AP Biology

1. AP Biology Exam Critical Concepts Chapter 17 & 20 Protein Synthesis and Biotech

2. Chapter 17 Protein Syntheis • RNA is the intermediate between genes and the proteins for which they code • Protein synthesis is two steps • Transcription: synthesis of RNA from DNA • produces messenger RNA (mRNA) • Translation: synthesis of a polypeptides • occurs under the direction of mRNA • Ribosomes are the sites of translation • Prokaryotes: mRNA is immediately translated without more processing • Eukaryotes: nuclear envelope separates transcription from translation

3. Chapter 17 Protein Synthesis cont. • The central dogma: DNA to RNA to Protein • Codon: flow of information from gene to protein is based on this triplet code • 20 amino acids make up all proteins • Each codon specifies the addition of one of 20 amino acids • Of the 64 triplets: 61 code for amino acids • 3 triplets are “stop” signals to end translation • The genetic code is redundant but not ambiguous • no codon specifies more than one amino acid • The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals

4. Chapter 17 Protein Synthesis cont. • Template strand: one of the two DNA strands provides a template for ordering the sequence of nucleotides in RNA transcription • RNA polymerase: pries the DNA strands apart and hooks together the RNA nucleotides with the Same base pairing rules as DNA, except no thymine, uracil • attaches at the promoter • Transcription unit: stretch of DNA that is transcribe • The three stages of transcription: • Initiation • Elongation • Termination

5. Chapter 17 Protein Synthesis cont. • Initiation: begins transcription • Transcription factors: mediate the binding of RNA polymerase and the initiation of transcription • Transcription initiation complex: the completed assembly of transcription factors and RNA polymerase II bound to a promoter • TATA box: promoter made up of thymine and adenine is where transcription begins • Elongation: RNA transcript is “built” • As RNA polymerase moves along the DNA, it untwists the double helix • A gene can be transcribed simultaneously by several RNA polymerases

6. Chapter 17 Protein Synthesis cont. • Termination: RNA transcript is completed • Different in bacteria and eukaryotes • Bacteria: the polymerase stops transcription at the end of the terminator • Eukaryotes: the polymerase continues transcription after the pre-mRNA is cleaved • Transcript processing: modify pre-mRNA before the genetic messages are dispatched to the cytoplasm • both ends of the primary transcript are altered • some interior parts of the molecule are cut out, and the other parts spliced together

7. Chapter 17 Protein Synthesis cont. • Each end of a pre-mRNA molecule is modified in a particular way: • The 5 end receives a modified nucleotide 5 cap • The 3 end gets a poly-A tail • These modifications share several functions: • They seem to facilitate the export of mRNA • They protect mRNA from hydrolytic enzymes • They help ribosomes attach to the 5 end • Introns: noncoding stretches of nucleotides that lie between coding regions • Exons: coding regions eventually expressed

8. Chapter 17 Protein Synthesis cont. • RNA splicing: removes introns and joins exons • creating an mRNA molecule with a continuous coding sequence Exon Exon Intron 5’ Exon Intron 3’ Pre-mRNA Poly-A tail 5’ Cap 146 31 104 1 105 30 Introns cut out and exons spliced together Coding segment mRNA 5’ Cap Poly-A tail 1 146 5’ UTR 3’ UTR

9. Chapter 17 Protein Synthesis cont. • Spliceosomes: a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites • Ribozymes: catalytic RNA molecules that function as enzymes and can splice RNA • Alternative RNA splicing: some genes can encode more than one kind of polypeptide • depending on which segments are treated as exons during RNA splicing • the number of different proteins an organism can produce is much greater than its number of genes

10. Chapter 17 Protein Synthesis cont. • Importance of Introns: • Domains: Proteins have modular architecture consisting of these discrete regions • In many cases, different exons code for the different domains in a protein • Exon shuffling: may result in the evolution of new proteins

11. Chapter 17 Protein Synthesis cont. • Translation: mRNA into proteins • Cell translates an mRNA message into protein with the help of transfer RNA (tRNA) • Molecules of tRNA are not identical: • Each carries a specific amino acid on one end • Anticodon on the other end • base-pairs with a complementary codon on mRNA • Ribosomes: facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis • The two ribosomal subunits (large and small)

12. Chapter 17 Protein Synthesis cont. Amino acids • Ribosome Binding sites: 1. P site: holds the tRNA that carries the growing polypeptide chain 2. A site: holds the tRNA that carries the next amino acid to be added to the chain 3. E site: exit site tRNAs leave the ribosome Polypeptide tRNA with amino acid attached Ribosome Trp Phe Gly tRNA Anticodon Codons 5’ 3’ mRNA

13. Chapter 17 Protein Synthesis cont. • The three stages of translation: • Initiation • Elongation • Termination • Initiation: • A small ribosomal subunit binds with mRNA and a special initiator tRNA • The small subunit moves along the mRNA until it reaches the start codon (AUG) • Initiation factors bring in the large subunit that completes the translation initiation complex

14. Chapter 17 Protein Synthesis cont. • Elongation: • Amino acids are added one by one to the preceding amino acid • Each addition involves proteins called elongation factors • Termination: • Stop codon on mRNA reaches the ribosome A site • A site accepts a protein called a release factor • Release factor causes the addition of a water molecule instead of an amino acid • This reaction releases the polypeptide, and the translation assembly then comes apart

15. Chapter 17 Protein Synthesis cont. • Polyribosome (or polysome): A number of ribosomes can translate a single mRNA simultaneously • enable a cell to make many copies of a polypeptide very quickly • Often translation is not sufficient to make a functional protein • Polypeptide chains are modified after translation • Completed proteins are targeted to specific sites in the cell • During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape

16. Chapter 17 Protein Synthesis cont. • Proteins may also require post-translational modifications before doing their job • Some polypeptides are activated by enzymes that cleave them • Other polypeptides come together to form the subunits of a protein • Two types of ribosomes: • Free: in the cytosol • Bound: attached to the ER

17. Chapter 17 Protein Synthesis cont. • Mutations: changes in the genetic material of a cell or virus • The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein • Point mutations: chemical changes in just one base pair of a gene • Base-pair substitutions • Base-pair insertions or deletions

18. Chapter 17 Protein Synthesis cont. • Insertions and deletions are additions or losses of nucleotide pairs in a gene • have a disastrous effect on the resulting protein more often than substitutions do • frameshift mutation: alter the reading frame • Mutagens: physical or chemical agents that can cause mutations • Examples: Formaldehyde, benzene, and chloloform

19. DNA and RNA Chapter 17 Protein Synthesis cont.

20. Chapter 17 Protein Synthesis cont. DNA Makes RNA

21. Chapter 17 Protein Synthesis cont. Amino acids tRNA Ribosome large and small units mRNA DNA makes RNA (transcription); RNA makes protein (translation)

22. Chapter 20 Biotechnology • Recombinant DNA: nucleotide sequences from two different sources, combined in vitro • Genetic engineering: direct manipulation of genes for practical purposes • Biotechnology: manipulation of organisms or their genetic components to make useful products • Restriction enzymes cut DNA molecules at specific DNA sequences called restriction sites • Restriction fragments: cut pieces • Sticky ends: cut DNA in a staggered way producing fragments that bond with complementary sticky ends of other fragments

23. Chapter 20 Biotechnology cont. • DNA ligase: enzyme that seals the bonds between restriction fragments • Polymerase chain reaction, PCR: can produce many copies of a specific target segment of DNA • Gel electrophoresis: uses a gel as a molecular sieve to separate nucleic acids or proteins by size • DNA fragments produced by restriction enzymes • A current is applied that causes charged molecules to move through the gel • Molecules are sorted into “bands” by their size

24. Chapter 20 Biotechnology cont. • Restriction fragment analysis is useful for comparing two different DNA molecules, such as two alleles for a gene • The procedure is also used to prepare pure samples of individual fragments • Gene therapy is the alteration of an afflicted individual’s genes • holds great potential for treating disorders traceable to a single defective gene • Vectors are used for delivery of genes into specific types of cells, for example bone marrow

25. Chapter 20 Biotechnology cont. • Transgenic animals: made by introducing genes from one species into the genome of another animal • are pharmaceutical “factories,” producers of large amounts of otherwise rare substances for medical use • “Pharm” plants are also being developed to make human proteins for medical use • Most public concern about possible hazards centers on genetically modified (GM) organisms used as food