Chromatin Modification
1. Euchromatin - uncompact chromatin, accessible, loose prior to prophase so during
interphase, expressed, should be in this form if it is meant to be transcripted
2. Heterochromatin - compact chromatin, unaccessible, condensing during prophase of
mitosis, barr bodies (inactive X chromosome) have dense chromatin, not expressed
3. Gene Regulation: Gene Expression Regulation Through Chemical Modification
a. Histone acetylation
i. DNA typically wrapped around histone, loosely or tightly based on if it
wants to be expressed
ii. Acetyl groups attaches to positively charged lysine in histone tails
iii. Neutralizes charge
iv. Loosens chromatin structure
v. Euchromatin
vi. Should be this form for transcription to occur
b. DNA methylation
i. Adding methyl groups to certain bases of DNA
ii. Condenses chromatin structure
iii. Heterochromatin
iv. Transcription is not impossible but rather impeded
Dogma Model
4. DNA → RNA → protein/polypeptide → trait
a. Don’t always need to make the protein, could just want mRNA, tRNA, rRNA (for
ribosomes).
5. Transcription: DNA → RNA
6. Translation: RNA → protein
Transcription: DNA → pre-mRNA
7. Location: Nucleus
8. DNA needs to be relaxed for factors to bind and move along its length
9. DNA needs to have euchromatin (acetylation)
10. DNA → pre-mRNA aka an immature transcript
a. Not ready for translation yet
b. pre-mRNA in eukaryotes
11. DNA as a template to synthesize complementary pre-mRNA
12. Only one strand of DNA is the template
a. Template strand still being read as 3’ → 5’ and new RNA strand synthesized 5’
→ 3’ and they’re not interacting with each other after or being bound to each other
, b. Template strand can have either polarity though: 3’ → 5’ or 5’ → 3’, the RNA
polymerase will fix its orientation to match it
i. Different from DNA replication then
c. Nontemplate strand has information about a different gene of interest
d. Doesn’t interact with nontemplate strand
i. Different from DNA replication then
e. The same gene will always be found on the same template strand
13. Complementary Base Pairing
a. AU and CG
b. New strand looks just like nontemplate strand but U’s where there were T’s
14. Will never transcribe the entire DNA sequence or an entire chromosome but rather small
segments of the chromosome
a. Transcript strand shorter than replicated DNA strand
15. Constantly unwinding and winding instead of just staying unwinded because DNA is very
stable as a helical structure, if they’re apart they’d want to form the hairpin structures and
thus be inaccessible to transcription
16. RNA Polymerase
a. RNA polymerase I focuses on synthesizing ribosomal RNA genes
b. RNA polymerase II focuses on synthesizing protein coding genes - most common,
the one we’re usually referring to
c. RNA polymerase III focuses on synthesizing transfer RNA genes and ribosomal
RNA genes
d. If we don’t want to end up synthesizing a protein, then RNA pol I and III are what
will be present in transcription
17. Initiation Stage
a. Starting process
b. Promoter Region
i. Special sequence always on template strand
ii. Promoter has region for transcription factors to bind, region for RNA
polymerase, and region for regulatory protein binding
1. Gene Regulation: Specific sequence that recruits regulatory protein
binding
a. Presence or absence of proteins that can activate or inhibit
gene and thus regulate the rate of transcription
b. Regulatory proteins may or may not be needed
2. Specific sequence that recruits RNA polymerase
a. Indicates RNA polymerase to bind tightly to the promoter
region on the template strand and unravel the double
stranded DNA
i. Capable of de novo synthesis
1. Euchromatin - uncompact chromatin, accessible, loose prior to prophase so during
interphase, expressed, should be in this form if it is meant to be transcripted
2. Heterochromatin - compact chromatin, unaccessible, condensing during prophase of
mitosis, barr bodies (inactive X chromosome) have dense chromatin, not expressed
3. Gene Regulation: Gene Expression Regulation Through Chemical Modification
a. Histone acetylation
i. DNA typically wrapped around histone, loosely or tightly based on if it
wants to be expressed
ii. Acetyl groups attaches to positively charged lysine in histone tails
iii. Neutralizes charge
iv. Loosens chromatin structure
v. Euchromatin
vi. Should be this form for transcription to occur
b. DNA methylation
i. Adding methyl groups to certain bases of DNA
ii. Condenses chromatin structure
iii. Heterochromatin
iv. Transcription is not impossible but rather impeded
Dogma Model
4. DNA → RNA → protein/polypeptide → trait
a. Don’t always need to make the protein, could just want mRNA, tRNA, rRNA (for
ribosomes).
5. Transcription: DNA → RNA
6. Translation: RNA → protein
Transcription: DNA → pre-mRNA
7. Location: Nucleus
8. DNA needs to be relaxed for factors to bind and move along its length
9. DNA needs to have euchromatin (acetylation)
10. DNA → pre-mRNA aka an immature transcript
a. Not ready for translation yet
b. pre-mRNA in eukaryotes
11. DNA as a template to synthesize complementary pre-mRNA
12. Only one strand of DNA is the template
a. Template strand still being read as 3’ → 5’ and new RNA strand synthesized 5’
→ 3’ and they’re not interacting with each other after or being bound to each other
, b. Template strand can have either polarity though: 3’ → 5’ or 5’ → 3’, the RNA
polymerase will fix its orientation to match it
i. Different from DNA replication then
c. Nontemplate strand has information about a different gene of interest
d. Doesn’t interact with nontemplate strand
i. Different from DNA replication then
e. The same gene will always be found on the same template strand
13. Complementary Base Pairing
a. AU and CG
b. New strand looks just like nontemplate strand but U’s where there were T’s
14. Will never transcribe the entire DNA sequence or an entire chromosome but rather small
segments of the chromosome
a. Transcript strand shorter than replicated DNA strand
15. Constantly unwinding and winding instead of just staying unwinded because DNA is very
stable as a helical structure, if they’re apart they’d want to form the hairpin structures and
thus be inaccessible to transcription
16. RNA Polymerase
a. RNA polymerase I focuses on synthesizing ribosomal RNA genes
b. RNA polymerase II focuses on synthesizing protein coding genes - most common,
the one we’re usually referring to
c. RNA polymerase III focuses on synthesizing transfer RNA genes and ribosomal
RNA genes
d. If we don’t want to end up synthesizing a protein, then RNA pol I and III are what
will be present in transcription
17. Initiation Stage
a. Starting process
b. Promoter Region
i. Special sequence always on template strand
ii. Promoter has region for transcription factors to bind, region for RNA
polymerase, and region for regulatory protein binding
1. Gene Regulation: Specific sequence that recruits regulatory protein
binding
a. Presence or absence of proteins that can activate or inhibit
gene and thus regulate the rate of transcription
b. Regulatory proteins may or may not be needed
2. Specific sequence that recruits RNA polymerase
a. Indicates RNA polymerase to bind tightly to the promoter
region on the template strand and unravel the double
stranded DNA
i. Capable of de novo synthesis
