Biology Midterm Review

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Biology Midterm Review by Mind Map: Biology Midterm Review

1. Eukaryotic Structure

1.1. Nucleus

1.1.1. DNA is located in here

1.2. Has a cytoplasm, ribosomes, DNA, and plasma membrane as well as a Prokaryote

1.3. Cytoplasm is located between nucleus and plasma membrane

1.4. Bigger and more complex than Prokaryotes

1.5. Organelles found

1.5.1. Centrosome

1.5.2. Ribosomes

1.5.3. Cytoskeleton

1.5.4. Surface Flagellum Plasmadesmoda Cell Wall Plasma Membrane Microvilli

1.5.5. Endomembrane System Endoplasmic Reticulum Rough Smooth Golgi Apparatus Vesicle Lysosomes Vacuole

1.5.6. Endosymbiosed Chloroplast Mitochondrion

2. History of Life on Earth & Organic Chemistry

2.1. Early Earth

2.1.1. Physical and Chemical Processes that Led to the First Cell in 4 stages: 1. Abiotic Synthesis of Small Organic Molecules 2. Joining of these Small Molecules into Macromolecules 3. Packaging of these Molecules into Protocells Protocells: droplets with membranes that maintained an internal chemistry different from surroundings 4. Origin of Self Replicating Molecules This eventually made inheritance possible

2.1.2. Conditions Earth was formed 4.6 billion years ago Earth was uninhabitable until 4.2-3.9 billion years ago The first atmosphere was thick with water vapor and various compounds were released by volcanic eruptions As earth cooled, water vapor condensed into oceans and lots of hydrogen escaped to space. Early earth is hypothesized to have been a reducing environment

2.2. Water

2.2.1. All properties of water are a result of its polarity High Specific Heat: Water heats very slowly and is therefore good at maintaining its temperature High Heat of Vaporization Perspiration Universal Solvent Capillary Action Cohesion: Water is attracted to itself Adhesion: Water is attracted to other polar substances

2.3. Organic Chemistry

2.3.1. Lipids Lipids are hydrophobic 5 Classifications Fats and Oils Cholesterol and Steroids Phospholipids Waxes Pigments

2.3.2. Carbohydrates Simple Sugars Monosaccharides Disaccharides Polysaccharides Storage Polysaccharides Structural Polysaccharides

2.3.3. Proteins Shape Dictates Function Structure Hormones Immune System Transport Muscle Enzyme Receptors Storage Backbone: composed of an amino group, a carboxyl group and an "R" group attached to a carbon Protein Folding Primary Structure Secondary Structure: maintained by hydrogen bonds of the backbone Tertiary Structure Quaternary Structure Chaperonins ensure proper folding Denaturation Can occur at high temperatures, too high or too low pH levels and at abnormal amount of salinity Polymers are called Polypeptides, held together by Polypeptide bonds

2.3.4. Nucleic Acids Function Make Proteins Make up Genes RNA Workers Examples of Nucleic Acids DNA RNA Structure: Made up of Nucleotides Each nucleotide consists of: Bonding Two strands of DNA wind together in an antiparellel double helix There are two ends to each strand

3. Eukaryotes Continued

3.1. Protein Synthesis

3.1.1. Transcription Prokaryotes DNA is not separated by nuclear Has 1 RNA Polymerase Intiation doesn't need any proteins or transcription factors mRNA Primary Transcript has few surplus nucleotides no RNA Processing Has termination sequence Uses operons Eukaryotes Starts with DNA inside nucleus RNA Processing Transcription Factors Pre-mRNA Has 3 RNA Polymerases Initiation requires transcription factors which help recognize TATA Box mRNA Primary Transcript has more surplus nucleotides than Prokaryotes Has Polyadenylation sequence No operons (transcription factors instead) General Overview Synthesis of RNA on a DNA template 2 nucleic acids are rewritten DNA strand serves as a template for RNA nucleotides Initiation Elongation Termination DNA to RNA

3.1.2. Translation Prokaryotes Synthesizes 20 amino acids per second 3 initiation factors Continuous process as it's all in the cytoplasm Eukaryotes Synthesizes about 1 amino acid per second 9 initiation factors Non continuous process because of transcription happening inside nucleus General Overview Synthesis of a polypeptide using the info in mRNA Sites of translation are ribosomes Translate nucleotide sequence of mRNA into amino acid sequence of polypeptide

3.1.3. RNA to Protein

3.1.4. `

3.2. Gene Expression

3.2.1. Allows cells to express proteins when needed

3.2.2. Operons in Prokaryotes Lac Operon Inducible Operon Trp Operon Repressible Operon

3.2.3. DNA Methylation Can put the genes in an "off position" (turn them off) Addition of a methyl (CH3) group to the DNA strand itself often to the fifth carbon atom of a cytosine ring Cytosine can methylate certain bases in DNA Occurs in most plants, animals, and fungi Long stretches of inactive DNA is usually more methylated than active DNA Individual genes are more heavily methylated in cells in which they are not expressed A methylation pattern that is passed on through daughter cells correctly accounts for genome imprinting in animals Methylation permanentely regulates expression of either the maternal or paternal allele of particular genes at the start of development

3.2.4. Histone Acetylation Acetyl groups are attatched to lysines in histone tails Lysines positive charges become neutral and histone tails no longer bind to neighboring nucleosomes Histone Acetylation enzymes promote the initiation of transcription Addition of methyl groups condenses the chromatin Histone Methylation Phosphate groups expand the chromatin (opposite of methyl groups) Phosphorylation

3.2.5. Epigenetic Inheritance Inhertiance of traits trasmitted by mechanisms not directly involving the nucleotide sequence Might help explain why 1 indentical twin acquires a genetic disease and 1 doesn't Inappropriate gene expression from from alterations in DNA Methylation can be found in some cancers Modifications in the chromatin can be reversed

3.3. Metabolism

3.3.1. Photosynthesis Light Dependent Reactions Step 1 Step 2 Step 3 Step 4 Step 5 Step 6 Step 7 Step 8 Step 9 Step 10 Calvin Cycle (Light independent) Carbon Fixation Reduction Regeneration of RuBP

3.3.2. Cellular Respiration Glycolysis Means sugar breaking Energy Investment Energy Payoff Link Reaction Purpose is to alter pyruvates CoEnzyme A is added to the Pyruvate Krebs Cycle 2 Carbon Dioxide is released What is Produced Electron Transport Chain Uses high energy electrons from Glycolysis and Krebs Cycle to convert ADP to ATP NADH and FADH2 pass electrons to the chain Composed of a series of electron carriers located in the inner membrane of the mitochondrion End of chain combines electrons with O2 to form H20 as water is then released Product

4. Prokaryotes: The First Life on Earth

4.1. Enzymes

4.1.1. biological catalyst increases rate of reaction by lowering activation energy not consumed by the reaction

4.1.2. Made of proteins or RNA shape determines function

4.1.3. biological importance Temperature: helps organism reach temperature needed for reaction Speed: can increase the rate of reaction helpful in maintaining homeostasis Specificity: only used when specific enzymes are needed

4.1.4. Structure Substrate and enzyme bind together at the active site fits together with coordinating charges and shape

4.1.5. How they work Induced fit adds stress to bonds so they are easier to break Proper orientation puts substrates into position to make new bonds Sheltering keeps internal environment different from surroundings, allowing reactions to occur

4.1.6. What affects activity Temperature pH Enzyme Concentration Substrate Concentration Cofactors enhance enzyme activity Coenzymes Inhibitors competitive noncompetitive/allostery

4.2. Free Energy

4.2.1. Types of Energy Potential Chemical Kinetic light thermal

4.2.2. Laws of Thermodynamics 1st Law Energy cannot be created nor destroyed, only transferred from one type to another 2nd Law entropy is constantly increasing in a closed system

4.2.3. Free Energy (G) energy available to do work Spontaneity negative change in G positive change in G Coupling the sum of energy in all reactants compared to products must be less than 0 ATP Early Earth lightning and thermal vents possibly provided the input of energy needed making complex molecules is unfavorable without the input of free energy all living organisms use ATP

4.3. Cell Membranes

4.3.1. Structure Phospholipid bilayer hydrophilic phosphate heads hydrophobic tails Proteins Integral Proteins Peripheral Proteins Proteins embedded in the membrane was supported by freeze fracturing Functions

4.4. Transport

4.4.1. Active Transport Pumps Sodium/Potassium Pump powered by ATP - work against the concentration gradient

4.4.2. Bulk Transport Phagocytosis "cell eating" Pinocytosis "cell drinking" Receptor-Mediated Endocytosis Exocytosis vesicle merges with membrane

4.5. Prokaryotic Structure

4.5.1. found in ALL cells cell membrane cytoplasm (cytosol and organelles) DNA (in nucleoid region) Ribosomes (make proteins)

4.5.2. other parts of prokaryotes Passive Transport no energy or coupling needed goes from high to low Simple Diffusion Facilitated Diffusion Osmosis pili capsid cell wall flagella

4.5.3. What are Prokaryotes? first membrane-bound organisms alive ancestors to all organisms Modern: Bacteria Eubacteria - true bacteria Archarbacteria - ancient bacteria cell wall made of peptidoglycan

4.6. Cell Division

4.6.1. Binary Fission Definition asexual production replicate genetic material, cell divides Steps and Processes 1. replication of DNA 2. replication enzymes move out in both directions until reach terminus of replication 3. cell elongates 4. new membrane and cell wall begin to grow 5. when complete, cell pinches in two Terms DNA Origin of Replication Terminus of Replication Septum Septation

4.7. DNA Replicaiton

4.7.1. Eukaryotes vs Prokaryotes Prokaryotes occurs in cytoplasm one origin of replication replication of DNA occurs at one point only two replication forks are formed and one replication bubble one replicon Okazaki Fragment is large replication is rapid Eukaryotes occurs in nucleus numerous origins of replication replication of DNA occurs simultaneously numerous replication forks and bubbles large number of replicons Okazaki Fragment is short replication is slow

5. Life Gets Complex: Eukaryotes

5.1. DNA Replication

5.1.1. Initiation of DNA Replication Helicase untwists double helix; separating two parental strands Single-strand Binding Proteins after parental strands separate, bind to the unpaired DNA strands to keep them from re-pairing Topoisomerase relieve strain by breaking, swiveling and rejoining DNA strands

5.1.2. Primase adds a short RNA sequence to a template strand of DNA

5.1.3. DNA Polymerase adds nucleotides to produce a double stranded DNA molecule

5.1.4. DNA Ligase joins the sugar of one nucleotide to the phosphate of another when the Okasaki fragments have been completed

5.1.5. Structure Antiparallel Elongation Direction Leading Strand Lagging Strand Origins of Replication site where replication of DNA begins eukaryotes has multiple whereas prokaryotes only have one Replication Bubble Replication Fork region where parental strands are being unwound Replicon a region of DNA or RNA, that replicates from a single origin of replication

5.1.6. Replication the Ends of DNA Molecule Telomeres special nucleotide sequences at the ends of DNA molecules to protect chrosomes doesn't contain DNA, consist of multiple repitition of one nucleotide sequence Telomerase catalyzes the lengthening of telomeres

5.1.7. Mutations Definition they are any changes in the sequence of bases of DNA How do they occur? sometimes during replication, the cell makes a mistake and adds the wrong base when the cell replicates its DNA again, the two strands produce are no longer exactly the same Types Deletion Insertion Subsitution Frameshift Repair Mismatch Repair Nuclease Nucleotide Excision Repair

5.2. Cell Division

5.2.1. Phases of the Cell Cycle Interphase G1 S G2 Mitotic (M) Phase Mitosis Cytokinesis Cell Cycle Control System 3 Internal Checkpoints Stop and Go Signs Lost of Control

5.2.2. Order of DNA Organization Chromatin together, the entire complex of DNA and proteins that is the building material of chromosomes Chromosome a molecule of DNA with associated proteins Sister Chromatids joined copies of the original chromosome, each duplicated chromosome has two

5.3. Endosymbiosis

5.3.1. the process by which smaller bacteria were engulfed by larger cells and continue to perform functions for the larger cell Mitochondria Chloroplast Evidence for Endosymbiosis these organelles contain prokaryotic DNA these organelles contain prokaryotic ribosomes these organelles replicate with binary fission - not mitosis

6. Basics of Biology as a Science

6.1. Ecology

6.1.1. Organization Individual Single organism comprised of one or more cells Biotic Population Many individuals of the same species living in a shared environment Biotic Community Many populations of species living together in a shared environment Biotic Ecosystem Community of species in a specific location along with abiotic factors such as sunlight, water, and soil Biotic and abiotic Biome Like ecosystems across the globe with similar abiotic and biotic factors Biotic and abiotic Biosphere A collection of the biomes on Earth; the entire planet Biotic and abiotic

6.1.2. Interactions Symbiosis Mutualism Commensalism Parasitism Predation True Predation Grazing Adaptations Competition Interspecific Intraspecific

6.1.3. Niche Influenced by abiotic and biotic factors Role a species plays in its ecosystem No organism can occupy the same niche at the same time Adaptation for one of the organisms to change something within their niche If adaption does not happen, one species will die

6.1.4. Flow of Energy Producers Photoautotrophs Chemoautotrophs Consumers Carnivores Omnivores Herbivores Decomposers Detritivores Scavengers Saprotrophs

6.1.5. Cycles Water Cycle Carbon Cycle Nitrogen Cycle

6.2. Natural Selection

6.2.1. "Survival of the Fittest"

6.2.2. Reproduction of individuals with advantageous traits survive Over time, as reproduction continues of these traits, leads to evolutionary change

6.2.3. 3 Principles: Characteristics are inherited from parents Resources for survival and reproduction are limited (not all offspring will survive) Offspring vary among each other

6.2.4. Only possible with variation in genetics

6.2.5. Charles Darwin Ground finch variation on the Galapagos Island Book: On the Origin of Species

6.3. Evolution

6.3.1. Processes and Patterns of Evolution Natural Selection Adaptation Heritable trait that helps in current environment Snow leopards have thick fur to survive their cold, snowy environment Divergent Evolution 2 species evolve in diverse directions from common point Common ancestor evolved into wooly mammoth and elephants Convergent Evolution 2 species evolve independently (w/o common ancestry) to obtain similar traits Bats and insects both evolved to have wings even though they share no common ancestor

6.3.2. Evidence of Evolution Fossils Show progression of change in species over time Age can be determined Locations can be compared to each other Similarities can be observed Anatomy Homologous Structures Vestigial Structures Embryology Biogeography Distribution of organisms on planet explained by tectonic plate movement Break-up of Pangaea= geographical isolation Endemic species Molecular Biology Common ancestor for all of life supported by universality of DNA Evolution supported by similar machinery of DNA replication and expression

6.3.3. Coevolution Evolution of traits in prey species leads to evolution of traits in predator species

6.4. Characteristics of Life

6.4.1. Maintain Homeostasis

6.4.2. Grow and Develop

6.4.3. Reproduce

6.4.4. Evolve as a Species

6.4.5. Obtain Materials and Energy

6.4.6. Respond to Stimuli

6.4.7. Genetic Material

6.4.8. Made of Cell(s)

6.5. Phylogeny

6.6. Scientific Method

6.6.1. Lab Practical Questions Labs we have Done Catalase Lab Osmosis and Diffusion Lab Potato Lab Jello Cube Lab Metabolism Lab Variables Relationship between variables