BIO311c Sata Final Review

What are the 3 different kinds of lipids, examples and their functions?

*Ester linkages between glycerol and fatty acids ~Fats (Triglycerides)- storage of energy, phospholipids, cell membrane [Ex- 3 fatty acids + glycerol] ~Phospholipids (polar- head; non-polar- tail) <-- amphipathic (selective permeability) [Ex- Glycerol + 2 fatty acids + a phosphate group; lipid bilayer of cell membrane, maintain compartments of membrane-bound molecules] ~Carotenoids- color pigments, photosynthesis, Vitamin A (synthesis in animals), products of secondary metabolism ~Steroids- cholesterol, testosterone or growth hormones, membrane lipids ~Saturated fats- saturated with hydrogens, no double bonds or kinks, usually solid at room temp, closely packed ~Unsaturated fats- not saturated with hydrogen, at least one double bond, liquid at room temp, not closely packed together [Ex- plant fats, canola oil] *The more saturated fat --> higher the melting temperature

How the fluidity of the membranes is affected by its composition and by temperature?

-Unsaturation and cholesterol- lowers melting temperatures (Tm), increases fluidity -Saturation- increases melting temperature (Tm), decreases fluidity

Be able to predict the pattern of inheritance in a given example based on the laws of inheritance.

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What are the features of various functional groups and their importance?

Acids ~Carboxyl: -COOH (acid), COO- (conjugate base) [Ex- fatty acid, amino acid], POLAR ~Phosphate: -PO4^2- [Ex- phospholipid, nucleotides] Bases ~Amine: -NH2 (base), -NH3+ (conjugate acid) [Ex- nitrogenous base, amino acid] Neither ~Sulfhydryl: -SH, R-SH + HS-R --> -R-S-S-R + H2 disulfide bond, THIOL, SLIGHTLY polar [Ex- Amino Acid, Cystine, Disulfide] ~Carbonyl: -C=O [Ex- Aldehyde if at end --> Aldose, Ketone if in middle --> Ketose] ~Hydroxyl: -OH, alcohols [Ex- alcohol, sugar, amino acid], POLAR Non Polar ~Methyl: -CH3, longer the hydrocarbon is, the more non-polar it becomes [Ex- hydrocarbons, fats]

Compare and contrast DNA and RNA.

BOTH ~Nucleic Acids ~polymers (DNA/RNA) made up of nucleotide monomers ~complementary base pairing RNA ~Ribonucleic ~Have nitrogenous base, ribose, phosphate ~single strand, variable structure ~Uracil instead of Thymine DNA ~Deoxyribonucleic ~Have nitrogenous base, deoxyribose, phosphate ~double strand helix ~codes for RNA ~stores genetic information ~more stable

Understand complementary base pairing of DNA and the three difference forms of DNA.

Complementary Base Pairing ~Adenine:Thymine 2 H-bonds ~Guanine:Cystine 3 H-bonds Different kinds of DNA ~A: Dehydrated DNA- turn right ~B: Most common DNA- turn right ~Z: Special cells, short oligonucleotides GCGCGC- turn left

Know the pathway of a secretory protein or a molecules coming from outside into the cell.

DNA --> RNA --> mRNA --> mRNA processing --> rough ER --> vesicle --> Golgi Apparatus --> lysosome, peroxisome, vacuole or secreted out

Understand the regulation of MPF activity that occurs as sharp peak during M phase.

Depending on cyclin levels, it binds to cdk. This stimulates auto-phosphorylation of cdk and phosphorylation of other proteins. Some of these proteins are proteases that can degrade cyclin and lower its levels to regulate the cycle.

Consider the possible ways errors in cell division may lead to an inherited disease.

Errors in cell division can result in cancerous tumors, an extra chromosome can result in down syndrome, higher susceptibility to alzheimers and leukemia through missing or extra chromosomes,

Classify all the different components of a eukaryotic cell with a concept map.

Eukaryotic Cell- Nucleus, Cytoplasm (1. Energy Organelles [1. Mitochondria, 2. Chloroplasts], 2. Endomembrane System [1. Endoplasmic Reticulum {Smooth and Rough}, 2. Golgi Apparatus, 3. Lysosomes, 4. Microbodies, 5. Vacuoles, 6. Plasma Membrane], 3. Ribosomes), Cytoskeleton (1. Microtubules, 2. Microfilaments, 3. Intermediate Filaments), Cell Surface (1. Cell Wall/ECM), 2. Cell Junction)

Where do the glycolysis, acetyl CoA formation, Krebs cycle and oxidative phosphorylation, (electron transfer and ATP synthesis) happen within a eukaryotic and prokaryotic cells?

Eukaryotic: ~Glycoloysis: cytoplasm ~Acetyl CoA Formation: inside mitochondria (matrix) ~Krebs Cycle: inner membrane of mitochondria (matrix) ~Oxidative Phosphorylation: inner membrane of mitochondria (electron transfer) and matrix (ATP synthesis) Prokaryotic: ~Glycolysis, Acetyl CoA Formation, and Krebs Cycle- cytoplasm ~Oxidative Phosphorylation- plasma membrane

How does the solute concentration affect the water movement in an animal or plant cell?

If the solution is.... -Isotonic (same)- the cell is stable (animal cell), flaccid (plant cell) -Hypertonic (high solute)- the cell will shrivel (animal cell), plasmolyze (plant cell) ~ less water -Hypotonic (low solute)- the cell is lysis (animal cell), turgid (plant cell) ~ lots of water

Know the energy released in vitro in ATP hydrolysis and the three types of cellular work for which ATP is used.

In Vitro ATP Hydrolysis --> ΔG= -7.3 kcal/mol Types of Cellular work for which ATP is used- ~Mechanical work: movement of cilia and flagella ~Active transport: Na+/K+ pump ~Chemical reactions: some metabolic reactions that need energy (sucrose biosynthesis)

Know the inputs and outputs of anaerobic fermentation (alcoholic and lactic acid)?

Lactate Formation ~Inputs: Glucose, ADP, Pi ~Outputs: Lactate, ATP Anaerobic Fermentation ~Inputs: Glucose, ADP, Pi ~Outputs: Ethanol, CO2, and ATP

Identify examples of monomers in each group based on their structure and functional groups.

Monomers for... ~Carbohydrate: Monosaccharide [Hydroxyl] ~Lipids: Glycerol [Hydroxyl] and Fatty Acids [Carboxyl, Methyl, Hydroxyl] ~Proteins: Amino Acids [Amine, Carboxyl, Hydroxyl] ~Nucleic Acids: Nucleotides [Phosphate, Amine, Hydroxyl]

Remember the inputs and outputs in light reactions (cyclic and non-cyclic).

Non- Cyclic light reactions ~Inputs: Light, H2O, ADP, Pi, NADP+ ~Outputs: ATP, Oxygen (O2), NADPH, H+, e- Cyclic light reactions: ~Inputs: Light, ADP, Pi ~Outputs: ATP

Understand the safety and ethical concerns of recombinant DNA technology.

Safety in... -Food: FDA, USDA -Research: NIH (regulates guidelines), OSHA (regulates other enforcement) -Environment: EPA, USDA Ethics... -Plants: genetic piracy -Animals: safety, treatment, rights -Human: medical ethics, rights, release of genetic information

Understand how the glycosidic, ester, peptide and phosphodiester bonds are formed.

They are all formed through condensation/dehydration synthesis (combined, water released).

What are the players and steps involved in amino acid activation and the whole protein synthesis process? Know the details in each step.

~Amino Acid Activation: the selection of a specific amino acid by attaching to the corresponding tRNA with the proper anticodon is very important for specificity, amino acids must be activated and attached to the 3'-OH group of tRNA for easy transfer to the elongating polypeptide; this activation and attachment are done by aminoacyl-tRNA synthetases; there is at least one enzyme for each amino acid and its appropriate tRNA, the enzyme binds to the right amino acid at its -COOH terminus and attaches an AMP by hydrolyzing an ATP, recognizes the tRNA by its secondary structure and anticodon, then transfers the amino acid to the 3-OH group of the correct tRNA and AMP is detached, and finally releases the aminoacyl tRNA Protein Synthesis Process: ~Initiation: the small subunit of ribosome first recognizes the ribosome binding site at the 5' non-translated region (NTR), the first codon is usually methionine, special tRNA caring a modified methionine binds to the P-site, and in addition 3 initiation factors (IF, proteins that help in starting translation), and GTP bind to form initiation complex, large subunit comes in and joins with the small subunit and rest of the imitation complex, the GTP is hydrolyzed ~Elongation: happens in 3 steps... 1. Codon recognition: an elongation factor (EF) helps to extend the polypeptide chain by bringing an appropriate aminacyl tRNA (tRNA for next codon + corresponding amino acid) and places it on the A-site. A GTP attached to EF is hydrolyzed for this step. 2. Peptide bond formation: the peptide transferase activity or ribosome transfers the first Methionine (or a growing polypeptide) from the P-site rRNA to the A-site and makes a peptide bond between the carboxyl terminus of previous amino acid and the amino terminus of incoming amino acid. The tRNA at the P-site (empty with no amino acid

How do cyclin and CDK serve as major components controlling check points.

~CDK + Cyclin --> MPF (maturation promoting factor); MPF --> initiates S-Phase or M-Phase OR activates protests which degrade cyclin) ~Cyclin and CDK combined make MPF which promotes DNA synthesis and mitosis. S-cyclin promotes S-Phase. M-cyclin promotes M-Phase.

What is the structure of DNA double helix? Pay attention to details.

~DNA consists of two strands that are H-bonded together with a width of 2 nm ~The two strands turn right to make a right-handed helix (turns clock-wise, when looked through cross section). The strands are like the ropes of a ladder with the bases making the rungs ~The hydrophilic sugar-phosphate is on the outside of helix. The negatively charged P-groups made DNA soluble in aqueous solution. ~The hydrophobic nitrogenous bases are stacked inside in a perpendicular manner to the strand. The distance between two base pairs is 0.34 nm. There are 10 base pairs per turn. ~Adenine pairs with Thymine with 2 H-bonds and guanine pairs with cytosine with 3 H-bonds. This is referred to as complementary base pairing and satisfies Charagaff's finding that the cellular ratios of A:T and G:C are equal (Chargaff's rule) ~The two strands run in opposite directions (i.e. have anti-parallel orientation), DNA starts with a phosphate group attached to the 5th C of ribose (5') and the other end has a -OH group attached to the 3rd C of ribose (3') ~The helical turns make a major groove and a minor groove between the adjacent turns. ~DNA stores information in its sequence of bases (four bases with infinite possibilities of various sequence and lengths). ~DNA replication is semi-conservative. New copy made is form a template DNA with high specificity.

Remember the inputs, outputs and the key regulatory step for glycolysis.

~First committed step: Glucose + ATP --> Glycolysis 6-P; catalyzed by Hexokinase ~Rate Limiting Step: Fructose 6-P + ATP --> Fructose 1, 6- BP +ADP; catalyzed by Phosphofructokinase (too much ATP will inhibit PFK, and too much Citrate/AMP/ADP will stimulate PFK) ~Inputs: Glucose, ADP, Pi, NAD+ ~Outputs: Pyruvate + ATP + NADH

Know examples of biological molecules containing such functional groups.

~Hydrocarbon: methyl group, cis configuration when the Hydrogens are horizontal with one another and the methyl groups are horizontal to one another ~Fatty Acid- carboxyl group ~Nucleic Acid- phosphate group ~Amino Acid- amine group, Hydroxyl, Carboxyl, can have other groups attached to the bottom hydrogen (like Sulfhydryl) ~Glucose, Carbohydrate- Carbonyl, Aldehyde (end), Hydroxyl

Remember the inputs and outputs of Calvin cycle.

~Inputs: CO2, ATP, NADPH ~Output: CH2O, ADP, Pi, NADP+

How the electron transfer helps in ATP synthesis? Know the chemiosmosis, inputs, and outputs of oxidative phosphorylation.

~Oxidation (NADH --> NAD+, 2e-, and H+ or FADH2 --> FAD, 2e-, and 2H+; the two electrons go through the ETC and either go to the Proton Concentration Gradient or are accepted by O2) --> Proton Concentration Gradient --> Chemiosmosis (protons moving from high --> low concentration) --> Results in ATP Synthesis (Phosphorylation) ~Inputs: NADH, FADH2, ADP, Pi, O2 ~Outputs: H2O, ATP, NAD+, FAD

Understand the ploidy levels and the need for meiosis (reduction division) in sexual reproduction.

~Ploidy levels show how many sets of chromosomes (N) are present in the cell. ~Haploid (1N): single set of chromosomes (ex: sperm and egg cells) ~Diploid (2N): two sets of chromosome (ex: body cells) ~Tetraploid (4N): four sets of chromosomes (ex: plants and tobacco) ~Polyploid (many N): several sets of chromosomes (ex: sugarcane) Meiosis is needed in sexual reproduction because it allows 2 parents' gametes to combine and make a new diploid zygote.

What are the different types of mutations? Learn how to use the universal codon table.

~Point mutations: single base pair change or substitution, sometimes has no effect on protein sequence or function if similar codons are substituted (Ex- GGC to GGG still codes for Glycine) ~HOWEVER: if the point mutation results in a different amino acids, it idc called a missense mutation (Ex- GGC to GAC will result in a glycine to aspartate substitution) ~If the change results in a stop codon, it is called non-sense mutation (Ex- GGA to UGA will result in a stop instead of coding for glycine) ~Insertions and Deletions- Frameshift mutation: one or more bases are inserted into or deleted from the coding sequence; these mutations have the worst possible effects on protein sequence and function. Insertions and deletions can also happen at a chromosomal level covering large regions ~Inversion or translocation: ~Inversion: two segments of a chromosome are inverted, results in flipping the order of genes (Ex. A-B-C becomes C-B-A) ~Translocations involve moving a part of chromosome from one place to another or to a different chromosome Point Mutations: Substitutions in single base ○Silent: No change in amino acid ○Nonsense: Change codes for early stop codon ○Missense: Change in amino acids ●Insertions/Deletions (Indels): Results in frameshift mutations that shift the reading from of the nucleotide sequence. 3 In/dels can correct a frameshift mutation.

What are exocytosis and endocytosis; phagocytosis, pinocytosis and receptor-mediated endocytosis?

-Exocytosis- vesicles from the ER or Golgi bodies carrying macromolecules and other materials to be secreted fuse with the plasma membrane and open outside to secrete the materials (Ex- sweat glands, tear glands secrete bacteriolytic enzymes, plant cell wall materials) -Endocytosis: ~Phagocytosis- macrophage enfolding bacteria (entire cell changes shape) identified for destruction (Ex- white blood cells) ~Pinocytosis- refers to cells gulping droplets of extracellular fluid (parts of cell change shape) *IF HE DOESN'T SPECIFY WHITE BLOOD CELLS THEN ENFULG REFERS TO PINOCYTOSIS ~Receptor Mediated Endocytosis- most specific; virus/LDL of HDL Cholesterol, change conformation and enfulg low density lipoproteins containing several cholesterol molecules and related proteins into the cell for processing

Define diffusion, osmosis, active transport and passive transport.

-Simple Diffusion: high --> low concentrations; directly through phospholipids, does not require ATP -Facilitated Diffusion: high --> low concentrations; through integral protein; still doesn't require ATP -Osmosis: transports only water through a semipermeable membrane, high --> low concentrations -Active Transport: low --> high concentrations; requires energy (ATP), through protein (endo/exocytosis) -Passive Transport: high --> low, does not require energy; molecules go down a concentration gradient

What is biological hierarchy? Know the levels and examples.

1. Atoms- C, H, O, N, S, etc. 2. Molecules- CO2, O2, H2O, Amino Acids, Sugars 3. Macromolecules- proteins, carbohydrates, lipids 4. Parts of a cell- membrane, nucleus, mitochondria 5. Cells- unicellular organisms and part of multicellular organism 6. Tissues- bone, muscle, nerve 7. Organs- heart, lung, brain 8. Organ Systems- circulatory, reproductive 9. Multicellular Organisms- plants, fungi, animals 10. Population- many individuals of same species 11. Ecosystem- collection of populations in limited area 12. Biomes- desert, tundra, forest 13. Biosphere- Living crust of the earth in air, water

Compare and contrast similar cell structures. For example - chloroplast vs mitochondria, microtubule vs microfilament and cell wall vs cell junctions etc.

1. Chloroplast- contains Stroma, Granum, Outer Membrane, Inner Membrane, Circular DNA, and Thylakoid 2. Mitochondria- Outer Membrane, Inner Membrane, Inner-Membrane Space, Circular DNA, Cirstae, and Matrix 1. Microtubule- cellular (flagella) and chromosome movement (centrioles), vesicle transport (motor proteins), tubular 25 nm, alpha and beta tubular 2. Microfilament- contains actin, cytoplasmic streaming, cleavage furrow, muscular contraction, filamentous 7 nm 1. Cell Wall- found in plant cells ~Plant cell wall- cellulose, hemicellulose, cutie, pectin, project cells, give physical support and help in water conservation, have plasmodesmata which are important for cell to cell transport and viral movement ~Fungal cell wall- contain chitin (NAG) ~Bacterial cell wall- contains NAM-NAG, degraded by lysozyme 2. Cell Junctions- found in animal cells, instead of cell walls its ECM (Extracellular matrix) ~Tight junctions: two membranes fused by integral membrane proteins to prevent movement of any solutes through the space between ~Gap junctions: connections between two cells through connections, challenges through chemical signals or solutes can pass from one cell to another, important for cell-to-cell communication ~Desmosomes: connected by keratin-like fibrous proteins, not as tightly sealed as tight junctions, some space exists

What are some examples of active transport and how do they work?

Active transport examples- go from low --> high concentrations with the addition of ATP (energy) -Uniport- single solute, one direction (Ex- H+ pump) -Symport- two solutes, moving in one direction (Ex- sucrose/H+ pump) -Antiport/electrogenic pump- Intrinsic membrane protein transfers 3 Na+ ions out of the cell, and brings 2 K+ ions against their concentration gradient into the cell (Sodium-Potassium pump) in order to maintain a net negative charge -Transport due to electric voltage difference -Coupled transport/cotransport- Primary active transport is coupled with secondary active transport which does not use ATP but depends on the primary active transport -Exocytosis and Endocytosis also active transport

Compare and contrast prokaryotic and eukaryotic cells; and plant and animal cells.

COMPARE (Prokaryotes and Eukaryotes) -Both contain DNA, plasma membrane, and ribosomes CONTRAST (Prokaryotes and Eukaryotes) -Prokaryotic- no nucleus, DNA in the nuclei region, no endomembrane system, no organelles, or protein attached to DNA, (1-10 nm) -Eukaryotic- have true nucleus, DNA within nucleus, vast endomembrane system, (10-100 nm), protein attached to DNA, membrane bound organelle (mitochondria and chloroplasts) COMPARE (Animal and Plant Cells) -Both Eukaryotic cells, plasma membrane, cytoplasm, nucleus, ribosomes, mitochondria, microtubule organizing system CONTRAST (Animal and Plant Cells) -Animal cells- no cell wall, have centrioles, lysosomes, food vacuole, peroxisomes, gap, tight, & anchor junctions -Plant cells- cell wall, central vacuole, chloroplast, glyoxysomes, plasma desmata

Understand how condensation synthesis and hydrolysis occur to make biopolymers.

Condensation Synthesis: H-___-OH + H ___-OH --> H-___-___-OH +H2O (monomer --> polymer) [Monomers -> Dimers -> Trimers -> Oligomers -> Polymer] Hydrolysis: H-___-___-OH + H2O --> H-___-OH + H-___-OH (breakdown polymer --> monomer) [Polymer -> Oligomers -> Trimers -> Dimers -> Monomer]

Remember all the enzymes and proteins involved in DNA replication, their roles and the sequence of events in DNA replication process.

DNA Replication Enzymes: ~Topoisomerase I: relaxes supercoiled or compact DNA ~Helicase: unwinds the double helix into single stranded DNA (ssDNA) ~SSB: single-stranded DNA binding protein; stabilizes the ssDNA ~Primase: synthesizes (makes) RNA primer that helps initiate DNA synthesis ~DNA Polymerase III: extends RNA primer with dNTPs, make new DNA on both strands (DNA replication), proof reads, and repairs ~DNA Polymerase I: erases RNA primers and replaces it with DNA ~DNA Ligase: connects DNA fragment with phosphodiester bond ~DNA gyrase: compacts DNA to supercoiled form DNA Replication: ~Initiation: -supercoiling relaxed at the origin of replication (ORI) by topoisomerase (single origin in prokaryotes and multiple origins in eukaryotes) -Relaxed DNA helix opened to make a replication fork by helicase -Resulting single stranded DNA is stabilized by single stranded DNA binding (SSB) proteins -Primase makes an RNA primer (providing a free 3'-OH group for the DNA polymerase to use) to start the new DNA synthesis. ~Elongation: -DNA Polymerase III (a complex protein) binds to the DNA template + RNA primer and adds nucleotides complementary to the template strand (at a rate of about 1000 nucleotides/sec in prokaryotes). -New DNA synthesis occurs in the 5' to 3' direction on a template that runs in the 3' to 5' direction. This is due to the nature of the enzyme DNA polymerase, which links new deoxy-nucloside triphosphate (dNTPs) to the 3'-OH group of the growing strand. Also, the H-bonding in the base pairing works only if the new strand runs in the opposite direction of the template DNA. -A leading strand is synthesized continuously from 5' to 3' based on the template -Since the opposite strand is not open to continue DNA synthesizes from 5' to 3' direction, DNA is synthesized in small fragments (100-200 bases in eukaryot

Know the components of a biological membrane and their specific functions.

In animal cell... -Phospholipid Bilayer: major structural component (Tm) based saturated/unsaturated, selective permeability of membrane, allow small, non polar molecules through, non polar/hydrophobic tails and polar/hydrophilic heads -Integral protein: structure, selective permeability, polar small molecules, enzyme, receptors -Anchored Protein and Peripheral Protein- structure, enzyme -Steroid- structure and fluidity (Tm), need optimal level -Oligosaccharides- cell to cell recognition In a plant cell... Going from outside to inside (cells connected by plasmodesmata)... Middle Lamella --> Primary Cell Wall --> Secondary Cell Wall --> Plasma Membrane

Understand sequence of stages of cell cycle, including the 3 phases of interphase and how each phase is defined, the visual and biochemical changes that take place at each stage and how cytokinesis takes place in animal and plant cells that leads to two daughter cells.

Interphase ~G1 (Gap 1)- growth, centriole replication ~S Phase- DNA Replication synthesis ~G2 (Gap 2)- growth, organelle replication M Phase (Mitosis) ~Prophase- preparation for cell division occurs, nucleus disappears, chromatids forms, centrioles mov to oppose poles, mitotic spindle forms ~Prometaphase (sometimes combined with prophase)- nuclear envelope disappears, microtubules connect to the chromosomes at kinetochore ~Metaphase- sister chromatids of replicated chromosomes align in the middle of the cell at the metaphase plate ~Anaphase- centromere of each chromosome divides, sister chromatids separate into two single-stranded chromosomes ~Telophase- two nuclei form to separate sister chromosomes, polar fibers use ATP to expand the cell and add more microtubules, nucleoli reappear inside each nucleus, chromosomes loosen to become chromatin again ~Cytokinesis: cell splits into two, cleavage furrow forms in animals, cell plate forms in plant cells

Remember all the stages of meiosis I and II and know the three causes of genetic variation in sexual reproduction and what stages these occur in sexual reproduction.

Meiosis I ~Interphase I) Chromosomes replicate into 2 identical sister chromatids attached at the centromere, centrioles and other organelles duplicate ~Prophase I) condensed chromosome attached to nuclear envelope, homologous chromosomes form tetrads, crossing over and recombination occur during synapsis, nuclear envelope eventually disappears, centrioles move apart eventually, and spindle fibers form eventually ~Metaphase I) Tetrads align themselves in the middle along the metaphase plate, random assortment of homologous chromosomes happens ~Anaphase I) Pairs of sister chromatids (homologs) separate and go to opposite poles ~Telophase I and Cytokinesis I) Nuclear envelope forms, cleavage furrow deepens to divide the animal cell or cell plate forms in plant cells, cell divides Meiosis II ~Interphase II) occurs sometimes but no DNA replication ~Prophase II) nucleus and nucleolus disappear if present, spindle fibers form; crossing over happens ~Metaphase II) sister chromatids align on the metaphase plate ~Anaphase II) centromeres of sister chromatids separate and individual chromosomes (1N) move towards opposite ends ~Telophase II and Cytokinesis II) 4 highly variable cells form

Know the types of amino acids based on the side chain properties (from a given figure)

Peptide bonds are found in proteins *The R-Group indicates which way the protein folds (interior or exterior based on solvent); IF THE R GROUP IS POLAR then it is Hydrophilic (exposed to water in aqueous surroundings)[Charged: (-,+), -COO-, -NH3+ & Uncharged: -OH, -SH] IF THE R GROUP IS NON POLAR then it is Hydrophobic (stay away from water in aqueous surroundings) [-CH3, linear chains of branched hydrocarbons]

How do the size and polarity of a molecule will affect ITS passage through biological membranes?

Polar: ~Small (1-100 Da)- Facilitated diffusion (aquaporins), Simple diffusion , active transport (H2O and charged ions) ~Medium (100-1000 Da)- Facilitated Diffusion; active transport depending on concentration gradient (Ex- amino acids, glucose) ~Large (>1000 Da)- Endo/exocytosis (Ex- soluble proteins, DNA, and RNA) Non polar: ~Small (1-100 Da)- Simple diffusion (Ex- CO2, O2, H2) ~Medium (100-1000 Da)- Simple diffusion (Ex- steroids, fatty acids, kerotenoids, monoglycerides, carotenoid ~Large (>1000 Da)- Endo/Exocytosis (Ex- triglyercides, non-soluble proteins)

Compare and contrast prokaryotes and eukaryotes in transcription and translation.

Prokaryotes: transcription and translation occur simultaneously in the same place (cytoplasm); no introns, hence no RNA processing Eukaryotes: Transcription, translation are separated in space and time, RNA needs to be safely transported from nucleus to cytoplasm, eukaryotic genes (mostly) contain introns (intervening sequences) that need to be removed, 5' G-cap and 3' polyA tail are added to mRNA to protect from degradation by RNases, introns are removed for all types of RNA, eons are joined together, alternate splicing happens

What are the enzymes, cis-acting elements, trans-acting/transcription factors and steps involved in transcription?

Transcription: DNA --> RNA; Gene is a fragment of DNA that contains information to encode RNA or protein which is expressed to make the gene product Prokaryotes: multiple genes are organized in units called operons Eukaryotes: a single gene is expressed in one transcription unit ~Initiation: RNA Polymerase binds to a sequence of DNA called promoter, found near the beginning of a gene; each gene has its own promoter; RNA polymerase separates the DNA strands to provide the single stranded template needed for transcription. ~Elongation: One strand of the DNA, the template strand, acts as a template for RNA Polymerase, "reads" the template one base at a time, the polymerase builds an RNA molecule out of complementary nucleotides, making a chain that grows from 5' to 3', RNA transcript carries the same information as the non-template (coding) strand of DNA, but it contains the base Uracil instead of Thymine. ~Termination: Sequences called terminators signal that the RNA transcript is complete. Once they are transcribed, they cause the transcript to be released from the RNA polymerase. ~cis-acting elements: set of regulatory DNA sequences, regulate Eukaryotic genes, DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression (Ex- enhancers or suppressors, promoter) ~trans-acting/transcription factors- factors, usually considered to be proteins, that bind to the cis-acting sequences to control gene expression (Ex- TATAA box binding protein (one of the two circles on promoter)

Know the variations of carbon fixation, namely, C3, C4 and CAM.

~C3: photorespiration, during arid (hot and dry) stomates close to save water, O2 concentration increases from light reactions and CO2 decreases as it is fixed in the Calvin Cycle, RuBisCo fixes oxygen into RuBP and results in CO2 and amino acid (consuming oxygen, releasing CO2) (Ex- rice, wheat) ~C4: evolved to fix CO2 into a 3-C molecule (PEP) by the enzyme PEP Carboxylase to make a 4-C molecule; C4 pathway happens in the mesophyll cells, C3 pathway happens in the Bundle sheath cells, both occur during the day (Ex- corn, sugarcane) ~CAM: Both the C4 and C3 pathway happen in the mesophyll cells, but C4 happens at night time and C3 happens in the day time (Ex- cacti)

Know terms and details of codons, anticodons, degeneracy, wobble, promoter and one gene-one polypeptide experiment.

~Codon: 3 nucleotides that code for an amino acid ~Anticodons: 3 nucleotides on the tRNA that are complementary to codon ~Degeneracy: One amino acid can have multiple codons; A code in which several code words have the same meaning. The genetic code is degenerate because there are many instances in which different codons specify the same amino acid. ~Wobble: flexibility of the third base to bond with more than one codon; Changes in the last nucleotide of a codon aren't that crucial to the tRNA recognizing which amino acid the codon is supposed to code for; A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). ~Promoter: a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand). One Gene - One Polypeptide ~One gene codes for one polypeptide chain in a protein; any mutation in the gene will cause a mutation in the polypeptide ~Beadle and Tatum treated neurospora (bread mold) with x-rays, mutating certain genes that created certain enzymes. Showed that specific enzymes stopped being synthesized if certain genes were mutated ~Unmutated mold samples were called prototrophs; mutated mold samples that needed external enzymes to survive were called auxotrophs

How ATP is made during photophosphorylation and how is it different from oxidative phosphorylation?

~During photophosphorylation, photosystem 1 and 2 are utilized, this all happens in the thylakoids ~Non-cyclic Photophosphorylation- light goes into the PSII and H2O --> 2H+ + 1/2O2, then 2 e- go into the Primary Electron Acceptor (pigment protein complex) and then travel down to PSI through the ETC located on the thylakoid membrane, making ADP + Pi --> ATP in the process, then light goes into PSI and through photophosphorylation go back up to another primary electron acceptor and get converted from NADP+ --> NADPH, then water is split to give PSII from PSI ~In Oxidative Phosphorylation, NADH --> NAD+ on the inner membrane of the mitochondria, releasing H+ and also producing a concentration gradient, water is split, and then through the H+ coming back into the matrix through ATP Synthase, ADP + Pi --> ATP ~Differences: Photophosphorylation happens during photosynthesis and oxidative phosphorylation happens during cellular respiration, the source of energy for oxidative phosphorylation is glucose while the source of energy for photophosphorylation is light, and in oxidative phosphorylation the final acceptor is oxygen whereas in photophosphorylation the final acceptor is NADP+

Remember all structures and functions for each cellular component.

~Energy Organelles 1. Chloroplast- contains Stroma, Granum, Outer Membrane, Inner Membrane, Circular DNA, and Thylakoid 2. Mitochondria- Outer Membrane, Inner Membrane, Inner-Membrane Space, Circular DNA, Cirstae, and Matrix ~Outside progressing inward of plant cells: Middle Lamella --> Primary Cell Wall --> Secondary Cell Wall --> Plasma Membrane ~Plastids 1. Chromoplast: color pigment 2. Chloroplast: Chlorophyl

Define entropy, enthalpy and free energy. Understand how they are related to each other in the free energy equation.

~Entropy- measure of randomness denoted by ΔS ~Enthalpy- heat content or the total potential energy denoted by ΔH ~Free Energy- the portion of a system's energy that is available to perform work when the temperature is uniform throughout the system; an expression combining the entropy and enthalpy denoted by ΔG (-ΔG= exergonic, net release of free energy; +ΔG=endergonic, net absorption of free energy) ~Free Energy Equation: ΔG=ΔH-TΔS

What are enzymes and how do they help in a catalytic reaction?

~Enzymes are biological catalysts that speed up reactions without being consumed in the reaction, predominantly made up of proteins and some are RNA based, create highly variable 3-D structure ~the functional groups at active site (the one that interacts with the substrate) help in the enzymatic reaction ~Factors that affect enzyme activity: temperature, ph, salt concentration (both affect the bonding and 3-D structure), and cofactors (both inorganic- Fe^2+, Cu^2+, Ca^2+, Zn+ and organic- NAD+, FAD, CoA) <-- participate in the reaction but are recycled in the process

Understand the experiments that proved DNA as the genetic material and semiconservative mode of DNA replication. Be able to predict the results, if the experimental conditions were changed.

~Fredrick Griffith's experiment on Streptococcus pneumonia; S: Smooth Strain: pathogenic (caused disease in mice); R: Rough Strain: nonpathogenic (did not cause disease in mice); Heat killed S-Strain --> did not kill mice or cause disease; Heat killed S-Straigh and R-Strain (live) --> caused disease --> isolated S-Strain from dead mice transformed the R-Strain to become pathogenic and smooth ~Avery, McClead, and McCarthy: Used heat killed S-Strain extract and treated with DNase, RNase, or Protease to degrade DNA, RNA, and proteins respectively, enzyme treated extracts were used to mix with R-Straing and infect mice, both RNase and Protease treated samples caused disease whereas DNase treated on did not; first in vitro transformation of on bacteria strain by introducing DNA from another bacterial strain ~Hershey and Chase- used bacteriophage T2 to study if DNA or protein is the genetic material, cultured two batches of the T2 phage separately in media containing 35S and 32P to label proteins and DNA respectively, isolated the phages and used them to infect bacteria cultured without any radioisotope, after infection they mixed the contents vigorously to shake off the phages from the bacteria, the mixture was centrifuged to pellet the bacteria and retain the phages in supernatant; the pellet fraction (bacteria) contained most of the 32P and the supernatant contained most of the 35S, indicating that DAN was the genetic material injected into bacterial cells to program the cells to make more viruses ~Erwin Chargaff: different species contained different compositions of DNA and the percent of A was equal to that of T and the percent of G was equal to that of C, also chromosomes go through duplication during cell division also supported the hypothesis that DNA is the genetic material and carries hereditary information ~James,

What are the uses of DNA gel electrophoresis, sequencing, PCR, microarray and RFLP?

~Gel electrophoresis: fractionate DNA or RNA fragments based on their size; polyacrylamide gels are used to fractionate proteins and DNA ~DNA, RNA, and Protein Sequencing: determine specific molecular sequence; DNA sequencing done by doing an in vitro DNA synthesis using a DNA template, a primer, dNTPs and DNA polymerase to extend the new strand of DNA from the primer in a suitable buffer ~Polymerase chain reaction (PCR): used to amplify large amounts of DNA from small amounts of samples; amplify DNA with thermostable DNA polymerase (Ex- used in forensics to identify suspects at crime scene), doubles DNA product about 32 times doubling the product each time and resulting in about 1 billion copes of the DNA fragment from each copy of the template ~Microarray: detect RNA samples that are expressed; DNA tags + labeled RNA ~Restriction fragment length polymorphism (RFLP): commonly used to identify differences in the restriction pattern of a specific gene or DNA region between several individuals of a species or several related species; used for protein or maternity testing, and finger printing

What are the structural components of a eukaryotic gene?

~Genes have the coding sequences for the amino acids and polypeptide chains (exons- transcribed and translated) interrupted by non-coding sequences (introns- transcribed but not translated) ~Promoter sequences (sequence of DNA nucleotides up-stream of the initial base of transcription at which RNA polymerase binds and initiates transcription, control individual gene expression)), terminator sequences (a DNA sequence just downstream of the coding segment of a gene, which is recognized by RNA polymerase as a signal to stop transcription) ~Enhancers (A regulatory DNA sequence that greatly enhances the transcription of a gene) or silencers (A DNA sequence that helps to reduce or shut off the expression of a nearby gene) regulatory sequences which may be up stream or down stream, near or far from the gene ~Signals: Up stream- sequence signal for addition of Cap to the 5' end of mRNA, facilitates the initiation of translation; addition of cap and tail to primary RNA occur after transcription Down stream- sequence signal for addition of poly A tail ~TATA or hogans box- between 30-80 nucleotides upstream from the transcription site, located in the promoter ~ALL OF THESE TOGETHER WITH GENERAL TRANSCRIPTION FACTORS ARE RESPONSIBLE FOR BINDING OF THE ENZYME RNA POLYMERASE II WHICH IS RESPONSIBLE FOR TRANSCRIPTION

Understand the terms; genes, alleles, genotype, phenotype, dominance, recessive, homozygous and heterozygous.

~Genes: the unit of heredity according to classical genetics, based on the expression of a specific trait of an organism ~Alleles: alternate forms of a gene, responsible for a particular trait, present in two different chromosomes which are derived from mother and father, may code for the same protein with slightly different amino acid sequences and many result in different traits; alleles may be exchanged during meiosis in the crossing over and recombination process ~Genotype: the assorted collection of various genes in the chromosomes, represented by capital or small letters to notate dominant and recessive alleles respectively (ex- AA, Aa, bb, etc) ~Phenotype: a physical trait, physiology condition or biochemical aspect determined by the genes at the molecular level according to its genotype (Ex- eye color (physical), sickel cell anemia (physiological) and herbicide resistant enzyme (biochemical)) ~Dominance: the allele of a gene that is expressed under both homozygous and heterozygous condition due to the DNA sequence of the particular gene and the nature of the protein coded by such gene, denoted in capital letters (Ex- AA, BB, CC) ~Recessive: the allele of a gene that is expressed only under homozygous condition (Ex- aa, bb, cc), an organism may contain a dominant allele for one gene and recessive for another ~Homozygous: an organism with a pair of identical allele for a particular gene in both the homologous chromosomes (Ex- AA, aa, BB, bb) ~Heterozygous: an organism with mixed allele pairs for a particular gene (Ex- Aa, Bb), an organism may be homozygous for one gene and heterozygous for another

Remember the examples of protein processing in eukaryotes.

~Glycosylation: addition of oligosaccharides --> glycoprotein ~Myrstilation: addition of lipids --> lipoprotein (Ex- HDL, LDL) ~Zyomegen activation: removal of amino terminus segment to make an inactive precursor protein (zymogen) active ALL OF THE ABOVE CAN CHANGE THE SIZE OF THE PROTEIN ~Hydroxylation: addition of hydroxyl groups ~Phosphorylation: addition of phosphate groups ~Acetylation: addition of acetyl groups ~Conversion of L-amino acid to D-amino acid, rare (ex- snake venom)

What happens (specifically) during RNA processing in eukaryotic cells?

~Happens in the nucleus ~Capping and Polyadenylation: after transcription, the phosphate group of a modified form of guanosine triphosphate (GTP) is added to the 5' end of RNA (this is called capping), helps protect the mRNA and mark the 5' end as starting point for translation; at the 3' end a stretch of polyA tails (adenines) are added by an enzyme polyA polymerase, the polyA tail protects from mRNA from being degraded ~Splicing: introns are intervening sequences that generally do not code for a protein, erosions are expressed regions coding for a protein or a segment of a protein; during splicing introns are removed and exons are joined together; NTR (non translated regions) are present in processed RNA at 5' and 3' ends but they do not code for a protein; some RNAs splice themselves and they are called autocatalytic RNAs (self-splicing); in other RNAs splicing occurs in a splicesome made up of smaller RNAs (snRNAs), small nuclear ribonucleoproteins (snRNPs- called "snurps") and proteins ~Addition of 5' cap: ribosome binding site ~Addition of 3' Poly-A tail (100-200 Adenines): stabilization, guidance out of nucleus, protection for degradation ~Splicing: removal of introns by spliceosomes (ribozymes)

In general, know the practical uses of various techniques and now how they work.

~Humans: identification of genetic diseases by discovering the specific givens involved; diagnostics of diseases or infection such as HIVl development of recombinant vaccines by engineering various antigens in on plasmid to develop multiple vaccines; gene therapy techniques to rectify genetic errors; DNA detection techniques are extensively used in forensics and in paternity testing, identification of new viruses (such as SARS); developing gene therapies ~Animals: proteins in animals have been developed by introducing genes at an early embryonic stage, some hormones developed by recombinant DNA techniques to increase milk production or meat production; vaccines developed to prevent some diseases that can be difficult to treat ~Plants: herbicide resistance, insect resistance, disease resistance, and improved storage quality; transgenic plants being approved by the FDA (Ex- the Flavr-Savr tomato with long storage life, golden rice with high beta-carotene content, and insect- and herbicide-resistant crops)

Know the examples of non-mendelian inheritance patterns such as incomplete dominance, codominance, epistasis, plieotropy

~Incomplete dominance: the homozygous have a particular phenotype, and the heterozygotes have an intermediate phenotype meaning that no single gene is completely dominant (Ex- snapdragon flowers have RR red and rr White, but when crossed they make pink) ~Codominance: both phenotypes are expressed at about equal levels by the expression of two types of proteins by two alleles (Ex- AB blood types express proteins for both types A and B) ~Epistasis: one gene interferes with the expression of another gene, several pairs of alleles may interact to affect a single phenotype (Ex- in a biosynthetic pathway, if one enzyme is defective it defects the others, if a mice is affected by two pairs of alleles and on locus (pair of alleles) is homozygous recessive, mice are always albino irrespective of the other locus) ~Plieotropy: one gene or allele codes for more than one phenotype (Ex- in sickle cell anemia or cystic fibrosis, several symptoms can be traced to one or a few genes; may be due to the nature of an individual gene affecting many phenotypes or several genes in one locus being responsible for the varied effects)

What is the key regulatory step and enzyme in Calvin cycle?

~Key regulatory step: carbon fixation, the carbon dioxide is combined with ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules (3-PG). ~Key Enzyme: ribulose bisphosphate carboxylase (RuBisCO).

Understand the two laws of inheritance and examples of monohybrid and dihybrid crosses.

~Law of segregation: allele pairs segregate (separate) during gamete formation and the paired condition is restored by the random fusion of gametes at fertilization (monohybrid crossing) ~Law of independent assortment: the segregation of each allele pair is independent of other allele pairs; the individual allele pairs need to be located on separate loci, far from each other to allow independent assortment during gamete formation (dihybrid crossing) ~Examples of monohybrid crosses- crossing spherical seeds and dented seeds, then self-pollinated the results, and found that 3/4th of the second generation seeds had spherical seeds and 1/4th were dented; the ratio was 3:1 ~Examples of dihybrid crosses: considering two different traits by two allele pairs (SSYY and ssyy), have a 9:3:3:1 ratio

Know the basic details about leading, lagging strand synthesis and Okazaki fragments.

~Leading strand (3' to 5') copies DNA from 5' to 3' the easiest through DNA Polymerase III ~Lagging strand (5' to 3') is more difficult because the DNA Polymerase has to work backwards, RNA Primase lays the first 4 base pairs in sections, these fragments are called Okazaki fragments, DNA Polymerase I fills in the rest, then DNA ligase comes through to finally connect the fragments

Define metabolism, anabolism and catabolism and give examples for each.

~Metabolism- the sum of all biochemical reactions that take place in an organism, makes and sustains cells, produce and breakdown molecules, providing cellular energy for cells to move, transport, and do a variety of actions ~Anabolism- synthesis, synthetic of constructive biochemical reactions (Ex- photosynthesis) ~Catabolism- breakdown, degradative biochemical reaction facilitated by an enzyme for conversion of reactants into products (Ex- cellular respiration)

What are the three major types of DNA repair processes and what are some enzymes involved?

~Mismatch repair: done to correct errors made during DNA replication (Ex- done during DNA replications- S phase; also DNA Polymerase III proofreads and repairs; problems in mismatch repair causes colon cancer) ~Telomere repair or preservation- also occurs during DNA replication and is catalyzed by telomerase and helps prevent the telomere from getting shortened after each cycle ~Excision repair: occurs after a cell divides and is in the G1 phase or G2 phase, this damage is caused by carcinogens and mutagenic radiations altering the bases or making pyrimidine dimer (Ex- endonuclease removes mistakes, DNA Polymerase II, makes new DNA and & ligase connects DNA fragments; disease xeroderma pigmentosum is caused by a lack of enzyme(s) involved in excision repair)

How are the carbohydrates classified? Know specific examples.

~Monosaccharides (3-7 Carbons) [Ex- Glyceraldehyde <-- 3 Carbon sugar; Glucose, fructose, lactose <-- 6 carbon sugars; ribose, deoxyribose <-- 5 carbon sugars] ~Disaccharides [Ex- Maltose = Glucose + Glucose, Sucrose = Glucose + Fructose <-- Alpha-1, 4 linkages; Lactose = Glucose + Galactose <-- Beta-1 Linkage] ~Polysaccharides- >1000 Da in size; Storage for energy utilization- Starch (plants), Glycogen (animals) <-- Alpha-1,4 linkage which humans can digest; Structural to build cell walls and exoskeletons of insects- Cellulose, Callose, Chitin (NAM-NAG in cell wall) <-- Beta-1, 4 Linkage

Identify the eukaryotic cell components from a given diagram and assign their functions.

~Nucleus: stores DNA (genetic info), has double membrane, DNA replication, RNA synthesis and processing - Nucleolus: makes rRNA & assembles the subunits of ribosomes ~Cytoplasm: contain all of the organelles and compartments in the cell ~Cytoskeleton: (in order from biggest to smallest) 1. Microtubule- cellular (flagella) and chromosome movement (centrioles), vesicle transport (motor proteins), tubular 25 nm, alpha and beta tubular 2. Intermediate Filament- nuclear lamina, anchoring junctions (desmosomes), filamentous ~10 nm, keratin like protein 3. Microfilament- contains actin, cytoplasmic streaming, cleavage furrow, muscular contraction, filamentous 7 nm ~Cell Surface: cell wall/ECM, cell junction, keeps things out of the cell, protection ~Energy Organelles: double membrane organelle, mitochondria and chloroplasts, important for the utilization and generation of carbohydrates ~Endomembrane System: 1. ER: Smooth- synthesizes lipids, detoxes chemicals, Calcium storage, abundant in testes/ovaries, metabolism, no ribosomes Rough- membrane protein synthesis, attached to ribosomes, synthesizes proteins for secretion/modification 2. Golgi Apparatus- Receives proteins from Rough ER, modifies, sorts, and ships to target sites; glycosylation --> protein + carb --> glycoprotein; myristylation --> protein + lipid --> lipoprotein 3. Lysosomes- main site of digestion of macromolecules (breaks down all 4), acidic because of hydrolytic enzymes, digestion of food particles and damaged organelles 4. Microbodies: Peroxisomes- break down fatty acids (lipids --> carbs), active oxygen species- oxygen detoxification (Hydrogen Peroxide), found in animals Glyoxysomes- same as peroxisomes, but in plant cells 5. Vacuole: Large Central Vacuole- stores organic compounds and inorganic ions in plant cells Food Vacuoles- helps primitive (animals)

Know the details of prokaryotic operons- structure, inducible and repressible. Know specific examples and their regulation.

~Operon: bacterial genes organized into units called operons; constitutes the coding sequences of the genes in that unit, a promoter, and an operator; promoter and operator determine the accuracy and amount of transcription; many transcripts are made from one operon simultaneously as a single mRNA in a single transcription ~Inducible Operon: mostly turned off, they are turn on only when necessary (Ex- lac operon which is induced under two situations, either when lactose is present with glucose or alone; when the lactose is present along with glucose, the cells prefer glucose, however the expression of genes for lactose-utilizing enzymes is activated by removing a repressor that is bound to the operator of the lac operon, this lactose turns into allolactose and binds to the repressor molecule, and the operon is derepressed to start transcription; if there is no glucose and only lactose is present, it results in an increase of cyclicAMP levels in the cells. The cAMP binds to a CAP and that binds to the promoter to further enhance the activity of the lac operon above the basal level created from re-repression alone.); usually present to control catabolic pathways use to break down compounds ~Repressible Operons: use for anabolic pathways to synthesize compounds, mostly turned on, and they are turned off when not needed (Ex-Trp-operon to synthesize tryptophan, the enzymes are expressed only when trp is absent, when trp is absent a repressor protein is inactive and does not bind to the operator to repress transcription; when sufficient levels of trp are made, it binds to the repressor molecule and makes it an active repressor that now binds to the operator and stops transcription (this is similar to the feedback inhibition of enzymes except that it occurs at the gene level), trp acts as a corepressor and controls the transc

Define covalent bonds (polar, non-polar), ionic bonds, H bonds, Van der Waals interactions and hydrophobic interactions.

~Polar Covalent bonds- when two atoms have significantly different electronegativity, pair of electrons is unequally shared between two atoms ~Non-polar Covalent bonds- atoms have similar electronegativity, pair of electrons is equally shared between two atoms ~Ionic bonds- atoms have extreme electronegativity difference (>1.7), or a metal and nonmetal; the more electronegative atom pulls the electron away from the less electronegative atom to create an anion and a cation ~H bonds: chemical bond between an electronegative atom, such as fluorine, oxygen, or nitrogen, and a hydrogen atom bound to another electronegative atom; hydrogen attached negatively to a partial positive charge ~Van der Waals interactions- weak attractions due to constantly moving electrons/ constantly changing positive and negative charges, temporary (London Dispersion Forces) and dipole-dipole attractions ~hydrophobic interactions- non-polar molecules (Ex- water on leaf, water is not soaked up, it is repellant), lipid soluble ~hydrophilic interactions- polar molecules, water soluble

Know some biological examples of where these bonds and interactions occur.

~Polar covalent bonds- O-H bond in H2O or N-H bond in NH3 [ammonia] ~Non-polar covalent bonds- O=O [O2], C-H bond ~Ionic bonds- Cl + Na --> Cl- + Na+ ~H bonds- between other molecules, water, H2O can form up to 4 bonds, H-bonds of DNA, RNA, and proteins ~Van der Waals interactions- lipids in biological membranes and cellulose in plant cell walls ~hydrophobic interactions- the fatty acid tails inside the phospholipid bilayer ~hydrophilic interactions- heads of the phospholipid bilayer

What are the 4 different levels of protein structures? Know the bonds that stabilize them.

~Primary Structure: Amino acid sequence (stabilized by peptide bonds) [Ex- protein sequencing] ~Secondary Structure: interaction between Carbonyl (-C=O) and Amine (-NH) group of the polypeptide backbone [Ex- H bonds] ~Tertiary Structure: side chain interactions, disulfide linkages, ionic bonds, H-bond, hydrophobic, hydrophilic ~Quaternary Structure: interactions of the subunits (individual proteins) [Ex- complex proteins, hemoglobin, collagen, ATP Synthase, RuBisCo], there are 2 Sulfhydrl groups needed to make a disulfide bond, involve ionic and H-bonds

What are some examples of enzymes used in recombinant DNA work and their functions?

~Restriction endonucleases: recognize and cut specific sequences of DNA to insert foreign DNA fragment; enzymes isolated from prokaryotes that recognize a specific DNA sequence and cleave the DNA at that recognition site or another place; some protect cells from invading viruses and foreign DNA (Ex- type I and III recognize at one site and cleave at another place, have methyl's activity) (Ex- Type II most commonly used enzymes without methyl's activity, recognize and cleave at particular DNA sequence) (Ex- E Coli can recognize and cut DNA with a certain sequence, a six base pair recognition enzyme), sometimes leave 5' or 3' overhangs called sticky ends because they can anneal with similar sticky ends based on their complimentary or they can be 4 base pairs at 5' or 3' or blunt end ~DNA Polymerase: used to make DNA in vitro (commonly obtained from E. Coli, T7 bacteriophage, or thermostable bacteria and used for DNA synthesis, DNA sequencing, and polymerase chain reactions) ~DNA ligase: connect 2 DNA fragments through phosphodiester bond; can catalyze the covalent bonding of the 3' and 5' ends of two DNA strands; used to connect two DNA strands having blunt ends or complementary sticky ends created by restriction enzymes to make a recombinant DNA molecule (Ex- T4 DNA ligase obtained from the T4 phage is one of most commonly used ligases) ~Reverse transcriptase: mRNA --> cDNA; RNA-dependent DNA polymerase (it uses an RNA template to make a complementary DNA from RNA) (Ex- isolated from viruses such as AMV and MMLF, also some thermostable DNA polymerases also have reverse transcriptase activity under different salt conditions)

How the enzyme activity is regulated? (Simple, Allosteric, feedback and chemical modification)Note: There will be no calculations or questions on Keq, Vmax or Km.

~Simple: activators (km decrease and Vmax stays the same) and inhibitors (competitive- km increases and noncompetitive- Vmax decreases) ~Allosteric: complex proteins, switch between active and inavtice forms, sigmoidal response ~Feedback Regulation: A --> B --> C--> D --> back to A and recycles again, Ex- ATP and Citrate --> PFK ~Chemical Modification: Inactive Enzyme + ATP --> Active Enzyme + Phosphate + ADP (Ex- phosphorylation in cell signaling)

What are Southern, Northern and Western blots and what do you infer from them?

~Southern: Hybridization of probe with a target DNA; used to study the genome organization of a particular gene and determine the approximate number of copies of a specific gene; DNA-DNA hybridization techniques are commonly used in library screening and to find out if a particular gene is present in a genome or not. ~Northern: Hybridization of probe with a target RNA; used to determine the RNA levels for a particular gene at different stages or in different tissues or organs of an organism ~Western: Hybridization of probe with a target protein; specific protein (antigen) is recognized by a primary antibody which is then recognized by a secondary antibody conjugated to a fluorescent probe or an enzyme; can convert a chromogenic substrate into a colored substance for the detection

Remember the inputs, outputs and how the important steps are regulated in Krebs cycle.

~Step 1: Acetyl CoA + Oxaloacetate --> Citrate; catalyzed by Citrate Synthase ~Step 3: Isocitrate --> alpha- ketogluterite; catalyzed by isocitrate dehydrogenase ~Inputs: Acetyl CoA, NAD+, FAD, ADP, Pi, H2O ~Outputs: CO2, CoA, NADH, FADH2, and ATP

Learn the anatomy of a leaf and the components relevant to photosynthesis.

~Stomata- pores on the leaf, CO2, O2, and H2O are all non polar, so they go easily from cell to cell ~Mesophyll- middle tissue between epidermis ~Epidermis- two layers under waxy cuticle ~Waxy cuticle- outside of cells, protects from water loss ~Vein- in the Mesophyll, phloem transports sugar, and xylem transports water ~Mesophyll Cell: Nucleus, Chloroplasts, and Vacuole ~Chloroplasts: Outer and inner membrane, stroma, and thylakoids ~Stroma: calvin cycle/ carbon fixation happens ~Thylakoid: light reactions happen

Understand substrate level phosphorylation, chemiosmosis and reduction-oxidation reactions, in particular, how NAD+ and FAD are used in redox reactions.

~Substrate-level phosphorylation: a metabolic reaction that results in the formation of ATP or GTP by the direct transfer of a phosphoryl (PO3) group to ADP or GDP from another phosphorylated compound; occurs in Glycolysis and TCA Cycle, happens through Kinases ~Chemiosmosis: Hydrogen, protons move from high --> low concentrations ,results in ATP Synthesis -Reduction-Oxidation Reactions- an oxidation-reduction (redox) reaction is a type of chemical reaction that involves a transfer of electrons between two species. An oxidation-reduction reaction is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron; uses NADH and FADH2 and turns them into NAD+ and FAD; used in ETC

How is the eukaryotic genome organized? Identify the components at different levels of organization.

~The chromosomal DNA inside the nucleus is dispersed as chromatin during most of the cell cycle, double helix of DNA wraps around histone proteins to form nucleosomes (which condense further to make chromatin), eukaryotic chromosomes are linear with definite ends called telomeres, genome size is not a representation of organismal complexity, it is the sequence of DNA and the proteins coded by them and not the amount of DNA alone that determines how complex a species is (much of the excessive DNA is made of repetitive sequences that generally do not code for proteins) ~Most of the DNA in eukaryotic genomes (in contrast to prokaryotes) is made of DNA sequences that do not code for an RNA or protein, repetitive DNA can be identified by reannealing denatured DNA (dsDNA can be denatured and renatured by heating and cooling), receptive sequences are found near telomeres and are useful in the DNA replication process because they fold onto themselves to provide a 3'-OH group for DNA synthesis ~Gene families: the result of gene duplication during cross over, or a result of transposable elements translocating a gene from one chromosome to another, or to a different location on the same chromosome, genes essential to survival are highly duplicated during evolution, sometimes they lose their regulatory sequences (promoter and other cis-elements) and they are not expressed at all (these are calle pseudogenes), mulitgene family members may be located together on a chromosome or spread out in d different chromosomes, the expression of multilane family members is regulated by common cis-acting elements recognized by common trans-acting facts specific for that gene family. This is referred to as coordinated gene expression (Globin genes are an example of these)

Know the terms such as tissue-specific gene expression, transposable elements, gene amplification and coordinated gene regulation.

~Tissue specific gene expression: depends on the promoter, chemical signals and transcription factors in each tissue; during and after development genes are expressed in a tissue-specific manner to facilitate the function of different cell or tissue types (Ex- leaf tissue in a plant will make proteins for photosynthesis, and storage tissues in the seed will make storage proteins); this is controlled by the transcription factors being selectively active in specific tissues ~Transposable elements: provide the opportunity for various genes to be moved from one place to another; do not exist independently, but move with RNA as an intermediate and lack antibiotic genes, these elements can be integrated randomly or in hot spots by chromosomes, sometimes genes are interrupted and inactivated by transposable elements; may be to create a variation among the gene pool so that organisms can adapt to varying environments ~Gene amplification: sometimes certain genes are duplicated several times to amplify their number so that enough copies of mRNAs can be produced, genes for ribosomal RNA are amplified at earlier stages of development so that there are enough copies of rRNA genes to make rRNA for ribosomes and mRNA for ribosomal proteins; (Ex- genes for herbicide resistance are amplified to survive the chemical) ~Coordinated gene regulation: multiple genes are expressed in a synchronized manner by having similar regulator sequences recognized by a common transcription factor, controlled by promoter and transcription factors

What are the four levels of gene regulation in eukaryotes? Know specific examples.

~Transcriptional Regulation: regulated at the gene level with different mechanisms operating for long-term and short-term controls 1. long term transcriptional control: chromosomes are condensed during cell division, but gradually uncoil again to become dispersed as chromatin (COMPACTION AND RELAXATION), but a portion of chromatin remains condensed as heterochromatin (which is not readily accessible by RNA polymerases and other proteins), some regions are more diffuse and are accessible for transcription (euchromatin) (Ex- one of the x chromosomes in females is inactivated and such condensed chromosomes are called Barr bodies) -METHYLATION OF DNA- methylation is another way to control transcription on selected chromosomes, done by DNA methylates (such as DCM or DAM which add to methyl groups to the C and A bases), results in the prevention of such regions from being transcribed (Ex- humans 5% of DNA is methylated and 3-5% of genes are actively transcribed at any time), helps DNA polymerase to distinguish the old strand from the new strand (Ex- in bacteria, DNA methylation is critical for recognizing cellular verses viral DNA) -ACETYLATION OF HISTONES -GENOMIC REARRANGEMENTS (Insertion, Deletion, Transposition) 2. Short-term transcriptional control: some regions of chromosomes actively transcribed as transcription puffs, easily seen in the large multi stranded polytene chromosomes, transcription of genes in eukaryotes is controlled by the interaction between TRANSCRIPTION FACTORS and the regulatory elements on the genes (regulatory elements- promoter which s upstream of the start site, and enhancers or repressors which may be upstream or downstream from the start site), promoter only one at relatively fixed distance, trans-acting proteins recognize specific cis-acting proteins on the DNA by binding to a specific DNA ba

Define active site, substrate, competitive inhibitor, non-competitive inhibitor.

~active site: a region on an enzyme that binds to a protein or other substance during a reaction ~substrate: The substance acted upon by an enzyme; the more substrate, the more activity ~competitive inhibitor: compete with substrate for active site (raises Km- concentration of substrate at which the velocity = 1/2 of the Vmax) ~non-competitive inhibitor: bind to a site away from active site (lowers Vmax- maximum velocity at saturating substrate concentration)

Understand what is a checkpoint and internal and external conditions that are monitored by cell to determine whether to divide and whether to progress from one stage to another.

~checkpoint- control mechanisms in eukaryotic cells which ensure proper division of the cell ~There are checkpoints after G1, S-phase, G2, and M phase. The critical restriction point that controls cell division is the G1 phase because cells can go from here to G0 where there's no more division or it can carry on to other phases. Proteins regulate the main process of cell division. Maturation promoting factor (MPF), which is a combo of cdk and cyclin, promotes DNA synthesis and mitosis. S-cyclin promotes S-phase and M-cyclin promotes M-phase. Nutritional status, growth factors, hormones, cell density, and other environmental factors also influence cell division.

What are the roles the cis-acting elements (regulatory sequences) and trans-acting factors (transcription factors) in regulating gene expression?

~cis-acting elements: set of regulatory DNA sequences, regulate Eukaryotic genes, DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression (Ex- enhancers or suppressors, promoter) ~trans acting factors: recognize specific cis-acting elements on the DNA by binding to a specific DNA base sequence and inducing or inhibiting transcription; have unique secondary structures to recognize the DNA; bind to the cis-acting sequences to control gene expression (Ex- TATAA box binding protein (one of the two circles on promoter)

Understand coding strand, template strand and direction of transcription.

~coding strand: the coding strand is the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil), the strand used when displaying a DNA sequence ~template strand: The strand of DNA which is used during transcription to make mRNA. The mRNA made thus has the sequence of the antisense strand of DNA, and it codes for a sense strand of polypeptide (which eventually becomes a protein or part of a protein) during translation ~direction of transcription: 5' to 3' always ~Eukaryotes are monocistronic (one gene transcribed per transcription, each transcript coding for one protein), Prokaryotes are polycistronic (many messages per transcription)

What are the 3 types of RNA and their functions?

~mRNA: carries the message from the gene to be translated into protein, the mRNA alone has a plyA tail and travels to cytoplasm to be translated, processed mRNA carry regions that are recognized by the ribosomes to start protein synthesis; in prokaryotes the ribosome recognition site is called the Shine-Delgarno region, the translation in all organisms starts with an AUG cocoon; essentially protein synthesis- contains code for amino acid sequence ~rRNA: major component of ribosomes and the most abundant form of RNA in cells; makes up the ribosomal subunits (most of RNA in the cell is this type) ~tRNA: bring amino acids from cytosol to translation complex during protein synthesis, clover leaf shape, each tRNA has an anticodon that is complementary to an mRNA codon

What are nucleosides, nucleotides, NTPs and dNTPs?

~nucleosides- nitrogenous base + ribose sugar ~nucleotide- nitrogenous base + ribose sugar + phosphate ~NTPs- nucleoside triphosphate, has 3 phosphates ~dNTPs- deoxynucleotide triphosphate, if the sugar is deoxyribose as in DNA

What are the different factors affecting enzyme activity?

~pH, salt concentration, temperature (affect the H-bonds, ionic bonds, and even the covalent bonds), and cofactors (inorganic or organic) ~pH, temperature, and salt concentration affect the bonding and 3-D structure