DB014 Chapter 5: Expression of Biological Information

Db014 2021/2022

Chapter 5 Expression Of Biological Information

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Recap Lesson

​5.2 DNA Replication

​Learning outcomes:

​

1. ​Describe semi-conservative replication of DNA.

2. State the enzymes and proteins involved in DNA replication.

3. Describe the mechanism of DNA replication and the enzyme involved.

​Overview: Mechanism of DNA Replication

​1. DNA helicase untwists and unzip double helix DNA at the origin of replication.

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​Both DNA strands become templates.

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​2. SSBP molecules bind to the unwound DNA to stabilise the replication bubble.

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This step is necessary because unwound DNA strands have high tendency to re-wind and re-form the double helix.

​3. Supercoiling of DNA strand occurs ahead of the fork.

​

Topoisomerases will relief the strain by breaking, swiveling and rejoining DNA strands.

4. RNA primase will synthesise RNA primer, which are short RNA strands.

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​The purpose of this is to make a free 3' end available.

5. DNA polymerase III will add DNA nucleotides to the 3' end of the RNA primer, producing a DNA strand.

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​A growing DNA strand only elongate in the 5'-3' direction because new nucleotides can only be added to the 3' end.

6. The leading strand will continuously elongate in the 5'-3' direction, in the same direction as the replication fork.

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7. The lagging strand will discontinuously elongate in the 5'-3' direction, in the opposite direction of the replication fork.

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8. Each Okazaki fragment of the lagging strand requires an RNA primer.

9. DNA polymerase I will replace all the RNA primers with DNA nucleotide.

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10. DNA ligase will seal all the gaps between Okazaki fragments by forming phosphodiester bond.

​

​Note: be very careful with the spelling of

phos-pho-di-es-ter bond.

11. Two DNA molecules are produced with each of them containing one old parental strand and one new daughter strand.

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​This is known as the semiconservative replication.

​SUMMARY: DNA Replication

NEXT: DNA Replication Short Quizzes​

​Get your notes ready.

Multiple Choice

Which one of these will unwind a double helix DNA molecule prior to replication?

• Topoisomerases

• DNA helicase

• Single stranded DNA binding protein

• DNA ligase

Multiple Choice

Which sequence of DNA bases would pair with this partial strand CAT TCA CTG

• ATG TGA CAG

• TAC ACT GTC

• GTA AGT GAC

• CAT TCA CTG

Multiple Choice

What will the first four bases of the new DNA strand look like after the template strand is copied?

• TGGT

• ACCA

• GTTG

• CAAC

Multiple Choice

Site where replication begins

• Polymerase action site

• Replication fork

• Replication origin

• In the front

Multiple Choice

Object numbered as 2 in the picture is a

• Polymerase

• Primase

• Helicase

• Ligase

Multiple Choice

DNA strands elongate in the direction of

• 5' - 3'

• 3' - 5'

Multiple Choice

The lagging strands elongate _____ in the _____ direction as the replication fork.

• continuously;

  same

• continuously;

  opposite

• discontinuously;

  same

• discontinuously;

  opposite

Multiple Choice

The leading strands elongate _____ in the _____ direction as the replication fork.

• continuously;

  same

• continuously;

  opposite

• discontinuously;

  same

• discontinuously;

  opposite

​5.3.1 Protein synthesis

​Learning outcomes:

​

1. ​Give an overview of the relationship between DNA and protein synthesis.

2. ​Explain transcription which involves RNA polymerase to form mRNA.

​Part 1: TRANSCRIPTION

​Overview: DNA Transcription

​Step 1: Initiation

​1. RNA Polymerase (RNAP) binds to the promoter region.

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​Start signal is found within the promoter region.

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Start signal is the point where transcription begins.

2. RNAP will unwind the parental DNA helix. Only one DNA strand acts as a template.

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The template DNA strand is known as the non-coding strand.

The non-template DNA strand is known as the coding strand.

​Step 2: Elongation

​3. RNAP starts the synthesis of RNA transcript complementary to the DNA template strand.

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​Adenine will be transcribed with uracil, while cytosine with guanine.

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​4. RNAP moves downstream, elongating the RNA transcript in the 5' - 3' direction.

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​Note:

​Elongation of transcript: 5'-3'

​Reading of DNA template: 3'-5'

​5. Behind the point of transcription (or transcription bubble), the unwound DNA will re-wind to form double helix.

​Step 3: Termination

​6. RNAP detects the terminator region.

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​Stop signal is found within the terminator region.

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​7. RNA transcript will be released from the transcription bubble. RNAP and sigma factor will detach from DNA strand.

​Summary: DNA Transcription

NEXT: DNA Transcription Short Quizzes​

​Get your notes ready.

Multiple Choice

Which of these bases does not exist in RNA?

• Cytosine

• Thymine

• Uracil

• Adenine

Multiple Choice

What happens to the mRNA sequence after it has been synthesised?

• stays in the nucleus

• leaves the cell

• leaves the nucleus

• separates into smaller pieces

Multiple Choice

During protein synthesis, an RNA strand is transcribed from one strand of DNA (GCG TTA CCT) What is the complementary RNA strand?

• CGC UUT CCT

• CGC AAU GGA

• GCG UUA CCU

• CGC AAT GGA

Multiple Choice

Which enzyme creates the new mRNA polyer by adding the complementary free RNA nucleotides?

• RNA polymerase

• DNA polymerase

• Exonuclease

• DNA Helicase

Multiple Choice

Where does transcription begin?

• Transcription origin

• Promoter region

• Start signal

• Start codon

Multiple Choice

Where does transcription end?

• Terminator region

• Stop signal

• Stop codon

• At the end of the gene sequence

Multiple Choice

Transcribe the following DNA sequence to the complementary mRNA sequence.

TAC CGG CTG

• AUG GCC GAC

• AUG GCC GAG

• AUG CGG GAC

• GUA GCC GAC

Multiple Choice

Which type of RNA is synthesised during transcription?

• messenger RNA (mRNA)

• transfer RNA (tRNA)

• ribosomal RNA (rRNA)

• small nuclear RNA (snRNA)

Multiple Choice

A eukaryotic transcription takes place in the ____, while a prokaryotic transcription takes place in the ____.

• Cytoplasm;

  nucleus

• Cytoplasm;

  cytoplasm

• Nucleus;

  cytoplasm

• Nucleus;

  nucleus

​5.3.2 Protein synthesis

​Learning outcomes:

​

1. Show the relationship between codon on mRNA with sequence of amino acid using genetic code table.

2. Explain translation of mRNA forming polypeptide chain.

​Part 2: TRANSLATION

​Overview: Translation

​Step 1: Initiation

1. The translational initiation complex will assemble.

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The complex comprises of:

• ​small ribosomal subunit

• ​large ribosomal subunit

• ​mRNA strand

• ​initiator tRNA with UAC anticodon & carrying Met amino acid

2. The codon AUG will bind to the P-site of the ribosome.

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​tRNA with anticodon UAC will base-pair with codon AUG.

​Step 2: Elongation

​3. Elongation of translation comprises of three sub-steps:

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​i. Codon recognition

​ii. Peptide bond formation

​iii. Translocation

​4. During codon recognition, tRNA with anticodon will base-pair with the complementary codon in A-site.

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​Example:

​If the codon in A-site is AUG, then the tRNA with UAC anticodon will base-pair with the codon.

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​5. Peptide bond will be formed between the new amino acid in A-site and the existing ones in P-site.

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​As a result, the polypeptide strand in P-site will be removed and bonded to the amino acid in A-site.

​6. The tRNA in A-site will be translocated to P-site.

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7. This will push the empty tRNA in P-site into the E-site. Eventually, it is released from the translational complex.

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​These series of events will repeat until stop codon binds to A-site.

​Step 3: Termination

​8. Termination of translation begins when the stop codon binds to the A-site of ribosome.

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Note:

Stop codon (on mRNA):

• ​UAG

• ​UAA

• ​UGA

9. Instead of a tRNA, a release factor will base-pair with the stop codon in A-site.

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This results in the disassembly of the translational machinery.

​Summary: Translation

​Genetic code table

​Polypeptide chains are synthesised based on the codon that are read on the mRNA strands.

​The corresponding amino acid is determined based on the genetic code table.

​

​Genetic code table

Some examples:

​

• AUG: Methionine​ (starting amino acid)

• ​GAU: Tyrosine

• ​CUA: Leucine

• ​AAA: Lysine

• ​UGA: Stop codon - release factor

NEXT: Translation Short Quizzes​

​Get your notes ready.

Multiple Choice

When the mRNA sequence leave the nucleus, what organelle does it travel to?

• mitochondria

• smooth ER

• ribosome

• vacuole

Multiple Choice

What does tRNA "transfer"?

• amino acids

• nucleic acids

• nucleotides

• AUG

Multiple Choice

A polypeptide only becomes a functioning protein after it has folded into its exact 3D shape.

• True

• False

Multiple Choice

Codons are located on __________

• mRNA

• tRNA

• rRNA

• snRNA

Multiple Choice

Anticodons are located on __________

• mRNA

• tRNA

• rRNA

• snRNA

Multiple Choice

How many nucleotides make up a single codon?

• 3

• 5

• 4

• 1

Multiple Choice

Where does translation begin?

• Translation origin

• Start signal

• Codon AUG

• First codon on mRNA

Multiple Choice

Which one of these will stop translation?

• Terminator region

• Stop signal

• The last codon on mRNA strand

• Codon UAA

Multiple Choice

Which mRNA sequence always marks the beginning of a new polypeptide chain?

• UAG

• AUG

• GAU

• UGA

Multiple Choice

How many codons code are there for phenylalanine?

• 2

• 3

• 4

• 1

Multiple Choice

The following codon is translated into which amino acid?

AUU

• Methionine

• Isoleucine

• Histidine

• Arginine

Multiple Choice

The following codon is translated into which amino acid?

CAU

• Methionine

• Isoleucine

• Histidine

• Arginine

Multiple Choice

The following codon is translated into which amino acid?

UUU

• STOP

• Phenylalanine

• Valine

• Aspartic acid

Multiple Choice

The following codon is translated into which amino acid?

AGU

• Methionine

• Isoleucine

• Serine

• Arginine

Multiple Choice

The following codon is translated into which amino acid?

UAA

• STOP

• Phenylalanine

• Valine

• Aspartic acid

Multiple Choice

The following codon is translated into which amino acid?

ACA

• Threonine

• Phenylalanine

• Valine

• Aspartic acid

Multiple Choice

If an mRNA sequence consist of 171 nucleotides, how many amino acids can be synthesised for the polypeptide chain?

• 57

• 71

• 55

• 171

​SUMMARY: Transcription versus Translation

Poll

How confident are you with this chapter?

• 0-25%

• 26-50%

• 51-75%

• 76-100%

Open Ended

Which part(s) of this chapter that you feel like you need most work on?

Note: be specific and not just write down the subtopic