Chapter 15 Flashcards
(42 cards)
1
Q
What is translation?
A
the process through which the genetic code carried by messenger RNA (mRNA) is decoded to produce a specific sequence of amino acids, resulting in the formation of a protein
2
Q
why are proteins important?
A
active participants in cell structure and function
3
Q
What did Archibald Garrod do?
A
theory of a relationship between genes and production of proteins
4
Q
What did Beadle and Tatum do?
A
developed the one-gene/one-enzyme hypothesis
5
Q
What is the one-gene one-enzyme hypothesis?
A
the idea that was later expanded on that one gene encodes one enzyme
6
Q
How was the one-gene one-enzyme hypothesis modified?
A
- enzymes are one category of proteins, all proteins are encoded by genes, many of which don’t function as enzymes
- some proteins can be composed of 2+ different polypeptides
- One gene can encode 2 or more polypeptides due to alternative splicing or RNA editing
- many genes do not encode polypeptides
7
Q
What is the genetic code?
A
correspondence between a codon and the functional role that the codon plays during translation
8
Q
What is a codon?
A
A sequence of 3 nucleotides within mRNA
9
Q
How many codons are there?
A
64
10
Q
How many codons code for amino acids?
A
61 codons correspond to the 20 amino acids
10
Q
What are synonymous codons?
A
two or more different codons that specify the same amino acid
10
Q
What is a start codon?
A
a three-base sequence in mRNA that initiates translation, usually AUG
10
Q
What is a sense codon?
A
a codon that specifies an amino acid
10
Q
What are anticodons?
A
3-nucleotide sequence in tRNA that is complementary to a codon in mRNA
10
Q
What does it mean to say that genetic code is degenerate?
A
the characteristic of genetic code that more than one codon specifies the same amino acid
11
Q
What is the sequence that is always complementary to the codon on the mRNA?
A
The sequence that is always complementary to the codon on the mRNA is called the anticodon, which is located on the transfer RNA (tRNA) molecule.
12
Q
what are isoaccepting tRNAs?
A
Isoaccepting tRNAs are different tRNA molecules that accept the same amino acid but have different anticodon sequences. They play a role in recognizing different codons that code for the same amino acid
13
Q
How does the number of tRNAs compare to the number of amino acids?
A
There are 20 standard amino acids, but the number of tRNAs is greater than 20. The exact number of tRNA types in a cell can vary depending on the organism. For example, in humans, there are about 50 to 60 distinct tRNAs, while bacteria might have around 30 to 40.
14
Q
What does it mean to say that the genetic code has a “wobble”?
A
The third base in a codon which can vary without affecting the recognition between codon and anticodon during translation
15
Q
what are the characteristics of the genetic code?
A
- universal
- multiple codons can code for the same amino acid
3.codons are nonoverlapping - each codon only specifies 1 amino acid
- start and stop signals for translation
16
Q
what is meant by the genetic code is pretty much universal?
A
The genetic code is nearly universal across all living organisms, meaning that the same codon codes for the same amino acid in most species
17
Q
What are the basic subunits of a protein? what bond binds them together?
A
amino acids linked together by peptide bonds
18
Q
What is the basic structure of an amino acid?
A
contain both an amino group (-NH2) and a carboxyl group (-COOH), along with a unique side chain (R-group) that determines the properties and identity of each amino acid
19
Q
What is the amino terminal end and carboxy terminal end of a protein?
A
Amino terminal is the location of the first amino acid in a polypeptide
Carboxy terminal end is the location of the last amino acid in a polypeptide
20
What are the levels of conformation of a protein?
primary, secondary, tertiary, and quaternary
21
What is responsible for each level?
1- a chain
2 and 3: folding
4- associating with another structure
22
What is the basic structure of a tRNA molecule?
1. cloverleaf pattern of secondary structure
2. sequence CCA at 3' ends, where an amino acid can become attached
23
What is meant by tRNA charging?
a tRNA that has an amino acid covalently attached to its 3' end
24
What enzyme is involved in the charged tRNA?
aminoacyl-tRNA synthetase
25
What is the structure of a ribosome?
The ribosome is a complex molecular machine responsible for protein synthesis in cells. It is composed of ribosomal RNA (rRNA) and proteins and consists of two main subunits. The structure of a ribosome varies slightly between prokaryotes and eukaryotes, but they share many structural similarities. Here is an overview of the ribosome's structure:
General Structure:
Two Subunits:
The ribosome is made up of two subunits, one large and one small. These subunits come together during protein synthesis and separate when the process is complete.
In prokaryotes (e.g., bacteria), the ribosome is 70S, composed of a 50S large subunit and a 30S small subunit.
In eukaryotes (e.g., animals, plants, fungi), the ribosome is 80S, composed of a 60S large subunit and a 40S small subunit.
The "S" (Svedberg unit) represents the sedimentation rate during ultracentrifugation, which reflects the size and shape of the particle.
Composition of the Subunits:
Small Subunit:
Contains rRNA and proteins.
Its primary role is to bind to the mRNA and ensure the correct alignment of the mRNA and tRNA during translation.
In prokaryotes, the 30S subunit consists of 16S rRNA and about 21 proteins.
In eukaryotes, the 40S subunit consists of 18S rRNA and about 33 proteins.
Large Subunit:
Contains rRNA and proteins.
It plays a key role in catalyzing peptide bond formation between amino acids, a function known as peptidyl transferase activity.
In prokaryotes, the 50S subunit is composed of 23S rRNA, 5S rRNA, and about 34 proteins.
In eukaryotes, the 60S subunit is composed of 28S rRNA, 5.8S rRNA, 5S rRNA, and about 49 proteins.
26
What is a polyribosome?
mRNA transcript that has many bound ribosomes in the act of translation
27
What are the steps involved in translation?
1. Initiation
2. Elongation
3. Termination
28
What are some differences between initiation of translation in bacteria and eukaryotes?
1. Initiation Factors:
Bacteria: Use three main factors (IF-1, IF-2, IF-3).
Eukaryotes: Use many more initiation factors (eIFs, such as eIF-1, eIF-2, eIF-3, eIF-4 complex, etc.).
2. Ribosome Binding:
Bacteria: The small ribosomal subunit binds directly to the Shine-Dalgarno sequence on the mRNA to align with the start codon.
Eukaryotes: The small ribosomal subunit binds to the 5' cap of the mRNA and scans for the start codon (often within a Kozak sequence).
3. Initiator tRNA:
Bacteria: Use N-formylmethionyl-tRNA (fMet-tRNA), which carries a modified methionine.
Eukaryotes: Use methionyl-tRNA (Met-tRNA), which carries unmodified methionine.
4. Initiation Complex Assembly:
Bacteria: The 30S subunit binds to mRNA and initiator tRNA, then joins with the 50S subunit to form the 70S initiation complex.
Eukaryotes: The 40S subunit binds with the initiator tRNA and eIFs to form a pre-initiation complex, scans the mRNA, and then joins with the 60S subunit to create the 80S initiation complex.
5. Energy Requirements:
Bacteria: Use GTP hydrolysis facilitated by IF-2 for assembly.
Eukaryotes: Require multiple GTP hydrolysis steps, involving eIF-2 and eIF-5B.
6. Regulation:
Bacteria: Primarily regulated by mRNA accessibility and binding.
Eukaryotes: More complex regulation involving phosphorylation of eIFs and control over eIF-4E, adapting to stress and nutrient changes.
29
What are the different components of the initiation complex?
1. Initiation Complex in Bacteria (Prokaryotes):
Small Ribosomal Subunit (30S): The smaller subunit of the ribosome where initiation begins.
mRNA: The messenger RNA with the Shine-Dalgarno sequence that aligns the ribosome with the start codon.
Initiator tRNA (fMet-tRNA): Carries N-formylmethionine, which is the first amino acid in bacterial protein synthesis.
Initiation Factors:
IF-1: Binds to the 30S subunit and prevents tRNA binding to the A site prematurely.
IF-2: A GTP-binding protein that assists in the binding of fMet-tRNA to the 30S subunit.
IF-3: Prevents the premature association of the 30S and 50S subunits and helps the 30S subunit bind to mRNA.
Large Ribosomal Subunit (50S): Joins to form the complete 70S initiation complex once the components are correctly assembled and initiation factors are released.
2. Initiation Complex in Eukaryotes:
Small Ribosomal Subunit (40S): The smaller subunit that starts the initiation process.
mRNA: Contains a 5' cap structure and often includes a Kozak sequence around the start codon for recognition.
Initiator tRNA (Met-tRNA): Carries methionine (unmodified) and pairs with the start codon.
Eukaryotic Initiation Factors (eIFs):
eIF-1, eIF-1A: Assist in scanning and start codon recognition.
eIF-2: Binds to GTP and the initiator Met-tRNA, forming a ternary complex.
eIF-3: Prevents the premature joining of the 40S and 60S subunits and helps recruit the 40S subunit to the mRNA.
eIF-4 Complex (eIF-4A, eIF-4E, eIF-4G): Binds to the 5' cap of the mRNA and helps in unwinding secondary structures for scanning.
eIF-5: Promotes the release of initiation factors and assists in joining the 60S subunit.
eIF-5B: Facilitates the final joining of the large subunit (60S).
Large Ribosomal Subunit (60S): Joins to form the complete 80S initiation complex after start codon recognition and factor release.
30
What are the major events that happen in initiation?
1. Assembly of the Pre-Initiation Complex:
Bacteria: The 30S ribosomal subunit binds to the mRNA, assisted by initiation factors IF-1 and IF-3. The Shine-Dalgarno sequence on the mRNA helps align the mRNA with the ribosome.
Eukaryotes: The 40S ribosomal subunit associates with several eukaryotic initiation factors (eIFs), including eIF-1, eIF-1A, eIF-3, and eIF-2 (bound to GTP and initiator tRNA carrying methionine). This forms the 43S pre-initiation complex.
2. Binding of mRNA to the Ribosome:
Bacteria: The 30S subunit binds directly to the mRNA with the help of the Shine-Dalgarno sequence. This step positions the start codon (usually AUG) in the correct place to start translation.
Eukaryotes: The 43S complex binds to the 5' cap of the mRNA with the assistance of the eIF-4 complex (eIF-4E, eIF-4G, and eIF-4A). The complex then scans the mRNA in the 5' to 3' direction to find the start codon, typically within a Kozak sequence.
3. Recognition of the Start Codon:
The small ribosomal subunit, with its bound initiator tRNA, locates the start codon (AUG). This codon pairs with the anticodon on the initiator tRNA, ensuring the correct amino acid (methionine in eukaryotes, N-formylmethionine in bacteria) is in place to begin protein synthesis.
4. Joining of the Large Ribosomal Subunit:
Bacteria: The binding of fMet-tRNA to the start codon prompts the release of IF-1 and IF-3. IF-2 hydrolyzes GTP, which facilitates the joining of the 50S subunit to form the complete 70S initiation complex.
Eukaryotes: Once the start codon is recognized, eIF-2 hydrolyzes GTP, releasing the associated eIFs. The 60S subunit joins the 40S subunit, forming the complete 80S initiation complex. eIF-5B assists in this joining, and the remaining eIFs are released.
5. Establishment of the Initiation Complex:
The ribosome is now fully assembled and positioned at the start codon, with the initiator tRNA in the P site of the ribosome.
The initiation phase concludes with the ribosome ready for the elongation phase, where amino acids are sequentially added to build the polypeptide chain.
31
On a ribosome, what are the A, P, and E sites?
A- aminoacyl site where a charged tRNA initially binds
P- peptidyl site that carries a tRNA along with a polypeptide
E- exit site where an uncharged tRNA exits
32
What are the steps involved in elongation in translation?
1. Binding of Aminoacyl-tRNA to the A Site:
The ribosome has three sites: A (Aminoacyl), P (Peptidyl), and E (Exit).
An aminoacyl-tRNA with an anticodon complementary to the mRNA codon enters the A site.
Elongation factors:
Bacteria: The entry of aminoacyl-tRNA is facilitated by elongation factor EF-Tu, which binds GTP.
Eukaryotes: This step is mediated by eEF-1α, also bound to GTP.
Once the correct tRNA is in the A site and base-pairs with the codon, GTP is hydrolyzed, and the elongation factor is released.
2. Peptide Bond Formation:
A peptide bond is formed between the amino acid attached to the tRNA in the P site and the amino acid in the A site.
This reaction is catalyzed by peptidyl transferase, an enzymatic function of the large ribosomal subunit (23S rRNA in prokaryotes and 28S rRNA in eukaryotes).
The polypeptide chain is transferred from the tRNA in the P site to the amino acid on the tRNA in the A site, extending the chain by one amino acid.
3. Translocation:
The ribosome moves one codon down the mRNA in the 5' to 3' direction.
Elongation factors:
Bacteria: EF-G facilitates translocation, using energy from GTP hydrolysis.
Eukaryotes: eEF-2 performs the same function.
This movement shifts the tRNA carrying the polypeptide from the A site to the P site, and the now-empty tRNA in the P site moves to the E site before it exits the ribosome.
4. Exit of the Empty tRNA:
The tRNA in the E site is released, making the site available for the next round of elongation.
The A site is now vacant and ready to accept the next aminoacyl-tRNA corresponding to the next codon on the mRNA.
33
What is elongation in translation?
stage where the polypeptide chain is formed as amino acids are sequentially added, guided by the mRNA sequence. This phase follows initiation and precedes termination. The process is similar in both prokaryotes and eukaryotes, though some specific factors and details may differ
34
What is a release factor?
a protein that recognizes a stop codon and promotes translational termination and the release of the completed polypeptide
35
what is the difference between a peptide bond and a phosphodiester bond?
A phosphodiester bond is a covalent bond that links the 3' carbon atom of one sugar molecule to the 5' carbon atom of another in the backbone of nucleic acid strands (DNA and RNA). It forms between a phosphate group and two sugar molecules (deoxyribose in DNA and ribose in RNA).
A peptide bond is a covalent bond that forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another amino acid during protein synthesis.
36
What are some examples of post-translational modifications?
1. Phosphorylation:
Added Group: Phosphate.
Amino Acids Affected: Serine, threonine, tyrosine.
Function: Regulates protein activity, signaling, and cell processes.
Example: Activation of protein kinases in signaling pathways.
2. Glycosylation:
Added Group: Carbohydrate chains.
Amino Acids Affected: Asparagine (N-linked), serine/threonine (O-linked).
Function: Affects protein folding, stability, and cell-cell recognition.
Example: Glycosylation of antibodies for enhanced function.
3. Ubiquitination:
Added Group: Ubiquitin protein.
Amino Acids Affected: Lysine.
Function: Marks proteins for degradation, regulates cellular processes.
Example: Degradation of cyclin proteins during cell cycle control.
4. Methylation:
Added Group: Methyl group.
Amino Acids Affected: Lysine, arginine.
Function: Affects gene expression and chromatin structure.
Example: Methylation of histones in epigenetic regulation.
5. Acetylation:
Added Group: Acetyl group.
Amino Acids Affected: Lysine.
Function: Influences protein function and gene expression.
Example: Histone acetylation for relaxed chromatin and active transcription.
6. Proteolytic Cleavage:
Type: Removal of peptide segments.
Function: Activates or matures proteins.
Example: Activation of proinsulin to form insulin.
37
What are the ways that antibiotics can inhibit translation?
Erythromycin: binds to the 23S rRNA and blocks elongation
Tetracyclines: blocks elongation by inhibiting the binds of aminoacyl tRNAs to the ribosome
