Exam 3 Study Guide: Anabolism and Gene Regulation

Phototrophs get energy from ___ whereas chemotrophs get energy from ____.

sunlight, chemicals

Why is phototrophy NOT photosynthesis?

Photosynthesis confuses catabolic energy production and anabolic carbon fixation (building sugars)

Phototrophy

how organisms use light energy

Chlorophyll

Cofactor

Where is chlorophyll located?

Reaction center (holds closely arranged chlorophyll molecules)

What happens when chlorophyll absorbs light?

Different modifications on ring allow bacteria to take in different wavelengths (quality of light absorbed), light harvested to excite electrons on chlorophyll to act as electron donor

Since too much light can destroy chlorophyll molecules, where does the excess light go?

Move energy to carotenoids

Which energy intermediate(s) does cyclic phototrophy produce?

ATP and PMF

What is both the electron donor AND acceptor in cyclic phototrophy?

Chlorophyll

Describe how PMF and ATP are made in cyclic phototrophy

1. Excited electrons passed to membrane carriers

2. ETC makes PMF

3. PMF drives ATP synthesis through F1F0 ATPase

4. Electrons can return to any reaction center

Which energy intermediate(s) does acyclic phototrophy produce?

NADH

What is the electron donor in acyclic phototrophy?

Water

What is the electron acceptor in acyclic phototrophy?

NAD+

Describe how PMF and ATP are made in acyclic phototrophy

1. Excited electrons passed to membrane carriers

2. ETC makes PMF

3. PMF drives ATP synthesis through F1F0 ATPase

4. Electrons filled in from another source to complete cycle

Describe how NADH is made in acyclic phototrophy

Reducing NAD+

What are the three ways in which acyclic phototrophs complete the "cycle" of getting electrons from donor to acceptor?

strong reaction centers with enough energy to reduce NAD+, weak reaction centers and use reverse ETC, Oxygenic phototrophy

Why is oxygenic phototrophy called oxygenic?

Takes electrons off water and gives off oxygen as a byproduct

Which energy intermediate(s) does bacteriorhodopsin-based phototrophy produce?

ATP (and PMF)

What does bacteriorhodopsin-based phototrophy NOT use?

ETC

Briefly describe how bacteriorhodopsin-based phototrophy works.

Simple proton pump directly coupled to light absorption

What's the problem with reaction centers?

relatively small target

What do phototrophs do to solve relatively small targets in reaction centers?

increase surface area

How can phycobiliproteins absorb different wavelengths of light?

Carotenoids, different light-harvesting pigments

Explain how a chloroplast came to be in eukaryotic cells.

Eukaryotic cell containing mitochondria engulfed a photosynthetic cyanobacteria cell

In what ways is H. salinarum an extremophile?

extremely halophilic, desiccation/radiation resistant, has one large and two mini chromosomes

How is H. salinarum unusual in its phototrophy?

Requires carotenoids (photo-pigment cofactor found in the human eye

heterotrophs get carbon from

organic chemicals

autotrophs get carbon from

CO2

How are fatty acids activated for lipid synthesis?

Attaching Acyl Carrier Protein (ACP)

What are the two types of ACP, and how many carbons do they have?

"Primer"(2 Carbon)

"Extender"(3 Carbon)

What happens when malonyl-ACP (extender) donates to acetyl-ACP (primer)?

CO2 liberated and chain elongated by 2 carbons

What reducing steps are involved when malonyl-ACP (extender) donates to acetyl-ACP (primer)?

Chain reduced twice

What do cells vary in order to change the type of fatty acid being built?

Primer variation (even vs odd branching)

What are two ways in which cells introduce unsaturation to fatty acids?

skip reduction step, monooxygenase

What happens when the reduction step is skipped?

Reducing enzyme fails at low temperatures so double bond is preserved in elongation

Monooxygenase

Enzyme made at lower temperatures and adds oxygen to bring double bond after chain is completed

What are the monomers used to build polysaccharide macromolecules?

sugars

How are sugars activated for polysaccharide synthesis?

Attaching nucleotides

Peptidoglycan is a repeating subunit of ___ and ___.

NAG and NAM

Step 1 of peptidoglycan synthesis

NAM is activated with UDP

Step 2 of peptidoglycan synthesis

5 AAs are attached sequentially to NAM-pentapeptide

Step 3 of peptidoglycan synthesis

NAM-pentapeptide transferred to a membrane carrier lipid which becomes new monomer activator

Step 4 of peptidoglycan synthesis

NAG is activated with UDP

Step 5 of peptidoglycan synthesis

NAG is attached to NAM-pentapeptide

Step 6 of peptidoglycan synthesis

Lipid carrier and NAG-NAM-pentapeptide are flipped to the opposite side of the membrane through flippase enzyme

Step 7 of peptidoglycan synthesis

NAG-NAM-pentapeptide polymerized onto existing chain in wall

Step 8 of peptidoglycan synthesis

Pentapeptides are crosslinked by penicillin-binding proteins (PBPs)

What are the four macromolecules that can be generated by anabolism?

Lipids (phospholipids), carbohydrates (peptidoglycan), proteins, and nucleic acids (RNA and DNA)

Write out the equation for RuBisCO.

6CO2 → C6H12O6 (turns inorganic carbon into organic carbon)

Steps of RuBisCO.

1. RuBisCO carboxylates ribulose

2. Attach one CO2 molecule to the end of a five-carbon sugar

3. Reduction "fixes" the carbon atom biologically into two three-carbon sugars

4. 6x through cycle b/c one extra carbon comes from each (Calvin Cycle)

RuBisCO intermediates and products

18 ATP and 12 NADPH to make 1 glucose

Regarding carbon fixation, what can happen when CO2 levels are low?

photorespiration and/or oxygen can compete with the enzyme leading to toxic byproduct (glycolic acid)

Where can reduced nitrogen (ammonia) come from?

Mostly lightning or geothermal, man-made

What is the enzyme used for nitrogen fixation?

Nitrogenase

How do nitrogen-fixing bacteria deal RuBisCo (3 ways)?

1. Oxygen reacts with iron, exposing the active site of the iron protein to the cytoplasm

2. Live in anaerobic conditions where oxygen can't grow

3. Extremely rapid respiration

What molecule inhibits nitrogenase (like RuBisCO)?

oxygen

What does S. meliloti have a symbiotic relationship with?

Legumes

What is exchanged in S. meliloti relationship?

Plant gets nitrogen, bacterium gets carbon

What is the purpose of leghemoglobin in S. meliloti symbioses?

Controls oxygen so it doesn't destroy nitrogenase, nodulation

Anabolism

Reactions assembling small molecules into macromolecules and biomass.

Carbon Fixation (autotrophs)

making reduced carbon from CO2 gas

Nitrogen Fixation (nitrogen fixers)

making reduced nitrogen from N2 gas

Heterotrophs

obtaining carbon from organic sources.

Autotrophs

obtaining carbon from CO2.

Macromolecules

Large molecules like proteins and nucleic acids.

Phycobiliproteins

Light-harvesting pigments that absorb different wavelengths.

NADH is generally used for

catabolic reactions.

NADPH is generally used for

anabolic reactions.

RuBisCO

Enzyme that catalyzes carbon fixation.

Carboxysomes

Structures that prevent photorespiration in autotrophs.

Fe protein

Delivers electrons in nitrogen fixation.

FeMo protein

Reduces nitrogen in nitrogen fixation.

Homopolymer of glucose for energy storage.

glycogen

UDP

Activates NAM and NAG for synthesis.

Undecaprenyl

Anchors NAM-pentapeptide to the membrane.

Flippase enzyme

Transports NAG-NAM-pentapeptide across the membrane.

Penicillin binding proteins (PBPs)

Enzymes that crosslink amino acids in peptidoglycan.

Replication

Process of creating DNA from DNA.

Transcription

Process of creating RNA from DNA.

Translation

Process of creating protein from RNA.

Plasmids

Small circular dsDNA encoding non-essential genes.

oriC

DNA sequence where replication begins.

terC

Region where replication forks end.

dif

Site signaling to stop replication.

DnaA protein

Binds to oriC, recruits DNA polymerase to begin replication.

What Greek letter does this make the replicating chromosome resemble?

Theta

Catenation

Issue between old and new chromosomes post-replication.

Decatenation

Process resolving catenated chromosomes using topoisomerase and XerC/XerD proteins.

On the chromosome, which genes are at the highest copy number?

genes near origin

What kind of replication is used to replicate plasmids?

rolling circle replication

Theta replication

Involves two replication forks and bidirectional synthesis.

informational message mRNA (Has SD sequence)

Contains all the info coding a protein's primary sequence

transfer tRNA (no SD or start codon)

activates AAs and mRNA, decodes mRNa

ribosomal RNA (no SD or start codon)

Forms structure of the ribosome, recognizes transcript, catalyzes peptide bond formation

SD sequence

ribosomal binding site in mRNA

Shared pool

tRNA and rRNA.

RNA Polymerase

Enzyme that catalyzes transcription of RNA.

σ factor proteins bind

promoters

What is the function of Sigma (σ)?

Determines which promoters RNA polymerase binds to and controls specificity

Promoters

DNA sequences indicating transcription start points.