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Biology Lesson 1 – Chemistry Review and Enzymes

Thermodynamics
G = H - TS
G = G + RTlnQ
G = -RTlnKeq

H
+
+

S
+
+

G<0 Keq>1
G>0 Keq<1
G=0 Keq=1

-TΔS
+
+
-

Spontaneous at all temperatures
Non-spontaneous at all temperatures
Spontaneous at low temperatures
Spontaneous at high temperatures
Keq
K >> 1
K << 1
K~1

Meaning
Products favored at eq.
Reactants favored at eq.
Considerable Prod/React
present at eq.

Kinetics
Catalyst – speeds up a reaction by lowering the activation energy by providing an alternate mechanism
(pathway) for the reaction to occur
A catalyst lowers the Ea in both directions, is not consumed in a rxn, and does not shift the equilibrium.
Reaction Coordinate Diagrams

Enzyme Kinetics
Michaelis-Menton Kinetics
Higher Km, lower affinity for substrate
Substrate Specificity

V 

Vmax [ S ]
K m  [S ]

Competitive Inhibition
-Inhibitor binds to the active site
-Changes Km but not Vmax

Non-competitive Inhibition
-Inhibitor binds somewhere other than the active site
-Changes Vmax not Km

Cooperativity
Sigmoidal curve
Hemoglobin vs. myoglobin
Bohr Effect - H+ and CO2 decrease the affinity of
hemoglobin for O2

Enzyme Regulation
1) Allosteric Regulation (ex. feedback inhibition)
2) Phosphorylation (covalent modification)
-Ser, Thr, and Tyr residues can be phosphorylated by kinases (use ATP hydrolysis) or phophorylases
-Phosphatases dephosphorylate enzymes
-Phosphorylation can either activate or inhibit an enzyme depending upon the enzyme
3) Zymogens – inactive precursors that become active upon proteolytic cleavage
4) Cofactors – involvement of metal ions or organic molecules (coenzymes)
5) Association with other peptides

Biology Lesson 2 – Cellular Metabolism
Metabolism
Catabolism vs. Anabolism
Oxidation/Reduction
Catabolism of Glucose (oxidation of glucose):
C6H12O6 + 6O2 → 6CO2 + 6H2O
Anaerobic Catabolism of Glucose
1) Glycolysis (cytosol) – substrate-level phosphorylation
2) Fermentation (production of ethanol) or production of lactate
Aerobic Catabolism of Glucose
1) Glycolysis (cytosol) – substrate-level phosphorylation
2) PDC (Mitochondrial Matrix)
3) Kreb’s Cycle (Mitochondrial Matrix)
4) Electron Transport Chain (Mitochondrial Inner Membrane) – oxidative phosphorylation
Mitochondrial Structure
Outer membrane, intermembrane space, inner membrane, matrix
Regulation of Glycolysis

ENZYME

ACTIVATED BY

Hexokinase

PFK-1
Pyruvate Kinase

AMP
Fructose-6-P
Fructose-2,6-BP (liver)
Insulin
AMP
Fructose-1,6-BP

INHIBITED BY
Glucose-6-P (minor)
ATP
Fructose-1,6-BP
Citrate
Glucagon
ATP
Acetyl CoA
Phosphorylation
Alanine

Gluconeogenesis – Production of glucose; the reverse of glycolysis (uses a few different enzymes)
-occurs mainly in the liver (but also the kidneys)
Glycogen Metabolism – glucose polymer for glucose storage in the liver and muscles
-insulin activates glycogen synthesis
-glucagon and epinephrine promote degradation
Cori cycle – lactate transported to the liver for conversion back to glucose

5 ATP 1FADH2 = 1.Glucose Catabolism FAD FADH2 2ATP 2ADP 3NAD+ 3NADH (1 for each pyruvate) 2CO2 2 Acetyl-CoA 2 Pyruvate (2C) (3C) 2NAD+ 2NADH Glycolysis (cytosol) 4ADP 4ATP 2NAD+ 2NADH Anaerobic Conditions Glucose (6C) Lactate (3C) (per Acetyl-CoA) GDP GTP ADP ATP Ethanol + CO2 intermembrane space high [H+] Electron Transport Chain Yield Per Glucose 25ATP 3ATP 32ATP Total* 1NADH = 2.5 ATP 2CO2 (1 for each pyruvate) N DH ADH A + N NA D D+ A N 2ATP 2GTP 10NADH 2FADH2 TCA Cycle (Kreb's Cycle) e- H+ H+ ATP Synthase e- e+ NADH NAD+ FADH2 FAD 1/2O2+2H H2O ADP ATP mitochondrial matrix low [H+] .

Glucose ATP ADP Hexokinase Glucose-6-Phosphate (G-6-P) Glucosephosphate Isomerase Fructose-6-Phosphate (F-6-P) ATP ADP Fructose-1.3-Bisphosphoglycerate (BPG) ADP ATP ADP ATP Phosphoglycerate Kinase 3-Phosphoglycerate (3-PG) 3-Phosphoglycerate (3-PG) Phosphoglycerate Mutase 2-Phosphoglycerate (2-PG) 2-Phosphoglycerate (2-PG) Enolase H2O Phosphoenolpyruvate (PEP) Phosphoenolpyruvate (PEP) ADP ATP Pyruvate H2O Pyruvate Kinase Major Regulatory Step ADP ATP Pyruvate .3-Bisphosphoglycerate (BPG) 1.6-Bisphosphate (FBP) Aldolase Dihydroxyacetonephosphate (DHAP) Triosephosphate Isomerase Glyceraldehyde-3-P (G-3-P) Glyceraldehyde-3-P (G-3-P) NAD +NADH Glyceraldehyde-3-Phosphate Dehydrogenase NAD + NADH 1.

TCA Cycle (Kreb’s Cycle or Citric Acid Cycle) Regulation of the TCA Cycle ENZYME ACTIVATED BY INHIBITED BY Citrate Synthase ADP Acetyl-CoA Isocitrate Dehydrogenase ADP Ca2+ ADP Ca2+ Citrate Succinyl-CoA ATP and NADH (lesser extent) ATP and NADH (minor) -Ketoglutarate Dehyrogenase Pyruvate Carboxylase Succinyl-CoA NaDH ATP (minor) Acetyl-CoA Overall Regulation of Glucose Metabolism Low ATP/ADP and NADH/NAD+ Ratios – Catabolism activated and Biosynthesis inhibited High ATP/ADP and NADH/NAD+ Ratios – Biosynthesis activated and Catabolism inhibited .

Electron Transport Chain 1NADH = 2.5 ATP Chemiosmosis – The electron transport chain establishes a proton gradient (establishing an electrochemical potential) which ‘powers’ ATP synthase. .5 ATP 1FADH2 = 1.

Reassembled into triacylglycerides and transported via chylomicrons to adipose tissue for storage. or stress -Glycerol transported to liver for glycolysis or gluconeogenesis -Fatty acids transported through the bloodstream to tissues in need (heart and muscles primary) -oxidation -Unsaturated fatty acids produce 1 less FADH2 for each double bond . From Adipose Tissue to Energy Production Triacylglycerides converted to fatty acids and glycerol by hormone-sensitive lipases -Activated by glucagon and epinephrine in response to fasting. exercise.Lipid Metabolism Dietary Intake to Storage Triacylglycerides converted to fatty acids and monoacylglycerides for absorption out of the small intestine.

5 ATP) FADH2 8 9 17 (= 25.5 ATP) ATP -2 9 7 TOTAL: 120 ATP .Catabolism of Stearic Acid (18C) O O ATP 2Pi AMP + PPi (Equivalent to 2ATP consumed) O SCoA 8 NAD+ 8 FAD 8 Rounds of -oxidation 8 NADH 8 FADH2 9 Acetyl CoA 9 GDP 27 NAD+ 9 FAD CAC Cycle 27 NADH 9 FADH2 9 GTP (equal to 9ATP) 18 CO2 -oxidation CAC Cycle Total NADH 8 27 35 (= 87.

Dark reactions take place in the stroma. Chlorophylls absorb red light (600-700nm) and blue light (400-500nm). Chloroplasts Light Reactions . The proton gradient powers ATP synthase. Photophorphorylation Photosystems are part of an electron transport chain that creates a proton gradient. Antennae chlorophyll molecules pass light energy to reaction centers.Photosynthesis 6CO2 + 6H2O → C6H12O6 + 6O2 Light reactions take place in the thylakoid membrane.

Dark Reactions (Calvin Cycle) 3 CO2 + H2O Ribulose-1.5-bisphosphate (5C) 3-Phosphoglycerate (3C) 6 ATP 3 ATP 6 ADP 3 ADP 6 NADPH 6 NADP+ stay in the cycle Glyceraldehyde-3-phosphate (3C) Dihydroxyacetone phosphate (3C) Carbohydrates Glyceraldehyde-3-phosphate (3C) Glycolysis .

and uracil) Nucleoside Nucleotide O triphoshpate O - O P O- O O base NH N O P O P O- O- Pyrimidines (CUT the PY) O O NH2 O O O H H H OH H H sugar C N H NH N T U O N H O DNA double helix (right-handed helix) Antiparallel strands Complementary Held together by H-bonding Base stacking Watson-Crick base pairing G-C: 3 Hydrogen bonds A-T: 2 Hydrogen bonds Chromosome Organization Prokaryotes . nucleotide (ribose + base + 3 phosphates) Purines (guanine and adenine) and pyrimidines (cytosine. thymine.One circular chromosome (supercoiled by DNA gyrase) Eukaryotes – Many linear chromatin (called chromosomes when condensed during mitosis) Wrapped around nucleosomes (histone octamers) Have centromeres and telomeres N H NH O .Biology Lesson 3 – Molecular Biology DNA and RNA Nucleoside (ribose + base) vs.

The fragments on the lagging strand are called Okazaki fragments.Replication (Making DNA from a DNA template) 1) Helicase unwinds DNA helix and separates strands forming the replication fork at the origin. Topoisomerase ‘unravels’ DNA ahead of the replication bubble to relieve tension. 2) Single-strand binding proteins bind and stabilize the single stranded DNA. 6) DNA Polymerase (Pol I*) replaces the RNA primers with DNA Semiconservative – new DNA has one ‘parent’ strand and one ‘daughter’ strand Replication of the telomeres (by telomerase) in eukaryotes Energy provided by breaking high energy phosphate bonds during formation of phosphodiester linkages. 3) Primase lays RNA primers on the leading (only once) and lagging strand (many times). 4) DNA polymerase (III*) elongates new strands complementary to the leading strand (continuously) and the lagging strand (discontinuously) in the 5’  3’ direction (for both). 5) DNA ligase joins the Okazaki fragments together (seals the backbone). Reverse Transcriptase – polymerase in retroviruses that synthesizes DNA from an RNA template Prokaryotic DNA polymerases DNA Pol Function Exonuclease Activity DNA Pol I Replace Primers and DNA repair 3’ to 5’ and 5’ to 3’ exonuclease DNA Pol II ??? SOS ??? ??? DNA Pol III Primary pol for elongation 3’ to 5’ exonuclease Differences between Prokaryotes and Eukaryotes Prokaryotes 1 Circular chromosome Supercoiled (by DNA gyrase) 1 origin of replication Bi-directional Eukaryotes Many linear chromatin Wrapped around nucleosomes (histone octamers) Many origins of replication Bi-directional .

DNA Repair Proofreading – 3’5’ exonuclease can remove the last nucleotide if an error occurs during replication. 3) DNA ligase seals the backbone. 4) DNA Pol I fills in the gap. 1) The area around the damage is removed. Nucleotide-excision Repair – most common form of repair for damage caused by UV light. 3) An exonuclease removes several more nucleotides. 2) DNA Pol III fills in the gap. 2) An AP endonuclease removes the rest of that nucleotide. Nick Translation – 5’3’ exonuclease activity of DNA Pol I following replication Mismatch Repair – DNA is methylated prior to replication (prokaryotes). 3) DNA ligase seals the backbone. this allows for the parent strand (methylated) and daughter strand (not methylated) to be distinguished after replication and any errors during replication in the daughter strand to be repaired. 1) The area around the mismatch is removed on the daughter strand. 2) DNA Pol I fills in the gap. 5) DNA ligase seals the backbone. Base-excision Repair – 1) A damaged base is removed leaving an AP site. . Several enzymes and proteins are involved.

3) Transcription is terminated at a special sequence. It is the template (or non-coding) strand only that is being transcribed. anti-sense) vs.Protein Synthesis Prokaryotes Eukaryotes Transcription (Making RNA from a DNA template) 1) RNA Pol binds promoter region and begins unzipping DNA. Promoter region often contains a TATA box in eukaryotes. Monocistronic (eukaryotes) vs. The repressor binds to operator preventing transcription. 2) RNA Pol begins transcribing (forming complementary RNA) at the start site (5’  3’ direction). splicing out introns Lac Operon (Transcription Regulation) The Lac genes allow for the catabolism of lactose. Template Strand (Non-coding. polycistronic (prokaryotes) Prokaryotes 1 RNA polymerase Promoter is -35 sequence and Pribnow box (-10) Occurs in the cytoplasm Coupled transcription/translation No mRNA processing Eukaryotes 3 RNA polymerases (RNA pol I for rRNA – nucleolus) (RNA pol II for mRNA) (RNA pol III for tRNA) Promoter is often TATA box (-25) Occurs in the Nucleus Not coupled (Occur in separate compartments) 5’CAP. Gene – a DNA sequence encoding for a protein. Lactose binds the repressor removing it from the operator. poly A tail. Promoter region contains a -35 sequence and Pribnow box in prokaryotes. . Coding Strand (Sense) Transcription is the principle site of gene regulation.

tRNA. Eukaryotic RNA polymerases RNA pol I rRNA RNA pol II mRNA RNA pol III tRNA rRNA. 5) Ribosome catalyzes peptide bond formation. other sequences in eukaryotes 2) Met-tRNA (fMet in prokaryotes) binds to the start codon (AUG) via its anticodon – will be the P site.Translation (Making a peptide from mRNA) 1) Initiation – Small ribosomal subunit binds to mRNA near the 5’ end (along with many initiation factors). Ribosomes – 70S (50S&30S) in prokaryotes and 80S (60S&40S) in eukaryotes) Post-translational modifications may be made at the ER or Golgi body. 4) Elongation . Genetic Code: Degenerate Begins at Replication Origin of Replication Transcription Start Site (upstream promoter region) Elongation Enzyme Where occurs (prokaryotes) Where occurs (eukaryotes) DNA Polymerase Cytoplasm Nucleus RNA Polymerase Cytoplasm Nucleus Genetic Code Start Codon AUG Stop Codons UGA – U Go Away UAA – U Are Away UAG – U Are Gone Translation Start Codon(AUG) (upstream ShineDalgarno seq (prok) acts as ribosome binding site) Ribosome Cytoplasm Cytoplasm . peptidyl site (P site) and exit site (E site) 3) Large ribosomal subunit binds.2nd charged tRNA binds at the A site (requires GTP hydrolysis). Aminoacyl site (A site). and mRNA Charging tRNA requires ATP hydrolysis. 7) Termination – release factor binds when stop codon appears in the A site. Shine-Dalgarno sequence at -10 in prokaryotes. 6) Translocation (APE) – requires GTP hydrolysis.

Hybridization – DNA microarrays can be used to detect the presence and amount of specific DNA or RNA sequences 1) PCR (DNA with Taq polymerase. Plasmids – small circular dsDNA that has an origin of replication. . The plasmid is used to ‘transform’ bacteria (bacteria take up the plasmid). and often antibiotic resistance and a promoter. Eco RI cuts at the palindromic sequence 5' GAATTC 3' Gene Cloning – Transferring a gene from one cell to another to impart the gene’s function. A gene is inserted into a plasmid using restriction enzymes and DNA ligase. Restriction Enzymes – endonucleases that cut dsDNA at a specific sequence leaving either sticky ends or blunt ends. RNA with Reverse Transriptase) 2) DNA is denatured and single strands are allowed to anneal (when complementary) to single stranded ‘probe’ DNA on an array 3) A marker (often a fluorophore) allows for the detection and quantification of hybridized sequences.Molecular Biology Techniques PCR (Polymerase Chain Reaction) – DNA amplification 1) Denaturation – DNA strands are separated with heating (>90C) 2) Annealing – The sample is cooled (~55C) to allow primers specific to the target sequence to anneal to the template strands of the target sequence. 3) Elongation – Taq polymerase replicates the templates (~70C) 4) ‘Thermal cycling” is repeated many times. many restriction sites. Can also be used in eukaryotes as well (needs eukaryotic promoter and poly A signal).

phenotype Law of segregation – separation of alleles in the haploid gametes Law of independent assortment – genes assort independently to the progeny Homozygous vs. yellow is dominant to green and round is dominant to wrinkled. What are the phenotypic ratios in the F1 generation? 3) How would you figure out if a yellow pea plant had the homozygous or heterozygous genotype? . one received from each parent Genotype vs. recessive Complete Dominance –when a heterozygote has the phenotype of only 1 of the alleles (the dominant one) Incomplete dominance – phenotypes of the progeny are blends of the parental phenotypes (ex. heterozygous “Pure breeding” or “True-breeding” strain Dominant vs. The F1 generation is then self-crossed.Biology Lesson 4 – Genetics and Evolution Genetics Gene – genetic material coding for a single gene product (peptide. blood types – ABO) 1) Homozygous yellow peas (dominant) are crossed with homozygous green peas (recessive). What will be the phenotypic ratios in the F2 generation? 2) For peas. rRNA or tRNA) Locus – the chromosomal location of a gene Allele – one variant of a gene Homologous chromosomes – chromosomes that code for the same set of genes (but may have different alleles). round pea plants are crossed (YyRr). snap dragons – homozygous red crossed with homozygous white gives pink progeny) Codominance – both inherited alleles are completely expressed (ex. Two heterozygous yellow.

sex chromosomes (X and Y) Sex-linked Genes Y-linked traits – rare as there are very few genes on the Y-chromosome All Y-linked disorders are passed on to all male offspring (but to no female offspring) X-linked traits – males only receive a single copy of the X-chromosome from their mother Mitochondrial inheritance from the mother – any genetic disorders coded by the mitochondrial DNA will be passed on to all offspring Turner Syndrome (X) – offspring (female) have only a single X chromosome resulting from nondisjunction Kleinfelter Syndrome (XXY) – offspring (male) have an extra X chromosome resulting from nondisjunction 3) Color-blindness is the result of an X-linked recessive allele.Pleiotropism – when a gene has multiple phenotypes associated with its expression Polygenism – when multiple genes affect a trait Penetrance – probability an organism with a specific genotype will express a particular phenotype Expressivity – term describing the variation of phenotype for a specific genotype Epistasis – occurs when the expression of a gene is dependent upon another gene Autosomes vs. insertion. deletion) – change of a single nucleotide Missense mutation –point mutation leading to a codon coding for a different amino acid Nonsense mutation – point mutation leading to a stop codon Frame-shift mutations – insertion or deletion leading to a change in the reading frame of a gene Mutations in replication – low level of ‘natural’ mutations that occur during replication Mutagens and carcinogens – agents causing mutation (carcinogens when they cause cancer) . What is the probability that a colorblind father and a normal mother (homozygous) have a colorblind child (son or daughter)? 4) What is the probability that a heterozygous mother (a carrier) and a normal father have a colorblind daughter? A color blind son? Mutations Most mutations are deleterious to the cell. Point mutation (substitution.

Interphase G1 S Prophase I Metaphase I Anaphase I Telophase I Prophase II Metaphase II Anaphase II Telophase II Protein and nucleic acid synthesis to prepare for replication. production of organelles DNA Replication Longest phase Chromosomes condense and tetrad formation (homologous pairs) Recombination Disappearance of the nuclear envelope and polarization of the centrioles (MTOCs) Chromosomes line up on metaphase plate Spindle fibers attach at centromeres via kinetochores Spindle fibers pull homologous chromosomes apart towards the centrioles Cleavage furrow begins forming Nuclear membranes reform Completion of cytokinesis Chromosomes condense Disappearance of the nuclear envelope and polarization of the centrioles (MTOCs) Chromosomes line up on metaphase plate Spindle fibers attach at centromeres via kinetochores Spindle fibers pull sister chromatids apart towards the centrioles Cleavage furrow begins forming Nuclear membranes reform Completion of cytokinesis .

Down syndrome – chromosome 21  14) Recombination (single and double crossovers) Linked genes – genes on the same chromosome that probably will not undergo independent assortment -the closer together on the chromosome the greater the linkage between genes -the likelihood of recombination increases with distance between genes 5) Lets say that the color and size gene for an organism lie on the same chromosome: B = blue. Kleinfelter Syndrome (XXY) – an extra X chromosome) Translocation – movement of a segment of one chromosome to another non-homologous chromosome (ex. Turner Syndrome (X) – only a single X chromosome) (ex. l = small Two organisms that are heterozygous for bothcolor and size with the dominant alleles paired on one chromosome and the recessive alleles paired on the other are crossed and the offspring are as follows: Phenotype Number Blue and Large 70 Blue and Small 3 Green and Large 4 Green and Small 23 Which are the recombinant phenotypes? . b = green. L = large.Nondisjunction – failure of tetrads to separate during meiosis I or sister chromatids in meiosis II (ex. Down syndrome—trisomy 21) (ex.

increased likelihood of mating between organisms with different genotypes Genetic Drift – random change in allele frequencies in a population -smaller populations are more susceptible to genetic drift Bottleneck – dramatic decrease in size of a population making it susceptible to genetic drift Ontogeny and Phylogeny – Similarities in stages of development (ontogeny) can be used to determine evolutionary relationships between organisms. No mutations 3. but doesn’t harm or benefit the host in the process 3) Mutualism – symbiotic relationship between two organisms that confers fitness on both . harming the host in the process 2) Commensalism – an organism requires another species as a host to live. Convergent Evolution – two species possess the same analogous structures unrelated to a common ancestor Divergent Evolution – divergent leading to distinct populations/species Parallel Evolution – similar evolutionary changes in different species due to similar environmental pressures Symbiosis 1) Parasitism – when a species requires another species as a host to live. Random mating 2. No selection (natural or otherwise) 4 No migration 5. Large population size (No genetic drift) Evolution Fitness – the ability of an organism to pass on its alleles Natural Selection – differential reproduction of an organism based upon fitness in its environment 1) Stabilizing Selection – Selection against the extremes (for the averages) 2) Directional Selection – Selection against one extreme (but favoring the opposite extreme) 3) Disruptive (Divergent) Selection – Selection against the averages (for the extremes) 4) Artificial Selection – directional selection done by humans with selecting for traits in animals and crops 5) Sexual Selection – Differential mating between males and females Species – organisms that are capable of reproduction of ‘fit’ offspring Speciation Polymorphism – when multiple phenotypes exist within a population Adaptation – an inherited trait that confers greater fitness Specialization – an adaptation to a specific function or environment Inbreeding –increased likelihood of mating between organisms with similar genotypes (limits genetic variation) Outbreeding .Population Genetics Hardy-Weinberg Equilibrium – allele frequencies remain constant in a gene pool for a population in equilbrium p+q=1 p = frequency of dominant allele q = frequency of recessive allele p2 + 2pq + q2 = 1 p2 = frequency of homozygous dominant genotype 2pq = frequency of heterozygous genotype q2 = frequency of homozygous recessive genotype Assumptions for equilibrium 1.

But it is still required material and I’ll let you find another resource for this section. .Origin of Life – Prebiotic Soup?—I decided not to present the current scientific beliefs regarding this topic as I simply don’t have a lot of faith in them. My apologies.

nucleic acid encased in a protein capsid (enveloped or nonenveloped) -Genome can be linear or circular and can be either dsDNA. Lysogenic Cycle 1) Adsorption – Bind cell surface via tail (host cell specific interactions) 2) Penetration – puncture cell wall and membrane and inject genome into the host cell 3) Integration of the phage genome into the host genome 4) Dormancy – viral genes not expressed by viral genome is transmitted to all progeny during cell division 5) Activation – excision of viral DNA and entrance into the lytic cycle Animal cell viruses have similar cycles to the lytic and lysogenic. Host cells contain restriction enzymes that will degrade viral DNA. -Viruses infect every type of living organism (plant. dsRNA. -Relatively small genomes that can often be read in different reading frames. Viruses of eukaryotes often have a lipid bilayer envelope and enter the host cell via endocytosis and exit by budding out of the host cell. -Typically uses host’s replication. Bacteria methylate their own DNA to distinguish it from foreign DNA. bacteria. and translation machinery. or ssRNA. . transcription. 4) Replication of the viral genome (many copies) and synthesis of much capsid protein 5) Assembly of new virus particles 6) Production of lysozyme to degrade the cell wall resulting in cell lysis and release of virus particles. animal. -Structure .Biology Lesson 5 . parasitic. ssDNA.Microbiology Viruses Non-living. archaebacteria). -Much smaller than prokaryotic or eukaryotic cells Bacteriophage Life Cycles Lytic Cycle 1) Adsorption – Bind cell surface via tail (host cell specific interactions) 2) Penetration – puncture cell wall and membrane and inject genome into the host cell 3) Hydrolase (a viral gene product) is produced and degrades the host’s genome. Transduction – transfer of genetic material via a virus in the lysogenic cycle. infectious agent that can only replicate within a host cell.

must encode an RNA-dependent DNA polymerase (reverse transcriptase) . Must code for an RNA-dependent RNA polymerase and include this polymerase in its capsid to be infectious tio sla n a tr [-] RNA n viral proteins RNA-dep RNA-dep RNA Pol [+] RNA RNA Pol [-] RNA (assembled (can serve into capsids as mRNA) for new viruses) Retroviruses – [+] RNA viruses that convert their genomes into dsDNA for incorporation into the host’s genome.Virus Types (by genome) [+] RNA viruses – viral genome is ssRNA which can also serve directly as mRNA -must code for an RNA-dependent RNA polymerase for viral replication [-] RNA viruses – viral genome is ssRNA which is anti-sense (-) and therefore complementary to the mRNA coding for the viral genes.

membrane bound organelles or mitotic apparatus.Prokaryotes plasmid ribosomes plasma membrane cell wall supercoiled circular chromosome flagellum cilia -Single circular dsDNA genome and possibly the presence of a plasmid(s). -No nucleus. -Coupled transcription and translation. cell wall and outer lipopolysaccharide layer (contains endotoxins) Flagellar Propulsion – bacterial flagellum used by motile bacteria for locomotion Chemotaxis.movement is directed toward chemoattractants or away from chemorepellents (sensed by chemoreceptors) -powered by ATP hydrolysis . Archaebacteria Classifications of Bacteria cocci (spherical) bacilli (rod-shaped) spirilla (spiral-shaped) Gram Positive Bacteria – stain dark purple during gram staining -have cell membrane and cell wall (peptidoglycan) Gram Negative Bacteria – stain pink during gram staining -have cell membrane. Eubacteria vs.

DNA replication.Fission Reproduction simply through growth. Doubling times vary but can be as short as 20 minutes under ideal conditions. and cell division. -have a thick peptidoglycan coat and can survive through extreme conditions Aerobes – can survive in an oxygen environment Anaerobes – do not require oxygen to survive Facultative Anaerobes – Can carry out out metabolic processes with or without oxygen Conjugation -way to share genetic information adding to diversity -common way of conferring antibiotic resistance genes . Endospores – dormant form produced by some bacteria under harsh conditions.

2) Spore Formation – procuded by mitosis.Fungi Eukaryotes including yeast (unicellular) and a variety of multicellular forms. Sexual Reproduction . spores will germinate under favorable condition to become active. Have a cell wall made of chitin. Asexual Reproduction 1) Budding – A fungal cell simply grows out of an existing fungal cell until distinct.

Biology Lesson 6 – Eukaryotic Cells Mitochondrial Structure -PDC and Kreb’s Cycle occur in the matrix -ETC Complexes are located in the inner membrane -Proton’s are pumped (actively) from the matrix to the intermembrane space -ATP synthase is located in the inner membrane and synthesizes ATP on the matrix side .

and various toxins Carry out the glyoxalate cycle in germinating plant seeds Source of the spindle apparatus used for cell division (acts as a microtubule organizing center a. chloroplasts and a central vacuole (not present in animal cells). amino acids. pumping excess water out of a cell. Cell Walls Bacteria Made of peptidoglycans Archaebacteria Polysaccharides (not peptidoglycans though) Fungi Made of chitin Plant cells Made of cellulose Animal cells None .k. and cell rigidity (in plants) Site of photosynthesis in plant cells Animal cells have lysosomes and centrioles (not present in plant cells).Organelle Nucleus Ribosomes Rough ER Smooth ER Golgi Apparatus Mitochondria Lysosomes Peroxisomes Centrioles Vacuoles Chloroplasts Function DNA storage and site of transcription Surrounded by a nuclear envelope (2 lipid bilayers) through which nuclear pores regulate traffic of large molecules Contains the nucleolus (dark spot which is the site of rRNA synthesis) Translation of mRNA into proteins (present in both pro. Plant cells have cell walls.a. MTOC) Not present in plant cells Fluid-filled membrane-bound vesicles used for transport. storage of nutrients and other substances.and eukaryotes) ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to form glycoproteins destined for secretion or integration into the membrane Synthesis of lipids (membrane) and hormones often for export from the cell Breakdown of toxins in liver cells Modification (glycosylation) and ‘packaging’ of proteins into vesicles for secretion or transport to cellular destinations (like lysosomes) Site of ATP synthesis via ATP Synthase as a result of oxidative phosphorylation (PDC. fatty acids. Kreb’s cycle and the Electron Transport Chain) Site of fatty acid catabolism (-oxidation) Have their own DNA (circular) and ribosomes for self-replication Contains acid hydrolases (digestive enzymes) and have pH~5 Degradation of old organelles or phagocytosed materials Produced from the Golgi Apparatus Not present in plant cells Involved in the breakdown (involving hydrogen peroxide) of many substances including.

translation stalls.Protein Trafficking SRP binds signal peptide. lysosomes. ER) . and the ribosome is transported to the ER ribosome mRNA signal recognition particle (SRP) nascent peptide signal peptide Rough ER N-terminus Translation resumes and signal peptide is cleaved SRP directs ribosome with nascent peptide to the ER membrane ER lumen signal peptide cleaved Golgi Apparatus cis trans plasma membrane (integral membrane or secreted) organelles (ex.

Plasma Membrane Fluid Mosaic Model – Components free to move in 2D throughout the membrane Composed of phoshpolipids. CO2. intestinal cells) Desmosomes – ‘spot welds’ between cells that adhere them to one another and give mechanical strength -anchored to the cytoskeletons of each cell (ex. barrier to infection. lipids (including certain hormones). porins Cell Receptors . carrier proteins. skin cells) Plasmodesmata – narrow channels allowing the exchange of nutrients in plant cells Glycocalyx – carbohydrate coating on the cell wall of some bacteria and the plasma membrane of some animal cells.recognition glycoproteins on the cell surface that interact with hormones or other molecules and relay signals into the cell Adhesion proteins Gap Junctions – allow exchange of nutrients and cell-to-cell communication (ex. O2. cardiac muscle cells) Tight Junctions – completely encircles cells and seals the space between them to prevent leakage -(ex. or cell-cell recognition . glycolipids and cholesterol Cholesterol adds rigidity to the membrane Unsaturated fatty acids increase membrane fluidity Hydrophobic molecules and small polar molecules (uncharged) can cross the membrane (ex. functions in adhesion. some drugs) polysaccharides transmembrane protein integral membrane protein peripheral membrane protein Membrane Proteins Peripheral membrane proteins – adhere to membrane surface via electrostatic interactions Integral membrane proteins – anchored to and embedded in the membrane Transmembrane proteins – Spans the membrane and includes channel proteins.

isotonic Exocytosis vs. some drugs) 2) Facilitated Diffusion – diffusion of ions/polar solutes via a carrier protein (channel protein) (ex. glucose) Active Transport . and cytokinesis .works against the concentration gradient and requires energy (ATP hydrolysis) 1) Primary (ex.Membrane Transport Passive Transport 1)Simple Diffusion (ex. Na/K pump—3Na+ pumped out and 2K+ pumped into cell fueled by ATP hydrolysis) 2) Secondary – uses one solutes gradient (established by ATP hydrolysis) to accomplish the transport of another (Na+/glucose cotransport) Cell Signaling and Second Messengers (G-Proteins) 1) Ligand binds G-protein receptor 2) G-protein receptor activates G-protein which binds GTP (exchanges GTP for GDP) 3) G-protein activates Adenylate Cyclase (ATP  cAMP) 4) cAMP acts as a ‘2nd messenger’ activating a series of proteins and transcription factors Osmosis and plasmolysis vs. hypotonic. cytolysis Hypertonic. lipids. O2. endocytosis Phagocytosis and pinocytosis Receptor-mediated endocytosis Cytoskeleton Microtubules – made from tubulin in a 9+2 arrangement -functions as a ‘railroad’ for intracellular transport -found in the spindle apparatus of mitosis (MTOCs/centrioles) and in flagella and cilia Intermediate filaments – support and maintain the shape of the cell Microfilaments – made from actin and involved in cellular motility. CO2. muscle contraction.

Mitosis prophase met an aphas e ap ha se Cell Cycle Mi tos is G2 e as h p lo te G1 S Interphase Summary of Mitosis Interphase G1 Protein and nucleic acid synthesis to prepare for replication. production of organelles S DNA Replication G2 Continued growth in preparation for mitosis Prophase Chromosomes condense Nuclear envelope disappears Polarization of the centrioles (MTOCs) Metaphase Chromosomes line up on metaphase plate Spindle fibers attach at centromeres Anaphase Spindle fibers pull sister chromatids apart towards the centrioles Cleavage furrow begins forming Telophase Nuclear membranes reform Completion of cytokinesis * * * prophase * metaphase anaphase telophase and cytokinesis .

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