1. Eukaryotic Genome Control Mechanisms for Gene Expression
AP Biology
Eukaryotic Genome Control Mechanisms for Gene Expression

2. What is the condition of DNA during transcription? It is loose
What is this loose condition called?
Chromatin
Why is this condition necessary during transcription?
It provides easy access for the RNA to get in to work and copy the DNA
Like a bowl of spaghetti

3. What is the condition of the DNA during mitosis and meiosis?
It is tightly wound up
What is the tightly wound condition called?
Chromosomes
Why is this condition necessary during mitosis and meiosis?
To allow for easy and equal separation of the DNA
Chromosomes form an X shape

4. A description of prokaryote chromosomes is that they are …..
Circular
The chromosomes of eukaryotes is….
Linear

5. What are histones?
Proteins that DNA wraps around in order to condense more easily
Why does DNA wrap around these proteins?
Because DNA has a negative charge (because of the phosphate groups)
The histone have a positive charge
This attraction (like a magnet) causes the wrapping

6. Both eukaryotes and archaebacteria have histones
Why do many scientists consider eukaryotes to be more closely related to archaebacteria than to eubacteria?
Both eukaryotes and archaebacteria have histones
histones

7. What is a nucleosome?
The whole unit of the DNA wrapped around a group of histones

8. The process by which the DNA condenses from chromatin to chromosomes
What is supercoiling?
The process by which the DNA condenses from chromatin to chromosomes
What is heterochromatin?
DNA that remains condensed, even during interphase (different than normal)
It is not active and no transcription can occur on it
heterochromatin

9. The loose DNA (true) that is active during interphase
What is euchromatin?
The loose DNA (true) that is active during interphase
Transcription actively take place on it
euchromatin

10. What is cell differentiation or specialization?
The process of making cells different
How does this happen?
Certain genes are “turned on” or “turned off”
This is called differential gene experssion

11. What occurs when genes are “turned on”?
They make proteins
What happens when gene control does not work properly?
Death or cancer can result

12. What are some gene control mechanisms that occur during transcription?
DNA methylation
Histone acetylation
Enhancers and activators
Repressors or silencers
Coordinated control
Micro RNA and small interfering RNA

13. What is DNA methylation?
A heavy coat of methyl groups is put around the DNA
This prevents transcription
The methyl group attaches to the cytosine or adenine
This is called genomic imprinting and effectively erases the information on the DNA at that point

14. What is histone acetylation?
The attachment of acetyl groups to the histones
This breaks the bond between the DNA and histone
The positive charge is covered up, so there is no attraction any more
This allows RNA Polymerase to attach to the DNA to free up the transcription process

15. What are enhancers and activators?
They control the rate of transcription
They move the transcription factory down the DNA faster
Often called “pushers” because they are always in front of the gene being transcribed

16. What are repressors or silencers?
They prevent transcription from occurring by sitting on the TATA box
This represses the gene from being expressed
They are also controlling the rate of transcription

17. What is coordinated control?
One chemical signal can cause expression of multiple copies of the same gene
This is referred to as the gene family
This is like the bell signaling all classes to move at the same time

18. What is micro RNA (miRNA) and small interfering RNA (siRNA)?
Little pieces of RNA that attach to the messenger RNA and control transcription

19. What is post transcription regulation?
Controls that occur after transcription
What is alternative RNA Splicing using splicesomones?
Changing the primary mRNA into the secondary mRNA

20. What is cytoplasmic degradation?
Removal of the caps and tails on the mRNA
Then nucleotides are catabolized and recycled
The longer the Poly A Tail, the longer the mRNA will survive in the cytoplasm

21. What are translation control mechanisms?
Building the translation initiation complex
Controls can occur in a step by step process
If there is a faulty 5’cap, translation will not occur

22. What is post translation control mechanisms?
Controls that function after the translation is complete
What are some examples?
Chaperonins
Phosphorylation
Proteosomes

23. What are chaperonins?
Proteins that provide a safe, protected area for newly produced proteins to fold up

24. What is phosphorylation?
Using an ATP molecule to add a phosphate group onto the protein

25. What determines the transport of the proteins?
Whether they will remain in the cytoplasm or will go out of the cell
If remaining in the cell, they will go to the chaperonin
If leaving the cell, they will go to the RER

26. What are proteosomes?
They are special lysosomes that will determine how long the protein will last
They digest the A’s off the Poly A Tail

28. Chromatin vs. Chromosomes appearance within the cell.

29. Histone Proteins and Supercoiling
2 nm
DNA double helix
His-
tones
Histone
tails
Histone H1
10 nm
Linker DNA
(“string”)
Nucleosome
(“bead”)
Nucleosomes (10-nm fiber)

30. Supercoiling of Chromatin

31. Euchromatin vs. Heterochromatin (The dark spots are the hetero)

32. DNA Control stages in Protein Synthesis
Signal
NUCLEUS
Chromatin
DNA
Gene available
for transcription
Gene
Transcription
RNA
Exon
Primary transcript
Intro
RNA processing
Tail
Cap
mRNA in nucleus
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypeptide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein

33. Methylation

34. . Histone tails DNA double helix Amino acids available for chemical
modification
Histone tails protrude outward from a nucleosome
Unacetylated histones
Acetylated histones
Acetylation of histone tails promotes loose chromatin
structure that permits transcription

35. “Build the factory”

36. Enhancers Distal control element Activators Promoter Gene DNA Enhancer
TATA
box
General
transcription
factors
DNA-bending
protein
Group of
mediator proteins
RNA
polymerase II
RNA
polymerase II
Transcription
Initiation complex
RNA synthesis

37. Notice the different nucleotide control sequences (red vs, pink)
Liver cell
nucleus
Lens cell
nucleus
Available
activators
Available
activators
Enhancer
Promoter
Control
elements
Albumin
gene
Albumin
gene not
expressed
Crystallin
gene
Albumin
gene
expressed
Crystallin gene
not expressed
Crystallin gene
expressed
Liver cell
Lens cell

38. miRNA &siRNA Protein complex Degradation of mRNA Dicer OR miRNA
Target mRNA
Hydrogen
bond
Blockage of translation

39. Control of exons

40. How many As on the tail?

41. “Build the factory”

42. Chaperonin Protein will stay in the cell

43. RER Protein will leave the cell

44. Proteosomes Proteasome and ubiquitin to be recycled Ubiquitin
Protein to
be degraded
Ubiquitinated
protein
Protein
fragments
(peptides)
Protein entering a
proteasome