Lab tomorrowResearch Write-up due Friday

You should review…• Garrod! (1902) uncovered clues..• Tatum and Beadle’s experiments with Neurospora

Figure 14.5

DNAtemplatestrand

Protein

mRNA

3

Trp

TRANSCRIPTION

TRANSLATION

Amino acid

Codon

5

35

3

5

Phe Gly Ser

GU G U UU G G UC C A

CA C A AA C C AG G T

GT G T TT G G TC C A

Figure 14.9

Transcription factors

TATA box

Promoter Nontemplate strand

Start point

Transcriptioninitiationcomplex forms.

Transcription initiation complex

DNA

RNA transcript

A eukaryoticpromoter

Several transcriptionfactors bind to DNA.

35

5 3 35

35

35

3

2

1

Templatestrand

Transcription factors

RNA polymerase II

35

35 TA T A A A A

A T A T T T T

Transcription starts at a start point within a big sequence called the promoter.

At the start of the promoter there is a TATA box

Transcription unit=sequence being transcribed

Figure 14.9

Transcription factors

TATA box

Promoter Nontemplate strand

Start point

Transcriptioninitiationcomplex forms.

Transcription initiation complex

DNA

RNA transcript

A eukaryoticpromoter

Several transcriptionfactors bind to DNA.

35

5 3 35

35

35

3

2

1

Templatestrand

Transcription factors

RNA polymerase II

35

35 TA T A A A A

A T A T T T T

In Eukaryotes transcription factors bind first then RNA polymerase.

Figure 14.9

Transcription factors

TATA box

Promoter Nontemplate strand

Start point

Transcriptioninitiationcomplex forms.

Transcription initiation complex

DNA

RNA transcript

A eukaryoticpromoter

Several transcriptionfactors bind to DNA.

35

5 3 35

35

35

3

2

1

Templatestrand

Transcription factors

RNA polymerase II

35

35 TA T A A A A

A T A T T T TTranscription factors plus RNA polymerase =transcription initiation complex

Figure 14.10

Nontemplate strand of DNA

Direction of transcription

RNA polymerase

3

53

5

RNA nucleotides

Template strand of DNANewly made

RNA

3 end

5

UC

U

G

A

A

A

A

AA

A

AA

A

T T T

TT

T

T

CC

C

CCC C

G

GG

U

A single gene may have multiple transcription points and multiple RNA polymerases working on it..”trucks in a convoy”

What does that mean for the product?

This initial RNA sequence is called pre-mRNA or the primary transcript. • This primary transcript is then processed!

• Ends modified (5’ cap, poly-A tail added)

WHY? • Interior sections or introns cut out and exons kept

and spliced together by spliceosome• This is called RNA splicing

• So mRNA molecule that enters cytoplasm is a very abridged version!

More RNA Splicing

A single gene can encode more than one kind of polypeptide!

So protein products are much more diverse than number of genes.

Figure 14.4b-3

Nuclearenvelope

Polypeptide

Ribosome

(b) Eukaryotic cell

What kind of cell is this and how do you know?

Figure 14.4a-2

mRNA

DNATRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

(a) Bacterial cell

Troubles with ends! During replication DNA polymerase can add only to 3’ end so cannot complete 5’end. Repeated rounds of replication produce shorter and shorter DNA molecules with uneven ends. P259 txt

Figure 13.16

53

5

3

Origin of replicationLagging strand Lagging

strand

Overall directionsof replication

Leadingstrand

Leadingstrand

Overview

Primase makesRNA primer.

RNA primerfor fragment 1

Templatestrand

Okazakifragment 1

DNA pol IIImakes Okazakifragment 1.

DNA pol IIIdetaches.

53

5

3

5

35

3

RNA primerfor fragment 2

Okazakifragment 2 DNA pol III

makes Okazakifragment 2.

Overall direction of replication

DNA pol Ireplaces RNAwith DNA.

DNA ligase formsbonds betweenDNA fragments.

5

35

3

5

35

3

5

35

31

2

3

4

5

6

Lets assume this is the end of the chromosome

1. RNA comes off….

2. DNA pol I is supposed to add by hooking onto 3’ piece of previous DNA stretch-oops

1. What are telomeres? Do they contain genes? Do bacteria have telomeres?

2. What is telomerase and what does it do? What would happen in germ cells if telomerase did not exist?

3. Telomerase is not usually active in somatic cells, but turns on in germ cells, why?

4. Unusual activity of telomerase is often seen in what condition?

5. Non coding repetitive sequences?…Apoptosis? What do these things mean?

6. What kinds of conditions are associated with shortened telomeres?

7. What did the researchers find? Can you make a sketch of the findings the way our textbook does for experiments it describes?

8. Look at Table 1. What are the numbers in the parentheses after the means! 9. Look at Figure 1. What does the little star on the line between the two elderly groups mean?  

Figure 1. Telomere length expressed as T/S ratio among athletes and non-athletes, stratified by age.

Østhus IBØ, Sgura A, Berardinelli F, Alsnes IV, et al. (2012) Telomere Length and Long-Term Endurance Exercise: Does Exercise Training Affect Biological Age? A Pilot Study. PLoS ONE 7(12): e52769. doi:10.1371/journal.pone.0052769http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052769

Figure 14.5

DNAtemplatestrand

Protein

mRNA

3

Trp

TRANSCRIPTION

TRANSLATION

Amino acid

Codon

5

35

3

5

Phe Gly Ser

GU G U UU G G UC C A

CA C A AA C C AG G T

GT G T TT G G TC C A

Figure 14.12

Introns cut out andexons spliced together

31–104

5 Cap

5 UTR 3 UTR

Poly-A tail

Codingsegment

1–146

AAUAAA

105– 146

5 Cap Poly-A tail

1–30

mRNA

Pre-mRNA

Intron Intron

OR Primary Transcript

RNA SPLICING

Translation

mRNA heads out into cytoplasm to attach to ribosome.

Figure 14.4b-3

Nuclearenvelope

Pre-mRNA

mRNA

DNA

RNA PROCESSING

TRANSCRIPTION

TRANSLATION

Polypeptide

Ribosome

(b) Eukaryotic cell

Figure 14.17

PE A

tRNAmolecules

A

Largesubunit

Smallsubunit

Growing polypeptide Exit tunnel

E P

mRNA5

3

Growing polypeptide

(a) Computer model of functioning ribosome

tRNA

5

3E

mRNA

(c) Schematic model with mRNA and tRNA

Codons

Amino end Next amino acidto be added to

polypeptidechain

Largesubunit

Smallsubunit

A site (Aminoacyl-tRNA binding site)

P site (Peptidyl-tRNA binding site)

Exit tunnel

E site (Exit site)

mRNA binding site

(b) Schematic model showing binding sites

What is a ribosome?? • are tons of these in cytoplasm • made up of a kind of RNA (ribosomal RNA)• two subunits or parts (a large and a small)

Anther kind of RNA (transfer RNA) is out in cytoplasm

Amino acids!

Anticodons!

CCG

mRNA GGC

A little more detail about codons..

Different anticodons of tRNA will match to different a.a.

Note that there are 64 possible codons (4 possible bases (A, G, C, U) and 3 per codon so 43)

3 are stop codons! (so actual possible is 64-3=61)

BUT THERE are not 61 different amino acids Hmmmmm?

mRNA Table

What is wobble?

GGU and GGC will also match to Glycine

More Translation….

• Start codon establishes reading frame

• Once hits start codon tRNA hauls appropriate amino acid to the ribosome

• As each codon is matched to anticodon ribosome attaches the amino acid to the growing string to make a protein!

Terminology!

Polypeptide refers to a chain of amino acids…

Protein is typically the finished product-how do you get that finished product?

Post Translational Modifications p285Polypeptide starts to coil and fold due to its primary structure (its amino acid sequence) (might be a chaperone protein that helps it fold correctly)

• Groups are added (sugars, lipids, phosphate groups)

• Parts might be removed (amino acids from leading end or middle -Insulin is formed after a chunk of a.a. are taken out of its middle.)

• Polypeptides may be joined together to become subunits of a protein like hemoglobin

How do these polypeptides/proteins know where to go after they are made?

Sometimes ribosomes are told by the polypeptide being made to attach to the endomembrane system-=BOUND.

These polypeptides then go to into the endomembrane system

Other ribosomes stay FREE and floating.

Their polypeptides send themselves or “target” themselves to some other sites like…. ?

Targeting is done by a signal polypeptide and it is kind of like a “zip code” that is part of the polypeptide itself.

Large and Small scale “mutations”

Abnormal chromosome NUMBER or STRUCTURE (CH12 p241)

• Abnormal NUMBER of chromosomes is called aneuploidy

Ex. Down’s syndrome and various fascinating disorders where are extra X’s or no Y

• Abnormal STRUCTURE issues such as a chunk is deletion, inversion, translocation, duplication

Figure 12.14a

(a) Deletion

A deletion removes achromosomal segment.

(b) Duplication

A duplication repeatsa segment.

What is this called?

Figure 12.14b

(c) Inversion

(d) Translocation

An inversion reverses a segmentwithin a chromosome.

A translocation moves a segmentfrom one chromosome to anonhomologous chromosome.

In addition to abnormal chromosome structure or number we also have POINT MUTATIONS (CH14 p288) a change in a single nucleotide

1. Substitutions 3 kinds…missense, nonsense, silent –

WHICH ONE IS WHICH?

2. Insertions/Deletions

Point mutations (a change in a single nucleotide)

1. Substitutions 2. Insertions and deletions-why are these often

worse!!!