Foundation of Biology--> Chapter 4

What is DNA most Common Structure across all organisms?

The double helix (B-form DNA) — two antiparallel strands twisted around each other.

What is DNA main two functions?

• Storing genetic information

• Copying itself

What are the Monomers of Nucleic Acids?

• Phosphate group (5’ end)

• Deoxyribose sugar (3’ end)

What are the Nitrogenous Bases?

• Purines

• Pyrimidines

How many rings does Purines Bases have?

Two rings

How many rings does Pyrimidines Bases have?

One ring

What are the Purines Bases?

• Adenine

• Guanine

What are the Pyrimidines Bases?

• Thymine

• Cytosine

What do Nucleotide sequences read from?

3’ to 5’

Where can Nucleotides be added?

Only on the 3’ -OH on the sugar

(This is why DNA Grows in a 5’-3’ direction)

Who created the structure of DNA?

Watson and Crick through a 3D model

Who found that DNA molecules form a helix with repeating structure?

Rosalind Franklin and Maurice Wilkins through X-ray crystallography

Who found the base paired rules?

Erwin Chargaff through Biochemistry experiments

What is the structure of DNA?

A highly stable double helix.

What three factors contribute to DNA stability?

• Phosphodiester bonds,

• Hydrogen bonds

• Base stacking

What type of bond connects adjects nucleotides in a DNA strands

Phosphodiester bonds

Are Phosphodiester bonds strong or weak?

Strong covalent bonds that hold the sugar phosphate backbone together

What bonds hold complementary DNA bases together across strands?

Hydrogen bonds

How many hydrogen bonds form between A-T and G-C pairs?

• A=T has 2 hydrogen bonds

• G=C has 3 hydrogen bonds

Are hydrogen bonds individually strong or weak?

Individually weak, but collectively strong

Why are hydrogen bonds important in DNA?

They stabilize the double helix but allow strand separation for replication and transcription

What property of nitrogenous bases allows base stacking?

They are flat and hydrophobic

How does base stacking stabilize DNA?

Bases pack tightly together using hydrophobic effects and van der Waals forces

Whats the rule of matching Base Pairs?

• Always match a purine with a pyrimidine

• Always match a two rind with a one ring

Which are DNA strands Pair with what?

• A pairs with T

• G pairs with C

• ON OPPOSITE STRANDS

How are DNA strands antiparallel from one another?

One runs 5’ 3’ and the other runs 3’ 5’

Which direction does the top strand run?

5’ → 3’ (left to right)

Which direction does the bottom strand run?

3’ → 5’ (left to right)

What type of replication does DNA use?

Semi-conservative replication

What does semi-conservative replication mean?

Each new DNA has 1 parent strand + 1 new strand

What ensures the fidelity (precision) of DNA replication?

Complementary base pairing

What is produced after DNA replication?

Two double helices that are exact copies of the original DNA

What are rare errors in DNA replication called?

Mutations

What can mutations be?

• Harmful

• Beneficial

• or Neutral

What is the Central Dogma of molecular biology?

The flow of genetic information

What is the flow of genetic information according to the Central Dogma?

DNA → RNA → Protein

What is transcription?

The process of using a specific region of DNA (a gene) as a template to make mRNA

What is produced in transcription?

mRNA (messenger RNA)

Where does transcription occur in prokaryotes?

In the cytoplasm, since prokaryotes lack a nucleus.

Where does transcription occur in eukaryotes?

In the nucleus; the resulting mRNA then leaves the nucleus to be translated in the cytoplasm.

What happens simultaneously in prokaryotes but not in eukaryotes?

Transcription and translation occur at the same time in the cytoplasm in prokaryotes.

Why can transcription and translation occur simultaneously in prokaryotes?

Because they both occur in the cytoplasm, and there is no nuclear membrane separating DNA and ribosomes.

What are the main requirements for transcription?

DNA template, RNA polymerase, and additional factors that help RNA polymerase know where to start.

What is produced during transcription?

RNA that is antiparallel and complementary to the DNA template strand.

How is RNA different from DNA?

RNA is single-stranded, has ribose sugar, and uses uracil (U) instead of thymine (T).

What is common to both DNA and RNA?

Both contain cytosine (C), guanine (G), and adenine (A).

What happens to pre-mRNA in eukaryotes before translation?

It undergoes processing — 5′ capping, 3′ poly-A tail addition, and intron removal — to form mature mRNA.

In which direction is DNA read during transcription?

DNA is read 3′ → 5′ to produce RNA in the 5′ → 3′ direction.

What strand of DNA serves as the template during transcription?

The template strand (read 3′ → 5′).

What strand of DNA has the same sequence as RNA (except U replaces T)?

The nontemplate (coding) strand.

What is a promoter?

A region on DNA at the start of a gene that signals where transcription begins.

Genes are said to be located in which direction relative to the promoter?

Downstream from the promoter.

When does transcription initiation occur?

Only when the gene product is needed.

What regulates the initiation of transcription?

Multiple proteins (transcription factors) control when transcription starts.

Which proteins are required for prokaryotic transcription initiation?

Sigma factor and RNA polymerase, which bind to the promoter sequence.

Which proteins are involved in eukaryotic transcription initiation?

General transcription factors (GTFs), transcriptional activator proteins (TAPs), and mediator complex proteins.

What is an enhancer?

An upstream region of DNA where transcriptional activator proteins bind to increase transcription.

What enzyme is responsible for elongation during transcription?

RNA polymerase — it moves along DNA and builds the RNA strand.

What does RNA polymerase do during elongation?

It separates DNA strands, reads the template strand (3′ → 5′), and synthesizes RNA (5′ → 3′).

How are RNA nucleotides added during elongation?

RNA nucleotides are added to the 3′ end of the growing RNA strand.

What are the base-pairing rules for transcription?

G pairs with C, A pairs with U, and T pairs with A.

What provides the energy needed for RNA elongation?

Nucleotide triphosphates (NTPs) — their phosphate bonds release energy when broken.

Where does transcription end?

At a terminator sequence on the DNA.

What are the three main types of RNA produced during transcription?

mRNA (messenger RNA), rRNA (ribosomal RNA), and tRNA (transfer RNA).

In which types of cells are mRNA, rRNA, and tRNA found?

In both prokaryotes and eukaryotes.

What RNAs are found only in eukaryotes?

snRNA (used to process mRNA), miRNA and siRNA (regulate translation and protein levels).

Does RNA processing occur in both prokaryotes and eukaryotes?

No, only in eukaryotes. Prokaryotic RNA is not processed before translation.

What is the name of the unprocessed RNA in eukaryotes?

Primary RNA or pre-mRNA (primary transcript).

What two main modifications happen to pre-mRNA during processing?

Addition of a 5′ cap and 3′ poly-A tail, and splicing out introns.

What is the function of the 5′ cap?

Increases mRNA stability and enables recognition by the ribosome.

What is the function of the poly(A) tail?

Allows transcription termination, increases mRNA stability, and aids mRNA export to cytoplasm.

What are introns and exons?

Introns are noncoding regions removed from pre-mRNA; exons are coding regions that remain.

What carries out RNA splicing?

The spliceosome, a protein and snRNA complex.

What is the result of RNA splicing?

Mature mRNA with joined exons, ready for translation.

Where does RNA processing occur in eukaryotes?

In the nucleus.

What is alternative RNA splicing?

Different combinations of exons joined to produce multiple mRNAs from one gene.

What does alternative splicing allow?

A single gene to code for multiple proteins with different functions.

Example of alternative splicing?

One gene can produce Protein A (E1E2E4) and Protein B (E1E2E3).

What is the RNA World Hypothesis?

The idea that the first nucleic acids were RNA molecules, not DNA.

Why do scientists think RNA was the first genetic material?

Because RNA has many types, participates in all central dogma steps, and some RNA can act as enzymes.

What experiment supports the RNA World Hypothesis?

Jack Szostak et al. showed RNA can catalyze reactions, such as cutting and joining nucleic acid strands.

Why is RNA’s dual role important?

It suggests early life could exist before DNA or proteins, with RNA storing information and catalyzing reactions.