BIOL1007 Lecture Notes - Lecture 7: Open Reading Frame, Start Codon, Reading Frame

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19 May 2018

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Explain the unique problems associated with converting the

information as a nucleic acid sequence to an amino acid sequence.

Describe how these issues are overcome, with reference to the

universality and redundancy of the genetic code

Outline the unique problems associated with protein synthesis, with

particular reference to the unfavourable thermodynamics of peptide

bond formation and the requirement for order. Describe the

strategies used by cells to overcome these problems.

Need to convert sequence of nucleotides (with 4 different bases) to a sequence of amino acids

(20 different bases)

Need to have correct order of amino acids -> order determines fold and function of the

protein

Peptide bond formation is very thermodynamically unfavourable

Must have precise start and stop for proteins -> extra amino acids may alter the fold and

function

Challenges of protein synthesis

4 different bases which use only one position so only 4 possible combinations (A, G, C, T)

4 different bases BUT 2 positions = 4 x 4 = 16 combinations (e.g. AA, AG, TC)

We will need a stop code so at least 21 combinations

○

64 is too many

○

There is redundancy in the code, so some amino acids have more than one code

○

3 combinations code for stop -> so we have 61 combinations coding for 20 amino acids

○

So if we have 20 amino acids -> needs minimum of 3 positions with 4 bases = 4x4x4 = 64

combinations

The combinations

Codon - Combination of 3 bases which codes for an amino acid (triplet codon)

Codon sequence is quoted 5' to 3' from the mRNA

Codon will have the same sequence as the DNA strand that WASN'T copied (non-template

strand)

Contains uracils instead of thymines (it is RNA)

Things to know

Stop codons

UAG

UGA

UAA

Start codon

AUG - also condes for methionine (so every protein starts with

methionine)

Leucine (just an

example)

CUU

CUA

CUC

CUG

UUA

The codon

L7 - Making proteins

Thursday, 24 August 2017

8:52 PM

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UUA

UUG

Reading the code

Screen clipping taken: 24/08/2017 9:44 PM

Screen clipping taken: 24/08/2017 9:45 PM

3 positions -> 3 reading frames

○

We want start and stop codon to be in the same reading frame ie. Open reading frame

Start codon determines reading frame

Read codon in triplets

If you insert or delete downstream -> reading frame shift, so every reading frame downstream

from that changes

Degenerate/redundant - more codons (61) than amino acids (20), so some amino acids have

more than 1 codon

Universal - same code is used by all life forms

Code can be described as…

Structure that bridges the nucleic acid and protein world

Small RNA molecule, 75-90 nucleotides with lots of intra-strand loops

3'OH - amino acid attaches

Anticodon loop - complementary code to the codon in the messenger RNA

tRNA - the adapter

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Screen clipping taken: 24/08/2017 10:24 PM

How does the correct amino acid get bonded to its matching tRNA?

e.g. leucine tRNA synthase will only bind to leucine

○

Different side chain helps with identifying correct amino acid

○

Correct amino acid binds to the enzyme

ATP molecule forms

Carboxylic acid reacts with first phosphate, activating the amino acid

Pyrophosphate is released, breaking down into 2 phosphates (thermodynamically favourable),

so removing product drives reaction forward

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Document Summary

Explain the unique problems associated with converting the information as a nucleic acid sequence to an amino acid sequence. Describe how these issues are overcome, with reference to the universality and redundancy of the genetic code. Outline the unique problems associated with protein synthesis, with particular reference to the unfavourable thermodynamics of peptide bond formation and the requirement for order. Describe the strategies used by cells to overcome these problems. Need to convert sequence of nucleotides (with 4 different bases) to a sequence of amino acids (20 different bases) Need to have correct order of amino acids -> order determines fold and function of the protein. Must have precise start and stop for proteins -> extra amino acids may alter the fold and function. 4 different bases which use only one position so only 4 possible combinations (a, g, c, t) 4 different bases but 2 positions = 4 x 4 = 16 combinations (e. g. aa, ag, tc)

Related Questions

Which of the following is NOT a direct consequence of the fact that DNA polymerase can only build onto the end of an existing nucleic acid?

Question 6 options:

	DNA replication requires primers
	Bits of DNA are lost from the ends of your chromosomes in each successive round of replication
	RNA is involved in DNA replication
	The enzyme "primase" is needed for DNA replication
	There are multiple origins of replication on each eukaryotic chromosome

How does a nucleotide sequence code for a protein in nearly all living organisms?

Question 7 options:

	a sequence of 3 nucleotides can code for one of 64 different amino acids
	a sequence of 2 nucleotides can code for one of 64 different amino acids
	a sequence of 2 nucleotides can code for one of 20 different amino acids
	a sequence of 3 nucleotides can code for one of 20 different amino acids
	a sequence of 3 nucleotides can code for 3 different amino acids

Fill in the blanks. To make one strand of DNA, _________ monomers are linked together in a chain, forming a polymer we call a(n) ________ .

Question 8 options:

	nitrogenous bases, hydrogen bond
	nucleotide, nucleic acid
	amino acid, nucleic acid
	nucleotide, nitrogenous base
	amino acid, protein

Which of the following was NOT part of the ideas that Darwin used in his book On the Origin of Species?

Question 9 options:

	organisms vary in characteristics that affect survival and reproduction
	variation in traits is often heritable
	descent with modification explains life's unity and life's diversity
	organisms inherit characteristics from their parents that the parents acquired in their own lifetimes
	natural selection is a cause of adaptive evolution

Here is a hypothetical mRNA sequence:

5' G G A U G C U A G U A U G A 3'

What is the amino acid sequence encoded by this mRNA?

Question 10 options:

	Met-Ile-Val
	Asp-Ala-Ser-Met
	Met-Leu-Val
	Ser-Met-Ile-Val
	Gly-Cys

1. _________________________ is the name of the process that produces proteins using RNA molecules.

a.Transcription

b Translation

c. Replication

d. Mutagenesis

2. The peptide bonding site on the ribosome:

a. A site

b. P site

c. E site

d. D site

3. The name given to the bond formed between two amino acids.

a. Hydrogen bond

b. Double bond

c. Peptide bond

d. Negative bond

4. __________________________ is the movement of the mRNA molecule on the ribosome to open up the A-site for the new incoming amino acid.

a. Transformation

b. Mutation

c. Translocation

d. Initiation

5. What does the term semi-conservative mean.

a. Replication of RNA is semi-conservative, each new strand consists of one old strand of RNA and one new strand of RNA.

b. Replication of DNA is semi-conservative, each new strand consists of one old strand of DNA and one new strand of DNA.

c. Replication of DNA is semi-conservative, each new strand consists of new strands of nucleotides.

d. Transcription of RNA is semi conservative.

6. This molecule functions during protein synthesis to recognize the codon and bring the proper amino acid back to the ribosome for translation.

a. mRNA

b. tRNA

c. rRNA

d. DNA polymerase

7. What is meant by the base-pairing rule.

a. Bases on a single strand of DNA are always found as pairs

b. Adenine always base pairs with guanine; cytosine with thymine

c. Adenine always base pairs with thymine; cytosine with guanine

d. Bases on a single strand of RNA are found in pair.

8. In this step of protein synthesis, amino acids are added to a growing polypeptide chain.

a. Initiation.

b. Elongation.

c. Termination.

d. Transpiration.

9. Three complementary bases found in a mRNA are called ____________________.

a. Anti-codon.

b. Triplet.

c. Doublet.

d. Codons.

10. Which statement best describes the job or function of the messenger RNA.

a. Carries the map of the gene sequence in the form of codons to the cytoplasm

for translation of the protein.

b. It transfers amino acids to the ribosome for protein synthesis.

c. It forms the ribosomes.

d. It helps replicate DNA.

ceruleangnat663

Is DNA a protein if so what makes up proteins, if not what it is and what are its monomers called? Describe the primary, secondary, tertiary, and quaternary structure of DNA (this sub-question is independent of the answer to the first question).

Describe electrostatic bonds, covalent bonds, van der Waals interactions, and hydrogen bonds and give an example of each.

Which of the four classes of amino acids has side chains with the greatest hydrogen-bond-forming potential?

Which has the greatest potential to form electrostatic interactions?

Which class has the greatest potential for hydrophobic interactions?

Of the following amino acids, (K), (Y), and (F), which side-chains would you expect to be the most soluble in a polar aqueous solution? Which the least?

Would you agree with the statement that many different amino acid sequences can fold into the same basic tertiary structure? What data can you cite as evidence for your position?

BIOL1007 Lecture Notes - Lecture 7: Open Reading Frame, Start Codon, Reading Frame

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