From Gene to Protein Chapter 2 and 7 of IB Bio book

Protein Synthesis: overview DNA has instructions for building proteins Transcription: the synthesis of RNA (especially mRNA) using the code of DNA as a template (pattern) Translation: actual synthesis of a polypeptide under the direction of mRNA From “language” of nucleic acids to “language” of proteins

The Triplet Code DNA has 2 strands: Codons mRNA base triplets antisense strand (template strand) gets transcribed to make mRNA (complementary to mRNA) sense strand (coding strand) has the same base sequence as the mRNA that is transcribed (with thymine instead of uracil). Codons mRNA base triplets Each codon codes for one amino acid.

Transcription: overview F:\Desktop\animations from bio powerpoints\Chapter 11 BDOL IC

Transcription, Details Gene: stretch of DNA transcribed into an mRNA molecule Promoter : region on DNA where RNA polymerase attaches and where initiation of transcription begins RNA polymerase: pries DNA apart hooks RNA nucleotides together (in 5’3’ direction) as specified in the DNA code Terminator region: sequence that signals the end of transcription

Transcription animation with more detail http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter15/stages_of_transcription.html

Eukaryotic cells modify mRNA after transcription RNA splicing (note: ONLY occurs in EUKARYOTES): exons (expressed sequences) kept, introns (intervening sequences) cut out; exons joined to form mature mRNA. Increases the number of different proteins that can be produced The human genome contains about 21,000 protein-encoding genes, but the total number of proteins in human cells is estimated to be between 250,000 to one million. (source: http://proteomics.cancer.gov/whatisproteomics National Cancer Institute http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html# Other stuff (interesting but not important to IB): 5’ cap: modified guanine; protection from degradation by enzymes; recognition site for ribosomes 3’ tail: poly(A) tail (adenine); protection; recognition; transport

Translation Production of a polypeptide (protein).

Translation: Important components mRNA is the instructions for how to build the protein. Each codon codes for 1 amino acid.

Translation: Important components tRNA Each tRNA can only bind one amino acid tRNA activating enzyme binds a specific amino acid to the tRNA, using ATP for energy. note: illustrates enzyme -substrate specificity and role of phosphorylation (new syllabus) The amino acid attaches to the side of tRNA opposite the anticodon. Anticodon = nucleotide triplet on tRNA note: CCA at 3’ end

Translation: Important components The Ribosome (made of proteins and rRNA)– consists of two subunits, small and large rRNA – a component of the ribosome that helps with making proteins. A site-- holds the tRNA carrying the next amino acid to be added to the chain P site -- holds the tRNA carrying the growing polypeptide chain E site- exit site where tRNA’s are released

Translation (animations) http://science.nhmccd.edu/biol/bio1int.htm C:\Documents and Settings\BBAUGHMAN\Desktop\bio powerpoints\Chapter 11 BDOL IC http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html

Translation (the process) Initiation~ involves assembly of components Start codon mRNA binding site-mRNA attaches to small ribosomal subunit tRNA also attaches small followed by large ribosomal subunit Elongation ~ codon recognition by anticodons peptide bond formation (catalyzed by rRNA) 5’ 3’ (ribosome moves along mRNA toward the 3’ end)

Translation (the process) Translocation– tRNAs move from A site to P site to E site Termination~ ‘stop’ codon reaches ‘A’ site After termination, disassembly of components occurs.

Translation in Prokaryotes Note… Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.

Skill: ID Polysomes on micrographs Polysome: a complex of an mRNA molecule and two or more ribosomes that is formed during translation. many copies of a polypeptide can be made very quickly A portion of an E. coli chromosome being transcribed (left to right) and being simultaneously translated. The arrow points to the putative site where RNA polymerase is first bound to the DNA. The chains of dark bodies are polysomes, that is, several ribosomes on the same mRNA molecule. http://schaechter.asmblog.org/schaechter/2013/03/pictures-considered.html

Skills: Using tables of mRNA codons (codon charts) Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid. Deduce the sequence of amino acids coded by an mRNA molecule using a table. See next page for charts…

Table of Codons and Amino Acids

Translation (animations) http://science.nhmccd.edu/biol/bio1int.htm C:\Documents and Settings\BBAUGHMAN\Desktop\bio powerpoints\Chapter 11 BDOL IC http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html

Peptide Bond

From Polypeptide to functional Protein Posttranslational Modifications occur to polypeptides after translation Folding to get secondary, tertiary structure Joining to other polypeptides and/or prosthetic groups (Quaternary structure)

Free Ribosomes vs. Bound Ribosomes… Free– proteins within cell Bound– secretory proteins

Summary of Central Dogma (including RNA processing) Good animation https://www.dnalc.org/resources/3d/central-dogma.html

RNAi video http://www.pbs.org/wgbh/nova/body/rnai.html

Mutations: genetic material changes in a cell Note: new alleles are formed by mutation! Base substitution Mutations (Point mutations): Changes in 1 or a few base pairs in a single gene This alters mRNA May result in altered protein due to amino acid difference

Important Point Mutation example: Sickle cell anemia GAG mutates to GTG So for the 6th amino acid… Glutamic Acid = replaced by Valine Causes shape change, resulting in disease. http://www.dnalc.org/view/15532-Sickle-cell-anemia-3D-animation-with-narration.html

Mutations (continued) not in IB syllabus Base-pair insertions or deletions: additions or losses of nucleotide pairs in a gene frameshift mutation alters the ‘reading frame’ of triplets~ Mutagens: physical and chemical agents that change DNA

Theory of knowledge: Discuss •The nature versus nurture debate concerning the relative importance of an individual’s innate qualities versus those acquired through experiences is still under discussion. Is it important for science to attempt to answer this question?

Don’t use next slides

The Triplet Code The genetic instructions for a polypeptide chain are ‘written’ in the DNA as a series of 3-nucleotide ‘words’ The two strands of DNA: antisense strand (template strand) gets transcribed to make mRNA (complementary to mRNA) sense strand (coding strand) has the same base sequence as the mRNA that is transcribed (with thymine instead of uracil). Codons (mRNA base triplets) Each codon codes for one amino acid. ‘U’ (uracil) replaces ‘T’ in RNA