Translation (written lesson)

Q: How are proteins (amino acid chains) made from the information in mRNA? A: Translation Ribosomes translate mRNA into protein

Translation has 3 steps also! 1. Translation Initiation: mRNA binds to a ribosome and a tRNA binds to the ribosome, bringing in the first amino acid (a.a.) 2. Translation Elongation: Ribosome covalently links a.a.'s together as additional tRNA's bring them to the ribosome in response to the message of the mRNA. 3. Translation Termination: When the "stop codon" of the mRNA gets to the ribosome, translation stops. mRNA is released from the ribosome; tRNA is released; newly synthesized protein is released. How does the mRNA sequence of nucleotides direct a ribosome to connect the proper protein sequence of amino acids??? The genetic code = the way that the 4 bases of RNA encode the amino acid sequence of protein. Proteins are made of monomers called amino acids. There are 20 different amino acids. Each protein is made of a different combination of a.a.'s.

A messenger RNA is actually a code language that tells the ribosomes which amino acid to add first, second, third, etc. in the protein chain. The "code words" of mRNA are called codons.

 3 nucleotides specify one amino acid = a codon *AUG does code for an amino acid, Methianine, therefore "Met" is always the first amino acid in a protein.

What is tRNA and what is its role in translation?  tRNA's carry amino acids (a.a.'s) to the ribosome during translation; the ribosome then links the a.a.'s together into a peptide chain.  tRNA is a single-stranded RNA molecule the folds on itself through H- bonds between internally complementary nucleotides. Once it has folded, a tRNA is shaped like a cloverleaf.  There are many different tRNA's. They are all similar to one another in their cloverleaf shape, but each one carries a different a.a.  Each tRNA has an "anti-codon" that is complementary to a specific codon of mRNA. The a.a. that a tRNA carries corresponds to the codon that its own anti-codon recognizes. e.g. A tRNA whose anti-codon is AAG will carry the a.a. “Phenylalanine/Phe” because AAG is complementary to the codon UUC, which is a codon for Phe (see genetic code chart above.)

GAC CUG CUG GAC 5’ 3’

AMINO ACID = NH2 AMINO ACID = ASPARTATE LEUCINE

What is the structure of the ribosome? How does a ribosome build proteins?  The intact ribosome is actually a combination of two subunits. The two subunits are named the "small subunit" and the "large subunit" and they must come together before translation can begin.  Ribosome subunits are made of 1) ribosomal RNA (rRNA) and 2) many different proteins. Together, the rRNA's and the proteins of a ribosome's subunits act as a huge enzyme complex that can create proteins by forming new peptide bonds between a.a.'s.  Every intact ribosome has three important active sites: 1) mRNA-binding site, 2) tRNA-binding site #1 (also called the "P" site) 3) another tRNA- binding site, #2 (also called the "A" site.)

How does the ribosome work with the tRNA's and with the mRNA to elongate a chain of amino acids? Please see cartoon!!! 1. mRNA binds to the small subunit of a ribosome, then the 1st transfer RNA (always carries INITIATION methionine) binds to the #1 binding site of the Of TRANSLATION ribosome and to mRNA's start codon 2. large subunit joins the complex 3. A second tRNA binds to the ribosome's #2 site and to the second codon of the mRNA. (The second tRNA is chosen by its anti-codon (because its anti- codon is complementary to the codon of the mRNA.))

Initiation of Translation:

Amino Acids

t-RNA’s m-RNA

START CODON

5’ 3’ Initiation Small Subunit Complex of Ribosome Large Subunit of Ribosome P Site A Site

The ribosome catalyzes a reaction: the two amino acids carried in by the two tRNA's are linked by a peptide bond. 4. The 1st tRNA is released, but the amino acid that it carried is now covalently linked to the second tRNA's amino acid. 5. The ribosome moves tRNA #2 over into ELONGATION Of tRNA-binding site #1. This leaves TRANSLATION tRNA-binding site #2 open for a third tRNA to bind. The shift of tRNA #2 also pulls the mRNA further into the ribosome. 6. tRNA's continue to deliver a.a.'s to the ribosome, and the ribosome continues to covalently link the amino acids by forming peptide bonds between them. Each time an amino acid is added to the growing chain, the ribosome shifts the tRNA that was in binding site #2 over into site #1, pulling the mRNA in a little and exposing site #2.

Elongation Phase of Translation:

Amino Acids

t-RNA’s

5’ 3’

New Protein

NH2

TERMINATION 7. When a stop codon is reached, the newly Of TRANSLATION formed protein chain is released by the

ribosome. The last tRNA is released by the ribosome. The two subunits of the ribosome fall apart. The mRNA is released by the ribosome. Amino Acids

t-RNA’s

5’ 3’

New Protein STOP CODON

NH2

Amino Acids

t-RNA’s m-RNA COOH

5’ 3’ New Protein

NH2

End of Translation Lesson

REPLICATION (written lesson with still pictures) How is the double helix/DNA replicated (during the S phase of interphase)?

The two strands of the parent DNA are antiparallel. This means that the 5’ end of one strand pairs with the 3’ end of the opposing strand. Adenine Hydrogen bonds to Thymine and Guanine H-Bonds to Cytosine. Thus we say that A and T are complementary and G and C are complementary. Steps in DNA replication (synthesis): 1. Parental (double-stranded) DNA molecule unwinds and hydrogen bonds between complementary pairs are broken leaving two separated, complementary backbones. The enzyme that performs the unwinding and separation is called DNA Helicase. This enzyme gradually "unzips" the two strands of the parent molecule. 5’ A T 3’ G C A T

T A G C DNA Helicase Enzyme C G A T A T T A

T A G C 3’ 5’ G C

2. Once the two parent strands have been separated by Helicase, new complementary strands are made, using the single- stranded parent strands as templates.

The enzyme that performs the synthesis of new, complementary strands is DNA Polymerase. (Creates a polymer from monomers) 5’ A T 3’ G C DNA Polymerase A T Enzymes

T A G C C G A T T A A T A T C 3’ G 5’ C G

Limitations of DNA Polymerase: 1) DNA Polymerase can only add free complementary nucleotides to parental strand's 3' end. Since the strands of DNA are anti-parallel, when Helicase opens the molecule one single-stranded parent has a free 3' end, but the other has a free 5' end. Only the parent whose 3' end is single-stranded will be copied continuously by DNA Polymerase. This strand is called the Leading Strand. DNA Polymerase simply binds to the open 3' end and adds complementary bases along toward the branch point. The other parent strand must be copied in short, discontinuous pieces; therefore, it is called the lagging strand. DNA polymerase "waits" for helicase to unzip an entire segment of the double helix, it binds to the lagging strand at the branch point, which is its 3' end, and adds nucleotides away from the branch point. This creates a short fragment of daughter strand. Then the enzyme waits for another segment of lagging strand to be exposed by Helicase, and then it binds near the branch point and adds nucleotides down toward the small fragment it previously created.

5’ T 3’ A On the “Leading Strand” G DNA Polymerase C continuously adds new A T T nucleotides, as it T A follows DNA Helicase A G C C C G G On the “Lagging Strand” A T A T DNA Polymerase 5’ A T runs in the opposite A T direction of the Helicase, T A T A and therefore must make T A a series of discontinuous T A pieces (or fragments). C G C G 5’ 3’ G C 5’ 3’ G C

5’ 5 A T 3’ A T G C G C A T A T

T A T A G C C C G G A T 5’ A T A T A T T A T A

T A T A C G C G 3’ 5’ 3’ G C 5 G C

2) The second limitation of DNA Polymerase is that it cannot form a covalent bond between the fragments it has created on the lagging strand. The enzyme that does connect the fragments is called DNA Ligase. 5’ 5 A T 3’ A T 3’ G C G C A T A T DNA Ligase enzyme T A can connect the two T A fragments by forming G C G C a covalent bond C G between them. 3’ C G A T 5’ A T A T A T T A T A A T A T G C G C 5’ 3’ G C 5 3’ G C

Since the two strands of the parent molecule were complementary, and since the two new strands are complementary to the parent, the two, double-stranded daughter molecules are identical to each other and to the original/parent DNA molecule. They are called sister chromatids.

5’ 5’ A T 3’ A T 3’ G C G C A T A T We now have two T A identical daughter T A molecules of DNA, G C G C and the cell is ready for C G a Mitosis or a Meiosis C G division. A T A T A T A T T A T A A T A T G C G C 5’ 3’ G C 5 3’ G C

End of Replication Lesson

Electron Transport in the Mitochondria (Written Lesson)

Most of the cell’s ATP is generated by a process called chemiosmosis or oxidative phosphorylation which occurs as a result of electron transport in the mitochondria.

IV. Electron Transport Chain/System (ETS) and Chemiosmosis 1. occurs in/across the inner membrane of the mitochondria The Mitochondria up

Inner

Outer Membrane

Matri

Inter Membrane Compartment

2. high energy electrons from NADH or FADH2 are transferred from one membrane-bound protein to the next

H+ H+ H+ H+ H+

When NADH gives up its high-energy electrons, it also - e loses an H+; this reaction also produces NAD+.

The high-energy electrons NADH are automatically passed (one electron at a time) from NAD+ + H+ one protein to the next.

3. at each pass... the electron becomes more stable, and a little bit of its high energy is released 4. that released energy is used to create an H+ ion gradient (forcing H+ ions into an area of high concentration by active transport) H+ H+ H+ H+ H+ H+ H+ e-

Each time the electron is passed, some of its energy is H+ used for the active transport of H+ into the inter-membrane Space.

5. the H+ ions build up in the inter-membrane compartment (between the two mitochondrial membranes) 6. Another membrane-bound protein/enzyme named ATP Synthase is used as a channel through which the protons can flow down their gradient and back into the matrix. 7. When the H+ ions flow down their gradient, they release Energy. That released energy is used by the ATP Synthase to phophorylate (add a third phosphate group to) ADP, producing ATP. H+ H+ H+ H+ H+ H+

2

As the H+ ions flow through the ATP Synthase, they release ADP + Pi energy. This energy is used by

the ATP Synthase to produce ATP ATP. H+ H+

8. At the end of the electron transport chain, the final

electron acceptor is oxygen gas, O2, and when O2 is reduced by accepting electrons, it also picks up Hydrogen

atoms, becoming H2O. H+ H+ H+ H+ H+ H+

e-

The final electron acceptor is O2 (Oxygen gas). O2 accepts the electron as it releases the last of its O2 + H2 energy. The O2 also picks up H O creating H2O. H+

End of Electron Transport in Cellular Respiration Lesson

The Light Reactions of Photosynthesis (Written Lesson)

The light reactions of photosynthesis occur in the thylakoid membrane of the chloroplast. Sunlight energy is absorbed by photosystems which are collections of chlorophyll pigment molecules embedded in the thylakoid membrane. There are two types of photosystem in the thylakoid membrane; Photosystem I and Photosystem II.

The Chloroplast up Close

Inner

Outer

Strom

Inter Membrane Compartment Thylakoid Membrane

Stroma The chloraphyll pigment molecules that are capable of capturing sunlight energy are clustered together in the Thylakoid Membrane. These clusters are called photosystems. This cluster is Photosystem II.

Thylakoid Membrane

II

Thylakoid space

Photosystem II (only called II because it was the second of the two to be understood) 1. the chlorophyll absorbs the energy from sunlight 2. the reaction center (a single chlorophyll) collects all the energy from surrounding chlorophyll molecules 3. two of the electrons of the reaction center chlorophyll absorb so much energy that they leave the chlorophyll altogether Stroma One of the reaction center’s electrons becomes so energetic that it jumps off the photosystem and onto the first carrier, and then is passed along horizontally by redox reactions.

e -

II

Thylakoid space

4. because the chlorophyll does not like losing electrons, it requires a replacement for it's lost electron... the replacement electron is produced by the splitting of one molecule of H2O (this is the step that produces oxygen gas) Stroma When water splits three products are formed: 1) O2 (this is the step where plants generate Oxygen gas) 2) H+ ions • Electrons that are immediately used to replace the reaction center’s lost electron.

e-

II 2e-

1/2O2 H+ Thylakoid space H2O H+ H+ H+ H+ H+

5. the excited electron from chlorophyll is accepted by a protein of the electron transport system 6. the same type of chemiosmosis that occurs in mitochondria also occurs in the thylakoid disc to produce ATP. Except here the Thylakoid Compartment is the Reservoir for H+ ions. Stroma As Photosystem II’s electron is passed along, it moves to carriers with higher and higher redox potentials (more electronegative). Therefore these redox reactions release energy. This energy is used to actively transport H+ ions into the thylakoid H+ space.

e-

II

H+ H+ H+ Thylakoid space H+ H+

Strom In the Chloroplast, the H+ ions flow down their gradient into the stroma, releasing energy as they go. This energy is used to drive synthesis of ATP.

H+ ATP

ADP + Pi e-

I

H+ H+ H+ Thylakoid H+

7. the final electron acceptor of Photosystem II is the reaction center chlorophyll in Photosystem I *In Photosystem I electrons are also excited by sunlight. An excited electron from Photosystem I is ultimately passed to NADP+ which also accepts 2 electrons and 1 H+ ion to form NADPH. Thus NADP+ is the final electron acceptor. Stroma In Photosystem I’s high energy electron is NOT used as an energy source to pump H+. Rather, it is passed to the “High-energy Electron Carrier” NADP+, which also picks up H +, generating NADPH.

NADP+ + H+ NADP H

e - II I e -

H+ H+ H+ Thylakoid space H+ H+

*The differences between Photosystem I and II are that the arrangement of the chlorophylls is different, and their associated electron transport systems are different *The main product that comes from Photosystem II is ATP from Photosystem I is NADPH

This ATP and NADPH will be used to power the reactions of the Calvin Cycle, the pathway where glucose is made.