Introduction to Cellular Metabolism and Protein Synthesis

1. Chapter 4 Cellular Metabolism

2. Nucleic Acids and Protein Synthesis

3. Introduction • Because enzymes regulate metabolic pathways that allow cells to survive, cells must have the information for producing these special proteins • Recall that proteins have several important functions in cells, including structure (keratin), transport (hemoglobin), defense (antibodies), etc

4. Genetic Information • DNA holds the genetic information which is passed from parents to their offspring • Offspring has a mix of the two parents’ DNA • This genetic information, DNA, instructs cells in the construction of proteins (great variety, each with a different function) • The portion of a DNA molecule that contains the genetic information for making one kind of protein is called a gene

5. Genetic Information cont. • All of the DNA in a cell constitutes the genome • Over the last decade, researchers have deciphered most of the human genome • The key to how DNA ,confined to the nucleus, can direct the synthesis of proteins, at ribosomes outside the nucleus, is in the structure of DNA and RNA molecules • i.e. the genetic code

6. Genetic Code • Specified by sequence of nucleotides in DNA • Each triplet (three adjacent nucleotides) “codes” for an amino acid • Many triplets code for many amino acids, which are hooked together to form a polypeptide chain • RNA molecules facilitate the conversion of DNA triplets to an amino acid sequence

7. Nucleic Acid Structure • Both DNA and RNA share the same basic structure • Both are made up nucleotides, which consist of: • A 5-carbon sugar • Phosphate group • Nitrogen containing base • These Nitrogen containing bases pair up in specific ways

8. Basic structure of DNA and RNA

9. Base Pairs • Nucleotides will always for pairs with the same complimentary nucleotide • Complementary base pairs • DNA • A pairs with T • C pairs with G • RNA • A pairs with U • C pairs with G

11. Deoxyribonucleic Acid: (DNA) • DNA is composed of nucleotides: a pentose sugar molecule (deoxyribose) • a nitrogen-containing base • a purine (double ring) • adenine (A) and guanine (G) • a pyrimidine (single ring) • cytosine (C) and thymine (T) • a phosphate group • The two strands are twisted into a double helix • Strands face opposing directions

12. Nucleotides (DNA and RNA)

13. DNA Structure

15. Ribonucleic Acid (RNA) • RNA (like DNA) is composed of nucleotides, each containing the following: • a pentose sugar molecule (ribose) • a nitrogen-containing base • purine: • adenine (A) and guanine (G) • pyrimidine: • cytosine (C) and uracil (U) • a phosphate group • Each RNA strand is made up of a backbone of ribose sugars alternating with phosphate groups. • Each ribose sugar is linked to either A, G, C, or U.

16. RNA cont. • Each RNA molecule consists of a single strand of nucleotides. • There are three types of RNA molecules which assist the cell in protein synthesis: • Messenger RNA (mRNA) carries the code for the protein to be synthesized, from the nucleus to the protein synthesizing machinery in the cytoplasm (i.e. ribosome).

17. RNA cont. • Transfer RNA (tRNA) carries the appropriate amino acid to the ribosome to be incorporated into the newly forming protein • Ribosomal RNA (rRNA) along with protein make up the protein synthesizing machinery, the ribosome

18. Protein Synthesis • Protein synthesis can be divided into two major steps, transcription and translation. • Transcription= The process of copying information from DNA to messenger RNA • Think of “transcribing (copying) from one nucleic acid to another” • Translation= The process of creating amino acid chains from messenger RNA • Think of “translating nucleic acid into protein”

19. Nucleus: Transcription Protein Synthesis Cytoplasm: Translation DNA mRNA RNA polym-erase mRNA Amino Acid chain (polypeptide) mRNA moves out of the nucleus Ribosomes

20. Transcription • Transcription=is the process of copying the information from a DNA molecule, and putting it into the form of a messenger RNA (mRNA) molecule • One gene is read, containing the information for a specific protein • occurs in the nucleus of the cell • The DNA strands unwind and the H-bonds between the strands are broken

21. Transcription cont. • Only one of the exposed templates of the DNA molecule (i.e. the gene) is used to build the mRNA strand • Template strand= strand that the mRNA is made from • Coding strand= strand that is not used to make RNA • RNA polymerase (an enzyme) attaches to the template strand • Then positions and links RNA nucleotides into a strand

22. Transcription cont. • The message (mRNA): • is complementary to the bases on the DNA strand • Matches up in the same was a bases in DNA match to each other • is in the form of a triple base code, represented by codons (i.e. AUG, CUA, ACG, GUU) • Each codon on mRNA codes for one amino acid in the protein to be synthesized

23. Transcription cont. • This code is redundant, meaning several codons can code for the same amino acid • Only 20 amino acids but many more possible combinations of codons • This is an advantage in a protection against mistakes in the next step, translation. • A mistake could be made in creating the mRNA, but the same amino acid may still be produced • The wrong one could result in a nom-functional protein

25. Transcription cont.

26. Translation • Translation =is the process by which the mRNA is "translated" into a protein. • occurs at ribosomes that are either free in the cytoplasm or are attached to ER (as RER). • can only start at the start codon AUG, which codes for methionine • Transfer RNA (tRNA) molecules assist in translation by bringing the appropriate amino acid for each codon to the ribosome. • Shape formed from hydrogen bonds

27. Translation cont. • The tRNA molecule has an anticodon which is complementary to the codon on the mRNA strand • Codon for Glycine = GGG • Anticodon on the tRNA =CCC • tRNA carries Glycine to the ribosome

28. Translation cont. • Two codons of mRNA are read in the ribosome at the same time. • The tRNA molecules deliver their amino acids to the ribosome, and a peptide bond is formed between adjacent amino acids. • The mRNA molecule is read codon by codon, with each corresponding amino acid being added to the chain of amino acids. • A protein is synthesized.

29. Translation cont. • The mRNA molecule is read until a stop codon (UAA, UAG, UGA) on the mRNA is reached: • The protein is released into the cytoplasm or RER • The mRNA molecule can be read again and again

32. DNA Replication

33. Introduction • DNA holds the genetic code which is passed from parents to their offspring. • Happens in the nucleus • During interphase (S phase) of the cell cycle, our DNA is replicated • so each new daughter cell is provided with an identical copy of this genetic material

35. Process of DNA Replication • DNA uncoils, and unzips (hydrogen bonds are broken between A:T and G:C) • The two strands separate • Necessary for enzymes to “read” the DNA • Each free nucleotide strand now serves as a template (a set of instructions) for building a new complementary DNA strand. • DNA nucleotides that are present in the nucleoplasm begin to match up with their complements on the templates.

37. Process of DNA Replication cont. • DNA polymerase (an enzyme) positions and links these nucleotides into a strand • This results in two identical DNA molecules, each consisting of one old and one newly assembled nucleotide strand. • This type of replication is called semi-conservative replication.

39. Changes in Genetic Information • If there is an error in the DNA code (i.e. in a gene), this is called a mutation. • Nature of Mutations • DNA replication errors • Proteins are altered • Usually repair enzymes prevent mutations

40. Effect of Mutations • One place mutations an occur is during DNA replication • There are several kinds of mutations that can effect the genetic code • Point mutations=single base pair change • Frame shift=insertion or deletion of a base • More dangerous • Mutations can also occur spontaneously • Mutagens=particular chemical substances • Mutations can effect the productions of proteins

42. Effects of Mutations • Protein may not be made at all • When an enzyme is lacking from a metabolic pathway, childhood storage diseases (accumulation of A or B, etc) result. • This occurs in PKU, Tay-Sachs, and Niemin-Pick disease. • A protein may have altered function • In cystic fibrosis (altered chloride pump) & sickle-cell anemia (altered hemoglobin structure) • A protein may be produced in excess • In epilepsy where excess GABA leads to excess norepinephrine and dopamine

43. Metabolic Processes

44. Metabolic Processes Metabolism =the sum of an organism's chemical reactions. • Each reaction is catalyzed by a specific enzyme • The reactions typically occur in pathways (i.e. in a sequence) • Reactions are divided into two major groups, anabolism and catabolism. • Products from one reaction can be the reactants for the next • New enzyme for each

45. Anabolic Reactions Anabolic Reactions = synthesis reactions: • Building complex molecules from simpler ones • (i.e. monomers into polymers) • Bonds are formed between monomers which now hold energy (= Endergonic reactions) • Water is removed between monomers to build the bond, termed Dehydration. • Used to make carbohydrate, lipid, and protein molecules

46. Anabolic Reactions cont. energy  C + D C---D  water • Example is to build a protein (polymer) from individual amino acids (monomers).

47. Catabolic Reactions Catabolic Reactions = decomposition reactions: • Breaking complex molecules into simpler ones • (i.e. polymers into monomers) • Bonds are broken between monomers releasing energy (= Exergonic reactions) • Water is used to break the bonds, termed Hydrolysis • Reverse of dehydration synthesis

48. Catabolic Reactions cont. water  A---B A + B  energy • Example is breaking a nucleic acid (polymer) into nucleotides (monomers)