large membrane. Essentially a big bag of cytoplasm. • Syngomy (two come together) (diploid), forms zygote (fertilized egg), divides. Interesting note: nucleus divides but it doesn’t go through cytokinesis so you end with a big cell with many nuclei but not really multicellular. Then fruiting body  spores  release individual amoebas.  Algae: photosynthetic protest (autotrophic) • Unicellular and Colonial: ○ Dino-flagellates: Unicellular ○ Diatoms: Unicellular ○ Unicellular and Colonial Green Algae • Multicellular ○ Brown algae: Kelp 

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Red algae: Sushi Multicellular-green

Chapter 17 – Fungi and Plantae

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Fungi: All heterotrophic (EATS THE SHIT THAT’S ROTTING) ○ Characteristics ○ Heterotrophic ○ Decomposers ○ Usually multicellular (not yeast) ○ Cell walls are made of CHITIN ○ Nonmotile (they don’t move) Most fungi have hypha ○ A mycelium is made of numerous hypha ○ They are kind of like roots on a plant, but for a mushroom The fruiting body of a mushroom is the part you see and eat Mycorrhizae: Fungus that grow underground around roots of plants forming a symbiotic relationship. They absorb necessary nutrients, while the plants make sugar for the fungus. Three Divisions of Fungus ○ Zygomycetes: Black bread mold ○ Ascomycetes: Yeast, penicillin ○ Basidiomycetes: Mushrooms Kinds of relationships ○ Symbiotic: We both prosper! (lichen) ○ Parsitism: I’m going to eat you while you die (malaria or athletes foot) ○ Commensalism: Since you don’t mind I’m going to live on you (algae on turtles back) Plantae: *ALL AUTOTROPHIC* ○ Characteristics: Vascular, multicellular, autotrophic, photosynthetic, cellulose, cuticle (waxy) ○ Adapted to land, most plants have vascular tissue (xylem for water, phloem for food)

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Lignin: Strengthens cell walls, lets shit grow to be like tree-sized and whatnot Roots, leaves Algae has no vascular system, so they gotta stay in the water. Plants do. Plants have indoor plumbing usually. Except the: Bryophytes: Nonvascular (liverworts, hornworts, mosses) WORTS’N’MOSSES  They’re small, because they aren’t vascular, so they can’t pump water up too far, have to rely on just absorbing like a sponge  They aren’t well-adapted to land  They killed your mother Vascular seedless: Ferns and club mosses (black dots under fern leaves are spores) Vascular seeded: Gymnosperms and angiosperms (all the normal plants)  Gymnosperm: Cone-bearing plants (G  C)  Angiosperm: Flowering plants (Angie likes flowers) Alternation of Generations: Haploid/diploid stages plants go through  Gametophyte: Haploid, produces gametes  Sporophyte: Diploid, produces spores  All plants have these, however in some plants one or the other is more dominant (LOOK UP IMAGE) Google -> Alternation of Generations Structure of a flower: LOOK THIS IMAGE UP TOO When you see a fern, that is sporaphyte stage Fertilization in water Cones protect and cover seeds  There are male and female cones Plant model:  Filament goes to anther (tube)  Style goes to stigma  Receptable below the ovary  Carpel: All female reproductive structures on the flowering plant (stigma, style, ovary)  Stamen: Male parts (sta MEN), anther + filament

Chapter 18 – Animalia • •

Animalia: Multicellular, heterotrophic, mostly diploid, most have muscle and nerve cells Zygote  blastula  gastrula

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Embryonic stages and layers ○ Blastula: Hollow ball of cells developed from single zygote cell (fertilized egg) ○ Gastrula:  Outermost layer: Ectoderm (nervous system, outer covering like skin)  Middle layer: Mesoderm (forms muscle and connective tissue)  Inner layer: Endoderm (digestive tract) Classification of animal body ○ Symmetry:  Radial: Cut like pie, symmetrical (jellyfish)  Bilateral: Cut down the middle (lobster and most) ○ Body Cavities: can be “no”, pseudocoelum, true coelum  No: Means no body cavity or separate digestive tract (flatworms)  Pseudocoelum: Does not have mesoderm covering both sides within body cavity (round worm)  True coelum: Does have mesoderm on both sides of digestive tract (segmented worms) ○ Protostome: If the opening of the gastrula becomes the mouth ○ Deuterostome: If the opening of the gastrula becomes the anus and a 2nd opening forms the mouth. Different classes within the phylum chordate ○ Fish ○ Amphibians ○ Reptiles ○ Birds ○ Mammals  Characteristics of all of them • Dorsal nerve cord (like spinal cord) • Notochord (flexible rod between digestive tract and nerve chord) • Pharyngeal slits (gills, we got them shits in embryonic stages) • Post-anal tail (tail after anus)