Genetic Code and Genome

Question 1

Transcription and Translation Definition

Answer 1

Transcription: involves copying the code for a gene into mRNA
Translation: involves interpreting the code into a sequence of amino acids

Question 2

mRNA function

Answer 2

The template for protein synthesis (aka translation): codes for proteins (codons)

Question 3

difference between mRNA in prokaryotes and eukaryotes?

Answer 3

mRNA in prokaryotes: can be produced for each gene or group of genes (aka operon) that is to be expressed in E. Coli
- operon: a group of genes that can be transcribed together into a single mRNA
- multiple genes –> one mRNA

mRNA in eukaryotes: a distinct mRNA is produced for EACH gene
- one gene –> one mRNA
- Has structural features (ie. Stem-loop structure) that regulate the efficiency of translation and the lifetime of the mRNA

Question 4

tRNA function

Answer 4

Serves as adapters between mRNA and amino acids during protein synthesis
- Carries amino acids in an activated form to the ribosome for the peptide-bond formation in a sequence dictated by the mRNA template
- Reacts with specific amino acids in a reaction catalyzed by aminoacyl-tRNA synthetases
- there is at least 1 tRNA molecule for each amino acid

Question 5

rRNA (ribosomal)

Answer 5

forms the core of the ribosome’s structure and catalyze protein synthesis (the major component of ribosomes)

Question 6

What are 7 general characteristics of tRNA molecules?

Answer 6

1. Each tRNA molecule is a single strand of RNA between 73-93 ribonucleotides long
2. The 3D structure of the molecule is L-shaped
3. tRNA molecules contain UNUSUAL BASES (ie. inosine) or bases that have been modified
4. In a 2D representation, all tRNA molecules appear as a CLOVERLEAF PATTERN that is stabilized by many hydrogen bonds
5. The 5’ end is phosphorylated; the 5’ terminal residue is usually pG (guanine)
6. The amino acid is attached to a hydroxyl group (OH) of ADENOSINE in the CCA region of the acceptor stem
7. The ANTICODON is in a loop near the center of the sequence

Question 7

What is the general 3D structure and 2D representation of a tRNA molecule

Answer 7

The 3D structure of the molecule is L-shaped
In a 2D representation, all tRNA molecules appear as a CLOVERLEAF PATTERN that is stabilized by many hydrogen bonds

Question 8

Where is the anticodon located in a general tRNA molecule?

Answer 8

The ANTICODON is in a loop near the center of the sequence

Question 9

anticodon

Answer 9

a template recognition site in tRNA molecules that consists of 3 bases and recognize a complementary 3-base sequence in the mRNA (aka the codon)
anticodons base pair with codons

Question 10

What can Inosine pair with?

Answer 10

Inosine can pair with cytosine, uracil, or adenine

Question 11

if the template DNA strand is 3’-ACC-5’, what is the coding DNA strand, mRNA codon, and tRNA anti-codon sequences?

Answer 11

DNA coding strand: 5’-TGG-3’
mRNA codon: 5’-UGG-3’
tRNA anticodon: 3’-ACC-5’

Question 12

aminoacyl-tRNA synthetases function

Answer 12

synthesize aminoacyl-tRNAs
- aka catalyzes the attachment of the appropriate amino acid to the tRNA molecule to produce a charged tRNA (aka aminoacyl-tRNAs)

Question 13

aminoacyl-tRNAs

Answer 13

the amino acid substrates for protein synthesis
aka the charged tRNA formed after an ester linkage is formed between the carboxyl group of the amino acid and either 1. the 2’ or 2. 3’ hydroxyl group of the terminal ADENOSINE of the TRNA

Question 14

what is the general structure of an aminoacyl-tRNA?

Answer 14

1. The amino acid is attached at the 3’ end of the RNA; the anticodon is the template-recognition site
2. tRNA has a cloverleaf structure with many HYDROGEN bonds (shown as green dots) between bases

Question 15

how is the mRNA decoded in protein synthesis? (translation)

Answer 15

mRNA is decoded in the 5’ to 3’ direction
decoded one codon at a time

Question 16

how do aminoacyl tRNA synthetases read the genetic code?

Answer 16

aminoacyl-tRNA synthetases catalyze the activation of amino acids

In order to be incorporated into proteins, amino acids must be ACTIVATED
–> Amino acids are activated by the formation of an ester linkage between…
The carboxyl group of the amino acid and…
Either the 2’ or 3’ hydroxyl (OH) group of the terminal adenosine of the tRNA

→ the ester linkage forms an aminoacyl tRNA (aka charged tRNA)
Each aminoacyl-tRNA synthetase is specific for a particular amino acid

Question 17

What are the 2 chemical reactions/steps for the activation of amino acids?

Answer 17

1. The formation of aminoacyl adenylate (aka aminoacyl-AMP)
   Amino acid + ATP → aminoacyl-AMP + PPi
2. The aminoacyl group is transferred to a specific tRNA recognized by the synthetase
   aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP

→ the sum of the two reactions:
amino acid + ATP + tRNA → aminoacyl-tRNA + AMP + PPi

Question 17

Charging

Answer 17

Charging: the process where each aminoacyl tRNA synthetases couples a particular amino acid to the proper tRNA
- Each aminoacyl-tRNA synthetase is specific for a particular amino acid

Question 18

What and how is the bond formed to activate amino acids?

Answer 18

–> Amino acids are activated by the formation of an ester linkage between…
The carboxyl group of the amino acid and either the 2’ or 3’ hydroxyl (OH) group of the terminal adenosine of the tRNA

→ the ester linkage forms an aminoacyl tRNA (aka charged tRNA) that can be incorporated into proteins

Question 19

what is aminoacyl adenylate?

Answer 19

aminoacyl adenylate is the ACTIVATED form of the amino acid (aka the form that will work thermodynamically in peptide-bond synthesis reactions)
- Acyl adenylate intermediates are also prominent in fatty acid activation for fatty acid synthesis reactions

Question 20

what is threonyl-tRNA synthetase and what does it contain in its active site?

Answer 20

an example of an aminoacyl tRNA synthetase: that is responsible for attached the amino acid threonine to its corresponding tRNA during translation
- threonyl-tRNA synthetase contains a ZINC ION at the active site that interacts with the hydroxyl (OH) group of threonine

Question 21

How do amino acids valine and serine interact with threonyl-tRNA synthetase?

Answer 21

Valine: valine is similar in overall structure to threonine but LACKS the OH group → valine is NOT joined to tRNA

Serine: although serine is smaller than threonine, it is occasionally linked to tRNA because of the presence of the hydroxyl OH group

Question 22

What is the “code” between DNA and amino acids?

Answer 22

There are FOUR nucleotides (A, G, C, T or U) but only TWENTY amino acids (21 counting selenocysteine)

the mRNA is read in groups of 3 (aka codons)

Question 22

what does the genetic code link?

Answer 22

The genetic code LINKS the nucleic acid sequence info and the amino acid sequence info

Question 23

why are there only 20 amino acids, but 64 different codons?

Answer 23

1. genetic code is degenerate: most amino acids are specified by more than one codon 2. among the 64 codons, 3 codons are stop codons 3. wobbling: the 3rd position in a codon is less critical for defining the amino acid --> allows tRNA molecule with an anticodon that matches 2 or more codons to still bind effectively ie. the codons GGU, GGC, GGA, and GGG all code for Glycine and a single tRNA with the anticodon CCI (inosine) can pair with all 4 Glycine codons

Question 24

inosine

Answer 24

The base in inosine is hypoxanthine, which is structurally similar to adenine but lacks an amino group (NH2) Formation: Inosine is created by a post-transcriptional modification in tRNA, where an enzyme deaminates adenosine (converts the amino group on adenine to a keto group) at specific positions in the anticodon loop of the tRNA molecule

Question 25

Nobel prize in physiology or medicine 1968

Answer 25

Awarded to Robert W. Holley, Har Gobind Khorana, and Marshall W. Nirenberg for “their interpretation of the genetic code and its function in protein synthesis”

Question 26

what are the 5 characteristics of the genetic code?

Answer 26

1. 3 nucleotides (aka a codon) encode an amino acid 2. The genetic code is NON OVERLAPPING - A base in a mRNA is NOT used for 2 different codons (aka 3 bases of one codon are DISTINCT from the bases of adjacent codons) - Ie. a sequence UGGAUCGAU is read UGG AUC GAU, and not as UGG GGA GAU, etc… 3. The genetic code as no punctuation: its representation is continuous and there is no punctuation mark to separate two codes 4. The code has DIRECTIONALITY: the code is read from the 5’ end to the 3’ end of the mRNA 5. The code is DEGENERATE: some amino acids are encoded by MORE than one codon - main idea: 4*4*4 = 64 codons > 20 amino acids

Question 27

what are the benefits of the genetic code being degenerate?

Answer 27

→ minimizes the deleterious effects of mutations This redundancy provides flexibility and error tolerance in the genetic code. Mutations that change one base in a codon may still result in the same amino acid being produced, helping reduce the likelihood of harmful effects from single-point mutations.

Question 28

what are synonyms in respect to codons?

Answer 28

Synonyms: codons that specify the SAME amino acid (ie. CAU and CAC are synonyms for histidine)

Question 29

The genetic code is nearly universal among most organisms but some organisms have slight modifications. give two examples of variations in genetic code.

Answer 29

Ie. in ciliated protozoa: codons that are stop signals in most organisms DO encode amino acids Ie. Mitochondria also uses variations of the genetic code

Question 30

wobble

Answer 30

a phenomenon where the recognition of the THIRD (3’-most) base in the codon by the ANTICODON is sometimes less discriminating - 3rd position in the codon <==> 1st position in the anticodon Wobble base pairing explains why many alternative codons differ in the 3rd molecule

Question 31

why is wobble tolerated in the 3rd position of the codon?

Answer 31

because although ribosomal RNA monitors fidelity of the base pairing in the 1st two positions of the codon-anticodon complex, ribosomal RNA does NOT evaluate the correctness of the 3rd position

Question 32

2 Generalizations of the codon-anticodon interactions are…

Answer 32

1. Codons that differ in either the 1st or 2nd position nucleotides MUST be recognized by DIFFERENT tRNAS 2. The 1st (5’-most) base of the ANTICODON determines the degree of wobble if the 1st base is INOSINE, the anticodon can recognize THREE codons: inosine can pair with C, U, or A

Question 33

Allowed pairings at the 3rd base of the codon according to the wobble hypothesis (given first base of anticodon, what can the third base of the codon be?) C --> A --> U --> G --> I -->

Answer 33

C --> G A --> U U --> A or G G --> U or C I --> U, C or A

Question 34

How do mRNA, tRNA, and rRNA differ in terms of abundance in cell, composition, stability, and structure?

Answer 34

abundance - mRNA: lowest - tRNA: slightly higher than mRNA - rRNA: most abundance composition - mRNA: AG CU - tRNA: AG CU and about 40 unusual bases - rRNA: AG CU stability - mRNA: unstable - tRNA: very stable due to intrastrand pairing - rRNA: very stable due to lots of intrastrand pairing structure - mRNA: mostly single stranded - tRNA: 50% double stranded, 50% single-stranded (2D cloverleaf structure; 3D L-shaped structure) - rRNA: mostly double stranded (the precursor sequences form extended double-stranded regions at the termini of each rRNA species --> these regions are important structural determinants for various processing events)

Question 35

what are the 3 stop codons?

Answer 35

TAA - UAA TAG - UAG TGA - UGA

Question 36

what is the start codon

Answer 36

AUG

Question 37

how do the 3 eukaryotic RNA polymerases differ in terms of genes transcribed and relative abundance of total mass in cells?

Answer 37

RNA polymerase I: most rRNA genes and around 98% abundance RNA polymerase II: all protein-coding genes (mRNA), miRNA genes, and genes for other noncoding RNAs (ie. those of the spliceosome) and < 1% abundance RNA polymerase III: tRNA genes, 5S rRNA genes, genes for many other small RNAs and around 1% abundance

Question 38

where on the tRNA molecule is the amino acid attached to?

Answer 38

The amino acid is attached to a hydroxyl group (OH) of ADENOSINE in the CCA region of the acceptor stem

Question 39

what are the 6 components of a regular tRNA molecule?

Answer 39

1. 3' terminus --> CCA region: (OH) amino acid attachment site 2. phosphorylated 5' terminus 3. DHU loop (on the left) 4. TψC loop 5. anticodon loop 6. "extra arm" (variable)

Question 40

how are the CCA region and anticodon loop located relative to each other on the tRNA molecule?

Answer 40

The CCA region is at the end of one arm and the anticodon loop is at the end of the other arm

Question 41

codon wobble explains what?

Answer 41

Wobble base pairing explains why many alternative codons differ in the 3rd molecule: have more than 20 tRNA (about 31 tRNA but varies between species) for 20 amino acids to their 61 codons

Question 42

TψC loop of tRNAs function

Answer 42

interacts with rRNA and proteins within the ribosome to position the tRNA correctly during translation plays a role in recognition by aminoacyl-tRNA synthetases which attach the correct amino acid to the tRNA helps maintain the L shaped 3D structure of tRNA