3. Termination

• Prokaryotes: terminator sequence causes hairpin loop
• Eukaryotes: cleavage signal, polyadenylation signal
• RNA polymerase releases
• RNA transcript complete

Prokaryotic vs. Eukaryotic Transcription

RNA Processing (Eukaryotes Only)

Primary transcript (pre-mRNA) must be processed before translation

1. 5' Cap

• 7-methylguanosine cap added to 5' end
• Functions:
  • Protects from degradation
  • Helps ribosome recognize mRNA
  • Aids in export from nucleus

2. 3' Poly-A Tail

• ~50-250 adenine nucleotides added to 3' end
• Functions:
  • Protects from degradation
  • Aids in export from nucleus
  • Helps ribosome locate start codon

3. RNA Splicing

• Introns (non-coding) removed
• Exons (coding) joined together
• Carried out by spliceosome (snRNPs + proteins)

Alternative splicing:

• Different combinations of exons
• One gene → multiple proteins
• Increases protein diversity
• ~95% of human genes alternatively spliced

Gene Structure (Eukaryotes)

Gene organization:

• Promoter
• 5' UTR (untranslated region)
• Exons (expressed sequences)
• Introns (intervening sequences)
• 3' UTR
• Terminator

Types of RNA

1. mRNA (messenger RNA)

• Carries genetic information DNA → ribosome
• Translated into protein
• ~5% of total RNA

2. rRNA (ribosomal RNA)

• Structural and catalytic component of ribosomes
• Most abundant RNA (~80%)

3. tRNA (transfer RNA)

• Brings amino acids to ribosome
• Has anticodon that pairs with mRNA codon
• ~15% of total RNA

4. Other RNAs

• snRNA: splicing (in snRNPs)
• miRNA: gene regulation (microRNA)
• siRNA: gene silencing (small interfering RNA)

Key Concepts

1. RNA polymerase synthesizes RNA 5'→3', reads DNA 3'→5'
2. Promoter is where transcription starts
3. Template strand is copied; coding strand has same sequence as RNA
4. Eukaryotic processing: 5' cap, poly-A tail, splicing
5. Introns removed, exons joined
6. Alternative splicing increases protein diversity
7. Three main RNAs: mRNA (message), tRNA (transfer), rRNA (ribosomal)

Step-by-step:

Template (3'→5'):  3'- T A C G C A A T G C G A -5'
                        ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓
mRNA (5'→3'):      5'- A U G C G U U A C G C U -3'

$\boxed{\text{mRNA: } 5\text{'-AUGCGUUACGCU-}3'}$

(b) Start and stop codons:

Start codon: AUG

• Position: First codon (nucleotides 1-3)
• Codes for: Methionine (Met)
• Signals: Translation start
• All proteins begin with Met (often removed later)

Looking for stop codons:

• UAA, UAG, UGA = stop codons
• Check the sequence: AUG CGU UAC GCU
• No stop codon present in this sequence!

Note: This appears to be partial gene sequence. A real gene would have:

• Promoter (before start)
• Start codon (AUG) ✓
• Coding sequence
• Stop codon (UAA, UAG, or UGA)
• Terminator

$\boxed{\text{Start: AUG (position 1-3); Stop: none in this sequence}}$

(c) Amino acid sequence:

Translation using genetic code:

Divide mRNA into codons (3-nucleotide groups):

mRNA:    5'- AUG  CGU  UAC  GCU -3'
Codons:      ↓    ↓    ↓    ↓

Using genetic code table:

Polypeptide:

$\boxed{\text{Met-Arg-Tyr-Ala}}$

Or using single-letter code: MRYA

Complete picture:

DNA coding strand:    5'-ATGCGTTACGCT-3' (not given, but complementary to template)
DNA template strand:  3'-TACGCAATGCGA-5' (given)
                           ↓ Transcription
mRNA:                 5'-AUGCGUUACGCU-3'
                           ↓ Translation
Polypeptide:          Met-Arg-Tyr-Ala (N-terminus → C-terminus)

Key Concepts:

Genetic Code Properties:

1. Triplet code: 3 nucleotides = 1 amino acid
2. Degenerate: Multiple codons for same amino acid
   • CGU, CGC, CGA, CGG all code for Arg
3. Universal: Same code in nearly all organisms
4. Unambiguous: Each codon specifies only ONE amino acid
5. Non-overlapping: Codons read in sequence, no overlap

Reading frame:

• AUG sets the reading frame
• Must read in correct groups of 3
• Frameshift mutation → wrong amino acids!

Example if we shift by +1:

• Normal: AUG CGU UAC GCU
• +1 shift: A UGC GUU ACG CU → different amino acids!

Why AUG is special:

• Only start codon (in eukaryotes)
• Also codes for Met in middle of protein
• Context determines if it's start or internal Met