MMBio Final Review Study Guide PDF

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MMBio Final Review Study Guide

MMBio 121 Test 1 Review Chapter 1: What is Life? - What elements are we made of? (HONC) o Carbon o Hydrogen o Oxygen Nitrogen - What are the necessary qualifications for life? (acronym - HOMGARR) o Homeostasis o Organization (ie cells) o Metabolism o  Growth and development o Adaptation/Evolution o Response to stimuli o Reproduction - What category do viruses fall under and why? o Not alive – they rely on other cells to function and reproduce. It cannot harness energy from the environment - What is the basic unit of life? o The cell - Where does the energy to support life come from? o The sun and chemical compounds - What are the essential features of a cell? ● Plasma Membrane, ● can store and transmit information, ● harness energy - How does the scientific method work? o Observation, hypothesis, predictions, experiment, support/refute hypothesis

Chapter 2: Molecules of Life - Be able to describe the general structure of atoms o N  eutron o E  lectron o P  roton

Know the difference between Covalent bonds, Polar Covalent Bonds, Hydrogen Bonds, Ionic Bonds ● Covalent Bond: ○ A chemical bond formed between atoms by the sharing of electrons ● Polar Covalent Bond: ○ A covalent bond between two atoms where the electrons forming the bond are unequally distributed. This causes the molecule to have a slight electrical dipole moment where one end is slightly positive and the other is slightly negative. ● Hydrogen Bond: ○ A type of attractive (dipole-dipole) interaction between an electronegative atom and a hydrogen atom bonded to another electronegative atom. ● Ionic Bond: ○ A chemical bond in which one atom loses an electron to form a positive ion and the other atom gains an electron to form a negative ion. - o o o o -

What are the four main building blocks of life? (New Children Play Lego’s) Nucleic acids Proteins Lipids Carbohydrates Draw out a general structure of an amino acid 

o  - What are the three main types of lipids we discussed in class? o Phospholipids (ie phospholipid bilayer, membranes) o Hydrophobic tail and Hydrophilic head o Steroids o Fatty acids - How do you determine an unsaturated lipid from a saturated lipid? o Unsaturated has at least one double bond

- Describe and draw out general nucleotide structure of pyrimidines and purines.Purines have two rings (GA = General Authorities who are married have two rings), pyrimidines have just one ring - How do you tell the difference between an RNA nucleotide and a DNA nucleotide o There is an oxygen missing from the 2’ carbon of the sugar on DNA o Ribose sugar vs. Deoxyribose sugar o A-U, G-C vs A-T, G-C

Chapter 3: DNA Discovery, Replication, and Transcription

- Describe Griffith’s experiment and other experiments that lead to the discovery of DNA as the hereditary material o Griffiths found that traits could be transferred from one bacterium to the other o Smooth and rough experiment (THE MOUSE KILLER). Smooth was virulent and rough was non-virulent. The heat killed smooth bacterium with the rough still killed the mouse (the DNA from the smooth transferred to the rough but Griffith didn’t know it was DNA that was transferred at the time). o Avery, Macleod, and McCartney found that it was DNA that carried the genetic code (further developed what Griffith discovered) They extracted DNA as well as RNA and protein from heat-killed virulent cells and then added enzymes to degrade each component individually. - What is the central dogma? o DNA o Transcription o RNA o Translation o Protein - Describe the structure of DNA o Double helix o Antiparallel o Major and minor groove o Sugar backbone o Phosphodiester bond

o hydrogen bonds o Base stacking - Know all the protein machinery involved in DNA replication o Topoisomerase o Helicase o Single stranded binding proteins o Primase RNA o DNA polymerase o Ligase -Leading and lagging strands (not protein but still involved in DNA replication) - Why are the 5’ and 3’ so important in DNA replication? o We can only add to the 3’OH end - What are the major differences between RNA and DNA? o Double stranded (DNA) o Deoxyribose (DNA) o Thymine (DNA) uracil (RNA) o DNA longer than RNA o DNA more stable than RNA o DNA is monophosphate on the 5’ end while RNA is triphosphate on the 5’end - Describe the differences between the different types of RNA o mRNA –messenger (transcribed from DNA) o tRNA – helps decode mRNA→ brings amino acids (anticodon) to the mRNA to make the polypeptide chain o rRNA –ribosomes - Know the difference between the template and nontemplate DNA strands o Template is read 3’ to 5’ and is the one used to code mRNA -template strand=non coding= anti-sense=transcribed DNA strand -nontemplate strand=coding=sense=non-transcribed DNA strand - Describe the process of transcription including proteins involved, products, initiation and termination. o In a eukaryote, the protein RNA polymerase binds to a promoter in the DNA sequence. Once there, it begins synthesizing a mRNA strand by adding nucleotides opposite to those on the template strand. The mRNA is synthesized until it comes to a terminator sequence which causes a hairpin loop to form, ending transcription. The poly a tail is added to prevent degradation. - Know the function of the sigma factor in relation to transcription o In prokaryotes, the sigma factor signals to the RNA polymerase where to bind. - What are the differences between prokaryotic and eukaryotic mRNA?

o Eukaryotes have a 5’ cap on one end of the RNA and a poly-a tail at the other end. Also, eukaryotic mRNA contains introns, whereas the prokaryotes do not. In prokaryotes translation begins as transcription is still happening, but in eukaryotes it must be spliced, have a poly A tail and 5’ cap added and then transported out of the nucleus.

Chapter 4: Protein Structure and Translation - What is the general structure of proteins in terms of primary, secondary, tertiary, and quaternary structures? o Primary – amino acids o Secondary – alpha helices and beta pleated sheets interactions of nearby amino acids o Tertiary – folding of the protein into a general shape (three-dimensional shape of protein) Tertiary=function o Quaternary – tertiary structures are combined to form a more complex shape. Multiple proteins combined together. - How are amino acids linked? o Peptide bonds - What are the different RNA molecules used in translation? Describe their function and importance? o tRNA – carries amino acids to the ribosomes to be added to the primary structure of the amino acid chain o rRNA – a part of the ribosomes mRNA -- message RNA that is a copy of DNA that helps form ribosomes to build proteins off of - Describe basic ribosomal structure o The large subunit contains three sites where tRNA molecules bind. The A (Aminoacyl) site is where the tRNA- molecule enters. The P (Peptidyl) site is where the amino acid forms a peptide bond with the chain of amino acids. The e site is where the tRNA exits. The small ribosomal subunit attaches to the large subunit. - Describe basic tRNA structure and the difference between “charged” tRNA and “uncharged” tRNA o The tRNA molecule is in the shape of a clover, with three loops. The bottom loop has an anti-codon sequence which it uses to attach to the mRNA when it is inside of the ribosome. On the other side, there is a site for which an amino acid may bind to the tRNA. The tRNA is considered charged when it is bonded to an amino acid and uncharged when it is not. - Describe the initiation, elongation, and termination of translation

o Initation factors bind to 5’ cap of mRNA and moves until meeting AUG starting codon where ribosome attaches o tRNA moves into A position to join ribosome, transfers peptide when moving into P position and exits when entering E position which lengthens the polypeptide strand on the middle tRNA in the P position (this forms the protein) o a release factor enter…….s the A position in the ribosome which dissociates the tRNA,mRNA, and ribosome subunits and the polypeptide strand leaves

Chapter 5: Lipids, Membranes, and Cell Compartments - Why are phospholipids important in your cellular membrane? o Phospholipids are important in maintaining homeostasis of the cell by regulating much of what comes in and out of the cell. They are also self-healing. - What are the different type of cell membrane proteins and their functions? o Transport proteins- move compounds in and out of the cell o Receptor proteins – transmit messages into the cell o Anchor proteins – attach to other proteins that help maintain cell structure/shape o Enzyme – speeds up chemical reactions - Why are diffusion and osmosis important concepts? o These forces dictate how substances move in and out of the cell - What is active transport and secondary active transport? o Active transport utilizes ATP to move molecules against their concentration gradient. o Secondary transport indirectly uses ATP by using it to build up a concentration gradient of one substance which is the source of energy for moving another. - Know the differences between prokaryotic and eukaryotic cells ● Cell membrane vs. cell wall (bacteria) ● Prokaryotes have nucleoid of DNA as well as plasmids (circular DNA rings) ● Prokaryotes are typically about 1/10 the size of eukaryotes ● eukaryotes have a nucleus and prokaryotes don’t ● Prokaryotes form single-celled organisms, Eukaryotes can be single-celled or much more complex - Know the differences between plant and animal cells Plants have: - Chloroplasts - Mitochondria - Cell walls ● Vacuoles to store water ● Cellulose in cell wall ● Connected by plasmodesmata - passages through cell wall from one cell to the next, allowing the two plasma membranes to be continuous

Chapter 6: Energy - What is ATP and why is it important? o It is a way of storing and distributing energy to various reactions in the cell. o Adenosine TriPhosphate. It’s the currency of all cells!!! - What are the differences between a chemotroph and a phototroph? o Chemotroph – breaks down molecules to gain energy o Phototroph – uses the sun to obtain energy - What are the differences between an autotroph and a heterotroph? o An autotroph builds up molecules for cellular respiration using energy from the sun (Gets carbon from CO2) o Heterotrophs ingest these molecules and break them down for cellular respiration directly. (Gets carbon from organic molecules) - What is catabolism and anabolism and how are they related? o Catabolism – a system becomes less organized and energy is released (breaking food down into energy) o Anabolism – system becomes more organized as energy is put into the system (turning energy into food for later use) - Describe the general principles behind the first and second law of thermodynamics o First – energy is neither created or destroyed o Second – a system becomes less organized when it is transferred from one form to another. When energy changes form, the total amount of energy remains constant - How do enzymes relate to activation energy of reactions? o They decrease the activation energy needed to form a reaction - Endergonic vs. Exergonic reactions o Endergonic – requires (takes in) energy o Exergonic – releases energy - How are enzymes inhibited? Why is this important? o Enzymes are substrate specific o Competitive inhibitors – bind to the active site so that no substrate may react. o Noncompetitive inhibitors – bind to an enzyme at a place other than the active site which changes the shape of the active site. o This is important in regulating the speed of a chemical reaction and maintaining homeostasis.

Chapter 7 Review Cellular Respiration Cellular Respiration Type the responses in RED :)

Glycolysis- the partial breakdown of glucose.

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Location Cytoplasm · What is gained and what is lost Uses 1 glucose molecule and 2 atp ➡ creates 4 atp (2 net atp) and 2 NADH and 2 pyruvates Acetyl-CoA Synthesis- the oxidation and further breakdown of pyruvates produced in glycolysis. · Location - Begins in the cytoplasm then moves into the mitochondria. The vast majority of the synthesis occurs here. “In eukaryotes, this is the first step that takes place in the mitochondria” (pg. 7-7, 1st paragraph of section 7.3) · What is gained and what is lost 2 Acetyl-CoA molecules, 2 NADH and 2 CO2 are gained Krebs Cycle · Other names it could be called TCA Cycle, Citric Acid Cycle · Location “the citric acid cycle takes place in the mitochondrial matrix.” (pg. 7-8, 2nd paragraph of 7.4) · What is gained and what is lost gained 6 NADH 2 FADH2 and 2 ATP Electron Transport Chain · Location - The mitochondrial inner membrane. · What is gained and what is lost gained 28 ATP and water, all NADH and FADH2 are reduced · What is the electron acceptor o  xygen accepts electrons at the end of the ETC and synthesizes them into H2O · How does ATP synthase work It’s like a proton pump, for every 3 H+ molecules (or protons) that pass through, the synthase turns (like a revolving door) and adds a phosphate group to an adp molecule to make ATP. Uses the potential energy of the incoming protons from the proton gradient to create mechanical energy that turns the atp synthase and binds the extra phosphorus to ADP to create ATP · Which complexes can transport hydrogens c omplex I, III, IV · Important molecules involved: C  oenzyme Q or Ubiquinone. Cytochrome C. Oxidation and Reduction · What do they mean (Remember O.I.L. R.I.G., oxidation is losing, reduction is gaining) Oxidation is the loss of an electron

reduction is the gaining of an electron. · What is an example of both C 6H 12O 6 + 6O 2 → 6CO 2 + 6H 2O + 36 AT P The Glucose is oxidized and the Oxygen is reduced. reaction of iron with oxygen to make rust Acetyl-CoA is oxidized in the Krebs cycle. Electron Carriers · Examples of electron carriers NADH (in Cellular Respiration, in photosynthesis NADPH) and FADH2 (potential e- carriers) · Why are they important used in the electron transport chain to create a proton gradient **the reduced version of electron carriers have high potential energy used to synthesize ATP in the final stage of respiration. Fermentation · When and why is it used In the absence of oxygen it can partially break down glucose and create pyruvate in glycolysis; to generate a limited amount of ATP only using glycolysis jhmny 6 · How does it work regenerate the electron carriers when lactic acid or ethanol is formed so glycolysis can continue Lactic Acid Production · When and why is it used It is used when oxygen is not available to the cell. It is done because the body can at least produce some energy to work the cells when not enough oxygen is available · How does it work The body turns the pyruvate molecules built up from glycolysis into lactic acid. Only the two net ATP produced from glycolysis is created for every molecule of glucose. NADH can donate its electron to the lactate so that it becomes NAD+ and can accept another electron.

Chapter 8 Review Photosynthesis · Equation CO2 +  H2O ⟶ C6H12O6 +  O2 · Pigments: what they do

pigments are molecules that absorb some wavelengths of visible light they have different colors based on what wavelengths they reflect chlorophyll reflects green and yellow light · Photosystems: what they do a photosyst0em is a complex of proteins and pigments that’s embedded in the thylakoid membrane. PS II: supplies electrons to the beginning of the electron transport chain (ETC) breaks down water to steal electrons for the energy transport chain PS I: energizes electrons with a second input of light energy so they have enough energy to reduce NADP+ · Z scheme PS II absorbs light and energizes an electron pulled from water, allowing them to enter the photosynthetic chain (similar to the ETC). The electron is highly energized at the beginning of the chain, but decreases in energy as it flows down. A second input of light energy is needed when it arrives at PS I to raise the energy to an even higher level so that it can help reduce NADP+. This, when graphed according to an electron’s energy at any given time during the process, creates a z-scheme · Calvin cycle Occurs in the Stroma synthesize carbohydrates from CO2 1. Carboxylation: addition of CO2 to 5-carbon molecule RuBP 2. Reduction: NADPH transfers high-energy electrons 3. Regeneration: of the 5-carbon molecule needed for step 1 (RuBP) · Cyclic electron transport: what to do with excess electrons Simply stated, electrons, before going to reduce NADP+ can be sent back to the electron transport chain when ATP is needed. Plant Defense · How plants help us more than we think. We use plant compounds ALL THE TIME in medicine. Derived from different plants we are able to treat cancer, treat malaria, produce antibiotics, and other things with the proteins and chemical compounds they produce on a daily basis. Oxygen radicals · Why are they dangerous Beware of desperate bachelors...oxidative reactions are dangerous because they can create free radicals that can create cancer What can we do to prevent them antioxidants fight free radicals; that's why they are important to eat- and we get them from plants.

Surface Area · Why is surface area important when it comes to photosynthesis The more surface area there is, the more photosynthesis can take place. · What structure in the plant increases the surface area for photosynthesis The luma are stacked into Grana, making more surface area. The thylakoid has many folds as that increases the surface area

Chapter 9 Review Bacterial Cell · Competence factor: s urface protein that binds to extracellular DNA and enables cell to be transformed Signaling · 4 components needed for a successful signal 1. Signaling Cell 2. Signaling Molecule 3. Responding Molecule 4. Responding Cell · Steps of cell response 1. Receptor Activation 2. Signal Transduction 3. Cellular Response 4. Termination · What is a ligand Signaling Molecule · Types of signals o Endocrine: how does it work 0The signal comes from far away (through the bloodstream) o Paracrine: how does it work The signal comes from a nearby cell o Autocrine: how does it work The cell signals to itself o Juxtacrine: how does it work The two cells are connected. Cytokines · General characteristics/properties Most cytokines are soluble proteins released by one cell that bind to receptors on another cell and induce biological effects; Pleiotropy: having more than one effect

Redundancy: having the same effect as another signal Synergy: the property of two separate signals having an effect that is greater than the sum of the two signals Antagonism: a response that inhibits the effect of another response. Intracellular Signaling ·  Estrogen is an intracellular molecule it goes to the nucleus and there creates an effect it is part of the whole steroid hormones thing and is an endocrine signal as well. It’s a small non-polar molecule and so can pass through the cell membrane of the cell it wants to signal Cell surface receptors G proteins- 2  states active and inactive- GDP inactive- GTP-active; ligand binds to the G protein receptor, all bound to the alpha subunit have 3 subunits-alpha, beta, gamma, o Adrenaline example general- adrenaline is the example of a signal...aka it’s a ligand Receptor Kinases- it almost like a game of telephone- you are relaying the messagethey take a phosphate group from ATP and transfer it. This one is where the receptors dimerize, phosphorylate each other, and then phosphorylate the proteins that cause a response. o MAP kinase example general Ligand-Gated Ion channels- alter the flow of ions across the plasma membrane o Muscle example general t he neurotransmitters of your neurons work like this they are ions that pass through a ligand gated ion channel after a ligand has opened it and they ente-r ( the ions ) and then change the cell. Neurotransmitter binds to receptors on the ...