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

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1 ranslation (written lesson) Q: How are proteins (amino acid chains) made from the information in mrn? : ranslation Ribosomes translate mrn into protein ranslation has 3 steps also! 1. ranslation Initiation: mrn binds to a ribosome and a trn binds to the ribosome, bringing in the first amino acid (a.a.) 2. ranslation Elongation: Ribosome covalently links a.a.'s together as additional trn's bring them to the ribosome in response to the message of the mrn. 3. ranslation ermination: When the "stop codon" of the mrn gets to the ribosome, translation stops. mrn is released from the ribosome; trn is released; newly synthesized protein is released. How does the mrn sequence of nucleotides direct a ribosome to connect the proper protein sequence of amino acids??? he genetic code = the way that the 4 bases of RN encode the amino acid sequence of protein. Proteins are made of monomers called amino acids. here are 20 different amino acids. Each protein is made of a different combination of a.a.'s. messenger RN is actually a code language that tells the ribosomes which amino acid to add first, second, third, etc. in the protein chain. he "code words" of mrn are called codons. 3 nucleotides specify one amino acid = a codon *U does code for an amino acid, Methianine, therefore "Met" is always the first amino acid in a protein. What is trn and what is its role in translation? trn'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. trn is a single-stranded RN molecule the folds on itself through H- bonds between internally complementary nucleotides. Once it has folded,

2 a trn is shaped like a cloverleaf. here are many different trn's. hey are all similar to one another in their cloverleaf shape, but each one carries a different a.a. Each trn has an "anti-codon" that is complementary to a specific codon of mrn. he a.a. that a trn carries corresponds to the codon that its own anti-codon recognizes. e.g. trn whose anti-codon is will carry the a.a. Phenylalanine/Phe because is complementary to the codon UU, which is a codon for Phe (see genetic code chart above.) U U NH 2 MINO ID = SPRE MINO ID = LEUINE What is the structure of the ribosome? How does a ribosome build proteins? he intact ribosome is actually a combination of two subunits. he 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 RN (rrn) and 2) many different proteins. ogether, the rrn'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) mrn-binding site, 2) trn-binding site #1 (also called the "P" site) 3) another trnbinding site, #2 (also called the "" site.)

3 How does the ribosome work with the trn's and with the mrn to elongate a chain of amino acids? Please see cartoon!!! 1. mrn binds to the small subunit of a ribosome, INIIION Of RNSLION then the 1 st transfer RN (always carries methionine) binds to the #1 binding site of the ribosome and to mrn's start codon 2. large subunit joins the complex 3. second trn binds to the ribosome's #2 site and to the second codon of the mrn. (he second trn is chosen by its anti-codon (because its anticodon is complementary to the codon of the mrn.)) Initiation of ranslation: mino cids t-rn s m-rn SR ODON Initiation omplex P Site Site Small Subunit of Ribosome Large Subunit of Ribosome

4 ELONION Of RNSLION he ribosome catalyzes a reaction: the two amino acids carried in by the two trn's are linked by a peptide bond. 4. he 1st trn is released, but the amino acid that it carried is now covalently linked to the second trn's amino acid. 5. he ribosome moves trn #2 over into trn-binding site #1. his leaves trn-binding site #2 open for a third trn to bind. he shift of trn #2 also pulls the mrn further into the ribosome. 6. trn'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 trn that was in binding site #2 over into site #1, pulling the mrn in a little and exposing site #2.

5 Elongation Phase of ranslation: mino cids t-rn s New Protein NH 2

6 ERMINION Of RNSLION 7. When a stop codon is reached, the newly formed protein chain is released by the ribosome. he last trn is released by the ribosome. he two subunits of the ribosome fall apart. he mrn is released by the ribosome. mino cids t-rn s New Protein SOP ODON NH 2

7 mino cids t-rn s m-rn OOH New Protein NH 2 End of ranslation Lesson

8 REPLIION (written lesson with still pictures) How is the double helix/dn replicated (during the S phase of interphase)? he two strands of the parent DN are antiparallel. his means that the end of one strand pairs with the end of the opposing strand. denine Hydrogen bonds to hymine and uanine H-Bonds to ytosine. hus we say that and are complementary and and are complementary. Steps in DN replication (synthesis): 1. Parental (double-stranded) DN molecule unwinds and hydrogen bonds between complementary pairs are broken leaving two separated, complementary backbones. he enzyme that performs the unwinding and separation is called DN Helicase. his enzyme gradually "unzips" the two strands of the parent molecule. DN Helicase Enzyme

9 2. Once the two parent strands have been separated by Helicase, new complementary strands are made, using the singlestranded parent strands as templates. he enzyme that performs the synthesis of new, complementary strands is DN Polymerase. (reates a polymer from monomers) DN Polymerase Enzymes Limitations of DN Polymerase: 1) DN Polymerase can only add free complementary nucleotides to parental strand's 3' end. Since the strands of DN 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 DN Polymerase. his strand is called the Leading Strand. DN Polymerase simply binds to the open 3' end and adds complementary bases along toward the branch point. he other parent strand must be copied in short, discontinuous pieces; therefore, it is called the lagging strand. DN 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.

10 his creates a short fragment of daughter strand. hen 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. On the Leading Strand DN Polymerase continuously adds new nucleotides, as it follows DN Helicase On the Lagging Strand DN Polymerase runs in the opposite direction of the Helicase, and therefore must make a series of discontinuous pieces (or fragments).

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12 2) he second limitation of DN Polymerase is that it cannot form a covalent bond between the fragments it has created on the lagging strand. he enzyme that does connect the fragments is called DN Ligase. 5 DN Ligase enzyme can connect the two fragments by forming a covalent bond between them. 5

13 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 DN molecule. hey are called sister chromatids. We now have two identical daughter molecules of DN, and the cell is ready for a Mitosis or a Meiosis division. 5 End of Replication Lesson

14 Electron ransport in the Mitochondria (Written Lesson) Most of the cell s P is generated by a process called chemiosmosis or oxidative phosphorylation which occurs as a result of electron transport in the mitochondria. IV. Electron ransport hain/system (ES) and hemiosmosis 1. occurs in/across the inner membrane of the mitochondria he Mitochondria up Inner Outer Membrane Matri Inter Membrane ompartment

15 2. high energy electrons from NDH or FDH 2 are transferred from one membrane-bound protein to the next e - NDH ND + + H + When NDH gives up its high-energy electrons, it also loses an H +; this reaction also produces ND +. he high-energy electrons are automatically passed (one electron at a time) from 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 ion gradient (forcing ions into an area of high concentration by active transport)

16 e - Each time the electron is passed, some of its energy is used for the active transport of H + into the inter-membrane Space. 5. the ions build up in the inter-membrane compartment (between the two mitochondrial membranes) 6. nother membrane-bound protein/enzyme named P Synthase is used as a channel through which the protons can flow down their gradient and back into the matrix. 7. When the ions flow down their gradient, they release Energy. hat released energy is used by the P Synthase to phophorylate (add a third phosphate group to) DP, producing P.

17 2 s the H + ions flow through the P Synthase, they release energy. his energy is used by the P Synthase to produce P. DP + Pi P 8. t the end of the electron transport chain, the final electron acceptor is oxygen gas, O 2, and when O 2 is reduced by accepting electrons, it also picks up Hydrogen atoms, becoming H 2 O.

18 e - he final electron acceptor is O 2 (Oxygen gas). O 2 accepts the electron as it releases the last of its energy. he O 2 also picks up H + creating H 2 O. O2 H2 O End of Electron ransport in ellular Respiration Lesson

19 he Light Reactions of Photosynthesis (Written Lesson) he 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. here are two types of photosystem in the thylakoid membrane; Photosystem I and Photosystem II. he hloroplast up lose Inner Outer Strom hylakoid Membrane Inter Membrane ompartment

20 Stroma he chloraphyll pigment molecules that are capable of capturing sunlight energy are clustered together in the hylakoid Membrane. hese clusters are called photosystems. his cluster is Photosystem II. hylakoid Membrane II hylakoid 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

21 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 hylakoid 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)

22 Stroma When water splits three products are formed: 1) O 2 (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 - H2O 1/2O2 hylakoid space 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 P. Except here the hylakoid ompartment is the Reservoir for H + ions.

23 Stroma s Photosystem II s electron is passed along, it moves to carriers with higher and higher redox potentials (more electronegative). herefore these redox reactions release energy. his energy is used to actively transport H + ions into the thylakoid space. e - II hylakoid space

24 Strom In the hloroplast, the H + ions flow down their gradient into the stroma, releasing energy as they go. his energy is used to drive synthesis of P. P e - DP + Pi I hylakoid 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. n excited electron from Photosystem I is ultimately passed to NDP+ which also accepts 2 electrons and 1 ion to form NDPH. hus NDP + is the final electron acceptor.

25 Stroma In Photosystem I s high energy electron is NO used as an energy source to pump H +. Rather, it is passed to the High-energy Electron arrier NDP +, which also picks up H +, generating NDPH. NDP + + H + NDP H II e - I e - hylakoid space *he differences between Photosystem I and II are that the arrangement of the chlorophylls is different, and their associated electron transport systems are different *he main product that comes from Photosystem II is P from Photosystem I is NDPH his P and NDPH will be used to power the reactions of the alvin ycle, the pathway where glucose is made.