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Biochemistry

• 4 organic compounds: – Proteins:

• made up of amino acids.

• Control all chemical reactions in the body.

• Enzymes: proteins that speed up the rate of a chemical reaction.

– Carbohydrates: examples are starch and sugar. • Building block monosaccarides

• Provide cell with energy

– Lipids: examples are fats • Insulate the body and serve as long term energy reserve.

• Make up of a glycerol and 3 fatty acid chains

– Nucleic Acids: examples are DNA and RNA • The genetic code for life.

• Basic building block is called nucleotide (sugar, phosphate, nitrogen base)

Characteristics of Life

• Living things…

– Are made of cells

– Reproduce

– Are based on a universal genetic code

– Grow and develop

– Obtain and use materials for energy

– Respond to their environment

– Maintain stable internal conditions (Homeostasis)

– Change over time

Cells • Eukaryote – has a nucleus and organelles (Protist, fungi, plant, animal

cells)

• Prokaryote – NO nucleus or membrane bound organelles (Ex. Bacteria)

• Animal cells vs. Plant cells – Plant cell has cell wall and chloroplast

– Animal has lysosome

– Cell Parts and Functions: • Nucleus- control center of cell

• Cell Wall- protects plant cell

• Cell membrane- allows materials to move in and out of cell

• Cytoplasm- holds organelles in place in the cell

• Endoplasmic Reticulum- contains ribosomes, transportation system of the cell

• Ribosomes- makes proteins

• Golgi Body- organizes and packages materials for cell

• Mitochondria- provides energy for cell

• Vacuole- stores materials for cell

• Chloroplast- site of protein synthesis in plant cell

• Lysosome- breaks down food in animal cell

• Chromosomes- found in nucleus, contain genetic information

• Cell Theory – All living things made of cells

– Cells are basic unit of structure and function of living things

– New cells are produced from living cells

• Diffusion

– Movement of molecules from an area of high concentration to an area of low

concentration across a membrane

– Passive transport (requires no energy)

• Osmosis

– Diffusion of water across a membrane

– Passive transport

• Facilitated Diffusion

– Diffusion of glucose (large molecule) across a membrane

– Passive transport

• Active Transport

– Movement from a low concentration to high concentration (against

the flow)

– Requires energy

Cell Processes

• Endocytosis

– Cell membrane engulfs particle to bring it

inside

– Active transport

• Exocytosis

– Cell membrane sends out particle to get rid of

it

– Active transport

Cell Processes

Photosynthesis

• 6CO2 + 6H2O C6H12O6 + 6O2

• Takes place in PLANTS (chloroplasts)

– Light Dependent Reaction (in Grana)

• Requires light energy

• NADP and H join to form NADPH

• Oxygen gas given off as a byproduct

– Light Independent Reaction (in Stroma)

• ATP + NADPH join, using CO2

• Sugars (C6H12O6) given off as a byproduct

Cellular Respiration

• Process of breaking down food molecules to release energy

• C6H12O6 + 6O2 6CO2 + 6H2O – Opposite of photosynthesis

• 3 main stages – Glycolosis - C6H12O6 broken in half to make pyruvic acid

• If oxygen present – goes to Krebs Cycle

• If no oxygen present – goes to Fermentation

– Krebs Cycle (Citric Acid Cycle) – takes out oxygen and pyruvic acid turned into CO2; enzymes combine hydrogen and oxygen to form H2O

– Fermentation

• Alcoholic fermentation – yeasts and other microorganisms use pyruvic acid to make CO2 (makes bread rise)

• Lactic Acid fermentation – muscle cells convert pyruvic acid to lactic acid

Cell Division • Mitosis

– Division of somatic cells (all cells in the body EXCEPT gametes (sperm/eggs)

– Interphase: chromosomes appear

– Prophase: chromosomes condense chromatin; pair up to make sister chromatids

– Metaphase: chromatids lined up in center (metaphase plate)

– Anaphase: chromatids separate and pull to opposite ends of cells

– Telophase: chromosomes uncondense; nucleus forms around them

– Cytokenesis: cell splits into two daughter cells

• End Result

– Two new daughter cells are formed.

– Each daughter cell has same number of chromosomes as parent cell

• Meiosis – Division of gametes (sperm and eggs)

– Same process as mitosis, but it does 2 cycles • Interphase 1 – Prophase 1 – Metaphase 1 – Anaphase 1 –

Telophase 1 – Cytokenesis – 2 daughter cells formed with 2 copies of every chromosome –

They go on to divide again

• Interphase 2 – Prophase 2 – Metaphase 2 – Anaphase 2 – Telophase 2 – Cytokenesis

– Now 4 daughter cells are formed (2 cells from cycle 1 have divided again)

– Each daughter cell now has 1 copy of every chromosome (will join with other chromosomes during fertilization)

• End Result –4 daughter cells are formed.

- Each cell has half the number of chromosomes as the parent.

Cell Division

DNA • Deoxyribonucleic Acid- double stranded.

• Found inside of nucleus in cells

• Cells read DNA code sequences and translate them using the sequences of 4 bases – Adenine, Guanine, Thymine, Cytosine

– A-T G-C

• The way these bases pair up determines what proteins are made

RNA

• Ribonucleic Acid- single stranded

• Messenger RNA – mRNA – reads DNA “code” and carries it to ribosome

• Ribosomal RNA – rRNA – makes up the ribosome where proteins are made

• Transfer RNA – tRNA – transfers each amino acid needed for protein synthesis as coded by mRNA from DNA

• No Thymine (T) Uracil (U) – A-U G-C

Genetics

• The scientific study of heredity (passing of traits from one generation to the next)

• Dominant Allele: the trait that always shows physically and is represented by a CAPITAL LETTER. – Example: BB or Bb

• Recessive Allele: only shows if the dominant allele is not present and is represented by a lowercase letter. – Example: bb

• Punnett Square: diagram showing gene combinations that might result from a genetic cross.

• Homozygous: organism with 2 identical alleles (also called true breeding) – Example: TT or tt

• Heterozygous: organism with 2 different alleles (also called hybrid) – Example: Tt

• Phenotype: physical characteristic of the organism. – Example: Tall plant

• Genotype: genetic makeup of the organism. – Example: Tt, TT, tt

• Incomplete Dominance: one allele is not dominant over another. – Example: Red flower is crossed with white flower to

produce a pink flower.

Genetics

Genetics

• Codominance: both alleles of the genes contribute to the phenotype of the organism. – Example: Chicken with black feathers crossed

with white feathered chicken appears speckled with black and white feathers.

• Polygenic Traits: trait controlled by 2 or more genes that shows a wider range of phenotypes. – Example: range of skin color in humans.

• Gene Map: diagram showing the relative locations of each known gene on a particular chromosome.

Ecology • Study of interactions among organisms and their environment

• Abiotic factors – not living (water, air)

• Biotic factors – living (animals, plants)

• Levels of organization (smallest to largest)

– Individual Species (can breed & produce offspring)

– Population (same species in the same area)

– Community (different populations in the same area)

– Ecosystem (all organisms in a particular place – biotic only)

– Biome (group of ecosystems with same climate)

– Biosphere (all parts of earth – abiotic and biotic)

• Heterotrophs/Consumers – cannot make their own food (must eat something else) (humans)

• Autotrophs/Producers – make their own food (plants)

• Food web- overlapping food chains

• Biomass- total amount of living tissue at each level of a food chain. Highest amount of biomass is at producer level.

• Relationships between organisms

– Mutualism – both benefit

• Bees and flowers (bees get nectar from flower, flower

gets pollination done)

– Commensalism – one benefits and other is not

harmed or benefited

• Whales and barnacles (barnacles live on whales and

eat little organisms – whale not helped or harmed)

– Parasitism – one benefits one harmed

• Humans and tapeworms (tapeworm lives in intestines

and gets nutrients that are supposed to go to human’s

body – human suffers from malnutrition)

Ecology

• Biomes: – Tropical rain forest

• Hot, humid, lots of rain, lots of plants and animals

• Found in South America, SE Asia, Southern India, NE Australia (along equator)

– Deciduous forest • Warm year round, rainy/dry seasons, rich soils

• Found in Africa, Central America, Mexico, India, Australia, tropical islands

– Savanna (grasslands) • Warm, seasonal rain, isolated shrubs and trees (picture the setting of

The Lion King)

• Found in East Africa, Southern Brazil, Northern Australia

– Desert • Low/no rain, variable temperatures, soils have lots of minerals but no

nutrients (therefore, rare plant growth)

• Found in Africa, Middle East, U.S., Mexico, South America, Australia

– Tiaga • Long,/cold winters, mild summers, moderate rain, high humidity

• Found in North America (Canada and Alaska), Asia, northern Europe

Ecology

• Biomes (continued) – Grassland

• Warm/hot summers, lush grasses (fire and cold resistant)

• Found in central Asia, North America, Australia, Europe

– Chaparral • Hot/dry summers, wet winters, thin soils, evergreen shrubs and trees

• Western coasts of N. America and S. America, areas around the Mediterranean Sea, South Africa, Australia

– Temperate Forest (Alpine) • Cold to moderate winters, warm summers, year round rain, fertile soils

• Coniferous trees (produce cones), shrubs, deciduous trees

• Found in Eastern U.S., SE Canada, most of Europe, Japan, China, Australia

– Northwestern Coniferous Forest • Mild temps, lots of rain during fall/winter/spring, cool/dry summer

• Found in NW U.S., SW Canada (basically all along the coast of Northern California to Alaska)

– Tundra • Permafrost (permanently frozen), strong winds, low rain

• North America (northern Canada, Alaska), Asia, and Europe (towards North Pole)

Ecology

Classification • Taxonomy – process of classifying organisms into

similar categories (based on structure and function)

• 7 levels of classification (largest to smallest) – Kingdom-

• 6 kingdoms (Archaebacteria, Eubacteria, Protista, Fungi, Plantae, Animalia)

– Phylum

– Class

– Order

– Family

– Genus

– Species- 2 species that can interbreed and reproduce

Scientific name is the genus and the species name put together. Example: Canis lupus (common name is wolf)

Evolution

• Natural Selection – “survival of the fittest”

– Those organisms who are better adapted to live in their environments will survive, others less adapted will die off

• Mutations – Change in the sequence of DNA, creates variation in gene pool

• Variation – Differences among a population due to mutations and other members

coming in from surrounding areas

• Gene Shuffling – Genes shuffle around during the process of gamete formation, changes

the combinations possible during reproduction

• Immigration – New members of population move into area from outside areas – brings

in new genes

• Emigration – Members of population leave to go to a different area – takes genes to a

new area

Bacteria and Viruses

• Prokaryotes - bacteria

• Single celled organisms with no nucleus

• Autotrophs (can make their own food) OR Heterotrophs (cannot make their own food)

• Bacteria belong to kingdom Monera

• Viruses do not belong to a kingdom because they do not share enough characteristics with anyone, and they are not made of cells.

• Bacteria can be killed with antibiotics

• No treatment/cures for viruses

• Examples – Bacteria – sinus infections, pink eye, pneumonia

– Viruses – HIV/AIDS, herpes, flu, measles, mumps, chicken pox

Protists

• Kingdom protista

• Eukaryote

• Can be single celled or multicellular

• Groups – Animal like – animal characteristics

• Zooflagellates – have flagella, live in lakes and streams

• Sarcodines – amoeba, move by pseudopods, found all over the Earth

• Ciliates – paramecium, move by cilia, found in salt/fresh water

• Sporozoans – cause diseases (malaria), found in animals as parasites

– Plant like - plant characteristics • Euglenophytes – euglena, flagella, found in water

• Dinoflagellates – red tide

• Chrysophytes – green and golden algae

• Diatoms – glass cases, used in toothpaste/road paint

• Algae – Red algae – deep in ocean

– Brown algae (kelp) - oceans

– Green algae – water and moist lands

– Fungus like – fungi characteristics • Slime molds

• Water molds

Fungi

• Eukaryotes

• Heterotrophs (cannot make their own food)

• Have cell walls

• Types

– Molds (cheese, bread)

– Sac fungi

– Club fungi (what we know as mushrooms)

– Imperfect fungi (no known reproductive cycle)

Plants

• members of Kingdom Plantae

• multicellular eukaryotes

• cells walls made of cellulose

• develop from multicellular embryos

• carry out photosynthesis using green

pigments chlorophyll a and b

Plants • 4 groups of plants classified by water-

conducting tissues, seeds, flowers, and DNA – Bryophytes- no vascular tissue!

• mosses and relatives

– Seedless Vascular Plants • Club mosses, horsetails, ferns

– Gymnosperms • Cycads, Ginkoes, Conifers (produce cones)

– Angiosperms • Flowers

• Monocots - one seed leaf (cotyledon) in embryo (examples are corn, wheat, lilies, orchids)

• Dicots - two seed leaves (examples are roses, tomatoes, oaks)

Plants • Life Cycles

– Annuals – planted yearly, complete life cycle in

one year

– Biennials – plant every other year, complete

life cycle in two years

– Perennials – plant once, long life cycle over

many years

Invertebrates

• No backbone

• Phylums

– Porifera (Sponges)

– Cnidaria (jelly fish, sea anemones)

– Platyhelminthes (flatworms – planaria)

– Nematoda (roundworms – parasites that cause disease)

– Annelida (segmented worms – earthworms)

– Mollusca (squid, snail, slugs)

– Arthropods (crabs, lobster, spiders, insects)

– Echinoderms (starfish)

Vertebrates- have backbone • Belong to Phylum Chordata:

– Nerve cord

– Gills slits at some point in life

– Tail that extends beyond anus at some point in life

– Notochord- precursor to a backbone

• Classes – Agnatha- jawless fish

– Chondrichthyes- sharks, stingrays

– Osteichthyes- bony fish

– Amphibia- frog, toad, salamander

– Reptilia- turtle, snake, lizard, alligator, croc

– Aves- birds

– Mammals (Human, Bear)

Human Body • Humans are most complex organisms

• Body systems – Nervous (brain – controls body)

– Skeletal (bones – movement)

– Muscular (muscles – movement)

– Integumentary (skin – protection)

– Circulatory (heart – move materials around body)

– Respiratory (lungs – air movement)

– Digestive (stomach, etc. – digestion of food)

– Excretory (kidneys – remove waste from body)

– Endocrine (glands – regulate hormones)

– Reproductive (testes/ovaries – reproduction)

– Immune (many organs – protect against disease)