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Example research essay topic: Amino Acids Calvin Cycle - 2,100 words

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... E PHOTO REVIEW HANDOUT W/ EXPLANATION BELOW 6. Non-Cyclic electron Photo phosphorylation (Figure 13 - 34 = Z Scheme with electron volt ratings) (1) Mn -center - Water Oxidizing Enzyme (3) Plastoquinone e- carrier aromatic ring w/ long chair hydrocarbon not attached to PS II (4) Cytochrome b 6 - e- carrier Heme (Fe) containing protein Fe 2 + Fe 3 + (b) Sets up H+ gradient between Stroma and Thylakoid lumen (c) H+ pumped from stroma into lumen (d) Flow out through CF 0 CF 1 ATPase imbedded in thylakoid lumen. (7) PC = e- carrier - plastocyanin (a) Cu containing protein: Cu+ Cu 2 + (9) Ferrodoxin - Fe/S center mobile - not attached to PS I (10) NADP+ Reductase use electrons to reduce NADP+ to NADPH. a. electrons pass from Ferrodoxin to cytochrome b 6 c. may be used to produce the additional ATP needed to drive glucose production (~ 3: 2 ATP: NADPH).

E. LIGHT-INDEPENDENT REACTIONS (Calvin Cycle) 2. Use ATP and NADPH to reduce CO 2 to Glucose a. Reducing enzyme = Ribulose bisphosphate carboxylase (rubisco) e. Each turn of the cycle...

REFER TO HANDOUT. (1) 18 ATP 7. 3 kcal / mole x 18 = 131. 4 kcal (2) 12 NADPH 53 kcal / mole x 12 = 636 kcal (a) Note 53 kcal / mole - ref: Campbell pg. 178 for NADH to O 2 H 2 O (3) Takes 767. 4 kcal to make 1 molecule of glucose (686 kcal) F. PHOTORESPIRATION (Use Study Sheet) c. Produces a 2 -C compound (instead of 3 -C) d. This compound is sent to peroxisome and mitochondrion 4. Some plants waste as much as 50 % of the energy they make on this process 5.

For plants under ideal conditions photo respiration poses no problems 6. Some plants have evolved structures to reduce photo respiration. 1. Use spatial (C 4) isolation of Rubisco to prevent Photo respiration 2. Fix Carbon into 4 -Carbon organic Acids a. Rubisco sequestered away from O 2 in specialized cells BUNDLE SHEATH CELLS b. Capture CO 2 using shuttle molecules c.

C 4 use PEP (phospho enol pyruvate) and Pep (PEP carboxylase) to capture CO 2 and funnel it into Calvin Cycle. (1) C 4 comes from intermediates (oxaloacetate and malate) which are 4 -C molecules (2) Other plants called CAM plants. VIII. Oxidative Respiration - Overview A. Review cell organization and where reactions are taking place B. Emphasize role of ATP made in Photosynthesis A. Interested only in the big picture (see Figure 4 - 3, pg. 111) 2.

Cleavage of Glc into 2 3 -carbon sugars 1. If they want to learn the steps, thats fine. 2. Only be responsible for names in Figure. c.

Glyceraldehyde 3 -Phosphate (PGAL) 1. No involvement of molecular Oxygen 2. Direct dependence on the availability of NAD+ a. Use this as a lead into Fermentation.

X. Fermentation - Regeneration of NAD+ in the absence of Oxygen A. Discuss what is needed to keep Glycolysis going 1. ADP - no problem since cell is using ATP rapidly 3. NAD+ - must find a way to oxidize NADH to get to ATP generating step. B.

Review 2 Fermentation pathways with study sheet. XI. Mitochondrial Events - Oxidation of Pyruvate to CO 2 A. Review structure of Mitochondrion B. Transition Reactions - Review with Study Sheet 1. Enzyme - Pyruvate Dehydrogenase Complex 1.

Good overview - Figure 4 - 11 pg. 120 a. Students responsible for names and events. D. Chemiosmotic Phosphorylation - Chap. 13 - p. 410 - 429 1. Conversion of stored energy (NADH & FADH 2) into ATP 2. Stored Energy used to generate an a H+ gradient d.

Figure 13 - 21 - Shows Redox potentials a. Doesnt take into account ATP used for transport out of the Mitochondria d. See Problem 13 - 5 pg. 420 Yields are 2. 5 and 1. 5 (for NADH and FADH 2 and NADHcytosol. B. See Figure 4 - 18 p. 127 in text for similar but more detailed treatment. XIII.

DNA as the GENETIC MATERIAL A History Lesson (ref: Bio 120 Outline) XIV. Characteristics of the Genetic Material and the Central Dogma (ref: Bio 120 Outline) a. E. coli = 4. 3 x 106 nucleotide pairs / genome b. Humans = 2 x 108 nucleotide pairs / chromosome (3 x 109 genome) F. Packaging the Eukaryotic Chromosome (p. 250 - 255) a.

utilizes proteins called HISTONES b. amount of DNA amount of histones (1) high proportion of positively charged amino acids (a) allows for tight binding to negatively charged DNA (1) very similar from species to species (a) ex. some cow and pea histones differ by 2 aa) f. DNA + Histone core form NUCLEOSOMES (Figure 8 - 9) (3) Histone core = 8 "nucleosome" histone molecules (a) nucleosome histones = H 2 A, H 2 B, H 3, H 4 2. Level 2 - 30 nm fiber = SOLENOID (Figure 8 - 10) a. appear to be mediated by 5 th histone = histone H 1 a.

hetero = chromosomes in condensed state during interphase b. eu = chromosomes in less condensed state c. only euchromatin is actively transcribed d. may be a coarse form of gene control (a) one of two X chromosomes is always in most condensed form (during interphase) (b) Only genes on other chromosome are expressed (c) females are a mosaic since different X-chromosomes can be condensed in different cells... 1. Watson-Crick model implied Semi-Conservative a.

Use 15 N labeled DNA (14 N = normal) 1. Must take into account double helical structure 2. Step 1 - separate strands to access information 3. Step 2 - Make copies using old as model 4. Step 3 - Reform old and new as double helix. 1. unwind helix at specific starting point (s) 2.

stabilize unwound helix so it doesnt re anneal a. SINGLE STRAND BINDING PROTEINS (SSB) 3. Need enzyme that can make new DNA polymer. 4. DNA POLYMERASE (Figure 6 - 21 & 22) b. Sliding clamp protein moderates attachment of DNA pol to template.

c. uses 5 '-nucleotide triphosphate's (ATP, GTP, CTP, TTP) (1) provide energy for bond formation (2) DNA pol can only synthesis unidirectional (eg. 5 ' to 3 ') (3) Synthesis occurs continuously on 3 ' to 5 's than = leading strand (4) Synthesis occurs discontinuously on 5 ' to 3 's than = lagging strand (2) Private enzyme lays down RNA primer f. Replicating the ends of lagging strands (p. 249 - 250) (1) requires special enzyme to add tails onto template strand (2) Enzyme that duplicates them TELOMERASE (Figure 8 - 6) (c) Creates tandem repeats on ends of lagging strand (GGGGTTA) (d) allows the end of the chromosome to be replicated (3) leaves a 3 ' tail on template strand. (1) 3 ' to 5 ' exonuclease activity acts as proofreader (2) senses mismatch, backs up, removes mismatch, and corrects B. Mismatch Repair system catches errors Replication Machinery misses 1.

Rpn machinery error rate 1 in 10 7 nucleotides copies 2. Roughly 10 mistakes / chromosome /rpn cycle 3. Mismatch = mis paired nucleotide (Figure 6 - 25 A p. 201) 4. Mismatch repair enzymes recognize the mismatches c. Must be able to recognize the newly synthesized strand (1) Nick system - new strands have transient nicks (2) Methylation system - Parent is methylated 5. Reduces error rate to 1 in 10 9. 1.

Types of Damage (Figure 6 - 27 p. 202) a. Depurination - spontaneous loss of A or G b. Destination - loss of amine group on Cytosine c. Thymine Dimer formation due to UV light exposure d. Many other types caused by reactive metabolic by-products a. Single base pair changes (destination) (Figure 6 - 29 A) b.

Single-base pair deletions (deprivation) (Figure 6 - 29 B) c. Stalled or incomplete rpn (thymine dimers). D. DNA Repair Mechanism (Figure 6 - 30 p 204) a. Requires specialized nuclease's for each type of damage a. Uses DNA pol other than rpn DNA pol XVIII.

TRANSCRIPTION - ACCESSING THE CODE A. Central Dogma - From DNA to Protein Figure 7 - 1 B. Discuss this as the first step in Gene Expression PROCESSES INVOLVED IN GENE EXPRESSION Using Genetic Information to make the molecules necessary for cellular functions. Ultimately, every process within a living organism is controlled by the availability of specific gene products 1.

Region of DNA contains some information that needs to be accessed. a. Structure - Use Figure 7 - 3 to compare and contrast with DNA (1) gene is always read 5 ' to 3 ' regardless of which strand its on (2) template is always 3 ' to 5 ' regardless of which strand its on (3) Genes on different strands: Fig 7 - 10 b. More on this when we cover gene regulation. 1. Transcription factors & RNA Pol bind at promoter region a. More details when we cover gene regulation 2.

copies in 3 ' to 5 ' direction producing 5 ' to 1. Probably requires termination factors 2. Specific DNA sequence signals termination a. in eukaryotes - most common = AATAAA.

J. Compare Eukaryotic and Prokaryotic Transcripts K. The Eukaryotic mRNA - use Study Sheet (2) fixes length of UTR and site for 3 'tail attachment (2) mRNA w / o poly A degraded quickly. b.

mediated by a group of sn RNAs and proteins d. Several sn RNP's take part in each splicing event e. A complex of functioning sn RNP; 's is sometimes referred to as a Spliceosome (1) cis = connecting exons in same mRNA (2) trans = connection exons from different mRNAs g. Same mRNA can be spliced into different genes = ALTERNATIVE SPLICING 1. Includes promoter and termination regions a. minimum number to cover all AA = 64 c.

Advantage - can absorb some amount of mutation a. rRNA - serves to align ribosome with message and new evidence shows carries out the enzymatic reaction needed for peptide bond formation (ref: Science, 11 Aug 00, p. 878). b. Protein - Structural (Figure 7 - 26) (1) small - recognition and alignment ii) involved in binding t RNAs to Codon (mRNA) (2) large - binding tRNA and making peptide bond (a) peptidyl-transferase activity (rRNA) (b) GTP hydrolysis activity (proofreading) ii) binds majority of tRNA with AA attached (2) attach AA to correct tRNA in 2 step process (4) only process that ensures the correct codon / a . a. pairing. (5) Active site of enzyme screens Amino Acids based on size. (a) Coarse sieve removes AA too large for active site. (b) Fine sieve removes those small enough to fit but not correct d.

Joins 3 '-OH of tRNA to carboxyl group of Amino Acid. 1. Start - connect message with ribosome C. INITIATION - refer to Figure 7 - 28 1. Binding of small ribosomal subunit + initiator tRNA (tRNA met) + initiation factors (not shown in a. Initiator tRNA is only tRNA that can bind to small subunit alone 3. Complex scans mRNA 5 ' to 3 ' for start codon a.

When found, some IFs dissociate to allow for subsequent steps. 4. Large Ribosomal submit binds Translation begins 2. EF-tRNA NEXT-GTP binds at A site Use overhead in binder d. permits incorrect tRNA to diffuse out of ribosome 3.

Peptide Bond Formation - use overhead in binder a. Catalyzed by peptidyl transferase b. Aminoacyl (3 '-OH -- carboxyl) bond between rna-AAP (1) transfers chain from rna to rna 4. Small Ribosomal Subunit shifts down one codon (use Figure 7 - 27) b. Shifts tRNA attached to nascent chain to from A to P site c. Empty tRNA shifts to E site -dissociated d.

Small subunit shifts back 1 codon to realign with Large subunit e. Next tRNA binds at A site process continues f. Specific elongation factors (EF) have been identified for this process 5. A -site is now empty - next tRNA binds cycle repeats. E. Termination (refer to Figure 7 - 30) 1.

A-site is occupied by on of the termination codons 2. Release factor protein binds at A-site 3. Peptidyl transferase hydrolyses last amino-acyl bond 4. New protein is released -Ribosome/ mRNA complex dissociates 1. A region of DNA containing the code for a specific protein or RNA (e. g.

tRNA & rRNA, sn RNA) plus all the adjoining DNA sequences that act as controllers. G. Final Review of Process (use Figure 7 - 33) H. READING ASSIGNMENT - PG. 234 - 240 RNA AND THE ORIGINS OF LIFE Bibliography:


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Research essay sample on Amino Acids Calvin Cycle

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