MICB 3301 Exam 2 (1)

Metabolism (ch. 10)

100

Name the two components of metabolism. What happens during each process? What kind of reactions are they (do they require or release energy)?

(1)Catabolism: breakdown of complex molecules -energy is released, exergonic -"CATabolism- cats clawing things!" (2)Anabolism: synthesis of complex molecules -energy is required, endergonic

200

Define standard free energy. How is it different from free energy? What does it mean if it is positive vs. negative?

(1) Standard Free Energy: used to determine how much E is available to do work (measured at standard conditions- 298 K, pH 7, 1M) (2) Free Energy (G): E released to do useful work (3) negative => E released => exergonic => spontaneous (4) positive => E required => endergonic => not spontaneous

300

What is phosphorylation? Name and give examples of the three types of phosphorylation discussed in lecture.

(1) Phosphorylation: Addition of a phosphate group 1. Oxidative -aerobic and anaerobic respiration 2. Substrate-Level -fermentation 3. Photophosphorylation -photosynthesis

400

What are the 2 classes of electron carriers in REDOX rxns? Give 2 examples for each class (full names, not abbreviations).

(1) freely diffusible -NAD+ (nicotinamide adenine dinucleotide) -NADP+ (nicotinamide adenine dinucleotide phosphate) (2) membrane-bound -flavoproteins -cytochromes (proteins, use Fe to transfer electrons- hemegroups) -quinones (ex: coenzyme Q)

500

What are enzymes? How do they work? (Enzymes ____ by ____ ____ energy. They do this by (1) ___ and/or (2) ___)

(1) Enzymes are proteins that catalyze reactions (ex: Ribozymes- catalytic RNAs) (2) Enzymes increase reaction rates by lowering activation energy. They do this by (1) increasing local concentrations of substrates and/or (2) orienting substrates properly for reactions to proceed.

Catabolism (ch. 11)

100

What three things ('sources') do organisms require?

(1) energy source (2) electron source (3) carbon source These are obtained from the environment and used to drive fueling reactions!

200

What are the 3 common routes by which Glucose is broken down into Pyruvate?

(1) Embden-Meyerhof pathway ("glycolysis") (2) pentose phosphate pathway (3) Entner Duodoroff pathway

300

What is "put into" Glycolysis? (4 different molecules) What is the net yield of Glycolysis? (3 different molecules)

In: -glucose -2 ADP -2 Pi -2 NAD+ Out (net): - 2 pyruvate - 2 ATP (-2 ATP, +4 ATP) - 2 NADH

400

For (1) pentose phosphate and (2) Entner-Duodoroff: a: what goes into each? b: what comes out (net)?

(1) Pentose phosphate in: -glucose-6-phosphate -12 NADP+ -7 H2O out: -12 NADPH -6 CO2 -12 H+ -Pi -sidenote: ribulose-5-phosphate (intermediate metabolite sugar (2) Entner-Duodoroff in: -1 ATP -1 NADP+ -1 NAD+ -glucose out: -1 ATP (-1, +2) -1 NADH -1 NADPH -2 pyruvate

500

C, E, and e- : name and define the 2 categories that an organism my get each of these from. What order do you name organisms in?

(1) carbon -autotroph: CO2 principle C source -heterotroph: red, preformed ORGANIC molecules from other organisms (2) energy -phototroph: light -chemotroph: OXIDATION of organic or inorg. compounds (3) electrons -lithotroph: reduced INORGANIC molecules -organotroph: ORGANIC molecules Order: E source + e- source + C source

Photosyn. (ch. 11 +12)

100

What are the differences and similarities between cyclic and noncyclic photophosphorylation?

Noncyclic: ATP + NADPH prod., PSI +PSII Cyclic: Cyclic e- flow, ONLY ATP prod., ONLY PSI BOTH: generate a PMF used by ATP synthase to make ATP

200

What is the genus of the smallest known photosynthetic organism? Where is it found? What is the size of its genome?

Genus: Prochlorococcus Habitat: tropical oceans Genome of ~2000 genes

300

Define photosynthesis. Name to two parts of photosynthesis and outline each. (enxymes, structures, phases?)

Photosynthesis: E from light trapped and converted => ATP and red. P (NADPH); E then used to fix CO2 (1) Light rxns. -light E trapped and converted => chem. E and red. P -thylakoids-membranes where photosystems are -photosystems-assembly of: chlorophylls + accessory pigments => light harvesting arrays -PSI (P700) and PSII (P680) (2) Dark rxns. (TCA cycle/Calvin Cycle) -3 phases: 1-carboxylation, 2-reduction, 3-regeneration -needs 18ATP to make glucose from CO2 -often occurs in carboxysomes (RubisCO)

400

Some archaea use a special membrane protein for phototrophy. What is it called? How does it work?

-Bacteriorhodopsin -changes conformation upon absorbing light -funct: light driven proton pump => results in the generation of a PMF WITHOUT an ETC

500

Describe Gluconeogenesis. What does it require? How does it compare to glycolysis?

-Biosyn. of glucose from NON-carbohydrate substances -used to maintain blood glucose levels -requires both ATP and GTP -6 enzymes also used in glycolysis; 4 UNIQUE enzymes

Bact. Genome (ch. 13)

100

(1) Name + define the 3 processes of genetic info flow (2) Define the following: Gene, Genome, Genotype, Phenotype

(1) Genetic Info Flow: DNA replication (DNA => DNA), Transcription (DNA => RNA), Translation (RNA => protein) (2) Gene: Functional unit of genetic information Genome: All genetic material Genotype: specific set of genes Phenotype: set of observable characteristics

200

Describe Griffith's Transformation Experiments: (1) what organism was used? (2) what were the four setups? (3) what were the outcomes of each setup? (4) what conclusion was reached?

(1) Organism: Streptococcus pneumoniae (2) Setup: a: (S)- pathogenic capsule b: (R)- no capsule, not pathogenic c: heatkilled (S) d: heatkilled (S) + live (R) (3) Results: a: dead b: alive c: alive d: dead- isolated live (S) and live (R) (4) Conclusion: transformation: nonpathogenic => pathogenic (conjugation is occurring)

300

Describe (A) Avery, MacLeod, and McCarty + (B) Hershey and Chase's Experiments: (1) what organism was used? (2) what was the setup? (3) what were the outcomes? (4) what conclusion(s) were reached?

(A) Avery, MacLeod, and McCarty 1. used R and S Streptococcus pneumoniae 2. R alone, R + S DNA, R + S + DNase, R + S + RNase, R + S + protease 3. no growth on R alone or R + S + DNase 4. DNA is the transforming principal (B) Hershey and Chase: 1. used E. coli and T2 phages 2. labeled 35S protein or 32P DNA => blender 3. protein stayed on phage, not transferred to bacteria DNA from phage into bacteria 4. DNA is genetic info

400

Describe the composition of DNA in depth. Differentiate between nucleotides and nucleosides. Discuss base pairing. (@ least 5 things)

-DNA- polymer of deoxyribonucleotides linked by phsophodiester bonds -components: 1. deoxyribose sugar (no -OH on 2' C) 2. nitrogenous base: -Purines: adenine and guanine (Ag => silver is a "PURE" metal) (simpler word => more complex structure) -Pyrimidines: cytosine and thymine - A + T (2 H-bonds); G + C (3 H-bonds) 3. phosphate group -nucleotide= all 3 components, nucleoside = no P group -3' OH, 5' P -antiparallel -supercoiling (10.5 bp/turn typical) + => tighten - => loosen

500

How does RNA differ from DNA? (3 ways) Name three types of RNA and how they the 3 ways they differ from eachother.

(1) RNA vs. DNA -Ribose sugar (-OH on 2' C) -uricil (U) replaces T -usually single stranded -secondary structure= coiling back on itself (2) mRNA, rRNA, tRNA differ in: function, site of synthesis, and structure

DNA Rep. (ch. 13)

100

What does it mean when 2 DNA is catenated? How do we fix this?

-2 circular daughter chromosomes do not separate -topoisomerases break DNA so strand can sep.

200

Describe the structure of DNA Polymerase III Holoenzyme.

-Complex of 10 proteins -2 core enzymes, 3 proteins each- catalyze DNA syn, proofreading -clamp loader -beta clamp

300

Because prokaryotes lack a nuclear membrane, what can they do that eukaryotes cannot? (This is not a replication question...ran out of material...)

Bacteria and Archaea, translation and transcription are coupled. (Polyribosome= mRNA + seveveral ribosomes)

400

Name the main events that happen at the Replication Fork in E. coli. (6 things)

(1) DnaA proteins bind to oriC (2) DnaB (main helicase) and other helicases seperate strands, SSB attach (3) Primase synthesizes RNA primer (4) Lagging and Leading strands synthesized (5) DNA Polymerase I removes RNA primers, fills in gaps (6) Okazaki fragments joined by DNA ligase

500

Name 7 major proteins involved in DNA replication and give their functions.

(1) DNA polymerase III Holoenzyme syn. DNA polymer 5' -> 3'; needs: template, RNA primer, dNTPs; Pyrophosphate provides E (2) Helicases: unwind DNA (3) SSB proteins: keep strands apart (4) Topoisomerases:break DNA strand to prevent supercoiling, relieve tension (5) Primase: syn. short strands of RNA (6) Ligase: uses ATP to form phosphodiester bond in Okazaki fragments (7) DNA polymerase I: removes lagging strand primers, fills in gaps