Using DNA

-Transcription- RNA processing- Universality of the genetic code- Translation

Refer to chapter 12.3 to 12.6, and 13.2, 13.3 in text.

There are enzymes that can make proteins (nonribosomal peptides)without this process:

Those are enzyme-specific,and not what we are talking about here.

Review DNA structure(What does it look like?)

and RNA structure.

Recap DNA replication(Unzipping the... helix, etc.)

So... what do you recall/know about transcription and translation?purpose? location? general mechanisms?

Now go to animations.

TRANSCRIPTION/mRNA PROCESSING

Transcription and processing onlyhttps://www.youtube.com/watch?v=LPnz1i0Fr98

Also to processing onlyhttps://www.youtube.com/watch?v=eMYl0wjNc0U

‘realistic”https://www.youtube.com/watch?v=5MfSYnItYvg

You can also go to Crash Course or Bozeman of course

transcription: DNA to RNA

←sense strand

← antisense strand

NB →

http://www.google.com/imgres?imgurl=http://biology.kenyon.edu/courses/biol114/Chap10

… that promoter thing isn’t as simple as the previous picture suggests!

(You don’t need to worry about this. I just don’t want you to think you are responsible for everything!

There will still be stuff to learn in college!)

processing ofpre-mRNA:5’ cap, poly(A) tail ↑,and excision of introns →,leaving exons to move out of the nucleus…

snRNPs act as ribozymes:→

…like proteins

Called snRNAs in Mader

Some pre-mRNA are processed to include different exons -

One gene can code for multiple proteins.Some introns become microRNAs (miRNA)

that impact translation…

Are you accessing theIB syllabus at theStanton web site?

Transcription and RNA processing terminology (Read all as bold and underlined.)

initiationpromotertranscription factorelongation5’ to 3’RNA polymerasetranscription unitterminationterminatortermination pointsense strand

So now the message can leave the engineering libraryand go out onto the factory floor.

The ‘factory’ has 20 amino acids,while the plans only have 4 nucleotides....

antisense (template) strandpre-mRNAleadertrailerintronexonsnRNPsspliceosome5’ cappoly A tailmRNA

Genetic CodeDeciphered by

Marshall Nirenberg, 1966.Note- how table is read.- what it represents (RNA codons).- start codon- stop codons- redundancy: most amino acids have multiple codons…

(ramifications?)

What amino acid does UGU code for?What is the codon for alanine?What is a DNA sequence for met-ser-his?What a.a. sequence from TCAGGAACAATTTAG?

http://www.biology.lsu.edu/heydrjay/1201/Chapter17/SCI_Amino_Acid_CIRCLE.jpg

go to an animation for translation…

Same code, different presentation(Some tables have the DNA rather than the RNA sequences.)

Code is almost universal - exceptions usually mitochondrial - often involve a.a. for stop codon(s) - may swap in more stops - novel amino acids:

usually in prokaryotespyrrolysine for UAGselenocysteine for some UGA

(25 of your proteins have this last one!)

TRANSLATION

“Basic”, but fairly complete…https://www.youtube.com/watch?v=8dsTvBaUMvw

Virtual Cellhttps://www.youtube.com/watch?v=5bLEDd-PSTQ

Realistic viewhttps://www.youtube.com/watch?v=TfYf_rPWUdY

nobelprize.org/.../medicine/dna/a/translation/

translation:from the language of nucleic acids,

into that of protein.

riboso

mal su

bunits jo

in

after

small

er binds m

RNA →

←AUG codon = UAC anticodon (met)

5’ end→

polysome →

(multiple translational systems

on one mRNA)↑NB

close-up of tRNA →←NB

aminoacyl-tRNA synthetase ↓

This is happening on rER ↑ if the proteins are for export or are lysozymes; Local proteins are made on free ribosomes.The shift from the A to P site is translocation.

ww

w.n

sf.g

ov/n

ews/

over

view

s/bi

olog

y/in

tera

ct05

.jsp

Recall the peptide bond… and be able to draw it. →The energy required for the formation of one peptide bond includes the hydrolysis of 2 ATP and 2 GTP molecules.

Regulation of gene expression in eukaryoteschromatin structuremethylation/acetylation of histone tails,epigenetics, inherited factors

transcriptional controlmethylation of cytosines blocks reading role in cell specializationsee also slide 4

posttranscriptional controlalternate splicingcontrol of mRNA exiting nucleus

translational controlpersistence of 5’ cap and poly-A tailmicroRNA from introns → RISC

(RNA-induced silencing complex) posttranslational control

tertiary structure, prosthetic groups?coenzymes? proteases? lifted from p. 237 in Mader

Different genes coordinate whole structures Pax6 (eyes), Tbx5 (limbs), Hox (body shape)

Translation terminology (Read all as bold and underlined.)

initiationmRNAcodonstart codontRNAamino acidCCA tail (amino acid binding site)tRNA-activating enzyme (aminoacyl-tRNA synthetase)anticodonribosome rRNA

ribosomal proteinnucleolussmall ribosomal subunitmRNA binding siteelongationlarge ribosomal subunitA, P and E sitestranslocation 5’ to 3’ (reverse relative to DNA)polysometerminationstop codon

What are the three stages of DNA to protein?Where does each occur?

Walk through each.

Lots of proteins…Investigate any for which the namedoes not obviously lead to the job.

What is meant by the genetic code? How is it “universal”?

Give examples of form fitting function, for ribosomes and tRNA.

There were 4 different RNAs involved:Identify each along with its use.

transcription intron CCA tail

initiation exon amino acid binding site

promoter snRPs tRNA-activating enzyme

transcription factor spliceosome aminoacyl-tRNA synthetase

elongation 5’ cap anticodon

5’ to 3’ poly A tail ribosome

RNA polymerase mRNA rRNA

transcription unit start codon ribosomal protein

termination nucleolus

terminator (Arnold) redundancy small ribosomal subunit

termination point The Genetic Code mRNA binding site

sense strand translation elongation

antisense strand translocation large ribosomal subunit

pre-mRNA initiation A, P and E sites

leader codon polysome

trailer tRNA termination

amino acid