Post transcriptional processing includes modification of _____ _____ of an mRNA sequence. Even before the eukaryotic mRNA is completely transcribed, its ___ end is capped in a process using GTP. State 2 purposes of the 5' cap
- both ends
- 1. Serves as an attachment site in protein synthesis during translation and
- 2. As a protection against degradation by enzymes that cleave nucleotides, called exonucleases.
The 3' end of the transcript is similarly protected from exonucleases by the addition of a long series of _______ nucleotides. When this _____ ____ _____ has been added, the 3' end is said to be __________.
- poly A tail
The primary transcript is much _______ than the mRNA that will be translated into a protein. Before leaving the nucleus, portions of the primary transcript are excised and discarded through the process of ______. The portions of transcript that are removed are called _______, while the portions that become part of the mature mRNA and will code for proteins are called ______. Introns are generally much ______ than exons. They do not code for _______ and are _______ within the nucleus.
The process of splicing removes introns from the primary transcript and joins the ends of the ______ together to form one, uninterrupted coding sequence of ______.
The mechanism of splicing involves several _____ ______ __________ (_____). Each snRNP contains both an assortment of ______ and ______. During the splicing process, snRNA acts as a _______ (define)
- small nuclear ribonucleoproteins (snRNPs, "snurps")
- proteins and snRNA
- ribozyme: an RNA molecule capable of catalyzing specific chemical reactions.
- **(Note that this is one of the few enzymes that is not a protein.)
Splicing occurs when ______ recognize nucleotide sequences at the ends of the ______. The snRNPs pull the ends of the ______ together, forming an _____ _____ or ______
- intron loop or lariat.
The complex formed from the association of the snRNPs and additional associate proteins is called a ________. The spliceosome excises the ______ and joins the ends of the ______ together to form the _____ _____ strand that ultimately codes for a polypeptide.
**Remember that, in general, INtrons remain IN the _______, and EXons EXit the _______ to be translated.
- single mRNA
Eukaryotic cells exert control over gene expression and add to the variety of protein products possible through the process of ________ _______, one of the major mechanisms in the regulation of eukaryotic gene expression.
Alternative splicing allows the cell to incorporate different _______ _______ into the _______ mRNA. This highly regulated process can create a variety of ______ molecules for translation from a single DNA coding sequence.
**The mechanisms for creating this variability include omitting certain exons, incorporating certain introns, and utilizing variable splicing sites.
- coding sequences
Increasing evidence indicates that ______ play an important function in determining gene expression. The nucleotide sequences in both _____ & _____ determine the different ways a primary transcript may be spliced.
- introns and exons
Furthermore, sequences that contain ______ are associated with amplified protein production compared to sequences that lack _______.
Alternative splicing, together with other eukaryotic techniques such as the use of alternative _______ sites or _________ transcription at different sites, allows the cell to create from a relatively limited number of protein-coding nucleotide sequences. Although the human genome is estimated to contain only ______ to _____ protein-coding gene regions, it can code for more than _______ proteins. Alternative splicing is an important contributor to this diversity of protein products.
One reason there are more proteins than genes is that different splicing patterns of the same gene can create different _______.
Trancription and post transcriptional modifications take place in the _______ of eukaryotes. The ______ _______ between transcriptional and translational processes provided by the nuclear membrane is a form of regulation in eukaryotes. This separation allows the RNA transcript to be modified _______ it leaves the nucleus and _______ translation can begin. In contrast, prokaryotes have no nuclear membrane.
- spatial separation
The lack of ______ _______ means that prokaryotes can carry out transcription and translation concurrently and that they do not modify RNA transcripts prior to the start of _______.
- spatial separation
lntrons play a role in determining possible splicing patterns and promoting protein production. Because of their functional significance, many introns are highly ______ between species.
2.6 Translating RNA to Protein
When post-transcriptional processing is finished, a mature mRNA is ready for _______ (define). As described earlier in the lecture, it involves the " translation" of the nucleotide sequence of mRNA into the amino acid sequence of the corresponding protein.
Translation: the process through which a cell creates the protein products that are necessary to carry out the processes of life.
During the process of translation, the information contained in mRNA is used as a set of instructions to create a specific _______ nucleotides are strung together to form a ______ _____ consisting of four different nucleotides, as described in the Biological Molecules and Enzymes Lecture.
In nature, there are approximately ____ different amino acids that commonly make up ______ ______. The four RNA nucleotides (______, ______, ______, and _____) together must create a language that unambiguously codes for each of these common ______ ______
- functional proteins
- adenine, guanine, cytosine, and uracil
- amino acids
The genetic code of mRNA accomplishes this task by using a series of ______ nucleotides to code for each amino acid - a system known as the _____ _____
The number of possible combinations from a set of two nucleotides, where each nucleotide might contain any one of the four nitrogenous bases, is ___ = ___, which is still not enough to code for the 20 amino acids. Therefore, the code must use a combination of three nucleotides for each amino acid. However, the number of possible combinations of any three nucleotides gives ___ = ___, which is greater than the number amino acids.
- 42 = 16
- 43 = 64
The genetic code is therefore said to be _______ (define). However, any single series of three nucleotides will code for ____ amino acid(s). Therefore the code is also ________
- degenerative: more than one series of three nucleotides may code for the same amino acid
- one *and only one amino acid
Three consecutive nucleotides on a strand of mRNA comprise a _____. All but three possible codons code for amino acids. The remaining codons, ____, ___ and ___, are stop codons (also called ______ codons). Stop codons signal an end to ______ synthesis.
- UAA, UGA, and UAG
The start codon (also called the ______ codon), ____, indicates where translation will begin. The start codon codes for the amino acid _______, which is always the first amino acid incorporated into a polypeptide during protein synthesis. By convention, a sequence of RNA nucleotides is written ___ to __.
**Pay special attention to second pic
Translation is the process by which the cellular machinery "reads" the ____ ______ and translates it into a _______. Each of the three major types of RNA plays a unique role in translation, state each.
- mRNA transcript
- 1. mRNA is the template which carries the genetic code from the nucleus to the cytosol in the form of codons.
- 2. tRNA plays a vital role in actually rendering the triplet code of the mRNA into a specific amino acid sequence.
- 3. rRNA along with many separate proteins make up the small subunit and a large subunit, which compose a ribosome.
Each tRNA molecule has two distinct ends. One end contains a series of three nucleotides, called an _______ (state function). The other end of the tRNA carries the _____ _____ that corresponds to that codon, which can be added to a growing polypeptide chain as tRNAs bind to the codons along the mRNA strand (Figure 2.12).
- anticodon: binds to the complementary codon sequence on mRNA
- amino acid
The first two base pairs in the codon and anticodon must be strictly ________ (A with U and C with G). However, there is some flexibility in bonding at the _____ base pair position. This flexibility is called ______ pairing and helps explain why multiple ______ can code for the same amino acid.
All translation takes place using a specialized organelle called a ______. Ribosomes may be ____-_____ in the cytosol or attached to the outer surface of the ________ _______ to form rough ER, as described in the Cell Lecture in Biology 2: Systems.
- endoplasmic reticulum
The ribosome and its subunits are measured in terms of _______ _______ given in _______ units (S). The sedimentation coefficient gives the _____ of a particle in a centrifuge and is proportional to _____ and related to ______ and ______.
- sedimentation coefficients
- Svedberg units (S)
- shape and density
Prokaryotic ribosomes are _______ than eukaryotic ribosomes. Prokaryotic ribosomes are made from a ____ and a ____ subunit and have a combined sedimentary coefficient of ____. Eukaryotic ribosomes are made of ____ and ____ subunits and have a combined sedimentary coefficient of ____.
- 30S and a 50S subunit
- 40S and 60S
The complex structure of ribosomes requires a special organelle called the _______ in which to manufacture them. (________ do not possess a nucleolus, but synthesis of prokaryotic ribosomes is similar to that of eukaryotic ribosomes.) Although the ribosome is assembled in the nucleolus, the small and large subunits are exported _______ to the cytosol.
**Notice that the sedimentation coefficients don't add up: 40 + 60 ≠ 80.
The process of translation is divided into the same three stages as transcription (______, ______, and ______), but whereas transcription produces a strand of ____, the product of translation is a chain of _____ _____.
- initiation, elongation, and termination
- amino acids
After posttranscriptional processing in a eukaryote, mRNA leaves the nucleus through the _____ _____ and enters the ______.
Explain translation (13-story)
- 1. With the help of initiation factors (co-factor proteins), the 5' end attaches to the small subunit of a ribosome.
- 2. A tRNA containing the 5' -CAU-3' anticodon sequesters the amino acid methionine and settles into the P site (peptidyl site). This is the signal for the large subunit to join and form the initiation complex. This process is termed initiation. Most of the regulation of translation occurs during the initiation stage through the recognition (or lack of recognition) between the ribosomal subunits and the secondary structure of the mRNA transcript.
- 3. Once the initiation complex is fully formed, elongation of the polypeptide begins. During elongation, the ribosome slides down the mRNA strand one codon at a time in the 5 '~ 3' direction while matching each codon to a complementary tRNA anticodon.
- 4. The corresponding amino acids attached to these tRNAs are bound together into a growing polypeptide as the process proceeds. The mechanism of elongation requires the input of energy.
- 5. Once a methionine bearing tRNA has attached to the P site, a new tRNA, with its corresponding amino acid, attaches to the neighboring A site (aminoacyl site).
- 6. The amino acid attached to the tRNA in the A site becomes the second amino acid in the polypeptide sequence.
- 7. The C-terminus (carboxyl end) of methionine attaches to the N-terminus (amine end) of the amino acid at the A site in a dehydration reaction, forming a peptide bond.
- 8. The bond formation takes place through peptidyl transferase activity, which is catalyzed by rRNA in the ribosome, another example of ribozyme function.
- 9. After lengthening the polypeptide by a single amino acid, the ribosome shifts 3 nucleotides toward the 3' end of the mRNA.
- 10. The tRNA that carried methionine moves to the E site, from which it can exit the ribosome. The tRNA carrying the newly formed dipeptide moves to the P site, leaving the A site open for the next tRNA.
- 11. The elongation process is repeated until a stop codon reaches the P site.
- 12. Translation ends when the ribosome reaches a stop codon in a step called termination. When a stop codon (or nonsense codon) reaches the A site, proteins known as release factors (co-factor proteins) bind to the A site, allowing a water molecule to add to the end of the polypeptide chain.
- 13. The polypeptide is freed from the tRNA and ribosome, and the ribosome breaks up into its subunits to be reused in later rounds of protein synthesis.
Even as the polypeptide is being translated, it begins ______. The _____ _____ sequence determines the folding conformation, and the folding process is assisted by proteins called _______. For further information on protein folding and structure, revisit the Biological Molecules and Enzymes Lecture.
After Translation: The Fates of Proteins
Once a protein is completely synthesized, it can still undergo _____-_______ modifications. How are these modifications a mechanism for regulating gene expression?
- by affecting which products of translation ultimately become functional proteins
Sugars, lipids, or phosphate groups may be added to amino acids to influence _________. The polypeptide can be _______ in one or more places. Separate polypeptides may join to form the _______ structure of a protein.
The final destination of a protein is related to where it is translated. Proteins translated by free-floating ribosomes function in the ______, while proteins synthesized by ribosomes that attach to the rough ER during translation are injected into the ____ ______. Proteins injected into the ER lumen are destined to become _______ _____ proteins of the ______ ______, _____, ______, _______, or ______ ________ or, often, to be secreted from the cell. Free floating ribosomes are identical in structure to ribosomes that attach to the ER.
- ER lumen
- membrane bound
- nuclear envelope, ER, Golgi, lysosomes, or plasma membrane
The growing polypeptide itself may or may not cause the ribosome to attach to the ER, depending upon the _______. A 20 amino acid sequence called a ______ ______ near the front of the polypeptide is recognized by a protein-RNA _____-______ ______ that carries the entire ribosome complex to a ______ protein on the ER. There the protein grows across the membrane, where it is either released into the ______ or remains partially attached to the ____.
- signal peptide
- signal-recognition particle (SRP)
The signal peptide is usually _______ by an enzyme. Signal peptides may also be attached to polypeptides to target them to ________, the ______, or other _______. In this way, proteins end up in locations appropriate to their ________ and _______, and thus one of the main purposes of the genome, production and delivery of the products the cell needs, is achieved.
- structures and functions