MIC 230

Phototrophy and Photosynthesis

Use of light as an energy source

light energy --\> chemical energy

Chloroplast

organelle found in cells of plants and some other organisms that captures the energy from sunlight and converts it into chemical energy

Autotrophy

ATP + CO2 + electrons → Organic molecules (ex. glucose)

Path ways of CO2 fixation \= reductive

Not light dependent

Steps in phototrophic metabolism

light -\> ATP

light causes electron flow, electron flow in the membrane generates a current that drives the proton motive force (PMF) and creates ATP

What powers the electron transport chain?

light energy

Steps in autotrophic metabolism

CO2 -\> biosynthesis

CO2 causes carbon flow, causing biosynthesis. Carbon fixation is reductive and requires electrons (these electrons do not come from light)

Anoxygenic phototrophy

anaerobic process, no oxygen generated

Oxygenic phototrophy

aerobic process, oxygen generated

light -\> ATP

Electrons TO MAKE NAD(P)H from H2O!!!

Where do electrons come from in oxygenic phototrophy?

H2O

O2 is released in green plants and cyanobacteria

Where do electrons come from in anoxygenic phototrophy?

inorganic lithotrophs sources: sulfur, water, hydrogen, iron, nitrogen compounds

releases product in purple and green bacteria

Cyclic photophosphorylation

The reaction center is the e- donor and terminal e- acceptor

How are respiratory chains and cyclic photophosphorylation different?

Cyclic photophosphorylation has no net input or consumption of electrons, and respiratory chains do

Carbon Fixation

Light independent

CO2 → Organic molecules

Need energy and reducing power (electron source)

ATP and NADPH or NADH or Fd

Calvin Cycle (most common)

RubisCO

the most abundant enzyme on Earth

What uses the Calvin Cycle?

Cyanobacteria, Purple bacteria, Plants, Algae

Compare this cycle to the citric acid cycle

It's a cycle. Starting material needs to be recreated or the cycle stops

CO2 'fixed' to a \______ carbon sugar during the Calvin Cycle

six

Where does the 18 ATP and 12 NAD(P)H come from in the Calvin Cycle?

Proton motor force through light reaction

Photoautotrophs

•Example: cyanobacteria

•Energy source:

•Carbon source:

Photoautotrophs

•Example: cyanobacteria

•Energy source: light

•Carbon source: CO2

Chemolithoautotrophs

•Example: purple sulfur bacteria

•Energy source:

•Carbon source:

Chemolithoautotrophs

•Example: purple sulfur bacteria

•Energy source: chemical

•Carbon source: CO2

Since autotrophs are producing organic carbon (e.g. glucose) from CO2, are they reducing or oxidizing CO2?

A. Reducing

B. Oxidizing

A

DNA is composed of how many nucleotides? What are they composed of?

4 nucleotides (deoxynucleotides)

Composed of purines & pyrimidines

Sugar-phosphate backbone runs strands parallel or antiparallel?

antiparallel

Chargaff's Rule

A\=T

C≡G

What is the distance between a base pair?

1 bp \= 0.34nm

Topoisomerase

- Twists DNA to save space

- Supercoiling of DNA

Nick in DNA

Space

Meselson-Stahl discovered that DNA Replication is\_____?

semiconservative

Semiconservative

the new DNA strand contain one strand that is old and one that is new

DNA & RNA polymerases work in a \_______ direction always adding nucleotides to the 3'-OH

5' -\> 3'

Phosphodiester

bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide

Primase

Enzyme that makes RNA primers

Single-strand binding proteins (SSB)

stabilize ssDNA

& prevent re-forming dsDNA

Helicase produces?

single stranded regions (unwinds DNA)

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

What enzyme removes the RNA primer?

DNA polymerase I

5' -\> 3' proof reading

Cuts the RNA from the DNA and replaces the RNA with DNA, which leaves a gap

What enzyme closes the gaps left behind from DNA polymerase I?

DNA ligase forms phosphodiester bonds

Bidirectional

The replication fork moves in both directions simultaneously

Origin of replication (ori)

Specific site on the Bacteria and Archaea chromosome where replication starts.

Multiple "ori" in Eukaryal chromosomes

Transcription

Production of RNA from DNA

Gene

Any segment of DNA that is copied into RNA; plus all the associated DNA required for its transcription

Differences between DNA and RNA

U replaces T, deoxyribose (DNA) vs ribose (RNA), singe-stranded (RNA) vs double-stranded (DNA)

RNA polymerase (RNAP)

synthesizes RNA (DNA-dependent RNA polymerase)

Promoter

site on the DNA where the RNA Polymerase binds

Template strand

The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.

Coding strand

the strand containing the triplets that specify the sequence of amino acids in the polypeptide

Sigma factor (s)

Only in bacteria.

Subunit recognizes and binds to the promoter in complex with RNAP

Polycistronic

Multiple genes encoded on a single piece of RNA

Some polycistronic mRNA are arranged in operons....

A series of related structural genes (usually code for enzymes or proteins of a metabolic pathway) that are co-transcribed on a polycistronic mRNA.

Allows coordinated control of expression of related genes

Differences in Archaeal Transcription

Like Bacteria, Archaea contain a single RNAP, but it resembles the Eukaryotic RNAP II