PRINCIPLES OF BIOLOGY I ASYNCHRONOUS VIDEO
NOTES [MIDTERM 2]
WEEK 6: TRANSCRIPTION AND TRANSLATION
1. Each gene encodes a specific protein
a. Experiment: irradiated Neurospora Crassa with x-rays – causes mutations, these
mutations can inactivate genes
i. Isolated whole bunch of mutants and looked for mutants that could not
grow in the absence of nutrients
1. Neurospora can generally take arginine (nutrient used in
experiment) from the environment, or it can synthesize its own
arginine
2. Arginine synthesized in cells by a multi-step pathway, where a
precursor molecule is converted to ornithine by a specific enzyme;
ornithine is converted to citrulline by another enzyme, and
citrulline is then converted to arginine by a third enzyme
ii. Took classes of Neurospora mutants that were deficient in arginine
biosynthesis and noted that each of these mutants had a mutation in a
single gene
b. Found three classes of mutants
i. Wild type: UNMUTATED cells able to grow on minimal medium if
supplemented with either ornithine, citrulline, or arginine
1. Minimal medium: just what the cell needs to survive (nothing
additional added)
ii. When the MUTANTS were grown on minimal medium, the cells were
dead (unable to grow) because arginine biosynthesis pathway is broken,
and cells cannot make their own arginine
iii. Class I mutants: if supplemented with ornithine, citrulline, or arginine,
the cells were alive
iv. Class II mutants: if supplemented with ornithine, the cells were not able
to grow; but if supplemented with citrulline or arginine, the cells were fine
v. Class III mutants: whether given ornithine or citrulline, the cells could
not grow, but could grow if supplemented with arginine
,2. Conclusion of experiment
a. Class I mutants had mutation in enzyme that converted precursor molecule to
ornithine (thus only if it was given ornithine, it can still convert to arginine)
b. Class II mutants had mutation in enzyme that converts ornithine to citrulline (thus
if only given ornithine, cannot convert to citrulline, but if given citrulline, it can
still convert to arginine)
c. Class III mutants had mutation in enzyme that converts citrulline to arginine
d. Experiment shows that each strain had a mutation in one gene; the mutation in
one gene led to the specific inactivation of one enzyme
i. Thus, each gene codes a specific enzyme, and eventually broadened to the
concept that each gene codes a specific protein
3. DNA is transcribed to produce messenger RNA (mRNA), and this mRNA is translated to
produce a protein, which is the effector molecules
4. Transcription can generate several different kinds of RNA
a. mRNA (messenger RNA): codes for proteins
b. rRNA (ribosomal RNA): integral components of ribosomes
c. tRNA (transfer RNA): required for decoding in translation
, 5. mRNA synthesis
a. Genes have a beginning, middle, and end
i. Beginning: known as a promotor – where transcription starts is determined
by promotor
ii. Middle: gene body – part that encodes a protein; transcription produces
RNA copy of gene body
iii. End: terminator – where transcription ends
Note: examples of downstream = coding region and terminator are downstream the promoter;
promoter and coding region are upstream of the terminator
Note: untranslated region (UTR) does not get transcribed, so actual transcription region occurs
at beginning of coding region
6. Enzyme responsible for transcription is known as RNA polymerase
a. Catalyzes the reaction and can only move in the 5’ to 3’ direction
b. RNA polymerase is recruited to promotor of gene; RNA polymerase then moves
through the gene and makes a copy of one strand of the DNA
c. Only strand that is copied is the template strand of the DNA
d. When RNA polymerase reaches terminator at the end of transcription unit, it falls
off the DNA and will release completed RNA transcript that can go off to do its
job in the cell
7. RNA polymerase moves along the DNA (unwinding it as it goes)
a. Catalyzes the formation of an RNA molecule that sequences the reverse
compliment of the template strand
b. Sequence of the RNA that’s produced is the reverse compliment of the template
strand
i. This means it is the exact same sequence as the non-template / coding
strand
1. Only difference between RNA strand that is produced and coding
strand is that there are Ts in the DNA and Us in the RNA
, 8. Differences and similarities between DNA synthesis by DNA polymerase and RNA
synthesis by RNA polymerase
a. DNA synthesized (5’ to 3’) from 5’ dNTPs by DNA polymerase; RNA
synthesized (5’ to 3’) from 5’ NTPs by RNA polymerase
i. Essentially, they are chemically the exact same thing
1. Only difference is that the nucleotides involved in RNA have a 2’
hydroxyl
b. Both need topoisomerases to resolve the issue of supercoiling (topological issues)
9. There are specific sequences that determine promoter function and promoter location in
prokaryotes
a. If we mutate these sequences, we reduce the propensity of that region to act as a
promotor
b. The spacing between these two sequences is important
i. Ideal spacing between these two sequences is 17 base pairs
ii. Having specific DNA sequences a defined distance apart can be used to
recruit RNA polymerase
10. In prokaryotes, promoter sequences are recognized by RNA polymerase in complex with
an additional protein called the sigma factor
a. Sigma factor – accessory protein (not directly involved in catalysis of reaction /
not required for RNA polymerase to add NTPs to a growing chain)
i. Required to deliver RNA polymerase to promoter
ii. Without sigma factor, RNA polymerase cannot get to promoter, so you
cannot have transcription
iii. After it has delivered RNA polymerase to promoter, the sigma factor
leaves, and RNA polymerase can continue transcribing in absence of
sigma factor
NOTES [MIDTERM 2]
WEEK 6: TRANSCRIPTION AND TRANSLATION
1. Each gene encodes a specific protein
a. Experiment: irradiated Neurospora Crassa with x-rays – causes mutations, these
mutations can inactivate genes
i. Isolated whole bunch of mutants and looked for mutants that could not
grow in the absence of nutrients
1. Neurospora can generally take arginine (nutrient used in
experiment) from the environment, or it can synthesize its own
arginine
2. Arginine synthesized in cells by a multi-step pathway, where a
precursor molecule is converted to ornithine by a specific enzyme;
ornithine is converted to citrulline by another enzyme, and
citrulline is then converted to arginine by a third enzyme
ii. Took classes of Neurospora mutants that were deficient in arginine
biosynthesis and noted that each of these mutants had a mutation in a
single gene
b. Found three classes of mutants
i. Wild type: UNMUTATED cells able to grow on minimal medium if
supplemented with either ornithine, citrulline, or arginine
1. Minimal medium: just what the cell needs to survive (nothing
additional added)
ii. When the MUTANTS were grown on minimal medium, the cells were
dead (unable to grow) because arginine biosynthesis pathway is broken,
and cells cannot make their own arginine
iii. Class I mutants: if supplemented with ornithine, citrulline, or arginine,
the cells were alive
iv. Class II mutants: if supplemented with ornithine, the cells were not able
to grow; but if supplemented with citrulline or arginine, the cells were fine
v. Class III mutants: whether given ornithine or citrulline, the cells could
not grow, but could grow if supplemented with arginine
,2. Conclusion of experiment
a. Class I mutants had mutation in enzyme that converted precursor molecule to
ornithine (thus only if it was given ornithine, it can still convert to arginine)
b. Class II mutants had mutation in enzyme that converts ornithine to citrulline (thus
if only given ornithine, cannot convert to citrulline, but if given citrulline, it can
still convert to arginine)
c. Class III mutants had mutation in enzyme that converts citrulline to arginine
d. Experiment shows that each strain had a mutation in one gene; the mutation in
one gene led to the specific inactivation of one enzyme
i. Thus, each gene codes a specific enzyme, and eventually broadened to the
concept that each gene codes a specific protein
3. DNA is transcribed to produce messenger RNA (mRNA), and this mRNA is translated to
produce a protein, which is the effector molecules
4. Transcription can generate several different kinds of RNA
a. mRNA (messenger RNA): codes for proteins
b. rRNA (ribosomal RNA): integral components of ribosomes
c. tRNA (transfer RNA): required for decoding in translation
, 5. mRNA synthesis
a. Genes have a beginning, middle, and end
i. Beginning: known as a promotor – where transcription starts is determined
by promotor
ii. Middle: gene body – part that encodes a protein; transcription produces
RNA copy of gene body
iii. End: terminator – where transcription ends
Note: examples of downstream = coding region and terminator are downstream the promoter;
promoter and coding region are upstream of the terminator
Note: untranslated region (UTR) does not get transcribed, so actual transcription region occurs
at beginning of coding region
6. Enzyme responsible for transcription is known as RNA polymerase
a. Catalyzes the reaction and can only move in the 5’ to 3’ direction
b. RNA polymerase is recruited to promotor of gene; RNA polymerase then moves
through the gene and makes a copy of one strand of the DNA
c. Only strand that is copied is the template strand of the DNA
d. When RNA polymerase reaches terminator at the end of transcription unit, it falls
off the DNA and will release completed RNA transcript that can go off to do its
job in the cell
7. RNA polymerase moves along the DNA (unwinding it as it goes)
a. Catalyzes the formation of an RNA molecule that sequences the reverse
compliment of the template strand
b. Sequence of the RNA that’s produced is the reverse compliment of the template
strand
i. This means it is the exact same sequence as the non-template / coding
strand
1. Only difference between RNA strand that is produced and coding
strand is that there are Ts in the DNA and Us in the RNA
, 8. Differences and similarities between DNA synthesis by DNA polymerase and RNA
synthesis by RNA polymerase
a. DNA synthesized (5’ to 3’) from 5’ dNTPs by DNA polymerase; RNA
synthesized (5’ to 3’) from 5’ NTPs by RNA polymerase
i. Essentially, they are chemically the exact same thing
1. Only difference is that the nucleotides involved in RNA have a 2’
hydroxyl
b. Both need topoisomerases to resolve the issue of supercoiling (topological issues)
9. There are specific sequences that determine promoter function and promoter location in
prokaryotes
a. If we mutate these sequences, we reduce the propensity of that region to act as a
promotor
b. The spacing between these two sequences is important
i. Ideal spacing between these two sequences is 17 base pairs
ii. Having specific DNA sequences a defined distance apart can be used to
recruit RNA polymerase
10. In prokaryotes, promoter sequences are recognized by RNA polymerase in complex with
an additional protein called the sigma factor
a. Sigma factor – accessory protein (not directly involved in catalysis of reaction /
not required for RNA polymerase to add NTPs to a growing chain)
i. Required to deliver RNA polymerase to promoter
ii. Without sigma factor, RNA polymerase cannot get to promoter, so you
cannot have transcription
iii. After it has delivered RNA polymerase to promoter, the sigma factor
leaves, and RNA polymerase can continue transcribing in absence of
sigma factor
