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UIC / Biology / BIOS 100 / pyruvate processing

pyruvate processing

pyruvate processing


School: University of Illinois at Chicago
Department: Biology
Course: Intro to Biological Sciences
Professor: Tbd
Term: Fall 2015
Tags: Biology
Cost: 50
Name: BIOS 100 Exam 2 Study Guide
Description: This is a NINE page study guide that covers the information to be included in Exam 2. This is a much more in-depth study guide than the professors and it also includes several photos illustrating some of the cycles and processes we've discussed.
Uploaded: 02/22/2017
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Exam 2 Study Guide

What is Glycolysis?

Chp 9: Cellular Respiration and Fermentation

- Glucose = product of photosynthesis, break down makes ATP, needed constantly by cells - Cellular respiration- complete oxidation of glucose into CO2 and H2O - Fermentation- releases less ATP than cellular respiration, does not fully oxidize glucose - Cellular respiration steps:

1. Glycolysis- 1 6-C molecule of glucose> 2 molecule 3-C pyruvate; ATP and NADH formed

2. Pyruvate Processing- 1 molecule CO2 release, acetyl CoA formed, more NADH from NAD+

3. TCA Cycle- more ATP and NADH produced, FAD reduced to FADH2, CO2 produced

4. Electron Transport and Oxidative Phosphorylation- energy release in etc creates proton gradient across membrane; flow of protons across membrane makes ATP

What is Aerobic respiration?

- Catabolic pathways produce ATP and Anabolic pathway use ATP

- Glycolysis = sequence of 10 reactions (in cytosol), that oxidize glucose into pyruvate 1. Starts by using 2 ATP (energy investment phase), steps 1-5

2. Energy payoff phase- steps 6-10, substrate-level phosphorylation

enzyme-catalyzed reactions make ATP

- Substrate-level phosphorylation- enzyme catalyzes the transfer of a phosphate group from a phosphorylated substrate> ADP, forming ATP

- High levels of ATP inhibit phosphofructokinase, an enzyme that catalyzes reaction 3 in Glycolysis (feedback inhibition, ATP = allosteric regulator)

- Pyruvate produced by Glycolysis transported from cytosol> mitochondria, which has inner (filled with sac-like cristae) and outer membrane If you want to learn more check out bms 250

- Mitochondrial matrix- region enclosed within inner membrane, pyruvate processed here - Pyruvate starts with 3-C molecule and ends with 1 C released as CO2 and 2 C> acetyl CoA

What are the cellular respiration steps?

- TCA cycle completes oxidation of glucose

- Each C in cycle eventually released as CO2

- Reaction rates in cycle increase when ATP/NADH scarce and decrease when ATP/NADH abundant (feedback inhibition)

- Cycle starts with 2 acetyl CoA and ends with release of 2 CO2

- ETC- molecules responsible for oxidation of NADH and FADH2

- NADH donates electrons to FMN, FADH2 donates electrons to Fe-S; H2O formed as by-product and oxidation of glucose complete

- Cytochrome C- transfers electrons between 4 protein complexes

- Energy released from redox reactions used to actively transport protons across inner membrane from matrix to intermembrane space

- ATP synthase- stalk-and-knob component of protein, enzyme that synthesizes ATP - Chemiosmosis hypothesis- use of proton gradient to drive Energy-requiring processes (ATP); protein gradient alone can be used to synthesize ATP

- Chemiosmosis= dam and ETC pumps across inner membrane and when protons pass through ATP synthase, it spins and releases energy used to synthesize ATPWe also discuss several other topics like you have decided that you want to attend a costume party as iron man. you estimate that it will cost $40 to assemble your costume. after spending $40 on the costume, you realize that the additional pieces you need will cost you $25 more. the marginal cost

- Aerobic respiration- depends on O2 as an electron acceptor for ETC while anaerobic respiration does not use O2, but aerobic most efficient

- Fermentation- metabolic pathway that regenerates NAD+ by oxidizing stockpiles of NADH, occurs in cytosol

- Emergency-back up to produce ATP

- We use lactic acid fermentation and plants use alcohol fermentation We also discuss several other topics like which of the following bonds are arranged from strongest to weakest in a biological system?

- Facultative anaerobes- can use both types of fermentation

Chapter 10 Photosynthesis

- Photosynthesis- use of sunlight to manufacture carbs

- Autotrophs are self-feeding photosynthetic organisms and heterotrophs maintain necessary sugars from other organisms

- CO2 + H2O + sunlight> sugar + O2

- O2 comes from H20

- Calvin cycle- reactions that reduce CO2 and produce sugar

- Sunlight> light-capturing reactions (release O2 and H2O)> ATP becomes ATD and NADH becomes NAD+> CO2 goes in and sugar goes out

- Photosynthesis occurs in chloroplasts If you want to learn more check out comm 105 wvu exam 3

- Interior: thylakoids- flattened sac-like structures and space inside= lumen and stroma fluid-filled space between thylakoids and inner membrane

- Shorter wavelengths have more energy

- Chromatography: technique for separating molecules, pigments vary in size/solubility and solvent carries them at different rates

- 2 major pigment classes in plant leaves: Chlorophyll- absorb blue and red, plants reflect green and Carotenoids- absorb blue and green, plants reflect yellow, orange, or red; extend range of photosynthesis

- Pigments that absorb violet-to-blue and red wavelengths most effective at photosynthesis - Action spectrum- wavelengths that drive the light-capturing reactions and Absorbance spectrum- measures how wavelengths of photons influence amount of light absorbed by pigments If you want to learn more check out consimate

- Electrons promoted to high energy states when photons absorbed by Chlorophyll and if allowed to fall back down to ground state, energy released as heat and fluorescence - 4 possible fates of an electron in chlorophyll excited by photons; energy released: 1. Emitted in form of light- fluorescence

2. Given off as just heat

3. Excite an electron in nearby pigment> resonance

4. Transferred to an electron acceptor in redox reaction

- Photosynthesis more effective when PS I and II work together

- PS II feeds excited electrons to etc; plastoquinone carries electrons from PSII along with protons from stroma, cytochrome complex oxidizes PQ, releasing protons in thylakoid lumen that drive ATP synthase

- Photophosphorylation- synthesis of ATP in chloroplasts initiated by energy and light - PS II: Light> antenna complex> reaction center (electrons from H20 accepted here)> Pheophytin> etc> proton gradient> ATP synthase Don't forget about the age old question of a patient’s blood pressure is 118/82 mm hg. he asks the nurse, “what do the numbers mean?” the nurse’s best reply is:

- PS I produces NADPH for Calvin Cycle

- The Z Scheme: PS II(4 electrons> Pheophytin)> etc(Cytochrome complex and ATP produced)> PS I- 4 photons> 4 electrons->Ferredoxin> 2 NADPH

- Noncyclic electron flow- electrons pass from H2O> NADP+ through linear chain of redox reactions

- Antenna complex> PS II> Cytochrome complex> PS 1> 2 NADPH

- Cyclic electron flow recycles electrons, drives Photophosphorylation, and is alternative to Z-scheme

- Calvin Cycle fixes C- Carbon fixation- converts CO2 gas to biologically useful form; C in CO2 reduced

- Calvin Cycle:

- Calvin cycle manufactures carb and glycolysis breaks it down

- RuBP= initial reactant with CO2

- When rubisco catalyzes reaction with O2, photorespiration- undoes photosynthesis; regulates photosynthesis

Chapter 4 Nucleic Acids and the RNA World

- Deoxyribonucleic acid (DNA)- store genetic info and replicated using proteins - General structure nucleic acids: phosphate group, 5-C sugar at center, N2-containing base

- Nucleotides polymerize in condensation reactions via phosphodiester linkage- covalent bond between nucleotides

- Sugar-phosphate backbone of nucleic acids= unlinked 5 prime phosphate and unlinked 3 prime hydroxyl; sequence of bases written in 5 prime> 3 prime direction

- DNA’s Secondary Structure:

1. Sugar-phosphate backbone

2. # purines = # pyrimidines; # of T’s = # A’s, #C’s= #G’s

3. X-ray crystallography found DNA molecules have a regular repeating

structure- helical/spiral

- Purine- Pyrimidine pairs allow H bonds to form between complementary bases inside double helix

- 2 parallel strands of DNA run in opp. Directions: 1 runs 5>3 and other 3>5 (antiparallel) - Complementary/ Watson-Crick base pairing

- Double helix hydrophilic overall> soluble in water

- Tertiary Structure of DNA: supercoils or wraps around certain proteins - DNA copying:

1. Strand separation- H-bonds broken

2. Base-pairing- free nucleotides attach to 3 prime ends according to complementary base pairing

3. Polymerization- new strands polymerize to form sugar-phosphate backbone, secondary structure restored

4. Original molecule copied: each copy has 1 new strand and one original - Primary structure of RNA: ribose sugar-phosphate backbone and U instead of base T - Secondary structure: complementary base pairing between antiparallel regions from

double helix (stem) and unpaired regions form loop, entire structure= hairpin Chapter 16 How Genes Work

- Gene expression- process of converting archived info. Into molecules that actually do things

- null/loss-of-function alleles- don’t function at all

- One-gene, one enzyme hypothesis- each gene contains the info. Necessary to make an enzyme

- Genetic screen- any technique for picking particular types of mutations out of many randomly generated mutants> 1 gene, 1 polypeptide hypothesis today

- mRNA carry info. Out of nucleus from DNA to site of protein synthesis - RNA polymerase- polymerizes ribonucleotides into strands of RNA

- Central dogma of molecular biology- DNA>RNA>proteins

- Transcription- process of using DNA template to make RNA molec. with a base sequence complementary to DNA; RNA polymerase transcribes DNA>RNA

- Translation- process of using info. In mRNA to synthesize proteins; done by ribosomes

- DNA>RNA>proteins>phenotype

- Genotype= sequence of bases in DNA; phenotype= product of proteins produced - Exceptions to central dogma:

- Many genes transcribed from DNA but never translated

- Reverse transcriptase- viral enzyme that synthesizes DNA version of RNA genes - 4 RNA bases must specify 20 amino acids, so triplet- 3-base -code

- Group of 3 bases that specify particular amino acid= codon and diff. Codons in mRNA can code for same amino acid

- Start codon (AUG)- signals protein synthesis should begin at that pat on mRNA molec. - Stop codon (UAA, UAG, AGA)- signal end of translation

- Genetic code is redundant, ambiguous, nonoverlapping, nearly universal, and conservative

- Mutation- any permanent change in an organism's DNA; change in genotype creates new alleles

- Point Mutations- alter sequence of 1/small # base pairs

1. Missense- change identity of amino acid in protein

2. Silent- don’t change amino acid sequence of gene product

3. Frameshift- shift reading frame

4. Nonsense- codon that specifies an amino acid is changed to one that specifies a stop codon, usually resulting in nonfunctional protein

- Mutations can be beneficial, neutral, and deleterious and can occur anywhere in genome Chapter 17 Transcription, RNA Processing, and Translation

- Flow of information in cells: DNA> mRNA> protein

- RNA polymerase- synthesize RNA by polymerization reaction

- Transcription- synthesis of RNA from DNA template

- Template strand- strand of DNA read by enzyme

- Non-template strand/coding strand- sequence matches sequence of RNA transcribed from template strand and codes for polypeptide

- RNA polymerase performs template directed synthesis in 5>3 direction, but doesn’t need a primer (unlike DNA)

- In bacteria, transcription oriented when sigma binds to -35 and -b boxes in DNA 1. Initiation- sigma binds to promoter region of DNA

2. RNA polymerase opens DNA helix, transcription begins

3. Initiation complete- Sigma released from promoter, RNA synthesis continues from DNA

- Elongation phase of transcription- enzyme catalyzes + end of nucleotides to 3 prime end of growing RNA

- Termination:

1. Hairpin forms- transcription-termination signal codes for RNA that forms a hairpin

2. RNA hairpin causes RNA to separate from RNA polymerase, terminating transcription

- Transcription in Eukaryotes similar to bacteria, but:

1. More diverse promoters

2. Instead of sigma, basal transcription factors assemble at promoter and RNA polymerase follows

3. Transcription and translation separated in time and space

- Sharp discovered introns- DNA that are transcribed but not found in final mRNA - Gilbert found exons- regions of eukaryotic genes part of final mRNA - RNA Splicing- pieces of primary transcript removed (introns) and remaining segments joined together:

1. snRNPs bind to start of intron and an A base within intron

2. snRNPs assemble to form spliceosome- multipart complex

3. Intron cut, loop forms

4. Intron released as lariat, exons joined together

- Small nuclear ribonucleoproteins (snRNPs)- recognize RNA sequences critical for splicing

- After splicing, to become mRNA:

1. + 5 cap- enables ribosomes to bind to mRNA and protects end from attack by enzymes that degrade

2. poly(A) tail- needed for ribosomes to start translation and also to protect ends from attack by enzymes

- Biologists used Pulse-Chase experiment to find that ribosomes are the site of protein synthesis

- Polyribosome- 2/+ structures simultaneously translate 1 mRNA

- mRNA triplets specify amino acids when adapter molecules hold amino acids and interact with mRNA codons, as found by Crick

- Transfer RNA- transfer amino acids> proteins

- tRNA:

1. Secondary structure- cloverleaf; some sequences of bases form H-bonds with complementary base sequences; elsewhere in same molecule are stem-and-loop structures

2. Tertiary structure= L-shaped

- Anticodon- triplet of ribonucleotides able to form base pairs with codon for amino acid in mRNA (secondary structure)

- aminoacyl-tRNA synthetases- enzymes that catalyze + of amino acids to tRNAs - How many tRNA’s are there? Crick proposed wobble hypothesis:

- Bases in 3rd position of tRNA anticodons can bond to bases in 3rd position of codon that don’t match; tRNA can read more than 1 codon

- Translation of codon complete when peptide forms between tRNAs amino acid and growing polypeptide

- Ribosomes contain 3 tRNA binding sites:

1. A site- carries amino acid

2. P site- holds growing polypeptide chain

3. E site (exit)- no longer has amino acid attached and is about to leave ribosome - 3-step sequence for ribosome synthesis:

1. Aminoacyl tRNA diffuses into A site; if anticodon=codon in mRNA, stays 2. Peptide bond forms between amino acid held by aminoacyl tRNA in A site and growing polypeptide

3. Ribosome moves down mRNA by 1 codon and all 3 tRNAs move 1 position with in ribosome

- 3 phases of protein synthesis: initiation, elongation, and termination

- Translation initiation in bacteria:

1. mRNA binds to small ribosomal subunit

2. Initiator tRNA bearing f-Met binds to start codon

3. Large ribosomal subunit binds

- Elongation starts when aminoacyl tRNA binds to codon in A site by complementary base pairing between codon and anticodon; extends polypeptide chain

- Ribosome=ribozyme

- Translocation- protein elongation factor, helps move ribosome in 5>3 direction relative to mRNA

1. Arrival of aminoacyl tRNA

2. Peptide-bond formation

3. Translocation; repeat at each codon

- Translation terminated when translocating ribosome reaches 1 of stop codons and release factor recognizes stop codons and fills A site

- Major steps of gene expression in Eukaryotic cell:

1. Transcription> RNA processing (nucleus)

2. Translation> Post-translational modification (cytoplasm)

Chapter 18 Control of Gene Expression in Bacteria

- Bacteria turn their genes on and off to adapt to changing environment - Gene Expression- multistep process of converting info. that is archived in DNA into molecs. that actually do things in cell

- DNA>mRNA>protein>activated protein

- 3 possible mechanisms for gene regulation:

1. Transcription control- cell can only make mRNAs for particular proteins; affect RNAs polymerase’s ability to bind to a promoter and initiate transcription 2. Translational control- cell prevents mRNAs from unneeded proteins being translated; regulation of mRNAs survival time/ability to be translated

3. Post-translational control- after translation, protein must be activated by chemical modification to function

- some genes transcribed all the time- constituently

- Lactose=inducer for E. coli- small molec. that triggers transcription of a specific gene - Identifying regulating genes (Monod and Jacob)

1. Generate large # cells with mutations at random locations in genomes 2. Screen treated cells for mutants with defects in process/biochemical pathway in ? - Constitutive mutants- abnormal cells that produce a product at all times - 2 general ways to regulate transcription:

1. Negative control- regulating protein, repressor, binds to DNA and shuts down transcription

2. Positive control- regulatory protein, activation, binds to DNA and triggers transcription

- Transcription can be regulated by 1/both

- Operon- set of coordinately regulated bacterial genes transcribed together into 1 mRNA - Lac Operon- group of genes involved in lactose metabolism

- How does glucose regulate the lac operon?

1. Inducer Exclusion- glucose prevents transport of lactose when glucose low outside cell

2. Regulation of CAP- +control by catabolite activator protein allows transcription to begin more frequently

- Importance of lac Operon Model:

- Many bacteria genes and operons under - control by repressor proteins - Gene expression is regulated by physical contact between regulatory proteins and specific regulatory proteins and specific regulatory sequences in DNA

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