Translation

 Background knowledge

• The complete mRNA leave the nucleus and goes into the  cytoplasm
• polypeptide= many proteins
• The goal of translation is to create proteins

Act I
Initiation:



tRNA forms a complex with the with the ribosomal sub units
 this complex then binds with mRNA at the 5' cap and scans the mRNA

transfer RNA brings amino acids that correspond to the codons on mRNA
tRNA recognizes these codons by the anticodon loop attached to it
The starter codon is AUG which corresponds with the amino acid Methionine , the anticodon loop for it is UAC

Elongation
The polypeptide becomes longer one amino acid at a time
The first tRNA carrying the starter amino acid AUG goes to the P site
when the next tRNA brings the amino acid the previous tRNA goes to the E site

Termination
The codons UCC, UCA, UCG, UCU have no corresponding tRNA sequence so this process stops
Now the termination proteins release the ribosome from the mRNA, the polypeptide chain is released

Transcription

ACT I

• Transcription factors attach to the TATA box also known as the promoter
• The sequences before the TATA box are known as upstream, after the TATA box is known as downstream

• Transcription factors that bind to the the TATA box help attract RNA polymerase 2
• Once  RNA Polymerase 2 binds to transcription factors a transcription initiation complex is created and RNA starts transcribing
• A DNA strand can be transcribed  by several RNA polymerase 2, at a time

Act II

• The double stranded DNA is separated at certain points by RNA polymerase 2 
• The strand being transcribed is the template strand ( antisense) the other strand is the coding strand( sense) 
• The  RNA polymerase 2 binds RNA nucleotides to the template base pairs
• As the RNA strands grow they trail off from each polymerase and the DNA strands reform a helix 
• The RNA strand and template strand are anti-parallel
• Genes are read 3'-5' which creates a 5'-3' RNA molecule
• In RNA there is ''U'' instead of ''T" in the base pairs e.g A=U , T=A

Act III

• The terminator signals the end of transcription, it is the sequence AAUAAA
• At the end of the pre-mRNA molecule that was just synthesized a G cap is added to then of 5' and a Poly(A) tail is added at the end of the 3' 
• Introns (junk sequences that must be removed)
•  Extrons ( sequences that must be expressed) 
• The  spliceosome loops and cuts out the introns 
• It is composed of proteins and  snRNP
•  Every snRNPs has  a small nuclear RNA molecule/ snRNA
• The spliceosome also joins the exons, to create a mRNA molecule
• A messenger RNA has now been synthesized from the DNA strands

DNA Replication: Initiation,Elongation,Termination

Act I 

Initiation

Helicase splits/opens the template DNA strand at the replication fork = creation of bubble

Single-strand binding proteins stabilize the unwound parental DNA , otherwise there is a risk the strands will bond back together

A lot of tension has built up , from parts of the DNA strands being straightened. The gyrase cuts the stands to release tension

RNA primase creates RNA primers that act as a starting point for replication

The DNA polymerase III recognize the primers

Act II

Elongation 

The parental strands are replicated  in the direction of 5' to 3' 

Leading strand- Polymerase III begins adding nucleotides to the RNA primer in the direction of the opening  replication fork, it does this continuously

The lagging strand waits for enough of the replication fork to open ...... when it has opened sufficiently a DNA primer  attaches to the parental strand and polymerase III  makes a new starting point( discontinuous process)

The second strand is composed of  Okazaki fragments ( 100-200 nucleotides long) and RNA  primers 

Lagging= discontinuous, RNA primers, Okazaki fragments , polymerase III

Leading= continuous, 1 Primer, Polymerase III

The two new strands are assembled in the opposite direction

Act III

Termination 

Polymerase I removes the RNA nucelotides  one at a time, replacing them with DNA nucleotides, this process is catalyzed by DNA ligase 

Polymerase I and polymerase II( slow enzyme)  are repair mechanisms, they work to repair damage done to DNA during replication, and proofread

Catabolism & Anabolism

Catabolism

• Chemical reactions that result in the break down of complex organic molecules into simpler substances
• Releases energy that is used to start chemical reactions

Anabolism

• Simpler substances combine to become more complex
• requires energy
• build new molecules
• store energy

* Energy from catabolic reactions is used for anabolic reactions

Anabolic + catabolic=Metabolism 

Non-Cyclic

Anabolic reaction

Cyclic

Anabolic reactiom

Calvin Cycle

Anabolic reaction

Glycolosis

Catabolic reaction

Catabolic reaction

Krebs

Catabolic reaction

The Sad But True Story:Of The Passenger Pigeon

The Sad But True Story: Of The Passenger Pigeon (Ectopistes migratorius)





The passenger bird once constituted an estimated 25-40 % of America's bird population

When Europeans first discovered America there were 3-5 billion passenger pigeons

Never again will  a passenger pigeon soar through the sky... as 100 years ago they became extinct

Millions of these magnificent birds would travel in one flock.One flock traveling at sixty miles an hour would take several days to pass over a particular area.

 When they  migrated in  March and April one flock could block out the sun, making the sky dark for days.



The passenger pigeons had almost no defense mechanism, so they would travel in mass flocks as a means of protection against predators.

They would roost and feed in hardwood forests, until their natural habitat started being diminished and turned into farmland. Causing the pigeons to land on farmer's fields.

Humans started to kill passenger pigeons
- To protect their crop from being eaten
-  they were a cheap source of food , which was great for feeding slaves




The real slaughter of passenger pigeons started in the 1800's
They were :

• netted by baiting traps
• shot at nesting sites
• knocked out of  trees with long sticks
• the fumes of sulfur would case the birds to become dazed and fall out of trees

By using trains hunters could track and follow the flock giving them no rest and no time to mate and care for their young

In Michigan 50 000 pigeons were killed per day for 5 consecutive months.

In 1860 the decrease in population was noticeable, but nothing was successfully done to  protect their species

By 1890 they were considered a rare species, with only a few thousand remaining

A Glimpse of Hope

Finally the voice of conservationists was heard and a bill was passed  in Michigan,   making it illegal to net pigeons within two miles of a nesting area

However this law was hardly enforced... and the mass hunting continued

 In 1897 a ten year hunting ban on passenger pigeons began 

 It Was Too Late

 Despite conservationists efforts
 Not being able to breed and protect their blind and now defenseless young ,the population plummeted

Without a large flock the pigeons were defenseless to prey and unable to follow normal migration and mating habits

By 1914 only one of the species remained

Never again will man witness the beauty of  millions of passenger pigeons filling the sky above




Last of her species, died at 1 p.m.,
1 September 1914, age 29, in the
Cincinnati Zoological Garden.

Photosynthesis

Photosynthesis

- It was developed 450 million years ago 


Chemiosmosis:  The movement of chemicals from high to low concentrations via semi permable membranes

Oxidized = Giving away electrons
Reduced= Gaining electrons

PSI needs P700 from the sun
PSII needs to receive P680 from the sun

Chlorophyll is a green pigment found in chloroplasts









Thylakoids store molecules that absorb  energy from the sun


Light-dependent reaction
traps solar energy and uses it to generate ATP and NADPH

light- independent reaction
Assimilates carbon dioxide to produce an organic molecule that can be used to produce biologically important molecules

Hydrogen= single proton


NADP exists to carry energy around

ADP spins very fast and the protons need to slow it down to form ATP