A Biology Primer Part III: Transcription, Translation, and Regulation Vasileios Hatzivassiloglou University of Texas at Dallas

We have covered so far Biological classification Organisms, tissues, cells and organelles Cell, protein, DNA, RNA function, structure, and form DNA replication (In part) The mechanisms of reproduction

Mitosis

Distribution of chromatids Applies to diploid eukaryotic cells

Errors during mitosis Chromosome does not separate (non- disjunction), 3:1 imbalance in genes Deletion of part of a chromosome Attachment to non-homologous chromosome (translocation) Reversal of orientation (inversal)

Meiosis Two phases: Meiosis I separates homologous chromosomes, but with a twist – genes are exchanged between non-sister chromatids (from the two different parents) Meiosis II separates the sister chromatids in each chromosome

Meiosis vs Mitosis Cell has two chromosomes, 1 and 2; homologues come from F or M Cell: F1M1+F2M2 Replication: F1F1+M1M1+F2F2+M2M2 Meiosis I: 2 x (F1M1+F2M2) Meiosis II: random distribution of the four chromosome pairs, e.g., F1F1+M2M2 with transformations, then randomly F1+M2

Meiosis graphically

Gene expression DNA encodes proteins in genes Two stages: Transcription (from DNA to mRNA) and translation (from mRNA to proteins via tRNA) Somewhat simpler in prokaryotic organisms because there is no nucleus, everything happens directly in the cytoplasm

Transcription Similar to replication, DNA is “unzipped” with an RNA polymerase (another enzyme protein) One strand of the DNA is copied onto messenger RNA via the correspondence –C to G –G to C –T to A –A to U (replaces T in RNA)

Where to start and stop? Special DNA sequences tell the RNA polymerase where to start (transcription start site) and where to end (transcription end site) Additional control sections of DNA specify when the process will be initiated These are usually close to the gene

Transcription process

Translation mRNA now contains all the information from the gene Another RNA molecule attaches to mRNA – this is transfer RNA There are many kinds of transfer RNA, each capable of recognizing the code for a single amino acid (or for the stop signal)

Coding for amino acids DNA and RNA have four letters We need at least 21 specifications (20 amino acids plus a stop code) Two-base combinations not enough (4 2 = 16) Three-base combinations (codons) sufficient (4 3 = 64), introduces redundancy (synonymous codons)

The genetic code

Translation process Actual translation takes place in the ribosomes, made up of proteins and rRNA Yet another RNA type (ribosomal RNA) tRNA for each codon attaches to the mRNA on one side (via anti-codon) and attracts the appropriate amino acid on the other side

Translation

Complications in eukaryotes DNA is in the nucleus; ribosomes are in the cytoplasm mRNA has to be transported outside the nucleus Also, eukaryotic DNA contains mysterious regions that do not code (introns) in addition to the useful regions (exons) Average length of introns 10,000 bp, of exons 200 bp

Transcription in eukaryotes Normal transcription process in the nucleus produces pre-mRNA which still contains all the introns Splicing eliminates the introns and results in mature mRNA This travels outside the cell for translation

Intron elimination and splicing

Alternative splicing Allows for much variation in the end product of transcription Some introns behave like exons in different tissue, e.g., liver vs. brain This results in many more proteins than genes In humans, about 32,000 genes code for 1,000,000 proteins

Other complications Cannot translate in parallel with transcription Regulatory regions can be further upstream or downstream, even within the introns Genes much harder to identify (computational implications)

Protein diversity Two major mechanisms: –Alternative splicing; depends on variable function of introns in different cells within the same organism –Post-translational modification; changes to the protein after gene expression

Post-translational modifications Many proteins undergo further change after translation Removal of one or more amino acids Cutting the protein in two parts (e.g., insulin) Addition of non amino acid groups, in particular phosphates (phosphorylation) –Controls when a protein can bind to something –Controls where the protein goes (cytosol / membrane)

Expression regulation Promoters: Short DNA sequences that attract the RNA polymerase to bind to them and start the transcription In prokaryotes, typically like In eukaryotes, promoters are more diverse and further away

How expression is regulated RNA polymerase can bind to promoters, but it doesn’t always do so Proteins can activate or suppress expression Activator proteins enhance the promoter’s tendency to bind with RNA polymerase Repressor proteins bind with the promoter and make it unavailable for RNA polymerase

Examples of regulation Positive feedback / activation –When heat increases, a protein in E. Coli binds with its RNA polymerase and alters its properties so it can bind with promoters for heat-response proteins Negative feedback / repression –The protein lac repressor can bind either to lactose (if there is any) or to the promoters that produce enzymes that digest lactose

Ubiquitylation Ubiquitin is a small protein that occurs in all eukaryotic cells Human sequence: (76 amino acids) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK QLEDGRTLSDYNIQKESTLHLVLRLRGG Yeast sequence 96% similar Function: Attach to other proteins to mark them for destruction at the proteasome