Exam 1 is T 923 in class bring

• Exam #1 is T 9/23 in class (bring cheat sheet)

DNA is used to produce RNA and/or proteins, but not all genes are expressed at the same time or in the same cells. How do cells control which genes are expressed? Protein

Signal Transduction External Stimulus Internal Effector… Effector Perception (by receptor) Stimulus Response (change in cellular components and/or gene expression)

How do cells express genes?

The relationship between DNA and genes a gene promoter coding region terminator non-gene DNA

Combinations of 3 nucleotides code for each 1 amino acid in a protein. Fig 13. 2

• Overview of transcription Fig 12. 2

Fig 9. 8 Each nucleotide carbon is numbered

Fig 9. 22 Each nucleotide is connected from the 5’ carbon through the phosphate to the next 3’ carbon.

Fig 12. 8 The relationship between DNA and RNA

Fig 12. 8 What is so magic about adding nucleotides to the 3’ end?

How does the RNA polymerase know which strand to transcribe? Fig 12. 7

Reverse promoter, reverse direction and strand transcribed. RNA 5’ 3’ 5’

Why do polymerases only add nucleotides to the 3’ end? RNA DNA U U similar to Fig 11. 11

Error P-P P

Error P U P P-P-P The 5’ tri-P’s can supply energy for repair

similar to Fig 11. 11 Incoming nucleotide Error repair on 5’ end not possible. 5’ U 3’

Need for error repair limits nucleotide additions to 3’ end. RNA DNA U U similar to Fig 11. 11

When to express a gene is critical a gene promoter coding region terminator non-gene DNA

Promoter sequences in E. coli Fig 12. 5

Transcription initiation in prokaryotes: sigma factor binds to the -35 and -10 regions and then the RNA polymerase subunits bind and begin transcription Fig 12. 7

Transcription Elongation Fig 12. 8

Termination of Transcription Fig 12. 11

Fig 12. 13 Eukaryotic promoters are more diverse and more complex

in eukaryotes: transcription factors are needed before RNA polymerase can bind Fig 12. 14

Fig 12. 3 Transcription overview

RNA synthesis Protein Some genes code for RNA (t. RNA, r. RNA, etc) m. RNA is used to code for proteins

r. RNA is transcribed by RNA polymerase I

t. RNA is transcribed by RNA polymerase III

m. RNA is transcribed by RNA polymerase II

m. RNA is processed during transcription and before it leaves the nucleus. (transcribed from DNA)

Fig 12. 23 Addition of the 5’ cap, a modified guanine

Addition of the 3’ poly-A tail Fig 12. 24 After the RNA sequence AAUAAA enzymes cut the m. RNA and add 150 to 200 A’s

What do the cap and tail do? (transcribed from DNA)

Luciferase Gene (from fireflies) Expressed in a Plant

100% 4. 7% 0. 34% 0. 22%

The cap and tail have overlapping and distinct functions 5’ untranslated region Protects from degradation/ recognition for ribosome 3’ untranslated region Protects from degradation/ transport to cytoplasm

DNA Composition: In humans: • Each cell contains ~6 billion base pairs of DNA. • This DNA is ~2 meters long and 2 nm wide. • ~3% directly codes for amino acids • ~10% is genes • In a single human cell only about 5 -10% of genes are expressed at a time.

Introns are spliced out of most m. RNAs before they leave the nucleus. (transcribed from DNA)

• Conserved sequences related to intron splicing Sequences shown in bold are highly conserved Serve as recognition sites for the binding of the spliceosome

Splicing an intron: intron removal. Fig 12. 22

Splicing an intron: reattach exons. Fig 12. 22

Alternate splicing of introns/exons can lead to different proteins produced from the same gene. Fig 15. 16

Complex patterns of eukaryotic m. RNA splicing ( -tropomyosin) Fig 15. 16

Fruit fly DSCAM, a neuron guide, 115 exons over 60, 000 bp of DNA 20 exons constitutively expressed 95 exons alternatively spliced For over 38, 000 possible unique proteins

Size and Number of Genes for Some Sequenced Eukaryotic Genomes

RNA editing: Some m. RNAs are changed after transcription by guide RNA Tbl 12. 3 http: //www. cc. ndsu. nodak. edu/instruct/ mcclean/plsc 731/genome 9. htm http: //users. rcn. com/jkimball. ma. ultrane t/Biology. Pages/R/RNA_Editing. html

A processed m. RNA ready for translation 5’ untranslated region 3’ untranslated region

• Exam #1 is T 9/23 in class (bring cheat sheet)