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IB HL Biology > 7.3 Translation > Flashcards

7.3 Translation Flashcards

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1
Q

Diagram of the genetic code

A
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2
Q

When does translation start?

A

-When mature mRNA binds to a small ribosomal subunit at the mRNA binding site.

-All mRNA have an initiation (start) codon: AUG, which can be linked to the initiator tRNA.

-This specific tRNA always carries methionine.

-Thus, all proteins start with this amino acid.

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3
Q

How many stages are there of translation?

A

3

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4
Q

What are the three stages of translation?

A

-Initiation

-Elongation

-Termination

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5
Q

Diagram of the initiation stage of translation

A
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6
Q

Describe what happens to mRNA during initiation

A

-At initiation, the mRNA binds to a small ribosomal subunit.

-Next, the anticodon of the initiator tRNA binds to the codon of the mRNA.

-Finally, the large ribosomal subunit joins to complete the assembly of the translation complex.

-Now that each component is in its correct location, the process of translation can start.

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7
Q

What forms when a tRNA molecule binds to its corresponding amino acid?

A

A complex called an aminoacyl-tRNA.

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8
Q

Describe initiation (after each component is in its correct location)

A

-The space filled by the initiator tRNA is called the P site. E, P and A stand for Exit, Peptidyl-tRNA binding and Aminoacyl-tRNA binding site, respectively.

-As the name suggests, the E site is where the tRNA moves after transferring its amino acid to the growing polypeptide chain, ready to exit the ribosome.

-The A site is where the incoming tRNA with its attached amino acid binds, while the P site is where tRNA from the A site moves after its amino acid forms a peptide bond with the growing polypeptide chain.

-Therefore the P site is where the tRNA holding the growing polypeptide chain is found.

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9
Q

What should you know about the three tRNA binding states on a ribosome?

A

-The names of the three

-Their corresponding roles

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10
Q

Diagram of elongation stage of translation

A
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11
Q

Elongation involves a ___

A

Repeated cycle of events

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12
Q

Step 1 of elongation

A

-A new aminoacyl-tRNA comes in and binds to the A site ( step 1 ).

-This aminoacyl-tRNA carries a specific amino acid that matches the codon on the mRNA and the anticodon of the tRNA.

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13
Q

Step 2 of elongation

A

In step 2, the new amino acid is joined to the existing polypeptide chain by a peptide bond.

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14
Q

Step 3 of elongation

A

In step 3, the tRNA that was bound to the polypeptide chain is now ready to be recycled as it is no longer bound to an amino acid.

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15
Q

Step 4 of elongation

A

-In step 4, the ribosome translocates (moves) the tRNA holding the growing amino acid chain from the A site to the P site.

-This shifts the ‘empty’ tRNA to the E site, where it can leave the ribosome and be recycled.

-Now the whole process can start again until the ribosome reaches the termination codons: UAG, UAA, or UGA.

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16
Q

Do you need to know the base sequence of the start of stop codons?

A

No

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17
Q

Diagram of termination stage of translation

A
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18
Q

Describe termination

A

-Once the termination codon is reached, a release factor binds in the A site and causes the disassembly of the components of the translation complex.

-All of these components can be reused for another translation complex.

-This stage of translation is called termination.

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19
Q

A particular triplet of bases in a gene (DNA) reads 5’ AAA 3’.

The anticodon on the tRNA that binds to the mRNA codon is ___

A

UUU

AAA is the 5’ to 3’ sequence on the DNA, meaning that the mRNA reads: AAA (remember the 3’ to 5’ strand is the template for transcription which reads TTT so the mRNA that is transcribed reads AAA). A always pairs with U (in RNA).

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20
Q

What is the first event to take place in translation in eukaryotes?

A

The small subunit of the ribosome recognises and attaches to the initiator codon of mRNA.

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21
Q

What is the A site of the ribosome?

A

The site where a tRNA attached to an amino acid enters the ribosome.

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22
Q

During which stage of translation does a release factor bind to the ribosome?

A

Termination

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23
Q

Describe the structure of ribosomes

A

-Ribosomes are very complex structures, consisting of proteins and ribosomal RNA molecules.

-Ribosomes have a small and a large subunit, with three binding sites for tRNA molecules.

-The specific names and function of the three sites should be known.

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24
Q

Describe the structure of tRNA

A

-tRNA is a single-stranded RNA molecule that folds on itself to form a cloverleaf-shaped structure with double-stranded regions and three hairpin loops.

-One of these loops contains a sequence called the anticodon, which can decode and bind to an mRNA codon.

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25
Each tRNA has its corresponding ___
Amino acid attached to the 3' end of CCA (read 5' to 3').
26
What happens when a tRNA recognises and binds to its corresponding codon or mRNA in the ribosome?
-The tRNA transfers the appropriate amino acid to the end of the growing polypeptide. -The ribosome acts as an enzyme to catalyse this reaction.
27
Diagram of the structure of tRNA
.
28
Digaram of the structure of RNA
29
What is the triplet of bases at the amino acid binding site of tRNA?
5' CCA 3'
30
How many permanent loops does a tRNA molecule have?
3
31
When does translation only work well?
-If all of the thousands of tRNA molecules in the cells are loaded with the correct amino acid, corresponding to the codon on the mRNA. -This involves the enzyme aminoacyl-tRNA synthetase, which is also commonly referred to as the tRNA-activating enzyme.
32
How many different aminoacyl-tRNA synthetases are there and how many different amino acids do they correspond to?
There are 20 different aminoacyl-tRNA synthetases that correspond to the 20 different amino acids.
33
Describe the specificity of enzymes to tRNA molcules
-Each enzyme is highly specific for an amino acid and the corresponding tRNA molecule that has the matching anticodon. -This specificity is based on a match between the shape of the anticodon of the tRNA and the enzyme, as well as the match between the shape of the particular amino acid and the enzyme, thus illustrating the concept of enzyme–substrate specificity.
34
Diagram of the aminoacylation of a tRNA molecule
35
What does aminoacelytation of a tRNA molecule require? (reword?)
It requires the hydrolysis of an ATP molecule to provide the energy for the reaction: ATP + H2O → AMP and PP (pyrophosphate).
36
Give an example of the concept of phosphorylation
When phosphates are removed from ATP molecules energy is released for use by the cell.
37
Diagram of tRA with an attached amino acid
38
The enzyme attaches the specific amino acid to the ___ end of the tRNA
3'
39
Note that when reading the anticodon, we read ___ However, the mRNA codon (also read left to right on the diagram) is in the ___ direction on the mRNA molecule.
Left to right on the diagram, which is the 3’ to 5’ direction on the molecule. 5’ to 3’
40
What happens once the tRNA has attached an amino acid?
-It is called a charged tRNA molecule and can now be used in the initiation or elongation stages of translation. -Charged tRNA molecules are often written in this manner: tRNA-leu indicates a tRNA molecule that is attached to the amino acid leucine.
41
What will be the consequence if a mutation alters the formation of a single tRNA such that it still attaches to the same amino acid (phe), but its anticodon loop has the sequence AAU so it binds to the mRNA codon UUA (that usually specifies leucine)?
-One mutated tRNA molecule will be relatively inconsequential because it will compete with many 'normal' ones. -There are thousands of tRNA molecules in the cytoplasm of an organism involved in translation. -If one is mutated that would not have a great effect.
42
What is the anticodon loop of the tRNA that will complement the mRNA 5' CCG 3'?
-3' GGC 5' -The tRNA has an anticodon, so it runs in the opposite, i.e. 3' to 5' direction.
43
Based on the concept of enzyme specificity, if 20 different amino acids must be added to tRNA molecules, how many different types of aminoacyl-tRNA synthetase molecules would you expect to find in a cell?
-At least 20 -If each amino acid must be added to particular tRNA molecules, then there ought to be 20 aminoacyl-tRNA synthetase molecules; one to match each amino acid to the set of correct tRNA molecules. -You would also expect these molecules to be specific for the tRNA molecules that have the correct anticodons that match the correct amino acids.
44
Give an overivew of the function and place of proteins
-The cell has a set of organelles that function like a 'post office' that sorts proteins so that they end up in their proper place. -Proteins that function inside the endoplasmic reticulum (ER), Golgi apparatus, lysosomes and plasma membrane, or that are destined to be exported outside of the cell, are synthesised on the bound ribosomes attached to the ER.
45
What happens once the mRNA attaches itself to the ribosome?
-Translation starts immediately. -The beginning of the polypeptide contains the signal sequence, which is recognised by a signal-recognition particle (SRP). -The SRP then binds to the SRP recognition protein on the endoplasmic reticulum.
46
What does the SRP binding to the SRP recongnition protein on the ER allow?
This allows the polypeptide to enter the rough endoplasmic reticulum (RER) as it grows in length.
47
What happens to the polypeptide when translation ends and the translation complex disassembles?
The whole polypeptide is taken into the rER
48
Where does the post-translational modifications and sorting of newly formed proteins take place?
In the lumen of the ER
49
Diagram of protein synthesis on bound ribosomes
50
What happens to proteins that are translated on free (cytoplasmic or unbound) ribosomes?
-They are destined to function in the mitochondria, chloroplasts, cytoplasm or nucleus of the cell. -In the case of eukaryotes, once the mRNA moves into the cytoplasm from the nucleus, ribosomes attach to it and translation begins.
51
What is the difference between the function of bound and free ribosomes?
-Bound ribosomes synthesise proteins mainly meant for secretion or for use in lysosomes. -Free ribosomes produce proteins for use mainly within the cell.
52
Describe transcription and translation in bacteria (reword?)
-In bacteria, there is no separation between areas of the cell where transcription and translation take place, due to the absence of a nuclear membrane. -Once the mRNA is produced, and even before the whole molecule has been synthesised, small and large ribosomal subunits attach themselves to the beginning of the mRNA and translation starts immediately.
53
What is a polysome?
-To allow the production of polypeptides and hence proteins at a faster rate, multiple ribosomes can attach to the same mRNA. -The structure formed is called a polysome.
54
Diagram of polysomes attached to a growing mRNA molecule in a prokaryote
55
Electron micrograph of polysome in an eukaryotic cell (salivary gland). The green areas are proteins, blue are ribosomes and the areas in pink are mRNA.
56
What is a function of the signal recognition particle (SRP)?
To help translocate polypeptides across the ER membrane.
57
When translating secretory or membrane proteins, ribosomes are directed to the ER membrane by ___
A signal-recognition particle that brings ribosomes to a receptor protein in the ER membrane.
58
Actin and myosin are proteins found in muscle cells. Where would they be synthesised?
-Free ribosomes in cytoplasm of muscle cells. -Any protein to be used inside a muscle cell would be synthesised at free ribosomes in the cytoplasm of muscle cells. -Bound ribosomes are attached to the rough endoplasmic reticulum and sythesise proteins for export outside the cell.
59
What is a polysome?
A group of ribosomes working on the same mRNA molecule.
60
What is a difference between prokaryotic and eukaryotic translation?
Translation in prokaryotes can occur immediately after transcription due to the absence of a nuclear membrane.
61
How many amino acids to do polypeptides consist of?
Approximately 20 different amino acids
62
What is the primary structure of a protein?
-This refers to the sequence (order and identity) and the number of amino acids in the polypeptide. -It is maintained by peptide bonds between the subunits.
63
Diagram of the primary structure of a protein
64
When is the secondary structure of a protein formed and what is it stabilized by?
-It is formed when the polypeptide chain folds back on itself into α -helices or β -pleated sheets. -It is stabilised by hydrogen bonds between –NH groups (from the peptide bonds) and –C=O groups on another peptide bond, further along in the same chain.
65
Diagram of the secondary structure of a protein
.
66
What is the tertiary structure of a protein and what is it stabilized by?
-The tertiary structure is the further folding of the polypeptide, stabilised by interactions between R groups. -Generally, non-polar R groups will associate together as they are all hydrophobic, and polar R groups will associate together as they are all hydrophilic. -The polar R groups will be stabilised by interactions such as ionic interactions between acidic and basic R groups, or hydrogen bonding.
67
Describe covalent bonding in the tertiary structure of a protein
-Covalent bonds may form between R groups containing sulfur (these bonds are called disulfide bridges). -Only the amino acids cysteine and methionine have R groups that contain sulphur.
68
What is the result of tertiary structure?
-That, for a protein in the cytoplasm, it will fold in such a way that the hydrophilic amino acids are located on the outside of the protein, and the hydrophobic amino acids are located in the center of the protein, away from the watery cytoplasm. -A good example of such a single chain protein exhibiting many of these aspects of tertiary structure is a lysozyme.
69
Diagram of the tertiary structure of a protein
70
What is the quaternary structure of a protein?
-This exists in proteins with more than one polypeptide chain. -In this case, each folded chain is called a subunit, and subunits are joined together by strong bonds similar to those involved in the tertiary structure.
71
Give an example of a protein with quaternary structure
A good example is hemoglobin, which consists of two α -chains, two β -chains and four heme groups.
72
Diagram of the quaternary structure of a protein
73
What do quaternary proteins often also have?
-A non-protein molecular unit, called a co-factor or prosthetic group that is tightly attached to their polypeptides. -In the case of hemoglobin, heme is the iron-containing prosthetic group that helps the protein to transport oxygen.
74
What is a conjugated protein?
A protein with a prosthetic group attached.
75
What is denaturation?
Changes in parameters of the environment in which a protein functions, including pH, salt concentrations or temperature, immediately affect the secondary, tertiary and quaternary structures of proteins, and may inhibit their functioning.
76
What aspects of protein structure are stabilised or assisted by hydrogen bonds?
Secondary, tertiary, and quaternary structures, but not primary structures.
77
The amino acids of the protein keratin are arranged predominantly in an α-helix. This secondary structure is stabilised by ___
Hydrogen bonds
78
Aminoacyl-tRNA synthetases often associate with a Mg2+ ion in order to function properly. When a protein associates with a prosthetic group as in this example, what is it called?
Conjugated protein
79
Tertiary structure of proteins depends primarily on which structural component of amino acids?
R-groups
80
Describe the structure of a ribosome
-Ribosomes are composed of rRNA and proteins -There are two subunits: a large and a small subunit -On the small subunit, there is an mRNA binding site -On the large subunit, there are 3 tRNA binding sites: A, P, & E
81
Diagram of the 2D and 3D structure of a ribosome
82
Describe the steps in initiation
-The small subunit of the ribosome binds to the 5' end of the mRNA -The anticodon (UAC) of an initiator tRNA (carrying methionine) binds to the start codon (AUG) on the mRNA by hydrogen bonds -Anticodon to codon binding follows complementary base pairing rules -The initiator tRNA assists in the binding of the large subunit of the ribosome to the small subunit -The initiator tRNA is in the P site of the large subunit
83
What are the three things that the proteins synthesized by ribosomes (bound proteins, not free) can do?
-To be secreted (via exocytosis) e.g. antibodies -To be plasma membrane proteins -To function in membrane-bound organelles
84
What is the tertiary structure of a protein?
The further folding of the polypeptide stabilized by interactions between R groups.
85
What are the four types of interactions between R groups that hold the tertiary structure of a protein?
-Hydrogen bonds -Ionic bonds -Disulfide bridges (covalent bonds) -Hydrophobic interactions between amino acids and hydrophobic R groups -These hold different polypeptide chains together in the quaternary structure of a protein
86
Overview of the role of tRNA activating enzyme in transcription
-ATP «hydrolysis» provides energy for amino acid attachment -They attach a specific amino acid to the (3') end / free CCA of a tRNA -They do this repeatedly / they attach amino acid to all of the tRNA molecules that have anticodon corresponding to that amino acid
87
Diagram of tRNA activating enzyme
88
Describe the role of the tRNA activating enzyme in translation
-Each tRNA molecule binds with a specific amino acid in the cytoplasm in a reaction catalysed by a tRNA-activating enzyme -Each amino acid is recognised by a specific enzyme (the enzyme may recognise multiple tRNA molecules due to degeneracy) -The binding of an amino acid to the tRNA acceptor stem occurs as a result of a two-step process: -The enzyme binds ATP to the amino acid to form an amino acid–AMP complex linked by a high energy bond (PP released) -The amino acid is then coupled to tRNA and the AMP is released – the tRNA molecule is now “charged” and ready for use -The function of the ATP (phosphorylation) is to create a high energy bond that is transferred to the tRNA molecule -This stored energy will provide the majority of the energy required for peptide bond formation during translation
89
Diagram of tRNA activation

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