Energy and Cellular Metabolism

1. Energy and Cellular Metabolism 4

2. Enzymes: Types of Reactions

3. Chemical Reactions: Overview Activation energy is the energy that must be put into reactants before a reaction can proceed A + B  C + D Figure 4-3

4. Enzymes: Speed Up Reactions Enzymes lower the activation energy of reactions Figure 4-8

5. Enzymes: Overview • Speed up the rate of reactions- they reduce the activation energy making easier for a reaction to occur. They may also perform reactions that would not otherwise take place. • Isozymes • Catalyze same reaction but under different conditions -such as in different tissue cells • May be activated, inactivated, or modulated • Proenzymes and zymogens are synthesized as inactive and undergo proteolytic reactions to activate • Coenzymes usually vitamins, are needed for proper function, can carry atoms removed at the active site • Chemical modulators, temperature, and pH also affects enzyme activity

6. ENZYMES • Metabolism is defined as the many chemical reactions that occur in organisms • Few metabolic reactions occur without the assistance of enzymes • Enzymes are made up of proteins and have the following characteristics • They function at an optimal pH and Temperature • They are denatured or deactivated if exposed to extreme pH and temperature • They only bind a specific molecule • They only perform one specific reaction • While they change the reactants into new products enzymes themselves are not changed during a reaction • They can be re-used multiple times • They may be permanently or temporarily inhibited

7. The Enzyme Substrate Complex • Enzymes can be recycled • This is a key characteristic of enzymes Substrate (sucrose) Enzyme available with empty active site 1 2 Substrate binds to enzyme Active site Enzyme (sucrase) Fructose Glucose Substrate is converted to products 4 3 Product are released Figure 5.9

8. Cofactors and competitive Inhibition Figure 2-19

9. Allosteric Modulation Figure 2-20a

10. Physical Regulators • Temperature-each protein has a adequate temperature for it’s function. Outside of the range it may be denatured of inactivated. • pH- each protein has a adequate temperature for it’s function. Outside of the range it may be denatured of inactivated. • Concentration of protein –amounts in body vary over time to control physiological processes • Up-regulation – programmed production of protein • Down regulation – programmed removal of protein • Concentration of ligand – determines the magnitude of the reponse if the protein concentration is the same. • Reaction rates – speed up as ligand concentration increases up until saturation is reached.

11. A Review of DNA & RNA Structure • Nucleic Acids are ____? What does DNA stand for? How does DNA compare to RNA? Why is RNA needed? Cap End Tail Start of genetic message Visual Summary 3.3 Figure 10.17

12. Nucleotides, DNA, and RNA • Nucleotides are the monomers of nucleic acids. • DNA and RNA have different nucleotides . • In DNA A –T and C-G pair up. There is no pairing in RNA but RNA nucleotides pair up with DNA nucleotides

13. Synthesis: Protein Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression TRANSCRIPTION 2 mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus • rRNA in ribosomes • tRNA • Amino acids Cytoplasm 4 TRANSLATION Protein chain 5 POST-TRANSLATIONAL MODIFICATION Folding and cross-links Cleavage into smaller peptides Addition of groups: • sugars • lipids • —CH3 • phosphate Assembly into polymeric proteins The major steps required to convert the genetic code of DNA into a functional protein are done by enzymes We have20 different amino acids made from 4 nitrogenous bases Figure 4-24

14. Transcription and Translation • What is the language of nucleic acids? • In DNA, it is the linear sequence of nucleotide bases • When DNA is transcribed, the result is an RNA molecule • RNA is then translated into a sequence of amino acids in a polypeptide • Triplets of bases are called codons and they specify all of the amino acids DNA molecule Gene 1 Gene 2 Gene 3 DNA strand Transcription RNA Codon Translation Polypeptide Amino acid Figure 10.10

15. The Genetic Code • The genetic code is the set of rules relating nucleotide sequence to amino acid sequence • Use the RNA sequence in codons to determine the corresponding amino acid Figure 10.11

16. Synthesis: Protein Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA Nucleus Cytoplasm Figure 4-24, steps 1–2

17. Synthesis: Protein Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus Cytoplasm Figure 4-24, steps 1–3

18. Synthesis: Protein Gene Regulatory proteins 1 GENE ACTIVATION Constitutively active Regulated activity Induction Repression 2 TRANSCRIPTION mRNA siRNA 3 mRNA PROCESSING Alternative splicing Interference mRNA “silenced” Processed mRNA Nucleus • rRNA in ribosomes • tRNA • Amino acids Cytoplasm 4 TRANSLATION Protein chain 5 POST-TRANSLATIONAL MODIFICATION Addition of groups: • sugars • lipids • —CH3 • phosphate Cleavage into smaller peptides Folding and cross-links Assembly into polymeric proteins Figure 4-24, steps 1–5

19. Protein: Transcription • Transcription factors bind and activate promoter region • RNA polymerase binds and “unwinds” DNA • mRNA created from sense strand • mRNA is processed by • RNA interference • Alternative splicing RNA nucleotides RNA polymerase Newly made RNA Direction of transcription Template strand of DNA Figure 10.13a

20. RNA polymerase • Transcription of an entire gene • Three stages • Initiation of transcription • Elongation of RNA Strand • Termination of transcription DNA of gene Promoter DNA Terminator DNA Initiation RNA Area shown in part (a) Elongation Termination Growing RNA Completed RNA RNA polymerase (b) Transcription of a gene Figure 10.13b

21. The Processing of Eukaryotic RNA Intron Exon Exon Exon Intron • The eukaryotic cell processes the RNA after transcription • RNA processing includes • Adding a cap and tail • Removing introns • Splicing exons together DNA Transcription Addition of cap and tail Cap RNA transcript with cap and tail Tail Introns removed Exons spliced together mRNA Coding sequence Nucleus Cytoplasm Figure 10.14

22. Translation: The Players • Translation is the conversion from the nucleic acid language to the protein language • There are three types of RNA • mRNA is messenger RNA, it is created during transcription • tRNA is transfer RNA it carries the amino acid and an anticodon • rRNA is ribosomal RNA, it forms the units of the ribosome

23. Transfer RNA (tRNA) • tRNA • Acts as a molecular interpreter • Carries amino acids • Matches amino acids with codons in mRNA using anticodons Amino acid attachment site Hydrogen bond RNA polynucleotide chain Anticodon Anticodon Figure 10.15

24. Ribosomes • Ribosomes • Are organelles that actually make polypeptides • Are made up of two protein subunits • Contain ribosomal RNA (rRNA) • A fully assembled ribosome holds tRNA and mRNA for use in translation Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA (b) Figure 10.16b

25. Intiation of Translation • Translation is divided into three phases • Initiation • Elongation • Termination • The first phase brings together • The mRNA • The first amino acid with its attached tRNA • The two subunits of the ribosome • The process of initiation is the assembly stage and is signaled by the codon AUG that matches the anticodon UAC Met Initiator tRNA mRNA Start codon 1 Small ribosomal subunit Large ribosomal subunit A site P site Initiation 2 Figure 10.18.1

26. Formation of a polypeptide chain Amino acid • The process of elongation • The anticodon of an incoming tRNA pairs with the mRNA codon • The ribosome catalyzes bond formation between amino acids • A tRNA leaves the P site of the ribosome • The ribosome moves down the mRNA Polypeptide P site Anticodon mRNA A site Codons 1 Codon recognition Elongation 2 Peptide bond formation New peptide bond mRNA movement 3 Figure 10.19 Translocation

27. Termination RNA Polymerase 1 Transcription Nucleus RNA transcript DNA Elongation continues until the ribosome reaches a stop codon The stop codon signals all the pieces that come together at initiation to disassemble The end result is a polypeptide 2 Intron RNA processing Amino acid CAP Tail mRNA Intron Enzyme tRNA 3 Amino acid attachment Ribosomal subunits 4 Initiation of translation Stop codon Anticodon Codon 6 Termination 5 Elongation Figure 10.20

28. Protein: Transcription and Translation DNA 1 Transcription Nuclear membrane RNA polymerase mRNA processing 2 Figure 4-27, steps 1–2

29. Protein: Transcription and Translation DNA 1 Transcription Nuclear membrane RNA polymerase mRNA processing 2 3 Attachment of ribosomal subunits Figure 4-27, steps 1–3

30. Protein: Transcription and Translation DNA 1 Transcription Nuclear membrane RNA polymerase mRNA processing 2 Amino acid Growing peptide chain tRNA Incoming tRNA bound to an amino acid 4 Translation Lys Asp Phe Trp Outgoing “empty” tRNA 3 Attachment of ribosomal subunits U U U C U A Anticodon A A C C G A A A G A A G U G U C U U mRNA Ribosome Each tRNA molecule attaches at one end to a specific amino acid. The anticodon of the tRNA molecule pairs with the appropriate codon on the mRNA, allowing amino acids to be linked in the order specified by the mRNA code. Figure 4-27, steps 1–4

31. Protein: Transcription and Translation DNA 1 Transcription Nuclear membrane RNA polymerase mRNA processing 2 Amino acid Growing peptide chain tRNA Incoming tRNA bound to an amino acid 4 Translation Lys Asp Phe Trp Outgoing “empty” tRNA 3 Attachment of ribosomal subunits U U U C U A Anticodon A A C C G A A A G A A G U G U C U U mRNA Ribosome mRNA 5 Termination Each tRNA molecule attaches at one end to a specific amino acid. The anticodon of the tRNA molecule pairs with the appropriate codon on the mRNA, allowing amino acids to be linked in the order specified by the mRNA code. Ribosomal subunits Completed peptide Figure 4-27, steps 1–5

32. Protein: Post-Translational Modification • Protein folding • Creates tertiary structure • Cross-linkage • Strong covalent bonds  disulfide • Cleavage • Addition of other molecules or groups • Assembly into polymeric proteins