⭐ BIOL 1406 – Exam 4 Study Guide (Ch. 15, 17, 18, 19)

Proteins

chains of amino acids (polypeptides).

Each amino acid has..

• Amino group (NH₃⁺)

• Carboxyl group (COO⁻)

• R group (side chain) → determines shape & function
  (nonpolar, polar, charged, big/small)

Central Dogma

DNA → RNA → Protein

Transcription

DNA → mRNA

Translation

mRNA → protein (ribosomes link amino acids)

Genetic Code

Codon = 3 mRNA nucleotides = 1 amino acid

64 codons

→ 20 amino acids (redundancy)

Start codon

AUG

Stop codons

UAA, UAG, UGA

Reading frame matters.. T/F?

True

Frameshift mutation

 insertion/deletion → shifts codons

•  almost always destroys protein.

Initiation ( PROKARYOTIC TRANSCRIPTION )

• Promoter = DNA signal that tells RNA polymerase where to start.

• Sigma (σ) factor helps RNA polymerase attach → leaves after transcription begins.

• Transcription and translation happen at the same time.

Promoter

DNA signal that tells RNA polymerase where to start.

Sigma (σ) factor helps…

RNA polymerase attach

after RNA polymerase attach..

 leaves after transcription begins

Elongation ( PROKARYOTIC TRANSCRIPTION )

• RNA polymerase adds nucleotides in the 5′ → 3′ direction.

• Moves about 40 nucleotides per second.

Termination ( PROKARYOTIC TRANSCRIPTION )

• Rho-dependent: Rho protein stops transcription.

• Rho-independent: RNA forms a hairpin loop → stops transcription.

Rho-dependent ( PROKARYOTIC TRANSCRIPTION )

Rho protein stops transcription

Rho-independent ( PROKARYOTIC TRANSCRIPTION )

RNA forms a hairpin loop → stops transcription

How many RNA polymerases can work on the same gene?

Multiple ( PROKARYOTIC TRANSCRIPTION )

Multiple ribosomes can translate the same mRNA therefore..

fast protein production ( PROKARYOTIC TRANSCRIPTION )

Pol I

→ makes rRNA

Pol II

→ makes mRNA (codes for proteins)

Pol III

→ makes rRNA, tRNA, snRNA

Initiation ( EUKARYOTIC TRANSCRIPTION )

• Transcription factors bind the promoter.

• RNA Pol II attaches → transcription begins.

What binds the promoter?

Transcription factors

What is needed for transcription to begin? ( EUKARYOTIC TRANSCRIPTION )

RNA Pol II attachment

mRNA grows from..

 5′ → 3′

What does the FACT COMPLEX do to nucleosomes?

moves them out of the way

Elongation

• mRNA grows 5′ → 3′.

• FACT complex moves nucleosomes out of the way.

Termination

• Pol I: needs a termination protein

• Pol III: hairpin loop stops transcription

• Pol II: extra RNA made → cut during mRNA processing

mRNA Processing (Eukaryotes Only)

• 5′ cap (methylguanosine) added

• 3′ poly-A tail added

• Splicing: remove introns (non-coding), keep exons

• Done by spliceosomes (snRNA + proteins)

What is the 5’ cap also know as?

methylguanosine

What does splicing do?

• remove introns (non-coding)

• keep exons

• DONE BY SPLICEOSOMES

What are spliceosomes made up of?

snRNA + proteins

rRNA & tRNA Processing

• Cleavage, splicing, chemical changes.

• tRNA anticodon matches mRNA codon.

• Opposite end carries amino acid.

Ribosome Structure

• Small + large subunits

• A site: receives new tRNA

• P site: holds growing peptide chain

• E site: tRNA exits

A site

receives new tRNA

P site

holds growing peptide chain

E site

tRNA exits

Initiation ( Translation )

• mRNA binds small subunit

• Start codon (AUG) recognized

• Large subunit joins

Elongation ( Translation )

• tRNAs bring amino acids

• Peptidyl transferase forms peptide bonds

• Ribosome moves 3 nucleotides at a time

• Empty tRNA leaves

Termination ( Translation )

• Stop codon reached → release factor releases protein

• In eukaryotes: protein enters ER for folding/processing

Darwin studied animals & fossils on the..

H.M.S. Beagle

Natural selection

main way evolution happens.

Darwin’s 3 Postulates

1. Variation

2. Heritability

3. Overproduction

Adaptation

• Traits that help survival or reproduction.

• Spread through populations over generations.

Variation

individuals are different

Heritability

traits passed to offspring

Overproduction

more offspring than the environment can support → competition

Evidence for Evolution

1. Divergent evolution: related species become different

2. Convergent evolution: unrelated species become similar

3. Fossil record: shows changes over time

4. Homologous structures: same structure, different use → common ancestor

5. Vestigial structures: leftover parts from ancestors

6. Biogeography: species locations shaped by geography

7. Molecular biology: DNA/protein similarity shows relationships

Natural vs Artificial Selection

• Natural: environment selects traits

• Artificial: humans select traits

Common Misconceptions

• Evolution is not “just a theory”

• Individuals do not evolve—populations do

• Evolution doesn’t explain life’s origin

• Evolution has no goals

Speciation

Species = groups that can mate and produce fertile offspring

Allopatric Speciation (most common)

• Geographic barriers separate populations

• Causes:

  • Dispersal: group moves

  • Vicariance: barrier forms (mountain, river)

• Adaptive radiation: one species → many species in new environments

• Examples: Darwin’s finches, Hawaiian honeycreepers

Sympatric Speciation

• Happens without geographic separation

• A. Chromosomal errors

  • Aneuploidy: wrong chromosome number

  • Autopolyploidy: duplicate chromosomes in one species

  • Allopolyploidy: duplication + hybridization of two species

• B. Reproductive isolation

  • Prezygotic: prevent mating

    • Temporal, habitat, behavioral, mechanical, gametic

  • Postzygotic: hybrids fail

    • Hybrid inviability, hybrid sterility (mules)

Hybrid Zones

• Where two species meet and mate

• Outcomes:

  • Reinforcement: hybrids weak → speciation continues

  • Fusion: hybrids strong → species merge

  • Stability: hybrids continue steadily

Rates of Evolution

• Gradualism: slow, steady change

• Punctuated equilibrium: fast bursts + long stasis

Alleles & Gene Pool

• Allele: version of a gene

• Gene pool: all alleles in a population

• Allele frequency: how common each allele is

Hardy–Weinberg Equilibrium

• Population NOT evolving if:

  • No mutations, natural selection, gene flow

  • Random mating

  • Very large population

• Equations:

  • p + q = 1

  • p² + 2pq + q² = 1

• Used to detect evolution

Genetic Drift

• Random allele changes, bigger effect in small populations

Bottleneck Effect

Population drastically shrinks → lose genetic diversity

Founder Effect

Small group starts new population → limited alleles

Gene Flow

Alleles move between populations → populations become more similar

Types of Natural Selection

• Stabilizing: average traits favored

• Directional: one extreme favored

• Disruptive: both extremes favored

Stabilizing

average traits favored

Directional

one extreme favored

Disruptive

both extremes favored

Epigenetics

genes turned on/off by environment without changing DNA

Nonsense vs Missense mutations

• Nonsense: stop codon too early

• Missense: wrong amino acid

Wobble position

3rd base of codon often flexible → fewer mutation effects

Operons (Prokaryotes)

• group of genes transcribed together

  • Examples: lac operon (inducible), trp operon (repressible)

Review Summary (READ THEM)

• DNA → RNA → Protein

• Prokaryotes: fast, simultaneous transcription/translation

• Eukaryotes: processing (cap, tail, splicing)

• Mutations: frameshift = most dangerous

• Natural selection → adaptation over generations

• Speciation: allopatric vs sympatric

• Evolution supported by fossils, DNA, anatomy, geography

• Hardy-Weinberg = no evolution

• Drift strongest in small populations

• Selection: stabilizing, directional, disruptive