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Molecular Biology. > Translation. > Flashcards

Translation. Flashcards

1
Q

Define a codon?

A

A triplet of 3 nucleotides that codes for an amino acid.

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2
Q

What are monomers?

A

The individual building blocks in a polypeptide.

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3
Q

Define mutagens?

A

Chemical or physical agents that can cause DNA damage leading to mutations.

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4
Q

Define mutations?

A

Changes in the genetic material of a cell or virus.

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5
Q

Define point mutations?

A

Mutations in the genetic code that affect just 1 nucleotide.

E.g. A nucleotide that should be a T is changed to a C.

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6
Q

Define a polynucleotide?

A

A string of nucleotides that are been joined together.

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7
Q

How are nucleotides joined together in a polynucleotide?

A

By phosphodiester bonds at the 5 prime end and 3 prime end.

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8
Q

Define a polypeptide?

A

A string of amino acids that are joined together.

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9
Q

Do polypeptides have phosphodiester bonds?

A

No.

They molecules have peptide bonds which link an amino to a carboxyl end.

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10
Q

Define a polymer?

A

A substance that is composed of similar units e.g. a protein.

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11
Q

Define a polysome?

A

A collection of ribosomes that come together to synthesise a protein from 1 mRNA strand.

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12
Q

Define translation?

A

The process by which mRNA is translated to proteins.

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13
Q

When does translation occur?

A

After DNA has been transcribed to RNA.

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14
Q

Where does translation take place?

A

In the cytoplasm at the ribosomes.

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15
Q

What form of RNA will help the ribosomes translate mRNA to proteins?

A

tRNA will bring individual amino acids to the growing polypeptide chain.

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16
Q

How many known amino acids are there?

A

Over 300 amino acids.

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17
Q

How many amino acids can be made by the body?

A

20.

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18
Q

What will the body use individual amino acids to form?

A

As the individual building blocks for a protein.

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19
Q

What are the monomers that make up a protein?

A

Amino acids.

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20
Q

What are 5 examples of proteins that can be made from amino acids?

A

Enzymes.

Hormones.

Antibodies.

Spider webs.

Poisons.

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21
Q

What are the functional groups of an amino acid?

A

There is an amino end (NH3+).

A carboxylic acid end (COOH).

An R group.

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22
Q

What is the alpha carbon in an amino acid?

A

The carbon that is bound to the functional groups.

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23
Q

What is the alpha carbon on an amino acid bound to?

A

The carboxylic acid.

The amino group.

The R group.

A hydrogen.

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24
Q

What gives each amino acid their unique properties?

A

The R group.

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25
Q

What is used to classify each amino acid?

A

R groups.

E.g. if the R group is polar, then the amino acid is classified as a polar amino acid.

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26
Q

Is the alpha carbon found at carbon 1 in the amino acid?

A

No.

The carbon from the carboxylic acid is found at carbon 1 and the alpha carbon will be carbon 2.

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27
Q

What 8 amino acids make up the non-polar amino acids?

A

GAV The Lazy PIMP.

Glycine. (Gly.)

Alanine. (Ala.)

Valine. (Val.)

Tryptophan. (Trp.)

Leucine. (Leu.)

Phenylalanine. (Phe.)

Isoleucine. (Ile.)

Methionine. (Met.)

Proline. (Pro.)

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28
Q

What 3 amino acids make up the branched amino acids?

A

Leucine. (Leu.)

Isoleucine. (Ile.)

Valine. (Val.)

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29
Q

What 6 amino acids make up the polar uncharged amino acids?

A

CATS Grab Trout.

Cysteine. (Cys.)

Asparagine. (Asn.)

Threonine. (Thr.)

Serine. (Ser.)

Glutamine. (Gln.)

Tyrosine. (Tyr.)

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30
Q

What 3 amino acids make up the basic amino acids?

A

Basic HAL.

Histidine. (His.)

Arginine. (Arg.)

Lysine. (Lys.)

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31
Q

What 2 amino acids make up the acidic amino acids?

A

AGcidic.

Aspartic Acid. (Asp.)

Glutamic Acid. (Glu.)

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32
Q

What bonds join amino acids together?

A

Peptide bonds.

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33
Q

How is a peptide bond formed?

A

When a dehydration reaction allows the carboxylic end to bind to the amino end of another amino acid.

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34
Q

What functional groups are exposed in a polypeptide?

A

There will always be a terminal carboxyl and amino end.

The R groups will stick out to the side.

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35
Q

What is a dipeptide?

A

2 amino acids that are joined together.

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36
Q

What determines that nature of a polypeptide?

A

The R groups.

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37
Q

What is the beginning of a polypeptide marked by?

A

The amino group.

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38
Q

What is the end of a polypeptide marked by?

A

The carboxylic group.

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39
Q

Which 3 scientists cracked the genetic code and when?

A

Marshall Nirenberg.

Robert Holley.

Har Gbind Khorana

In 1968.

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40
Q

What 2 things did Nirenberg use to decipher the genetic code?

A

He used synthetic mRNA’s.

An in vitro translation system.

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41
Q

How did the synthetic mRNAs and the in vitro translation system work in Nirebergs experiment to decipher the genetic code?

A

He added mRNA sequences and then looked to see which amino acids were formed.

E.g. If he used mRNA this sequence UUUUUUUUUUUU he got PHE-PHE-PHE-PHE.

Or, if he used UCUCUCUCUCUC he got SER-LEU-SER-LEU.

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42
Q

What did the results of Nirenbergs experiment tell him about the genetic code?

A

Each mRNA codon is coded for by a triplet of three nucleotides.

E.g. AUG always codes for methionine and it is also the start codon.

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43
Q

How many triplets are there in the genetic code?

A

64 triplets.

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44
Q

How many of the 64 triplets code for amino acids?

A

61 code for amino acids and the other 3 are stop codons.

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45
Q

What are the 3 stop codons and what are their colours?

A

UAA (ochre).

UAG (amber).

UGA (opal).

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46
Q

How is the genetic code always produced?

A

As a line of single letters.

There is no punctuation or spaces in the code and it is non-overlapping.

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47
Q

How is the DNA code read?

A

It is read continuously at a rate of 3 nucleotides at a time and no nucleotides are ever skipped.

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48
Q

Why is the genetic code said to be degenerate?

A

As more than 1 codon can code for an amino acid e.g. UUG and CUC can code for leucine.

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49
Q

Which codons will not code for more than 1 amino acid?

A

AUG which codes for methionine and UGG which codes for tryptophan.

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50
Q

Why can the genetic code never be confused?

A

As one codon can only code for single amino acid.

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51
Q

What amino acid will always be the 1st to be produced in a polypeptide?

A

Because AUG is the start codon, it means that methionine will always be the start of a polypeptide sequence.

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52
Q

What tells us that a sequence of nucleotides in mRNA are read in sequences of 3?

A

The reading frame.

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53
Q

If the location of the start codon is unknown on a strand of mRNA, how many possible reading frames could there be?

A

There are 3 possible reading frames that can be used for any piece of mRNA if the location of the start codon is unknown.

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54
Q

What would be the 3 possible reading frames of the following mRNA?

-AGACUCAGCGUUACCAGA-.

A

-AGACUCAGCGUUACCAGA-.
The 1st sequence may be correct.

If it is incorrect, we can move the reading frame one letter to the right.

-GACUCAGCGUUACCAGAA-.
If it is still incorrect then we can move the reading frame one more nucleotide to the right.

-ACUCAGCGUUACCAGAAU-.

One of these 3 possibilities will be correct.

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55
Q

How many possible reading frames are found on a strand of DNA where the start codon is unknown?

A

DNA will have 6 possible reading frames as it has 2 strands.

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56
Q

What can a DNA mutation result in?

A

The formation of faulty proteins as the same mutation will be transcribed to the mRNA.

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57
Q

What is a point mutation?

A

A change to a single nucleotide in a DNA sequence.

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58
Q

Why can a point mutation affect how a protein is made?

A

As a new amino acid will be placed in the protein and this will change the structure of the protein.

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59
Q

What is a common disease that arises due to a point mutation?

A

Sickle cell disease.

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60
Q

What is the point mutation that occurs in sickle cell disease?

A

The normal gene for haemoglobin contains the sequence CTT in its DNA.

A person with sickle cell will have a codon reading CAT instead.

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61
Q

How does the CAT codon in people with sickle cell affect transcription?

A

The RNA transcript will contain the codon GUA instead of GAA.

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62
Q

How does the faulty RNA transcript affect transcription in people with sickle cell?

A

It will code for valine instead of glutamic acid which will make haemoglobin will faulty.

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63
Q

Can some DNA mutations occur spontaneously?

A

Yes.

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64
Q

What are physical or chemical agents that can cause mutations?

A

Mutagens.

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65
Q

What are the 2 categories of genetic mutations that can occur?

A

Substitution mutations.

Insertion and deletion mutations.

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66
Q

What are the 4 types of substitution mutations?

A

Nucleotide pair substitutions.

Silent mutations.

Missense mutations.

Nonsense mutations.

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67
Q

What are substitution mutations characterised by?

A

They are mutations where part of the genetic code is removed and replaced with different nucleotides.

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68
Q

Define nucleotide pair substitutions?

A

Where a complimentary pair of nucleotides in a DNA strand is substituted for another pair.

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69
Q

Define silent substitutions?

A

Mutations that have no effect on the amino acid that is produced.

This is due to redundancy of the genetic code.

70
Q

Define missense mutations?

A

These mutations will code for an amino acid, but it is the wrong amino acid.

71
Q

Define nonsense mutations?

A

They change a codon into a stop codon and they will almost always lead to a non-functional protein.

72
Q

What are insertion and deletion mutations?

A

They occur when parts of the genome are removed and not replaced.

Or when new nucleotide pairs are added to increase the size of the genome.

73
Q

Define a one or more nucleotide pair insertion or deletion mutation?

A

When more than 1 pair of nucleotides may be removed or added into the chain.

74
Q

Why can one or more nucleotide pair insertion or deletion mutations be disastrous?

A

Yes.

As they can change the reading frame meaning that the wrong proteins are synthesised.

75
Q

What are frameshift mutations?

A

Mutations that change the reading frame.

76
Q

Can both the insertion and deletion of nucleotides cause a frameshift mutation

A

Yes.

77
Q

Are substitution or insertion and deletion mutations often worse for the sufferer?

A

Insertion and deletion mutations tend to be much worse than substitution mutations.

78
Q

How can frameshift mutations be reversed?

A

By a process called a nearby addition mutation.

79
Q

How does a nearby addition mutation reverse a frameshift mutation?

A

They will add a pair of nucleotides to the DNA strand which will repair the mutation.

80
Q

What are the 2 subunits that make up the ribosome?

A

The large and small subunit.

81
Q

Which ribosomal subunit will read the mRNA?

A

Both subunits of the ribosome will read the mRNA.

82
Q

In what direction will the ribosomes read mRNA?

A

In the 5 to 3 direction.

83
Q

What happens as the ribosomes reads each codon of mRNA?

A

tRNA will bring the corresponding amino acids to form the polypeptide.

84
Q

What are the 3 sites that make up a ribosome?

A

The A site.

The P site.

The E sight.

85
Q

How are the amino acids separated into different forms?

A

Each form carries a specific amino acid on one end and an anticodon on the other end.

86
Q

How is the anticodon shown on a tRNA?

A

The nucleosides that make up tRNA will fold in such a way that the anticodon is shown.

87
Q

What does the anticodon on an amino acid consist of?

A

3 nucleotides that are used to base pair to a complimentary codon on mRNA.

88
Q

What are the last 3 nucleotides of tRNA at the 3 prime end?

A

The last 3 nucleotides of tRNA are always CCA-3.

89
Q

How is the unique amino acid on a tRNA attached to the tRNA?

A

The carboxyl group is attached to the ribose of the last ribonucleoside at the 3 prime end.

The last ribose is always adenine.

90
Q

How many structures does tRNA have?

A

A primary, secondary and tertiary structure.

91
Q

What is the primary structure of a tRNA?

A

A single strand that is around 80 nucleotides long.

It has the sequence CCA on the 3 prime end.

An anticodon that is complimentary to a codon on RNA.

92
Q

What is the secondary structure of a tRNA?

A

It is formed the pairing of some of the nucleotides within the RNA molecule causing the molecule to fold.

93
Q

What is the tertiary structure of a tRNA?

A

The twisting of the folded tRNA molecule to for a structure that looks like a cloverleaf.

94
Q

The activation of tRNA consists of how many steps?

A

2.

95
Q

What is the 1st step of the activation of a tRNA?

A

The attachment of an amino acid to the tRNA.

96
Q

How is the amino acid attached to the tRNA in step 1 of tRNA activation?

A

An enzyme recognises the amino acid to be attached.

It will bind to this amino acid and an ATP molecule.

97
Q

Which enzyme will attach the tRNA in step 1 of tRNA activation?

A

An aminoacyl-tRNA synthetase.

98
Q

What is step 2 of the activation of a tRNA?

A

The attachment of the tRNA to an amino acid.

99
Q

How does aminoacyl-tRNA synthetase recognise which tRNA to attach an amino acid to?

A

It contains an RNA codon which will scan a molecule of tRNA for its anticodon.

If the anticodon matches the RNA codon then the enzyme can attach the tRNA to the amino acid.

100
Q

What is the tRNA and amino acid complex also known as?

A

Aminoacyl tRNA (charged tRNA).

101
Q

Will cells carry a tRNA to match every RNA codon?

A

No.

102
Q

If a cell does not carry a tRNA to match every RNA codon, how does it add the correct amino acid?

A

By a property known as wobble.

103
Q

How does the wobble property allow a cell to receive the correct amino acids even if that cell doed not carry a tRNA to match an RNA codon?

A

A single tRNA molecule can bind to different codons.

104
Q

How can a single tRNA molecule can bind to different codons?

A

By forming non-traditional base pairs.

105
Q

What does the ability of tRNA to form non-traditional base pairs allow for?

A

For a single tRNA molecule to recognise multiple codons

106
Q

How does wobble affect an amino acid that is coded for by multiple codons?

A

The amino acid only needs 1 tRNA that will code for all those codons.

107
Q

When will the 2 subunits of a ribosome come together?

A

During protein synthesis.

108
Q

What are the ribosomal subunits composed of?

A

They are made up of specific proteins and rRNA.

109
Q

How does the mRNA fit into the ribosomal structure?

A

It will fit in between the 2 subunits.

110
Q

What do the differences in structure of prokaryotic and eukaryotic ribosomes allow Drs to do?

A

They can use drugs to target and destroy prokaryotic ribosomes without harming eukaryotic ribosomes.

111
Q

What is the structure of the prokaryotic ribosomal subunits?

A

Both subunits add up to 70S.

The small subunit is 30S.

The large subunit is 50S.

112
Q

What is the structure of the eukaryotic ribosomal subunits?

A

Both ribosomal subunits add up to 80S.

The small subunit is 40S.

The large subunit is 60S.

113
Q

How is the 30S subunit involved in the early stages of transcription in E.coli?

A

It is involved in the initial binding of the ribosome to mRNA.

114
Q

How is the 50S subunit involved in the early stages of transcription in E.coli?

A

It is involved in peptidyl transferase activity.

115
Q

Are the A, P and E sites of the ribosome found on any particular subunit?

A

Both subunits will contribute to the A, P and E sites.

116
Q

What is P site of the ribosome responsible for?

A

For holding the tRNA that carries the growing polypeptide chain.

117
Q

What is A site of the ribosome responsible for?

A

It holds the tRNA that is carrying the next amino acid to be added to the chain.

118
Q

What is E site of the ribosome responsible for?

A

It is the exit site where tRNAs that have dropped off their amino acids can leave the ribosome.

119
Q

What are the 2 different populations of ribosomes that are found in the cell?

A

Free and bound ribosomes.

120
Q

Where can the bound ribosomes be found?

A

They are attached to the ER.

121
Q

What proteins are made by bound ribosomes?

A

They make proteins that involved in the endomembrane system and proteins that are secreted from the cell.

122
Q

What proteins are made by free ribosomes?

A

Proteins that are found in the cytosol.

123
Q

Can a free ribosome become bound and vice versa?

A

Yes.

The types of ribosome are identical and interchangeable.

124
Q

When will free ribosomes become bound?

A

When they need to synthesise a polypeptide that is destined for the ER or to go outside of the cell.

125
Q

How do free ribosomes become bound?

A

When signal recognition particle binds to a signal peptide and will guide the ribosomal complex to the ER.

126
Q

How is a polypeptide that is made by a bound ribosome secreted?

A

The polypeptide will be secreted into the ER.

127
Q

What are polysomes?

A

Many ribosomes that come together and read the same mRNA so they can make proteins very quickly.

128
Q

What are the 3 stages of polypeptide formation?

A

Initiation.

Elongation.

Termination.

129
Q

Does translation require any additional helper proteins?

A

Yes.

All of the stages require helper proteins.

130
Q

What molecule will provide energy for polypeptide formation?

A

GTP.

131
Q

At what stage of translation will mRNA bind to a tRNA and the ribosomes?

A

The initiation stage.

132
Q

What is the 1st step of initiation of translation?

A

The small subunit binds to mRNA and to an initiator tRNA.

133
Q

What happens during the initiation of translation after the small subunit has bound to mRNA?

A

The small subunit will move along the RNA until it reaches the AUG start codon.

134
Q

What happens during the initiation of translation after the small subunit has reached the start codon on mRNA?

A

The initiator tRNA will bring the 1st amino acid which is always methionine.

135
Q

When will the large subunit bind to the small subunit during the initiation of translation?

A

They bind after the initiator tRNA has bought in methionine.

136
Q

What is the translation initiation complex?

A

The large and small ribosomal subunit bound to the mRNA and the initiator tRNA.

137
Q

Where does the small ribosomal subunit bind to mRNA in eukaryotes?

A

To the 5 cap on the mRNA.

It then migrates along the RNA to find the start codon and methionine can be bought in.

138
Q

How does the 30S subunit of prokaryotic ribosomes bind to mRNA?

A

It has a complimentary sequence to the Shine Delgarno sequence, allowing it to pair to the SDS.

139
Q

What kind of methionine is bought in as the first amino acid in prokaryotes?

A

F-methionine (formulated methionine) is always used as the 1st amino acid in prokaryotes.

140
Q

What is the 30S initiation complex?

A

F-methionine.

GTP.

The 30S subunit.

141
Q

What helps the prokaryotic 50S subunit to bind to the 30S initiation complex?

A

Initiation factors (proteins).

142
Q

What is formed when the 50S subunit binds to the 30S initiation complex in prokaryotes?

A

The 70S initiation complex

143
Q

What is the elongation stage of translation characterised by?

A

The addition of individual amino acids to the growing polypeptide.

144
Q

Where do individual amino acids enter the ribosome?

A

At the A site.

145
Q

How are the amino acids bought in to the ribosomal complex?

A

By tRNA molecules that use their anticodons to recognise complimentary codons on mRNA.

146
Q

What happens in the elongation stage of translation after the tRNA molecules have recognised their complimentary codons?

A

The tRNA molecules will bind to the mRNA.

147
Q

What happens in the elongation stage of translation after the tRNA molecules have bound to the mRNA?

A

The amino acids on the tRNAs are joined together by peptide bonds.

148
Q

Where on the ribosome are incoming amino acids added to the polypeptide?

A

The incoming amino acids are added at the A site.

149
Q

Where on the ribosome is the final amino acid of the chain where an incoming amino acid can be added to?

A

The amino acid that an incoming amino acid can be added to will be at the P site.

150
Q

What enzymatic activity forms peptide bonds between the amino acids during the elongation stage of translation?

A

Peptidyl transferase activity which occurs on the large subunit.

151
Q

What are the elongation factors that are used in translation?

A

Proteins that help the elongation process.

152
Q

What are the 3 ways that elongation factors help translation?

A

Codon recognition.

Peptide bond formation.

Translocation.

153
Q

How do elongation factors help with codon recognition?

A

The elongation factor EF-TU and a GTP molecule guide a tRNA to the A site of the ribosome.

154
Q

How do elongation factors help with peptide bond formation?

A

Peptidyl transferase forms the peptide bonds between amino acids.

155
Q

How do elongation factors help with translocation?

A

Peptide bond formation causes a tRNA in the P site to release its AA and leave the ribosome via the exit site.

The ribosome can move to the next codon where the process will repeat itself.

156
Q

When will termination of translation occur?

A

When a stop codon in the mRNA reaches the A site of the ribosome.

157
Q

Can tRNA’s recognise the stop codon?

A

No tRNA is able to recognise the stop codon.

158
Q

What happens when the ribosome reaches a stop codon?

A

It tells the A site to accept a protein called a release factor.

159
Q

What are the effects of the release factor during the termination of translation?

A

It adds water to the polypeptide and this causes the release of the polypeptide from the ribosome.

160
Q

What happens when the polypeptide is released from the ribosome?

A

The ribosomal complex will come apart.

161
Q

What is the release factor that is used in the termination of translation in eukaryotes?

A

eRF-1.

162
Q

What are the release factors that are used in the termination of translation in prokaryotes?

A

RF1 which will recognise UAA and UAG.

RF2 which recognises UAA and UGA.

RF3 which will stimulate termination.

163
Q

Where does the synthesis of polypeptides always begin and finish?

A

In the cytoplasm unless the polypeptide is destined to go outside of the cell.

164
Q

What often happens to the polypeptide after it has been released form the ribosomes?

A

It must be modified as translation is often not able to make a functional protein.

165
Q

When will the polypeptide formed in translation form its 3D structure?

A

During and after synthesis.

166
Q

What proteins will sometimes help the polypeptide form its secondary and tertiary structure?

A

Chaperone proteins.

167
Q

What kind of protein will not be functional?

A

A badly folded protein.

168
Q

What are some post translational modifications for proteins?

A

Phosphorylation.

Glycosylisation.

Lipid anchoring.

169
Q

What post translational modifications do trypsinogen and insulin need?

A

They need to be cleaved by enzymes so that they can be activated.

170
Q

What feature on some proteins allows them to perform self cleavage?

A

Intein.

Molecular Biology. (22 decks)

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