BIO 205 Unit 6 & 7

What are the 4 key intermediates in glycolysis?

(FBP) Fructose 1,6-Bisphosphate (DiHAP) Dihydroxyacetone (G3P) Glyceraldehyde-3-phosphate (G3P) (PEP) Phosphoenolpyruvate

How does ADP, AMP, and F-1,6-BP, and PEP regulate glycolysis?

- ADP activates glycolysis because it indicates that need more ATP and enzymes work as activator - AMP inhibits reversal of glycolysis (note ATP conservation!) - F-1,6BP activates glycolysis - PEP inhibits glycolysis and activates starch formation

What happens to pyruvate during the entry step before the citric acid cycle (Krebs)?

- CO2 is removed and NAD is reduced to NADH+H+ - This leaves a 2 carbon Acetyl group which is then joined to coenzyme A to form acetyl-CoA

What is the difference between direct control and genetic control of enzyme regulation?

- Direct control uses allosteric inhibition and activation - Genetic control - gene is only transcribed when there is need for the enzyme

What are the components of an operon?

- Promoter (P) Region binds RNA polymerase - Regulator (I) Gene codes for repressor protein - Operator (O) Region binds repressor and blocks transcription - Inducer

Describe DNA transcription.

- RNA polymerase binds to the promoter on DNA strand which it recognizes due to sigma factor - elongation: RNA polymerase moves along DNA (-) strand from the 3' to 5', synthesizing RNA molecule - termination site is encountered and newly synthesized RNA is released.

What are two main differences between aerobic respiration and anaerobic respiration?

- all the same except in anaerobic respiration the FEA is an inorganic molecule other than O2 and - ETS is shorter and energy drop is less, so smaller ATP yield. Thus each NADH or FADH2 is worth fewer ATPs.

What are the steps of DNA replication on the lagging strand after DNA gyrase and helicase break, unwind and unzip strands and why is this different from leading strand?

- an RNA primer initiates DNA polymerase to start adding nucleotides to lagging strand in the 3' to 5' direction. - as nucleotides are being added creating Okazaki fragments , DNA is unzipping behind the polymerase. RNA primer is formed every time there is a gap to keep the process going. - new DNA polymerase removes previous RNA primers as it moves down the strand and replaces them with deoxynucleotides - DNA ligase seals the gaps between Okazaki fragments by forming covalent bonds between them

What 2 ways does an inducer function to induce transcription?

- binds to the repressor protein, changing it's shape so that it can NOT attach to the operator and block transcription - binds to the activator so that it will attach to activator binding site and initiate transcription

Where is CO2 released during aerobic respiration?

- entry step to Krebs: pyruvate to acetal group - Twice in Krebs

How are proteins catabolized to enter glycolysis and Krebs?

- enzyme proteases break down protein into amino acids - amino group is removed by deamination - remaining carbon skeletons are converted into precursor metabolites and go through glycolysis and/or Krebs

How do antibiotic resistant bacteria

- first antibiotic kills all susceptible bacteria, leaving only the resistant cells to survive - resistant cells then reproduce and need a stronger antibiotic to kill them

How are lipids broken down to enter glycolysis?

- lipids (fatty acids and glycerol, a 3 carbon chain) are hydrolyzed by enzyme lipase. - the glycerol is converted to DiHAP and enters glycolysis - the fatty acids are goes through beta oxidation where 2-carbon units from each are transfered to coenzyme A forming acetyl-CoA which then enter TCA cycle

Where does transcription occur in a eukaryote? translation?

- mRNA transcription occurs in the nucleus - translation occurs in cytoplasm after mRNA transcript strand is transported out of nucleus

What are the main ways in which respiration and fermentation differ?

- presence or absence of electron transport chain - final electron acceptor - ATP output (yield)

What are 3 ways that cells evolve to resist antibiotic?

- pump ejects antibiotic - enzyme modifies shape of antibiotic inactivating it - shape of target molecule inside of cell is modified so antibiotic can't bind to it

What are the 3 ways cells develop antibiotic resistance?

- pump the antibiotic out - change shape of target molecule so antibiotic can't bind - porins in cell membrane

What does the pentose phosphate cycle produce?

- reducing power from 12 NADPH + (12)H+ - Pentoses (Carbon-5 sugars) Ribose and deoxyribose precursors metabolites - Precursor of some amino acid precursors (Pi)

What is the difference between RNA and DNA?

- sugar in the nucleotides of RNA contains ribose instead of deoxyribose (has an oxygen molecule the deoxy lacks) - RNA is a single stranded linear molecule shorter than DNA

Why is the ATP yield less in eukaryotic cells than in prokaryotic cells? What is the yield?

- yield is 36 - in eukaryotic cells the NADH+H+ can't cross the mitochondria membrane without a transfer of electrons to carrier

What is DNA polymerase III function?

-Joins nucleotides in 5' to 3' direction - 50,000 bp/minute at 37oC - Bacterial: 3' to 5' Exonuclease activity (proofreading)

What is the final electron acceptor (FEA) in aerobic respiration, anaerobic respiration, and fermentation?

Aerobic Respiration - O2 Anaerobic Respiration - inorganic molecule (N03, NO2, SO4 etc) Fermentation - organic molecule like pyruvate

What is the chemiosmotic theory?

Like a dam with energy - creating reservoirs, channels, and turbines: - (reservoir and channels) Proton (H+) pump creates H+ gradient across membrane (higher on outside of cell) - (Reservoir) Potential energy stored in the H+ gradient results in an energized state across the membrane capable of doing work - (channel and turbine) Controlled re-entry of H+ happens in association with a membrane-bound ATP synthase to phosphorylate ADP to ATP. Works like a turbine as H+ are brought in this energy is used to attach Pi to form ATP. - This is called Oxidative Phosphorylation due to use of an electron transport system - This Proton Motive Force (PMF) also drives bacterial flagella!

Why would an organism use fermentation instead of respiration?

organism lacks an electron transport chain with a final electron acceptor in order to recycle NADH+H+ for continuing glycolysis. So must use pyruvate or molecule derived from pyruvate

What is fermentation basically with regards to electrons?

oxidizing NADH+ H+ to NAD to make NAD available to accept electrons during glycolysis

What is substrate level phosphorylation and what is an example?

phosphates are added to ADP to create ATP from substrates of glucose. Energy to add the Pi comes from breaking bond from substrate.

What is translation?

protein synthesis, the process by which the information carried by mRNA (messenger RNA) is used to synthesize the encoded protein

Reactants of fermentation

pyruvate

What is a codon?

series of three nucleotides that code for a specific amino acid (GCAT in DNA, and GCAU in mRNA are the nucleotides)

Which of the 3 nucleotides in a codon are least important to identification of the amino acid?

the 3rd nucleotide - the first two nucleotides identify the amino acid, the third is like a second indentifier

What are the products (names and amounts) and reactants involved in glycolysis?

1 Glucose --> 2 Pyruvate 2 ATP --> 2 ADP 2 NAD+ --> 2 NADH+H+ 4 ADP --> 4 ATP

How many NADH+H+ and FADH2 are generated during beta-oxidation of fatty acids?

1 NADH+H+ and 1 FADH2

What are the steps of DNA replication on the leading strand?

1. DNA gyrase breaks the DNA strand and unwinds. 2. helicases unzips the two strands of DNA 3. As leading strand is exposed, DNA polymerase adds nucleotides onto the 3' end

Summarize steps of glycolysis with regards to ADP, ATPs, and phosphorylation.

1. Investment phase: 2 ATP phosphorylate the glucose molecule creating first intermediate fructose 6-phosphate, then fructose 1,6-bisphosphate. 2. 6-carbon glucose molecule splits in the middle into two 3-carbon molecules with a phosphate on each 3. Both 3-carbon molecules are oxidized as NAD is reduced. Another phosphate is added to each. 4. ADP takes phosphate off of each creating ATP 5. Another phosphate from each is transferred to ADP creating 2 more ATPs 6. Left with two 3-carbon molecule with no phosphates called pyruvates.

What is the net ATP produced during glycolysis (not including NAD-NADH+)?

2 ATP are used in the investment phase 4 ATP are produced in the payoff phase = 2 ATP produced

Describe the hydrogen bonds that hold together the double helix structure of DNA.

2 hydrogen bond between AT 3 hydrogen bond between GC

What is oxidative phosphorylation and what does it do?

2 processes involved: - first, proton motive force is generated by NADH donating their H across cell membrane by means of NADH dehydrogenase enzyme carrying across membrane. - second, enzyme ATP synthase uses the energy of the hydrogen outside of membrane to enter cell and attach a third phosphate to an ADP. - produces ATP

What are the subunits of Prokaryote ribosomes

30S and 50S subunits = 70S

What is the difference between the 5 prime and 3 prime end of DNA?

5 prime ends with a phosphate 3 prime ends with a hydroxyl (OH)

What are the components of a DNA nucleotide?

5-carbon sugar (deoxyribose), a phosphate group, and one of the four nucleobases (A, T, G, C)

How many different codons that code for amino acids are there?

61 (3 stop codons)

What is the start signal (codon) of translation process on mRNA?

AUG - methianine

What are the end products of fermentation and how do you detect them in a lab test?

Acid - pH indicator gas - durham tube alcohol - not routinely detected

What is the name for a set of genes transcribed as a single mRNA molecule whose transcription is regulated based on need?

operon

What are the 3 groups of enzymes according to their type of regulation?

Constitutive Inducible Repressible

How is DNA replication semi-conservative?

Each of the two molecules created contains one of the original strands (it's conserved) paired with a newly synthesized strand

What are the major difference in eukaryotes transcription and translation versus prokaryotes?

Eukaryotes: -mRNA contains introns which are removed by splicing -mRNA is monocistronic, and only begins at one AUG, versus any AUG that follows a ribosome-binding site - translation doesn't begin until mRNA transcript is transported out of nucleus into cytoplasm - a cap is added to the 5' end of mRNA and a poly A tail to the 3' end

Where is the ETC located in eukaryotic cells and prokaryotic cells?

Eukaryotic - mitochondria inner membrane Prokaryotic - cytoplasmic membrane

What are introns and exons and in what type of cell do you find them?

Eukaryotic cells only. Intron - non coding nucleotide sequences that must be removed by splicing before transcription can take place Exons - coding nucleotides

Which type of enzyme is NOT routinely produced at significant levels, instead their synthesis can be turned on when needed.

Inducible - their synthesis can be induced.

What are the 3 steps of mRNA transcription?

Initiation Elongation Termination

Describe the 3 steps of mRNA transcription.

Initiation: - ribosome 30s and 50s bind to mRNA - the anticodon of tRNA carrying a f-Met amino acid binds to mRNA start codon at the P-site Elongation: - another tRNA-amino acid with matching anticodon occupies the A-site - Peptidyl transferase forms a peptide bond between the two amino acids and releases the first AA from its tRNA - tRNA occupying A-site now has a growing protein chain - Ribosome advances one codon and first tRNA is ejected at the E-site; 2nd tRNA moves into P-site - a new tRNA comes into A-site and first two amino acids are attached to it's amino acid - process repeats as ribosome moves down mRNA Termination: - When ribosome hits a stop codon the process ends, polypeptide is released - ribosome subunits separate

In transcription, to what does the RNA polymerase bind to initiate RNA synthesis? Where does it end?

Promoter and Terminator

Of the nucleotides of DNA and RNA, which are the purines and which are pyrimidines?

Purines (A & T)- double rings molecular structure Pyrimidines (G & C) - single ring

What type of regulator enzyme is trp operon and what is it's function?

Repressible enzyme - trp operon codes for synthesis of tryptophan Enzymes are not produced if an adequate amount of tryptophan is present - Corepressor (e.g., tryptophan) binds to repressor and allosterically activates it; transcription is blocked

Which enzymes are produced routinely, but synthesis can be turned off when they are not required.

Repressible....they can be repressed

Describe the carbon exchange in a full pentose phosphate cycle from 36 to 30 carbons.

Six glucose 6-phosphate each lose a carbon to CO2 and they're left with six ribulose 5-phosphates (a 5 carbons molecule), which transfer carbons around until five glucose 6-phosphates are eventually formed.

What is the function of primase in DNA synthesis?

Synthesizes RNA primer at origin and at the beginning of each Okazaki fragment

Why is the net ATP production in Enter-Doudoroff pathway less than glycolysis?

The result of the split of the 6-carbon compound into two 3 carbon chains is 1 pyruvate (instead of DiHAP) and 1 G3P to go through further breakdown to pyruvate. Thus less ATPs are produced than in glycolysis

What is f-Met?

This is the amino acid attached to the initiating tRNA. It is a chemically altered form of amino acid methionine, the start codon on mRNA for transcription.

Unit 7

Unit 7

What are the three functional types of RNA molecules?

mRNA - messenger RNA rRNA - Ribosomal RNA tRNA - Transfer RNA

Describe an electron transport chain.

a series of membrane embedded electron carriers that accept electrons from NADH and FADH2, then pass those electrons from one carrier to the next. As energy is released protons (H) are able to be pumped across the membrane generating proton motive force.

What is the (ideal) ATP yield of aerobic respiration? anaerobic respiration? fermentation?

aerobic - 38 ATP anaerobic - less than aerobic fermentation - 2

What is an anticodon on tRNA?

amino acid at the end of tRNA which is complementary to a mRNA codon and binds

What is transcription?

mRNA synthesis - The process by which the information encoded in DNA is copied into a different molecule called RNA

Define reducing power?

molecule's ability to donate hydrogen atoms or electrons to another molecule with a more positive charge.

What is a base substitution and point mutation?

one nucleotide in base pair is changed or substituted during DNA replication and will generate a different codon, resulting in a mutant DNA

Which direction does DNA polymerases and RNA polymerases synthesize DNA and RNA?

created as 5' to 3' (*meaning it starts at the 3' on template strand)

What type of metabolic pathway and reaction is glycolysis?

glycolysis is exergonic/oxidation/catabolic

Does glycolysis require oxygen?

glycolysis is oxygen independent, but not anaerobic

What is meant by polycistronic?

in prokaryotes mRNA may transcribe multiple genes from a DNA

Of inducible and repressible enzymes which are catabolic and anabolic and what is an example of each?

inducible - catabolic - lac operon repressible - anabolic - lac ter

What type of regulator enzyme is lac operon and How it function in E. coli metabolism of glucose and lactose? And what is it's inducer called?

inducible enzyme: - enzymes are only turned on when glucose is NOT available, but lactose is present. Cell will use glucose first unless it is not available. - inducer is called allolactose

Where does the energy for phosphorylating ADP into ATP in glycolysis come from (where does the Pi come from)?

intermediates (which are just phosphorylated carbon chains) lose their phosphates as they are broken down

Describe constitutive enzymes with regards to regulation.

these are always produced and always active

What is one way that prokaryotes are more efficient than eukaryotes?

transcription and translation can happen simultaneously in prokaryotes

When is the Enter-Doudoroff pathway used to produce ATP?

when organism lacks glycolytic enzymes or used for sugars other than glucose