1. From Gene to Protein
Chapter 17

2. Warm Up Exercise What is a telomere?
Explain how DNA is packed tightly into a chromosome.

3. Gene Expression
Gene Expression- DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins. (Proteins therefore are the link between genotype and phenotype).
Gene expression occurs in two steps- transcription and translation.
We learned previously that traits are determined by genes and the information content of genes is in the form of a specific sequence of nucleotides in the DNA. Albinism for example results from a faulty protein, or enzyme that is required for pigment synthesis. This protein contains incorrect information due to a DNA mutation.
Many proteins are enzymes, but not all such as insulin and keratin, hemoglobin. Some are coded for by only one gene, some by more than one gene

4. Transcription and Translation
Transcription- the synthesis of RNA using information in the DNA.
Occurs in the nucleus.
Translation- the synthesis of a polypeptide from mRNA.
Occurs on the ribosome
Genes provide the instructions for making proteins but the gene does not build a protein directly. The bridge between the DNA and the protein is RNA. Similar to DNA except the base, single strand, and the sugar.
Genes are typically hundreds or thousands of nucleotides long- each with a specific sequence of bases (the proteins primary structure).
*specifically mRNA, although transcription in general refers to any type of RNA.

5. Transcription and Translation
Primary Transcript- the initial RNA from any gene. Includes RNA that is not translated into protein.
The instructions for making a protein
In bacterial cells there is no primary transcript or further editing of the RNA.
Exons are Expressed Introns are intervening between the coding sequences.

6. Transcription and Translation
Template Strand- the single DNA strand from which the mRNA is transcribed.
Only one of the two strands is transcribed.
For any given gene, the same strand is used as the template every time the gene is transcribed. For other genes on the same DNA molecule, the opposite strand may be the one that always functions as the template.
RNA is complementary to the template strand. (would be same as other strand with exception of T/U) because it uses the base pairing rules.
Triplet Code- three letters read at a time. Because there are 4 bases, read 3 at a time, there are 4^3 or 64 possible outcomes that code for 20 amino acids- so some are coded for more than once.
Within the 64 codons, 61 code for amino acids. There is 1 start codon and 3 stop codons.

7. Transcription and Translation
Codons- a series of 3 bases on the mRNA, read together to code for a specific amino acid.
Written and read in the 5’ to 3’ direction. Because it takes 3 codons to make an amino acid- a polypeptide that is 100 amino acids would be 300 nucleotides long.
AUG starts with methionine. So it is the first amino acid that is synthesized. Not all proteins need methionine as their first amino acid though- so there may be an enzyme that comes in and removes it.
Because the genetic code is the same for all organisms (or all that scientists have examined so far) species can express proteins/ genes taken from other species. This is a huge medical advancement. Bacteria are frequently programmed to make human insulin for medical use. (Very few exceptions exist- such as in mitochondrial/eukaryotic DNA or in some unicellular eukaryotes)
This similarity in genetic code of all organisms points toward a shared genetic relationship and common ancestry.

8. Codon Charts

9. Warm Up Exercise What is a codon?
What is meant by the term primary transcript?

10. Trascription
RNA Polymerase- pries two strands of DNA apart and joins RNA nucleotides that are complementary to the DNA template strand.
RNA Pol II specifically is used for mRNA synthesis.
Promoter- specific DNA sequence where RNA polymerase attaches and begins transcription.
Start Point- the nucleotide where RNA synthesis actually begins. Found on the promoter gene.
Transcription Unit- the stretch of DNA that is transcribed into RNA.
In 5’ to 3’ direction only. Unlike DNA though, there is no primer needed to start a chain of RNA. Specific sequences of nucleotides along the DNA mark where transcription begins and ends. In bacteria, the end of the sequence is marked by a “terminator”. Eukaryotes is not like that.
Bacteria have a single type of RNA polymerase that synthesize all types of RNA. Eukaryotes have at least 3 types of RNA polymerase that function in protein synthesis.
Transcription occurs “downstream” with the opposite direction being upstream. Thus the promoter is upstream from the terminator.

12. Stages of Transcription
Initiation
Transcription Factors- mediate the binding of RNA polymerase and initiate transcription (in eukaryotes).
Transcription Initiation Complex- Transcription Factors + RNA Pol II + Promoters
TATA Box- promoter DNA sequence
RNA polymerase binds in a precise orientation and locating on the promoter, determining where transcription starts and which of the 2 DNA strands as used as the template.
In bacteria, RNA polymerase recognizes and binds to the promoter. Once the transcription factors are firmly attached to the promoter DNA and polymerase is bound in the correct orientation, polymerase unwinds the strands and starts transcribing.
The TATA box is part of the promoter sequence (it is TATA on the non-template strand, ATAT on the template strand) it is usually about 25 nucleotides upstream from the start point. Transcription factors must bind to the promoter region, including the TATA box before rAN polymerase II can bind and start transcription.
Only after transcription factors are attached to the promoter does RNA pol II bind to it.

13. Stages of Transcription
Elongation
RNA Polymerase moves along the DNA, unwinding the double helix for pairing with RNA nucleotides.
Unwinds and exposes about nucleotides at a time. RNA Polymerase adds nucleotides of the 3’ end f the growing RNA molecule. Transcription occurs at about 40 nucleotides per second in eukaryotes.

14. Stages of Transcription
Termination
Terminator sequence in bacteria causes RNA polymerase to detach from DNA.
In eukaryotes, RNA pol II transcribes a polyadenylation signal. Proteins then cut the transcribed RNA free from polymerase, releasing the pre-mRNA (aka: primary transcript).
Termination sequence (on RNA) causes the Polymerase to detach from DNA and release the mRNA which is completely transcribed and gets no further modifications.
The pre-mRNA then goes through an editing process in eukaryotes to be modified. This is why the strand that is initially produced is called pre-mRNA.

15. Modifying RNA After Transcription
RNA Processing- modification of pre-mRNA before it is released from the nucleus.
5’ Cap- a modified guanine (G) nucleotide added on the 5’ end after transcription.
Poly-A Tail- a series of adenine (A) nucleotides added at the 3’ end of the pre-mRNA.
Both ends of the primary transcript are altered and some interior sections are cut out and the remaining parts spliced together.
5’ end is synthesized first.
Importance: 5’ Cap and Poly A Tail help pre-mRNA move from nucleus to cytoplasm, they help protect mRNA from degradation by enzymes, and they help ribosomes attach to the 5’ end of the mRNA once it reaches the cytoplasm.
UTR- untranslated region- not translated into a protein, but have other functions such as ribosomal binding.

16. Modifying RNA After Transcription
RNA Splicing- removal of large portions of the RNA molecule that is initially synthesized.
Introns- noncoding sequences in the DNA/RNA. (Intervening sequences)
Exons- coding sequences in the DNA/RNA (Expressed sequences)
Average length of transcriptional unit along human DNA is about 27,000 nucleotide pairs, so primary transcript is that long. It only takes about 1,00 nucleotides in RNA to code for the average size protein- of 400 amino acids, so most of the eukaryotic genes have long noncoding stretches.
Exception: the UTR of the exon at the end of the RNA strand. They are not cut out, but are still considered exons.
Exons are sequences that EXIT the nucleus, to be translated into a protein on the ribosome.
The pre-mRNA or primary transcript contains both the introns and exons, but introns are spliced out and exons joined together in the process of RNA Splicing.
This is hemoglobin- 146 aa long protein

17. Modifying RNA After Transcription
snRNPs (“snurps”)- a short nucleotide sequence at the end of an intron that recognizes splice sites.
Spliceosome- several snRNPs joined together with proteins. Interacts with sites along the intron, releasing the intron which is rapidly degraded- and joining the exons.
Small nuclear ribonucleoproteins – located in the cell nucleus, and are composed of RNA and protein molecules. It is called a small nuclear RNA because it is only about 150 nucleotides long.
Spliceosome- interacts with certain sites along an intron, releaseing the intron, which is rapidly degraded.
snRNA catalyzes this process and helps assemble the spliceosome and aide in splice site recognition.
snRNA base pairs with nucleotides at specific sites along the intron
Spliceosome disassembles.

18. Modifying RNA After Transcription
Ribozymes RNA molecules that function as enzymes.
Domains- a discrete structural and functional region of a protein- coded for by a specific exon.
Almost all enzymes are proteins- all except ribozymes. Ribozymes can sometimes catalyze the splicing of their own introns in some species. Still the RNA primary transcript has nucleotide sequences that indicate where the splicing begins.
Some exons may create the active site, others may allow an enzyme to bind to a specific membrane.

19. Warm Up Exercise Explain the difference between introns and exons?
What is a snurp? A spliceosome?

20. Translation
Transfer RNA (tRNA)- transfers amino acids from the cytoplasm to the growing polypeptide on a ribosome.
tRNA molecule has a specific amino acid at one end, and a nucleotide triplet, called an anticodon at the other end, which pairs with a complementary codon on the mRNA.
A cell keeps its cytoplasm stocked with all 20 amino acids, either b synthesizing them from other compounds, or taking them up from surrounding solution. Ribosome (made of proteins and RNAs) adds each amino acid brought it it by tRNA to the growing end of a polypeptide chain.
Each type of tRNA molecule translates a particular mRNA codon into a particular amino acid.
GCC on mRNA= amino acid glycine, tRNA would be CGG anticodon on one end and glycine on the other end. Glycine is added to the growing polypeptide chain