UNIT 2. NUCLEAR ACID STRUCTURE & FUNCTION

nucleotide

Building block of DNA and RNA

1. phosphate group

2. pentose sugar

3. nitrogenous base

3 composition of nucleotides

Pentose Sugar

3 composition of nucleotides:

• Ribose and deoxyribose

Adenine

Guanine

Cytosine

5 bases seen in DNA and RNA:

• found both in DNA and RNA

Uracil

pyrimidine that is special to RNA, can’t be found in DNA

Thymine

pyrimidine that is only found in DNA, not in RNA

Adenine

Guanine

Purines

Cytosine

Uracil (RNA)

Thymine

Pyrimidines

Deoxyribonucleic Acid (DNA)

• Composed of phosphate group, nitrogenous base and deoxyribose

• Exists as a double – helix

• Has directionality

5’ to 3’ Directionality

• based on the connection of phosphate group to pentose sugar of DNA

sense/coding strand

5’ to 3’ strand

Not used as the template during transcription

Antisense/ Template Strand

3’ to 5’ strand

Complementary to the mRNA sequence

Used by RNA polymerase during transcription

Hydrogen Bonds

Nitrogen bases are bound through ____________

A-T/ A-U = 2 H-bonds

C-G = 3 H-bonds

A-T/ A-U = ____________

C-G = ____________

10 base pair

For physiological DNA that we have, Each turn of the helix has ____________

1. B-form

2. A-from

3. Z-from

3 Forms of DNA:

B-form

3 Forms of DNA:

• Closest form to the one found in the physiological environment

• Relatively high humidity (92%)

• Aqueous form of DNA found in aqueous environment

A-form

3 Forms of DNA:

• Lower humidity (75%)

• Dehydrated form

z-form

3 Forms of DNA:

• Left-handed helix

• Usually man-made sequences

Pitch

• Refers to the length of one complete turn of the DNA helix

• measured in Angstrom (A)

chromosomes ;

nucleus

In eukaryotes, DNA is packed into ______________ and enclosed by the ________.

Ribonucleic Acid (RNA)

• Single-stranded nucleotides with 5’ to 3’ directionality

• Composed of a phosphate group, a pentose sugar (ribose) and bases (Adenine, Uracil, Cytosine, Guanine)

RNA molecules

Function as gene intermediates and for gene expression control through ______________

1. mRNA

2. rRNA

3. tRNA

3 Major Kinds of RNA:

messenger RNA (mRNA)

Major Kinds of RNA:

• Product of DNA transcription

• most code for proteins — Those that are not coding are either RNA regulatory elements or they can be other things

ribosomal RNA (rRNA)

Major Kinds of RNA:

• Form the basic structure of ribosomes

• catalyse protein synthesis

• They form loops and hairpins so they bind to each other and form this higher order of structure for their rRNA

Transfer RNA (tRNA)

Major Kinds of RNA:

• Looped structures that bring amino acids to the ribosomes during protein synthesis

small nuclear RNA (snRNA)

Other Kinds of RNA:

• For nuclear processing like splicing (of RNA)

small nucleolar RNA (snoRNA)

Other Kinds of RNA:

• For processing and chemically modifying rRNAs

• Found in nucleolus

microRNA (miRNA)

Other Kinds of RNA:

• Regulate gene expression usually by selective silencing of mRNA

• They usually do this by attaching themselves to the untranslated regions of gene

small interfering RNA (siRNA)

Other Kinds of RNA:

• Silence expression by degrading select mRNAs

• can help make compact chromosome structures

• A lot of this are used to make compact chromosomes structures as well as like x – chromosome inactivation

Gene

• Sequence of DNA which codes for an RNA product

• Product can be protein-coding, a regulatory RNA molecule, tRNA, rRNA, etc.

control elements

Genes are generally flanked by _________________

• upstream = before the gene

• downstream = after the gene

Control Elements:

• _____________ = before the gene

• _____________ = after the gene

Regulatory elements

Control Elements:

• modulate transcription

• can be negative or positive

• Positive (Enhancers)= increase transcription rate

• Negative (silencers) = decrease transcription rate

Regulatory Elements:

• ____________________ = increase transcription rate

• ____________________ = decrease transcription rate

1. Constitutively Expressed Genes

2. Facultative Genes

Types of Genes based on expression:

Constitutive / Housekeeping Genes

Types of Genes based on expression:

• Constitutively expressed means that they are always on, always needed by the cells

• Expression is constant, not influenced by external signals

• Ex: beta-actin in cytoskeleton, ubiqiutin in ubiquitin proteosome pathway

Facultative Genes

Types of Genes based on expression:

• Expressed only when needed

• Turned on or off depending on cell type, environment, or signals

• Ex: genes for lactose metabolism in bacteria, stress response proteins, hormone-induced genes

Prokaryotic cell

• No nucleus

• No membrane bound organelles

• No chromosomes

plasmids

Prokaryotes have Extrachromosomal DNA called ___________ for Antibiotic resistance, virulence, metabolism

nuclear region

in prokaryotes, There’s a _____________ where the DNA is, and plasmid scattered around the cytoplasm

T

There are simple eukaryotes that have smaller genomes compared to prokaryotes, but generally prokaryotes will always have a shorter genome

T or F
Prokaryotic genome is generally shorter than eukaryotes.

Prokaryotic Genome

• Generally exist as a single, circular piece of DNA (unipartite)

• shorter than eukaryotes

• Very compact in nature

• Some genes have no space between them

• Generally no discontinuous genes

• Generally low copy numbers with very few repeats

multipartite genome

• A small subset of prokaryotes have multiple DNA pieces that may be either circular or linear

• Allows gene specialization and adaptation

Vibrio, Brucella, Burkholderia

Examples of multipartite genome

Operon

• Adjacent genes under the control of the same promoter and make use of the same regulatory elements

• are transcribed together as one mRNA.

• Usually encodes proteins in the same biochemical pathway.

T

No introns → genes are continuous, all DNA sequences are functional.

Efficiency: Genome is small, so every gene is important.

T or F

Prokaryotic genome has no introns, and thus, they do not have any discontinuous strand.

E. coli (K12)

• Example of Prokaryotic whole genome

• 4.6 million nucleotide pairs

• Very small genome

• There’s an origin of replication and point of termination

• Example of a unipartite genome

Polycistronic Operons

• An operon that produces one mRNA encoding several proteins.

• Proteins are usually part of the same biochemical pathway, so expressing them together is efficient.

• Controlled by:

  • Single promoter

  • Same regulatory elements

1. Lactose (lac) Operon

2. Tryptophan (trp) Operon

2 Examples of Polycistronic Operons

Lactose (lac) Operon

2 Examples of Polycistronic Operons:

• Famous model in molecular biology

• used in blue-white assay

• Turning on the operon allows the cell to take in and digest lactose.

lacZ

lacY

lacA

3 Genes of lactose operon

β-galactosidase

3 Genes of lactose operon:

• lacZ: ________________ → breaks down lactose into glucose & galactose

Lactose permease

3 Genes of lactose operon:

• lacY: _______________ → transports lactose into the cell

Transacetylase

3 Genes of lactose operon:

• lacA: ______________ → helps lactose metabolism

Tryptophan (trp) Operon

2 Examples of Polycistronic Operons:

• Express different genes for tryptophan production

• Genes are expressed together because all are needed in the same pathway.

Activator

PROKARYOTIC GENE STRUCTURE:

• attaches to the enhancer (positive) to increase transcription

Repressor

PROKARYOTIC GENE STRUCTURE:

• sticks to the silences (negative) to put down transcription

Operator

PROKARYOTIC GENE STRUCTURE:

• regulatory element specific for operons, used by repressors.

Promoter

PROKARYOTIC GENE STRUCTURE:

• Sequence where RNA polymerase and transcription factors bind to start transcription.

5’ Untranslated Region (5’ UTR)

PROKARYOTIC GENE STRUCTURE:

• Part of transcript but is not translated into the protein

• still important

• contains sequences for signal peptides, ribosome binding sites, termination signals

Open Reading Frame (ORF)

PROKARYOTIC GENE STRUCTURE:

• A sequence of DNA or mRNA that can potentially code for a protein.

• Starts with a start codon (AUG) and ends with a stop codon (UAA, UAG, UGA).

• Each ORF corresponds to one protein in an operon.

the ribosome binding site

PROKARYOTIC GENE STRUCTURE:

After transcription, you’ll have ______________________ because you’ll need this because this is what the ribosome would recognize and attach to

Termination signals

PROKARYOTIC GENE STRUCTURE:

__________________ stop translation of each ORF.

Coupling of Transcription & Translation

• In prokaryotes, transcription and translation occur in the same place (no nucleus).

• Translation can start as soon as RNA emerges from RNA polymerase.

• nucleus

• mitochondria

• chloroplast

EUKARYOTIC GENOME:

DNA is compartmentalized into the

whole (eukaryotic) genome

EUKARYOTIC GENOME:

includes the nuclear DNA sequences and the organelle DNA sequences

linear chromosomes

EUKARYOTIC GENOME:

DNA is present as ___________________.

T

T or F

Eukaryotic Genes are distributed along the chromosome arms with gene density variable with each chromosome.

Multigene Families

EUKARYOTIC GENOME:

• Groups of genes that are identical or very similar in sequence.

• Often have high copy numbers, meaning multiple copies exist in the genome.

• Examples:

  • Globin genes → code for hemoglobin subunits

  • Aldolase genes → involved in glycolysis

T

T or F

Eukaryotic Genome have introns making genes generally discontinuous.

F

No operons so each gene has its own promoter and control region

T or F
Eukaryotic genome have operons and each gene also has its own promoter and control region.

Organelle Genome

EUKARYOTIC GENOME:

• Generally circular DNA molecules. o There are exceptions, but in general, they have circular DNA molecules similar to prokaryotes

• They have variable sizes that are generally not affected by organism complexity.

• Generally compact with very little space between genes

Yeast Mitochondrial Genome

ORGANELLE GENOME:

• circular DNA

• Genes for oxidative phosphorylation and the ETC (electron transport chain)

• Genes for transcription and translation

• expression occurs in the matrix

Chloroplast Genome

ORGANELLE GENOME:

• Genes for photosynthesis

• Genes for transcription and translation

• expression occurs in the stroma

• Proximal

• Core

Parts of promoter

• Splicing

• 5’-G Capping

• 3’ Poly-A Tail

Post transcriptional modifications:

Splicing

Post transcriptional modifications:

• Introns are removed, exons joined together.

• This produces a continuous coding sequence for the protein.

• Occurs in the nucleus.

5’ G cap

Post transcriptional modifications:

• Added to the 5′ end of mRNA.

• Protects mRNA from degradation.

• Helps ribosome recognize the mRNA for translation

3’ Poly-A Tail

Post transcriptional modifications:

• Added to the 3′ end of mRNA.

• Marks the molecule as mature mRNA.

• Stabilizes mRNA and protects it from degradation.

• Helps mRNA exit the nucleus and reach the cytoplasm for translation.

Signal Peptide

• Short sequence in mRNA/protein that directs the protein to its proper location (e.g., nucleus, membrane, or secretion).

• “locator”

Prokaryotic Genome

Prokaryotic Genome

Eukaryotic Genome

Eukaryotic Genome