Transcription and RNA Processing

Gene transcription, RNA processing in eukaryotes, and gene expression

📝 Transcription and RNA Processing

Overview

Gene expression: DNA → RNA → Protein

Transcription: DNA → RNA (this topic) Translation: RNA → Protein (next topic)

Transcription Process

Purpose: Synthesize RNA from DNA template

Key enzyme: RNA polymerase

Does NOT need primer (unlike DNA polymerase)
Synthesizes RNA 5'→3' direction
Reads template strand 3'→5'

Three Stages

1. Initiation

Promoter: DNA sequence where RNA polymerase binds
TATA box: common promoter element in eukaryotes (~25 bp upstream)
Transcription factors help RNA polymerase bind (eukaryotes)
RNA polymerase unwinds DNA

2. Elongation

RNA polymerase moves along DNA (3'→5' on template)
Adds RNA nucleotides (5'→3')
Coding strand (non-template) has same sequence as RNA (except T→U)
Template strand (antisense) used to make RNA

3. Termination

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

Prokaryotic vs. Eukaryotic Transcription

| Feature | Prokaryotes | Eukaryotes | |---------|-------------|------------| | RNA polymerase | One type | Three types (I, II, III) | | Promoter | -10, -35 boxes | TATA box, others | | Processing | None | Extensive | | Location | Cytoplasm | Nucleus | | Coupling | Transcription + translation | Separated |

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

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

📚 Practice Problems

1Problem 1medium

❓ Question:

A gene has the following DNA template strand: 3'-TACGCAATGCGA-5'. (a) Write the mRNA sequence transcribed from this template, (b) identify the start and stop codons, and (c) write the amino acid sequence that would be translated (use the genetic code).

💡 Show Solution

Given: Template strand: 3'-TACGCAATGCGA-5'

(a) mRNA sequence:

Transcription rules:

RNA polymerase reads template 3' → 5'
Synthesizes mRNA 5' → 3' (antiparallel)
Uses complementary base pairing:
- A (DNA) → U (RNA)
- T (DNA) → A (RNA)
- G (DNA) → C (RNA)
- C (DNA) → G (RNA)

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:

| Codon | Amino Acid | Abbreviation | |-------|------------|--------------| | AUG | Methionine | Met (M) | | CGU | Arginine | Arg (R) | | UAC | Tyrosine | Tyr (Y) | | GCU | Alanine | Ala (A) |

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:

Triplet code: 3 nucleotides = 1 amino acid
Degenerate: Multiple codons for same amino acid
- CGU, CGC, CGA, CGG all code for Arg
Universal: Same code in nearly all organisms
Unambiguous: Each codon specifies only ONE amino acid
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

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