chapter four
4.1 DNA and RNA—The Nucleic Acids
Expected Learning Outcomes:
Describe the structure of DNA and relate this to its function.
Describe the types of RNA, their structural and functional differences, and how they compare with DNA.
4.1a DNA Structure and Function 1
Deoxyribonucleic acid (DNA):
A long, thread-like molecule with a uniform diameter but variable length.
Most human cells have 46 DNA molecules (chromosomes).
The average human DNA molecule is about 2 inches long.
DNA Structure and Function 2
DNA and Nucleic Acids:
DNA and other nucleic acids are polymers made of nucleotides.
Each nucleotide consists of three components:
A sugar (deoxyribose)
A phosphate group
A nitrogenous base
DNA Bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)
Purines: Adenine (A) and Guanine (G) have a double-ring structure.
Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U) have a single-ring structure.
The Five Nitrogenous Bases found in DNA and RNA
Figure 4.1b:
Access text alternatives for the accompanying images.
DNA Structure and Function 3
Double Helix Structure:
The double helix shape of DNA resembles a spiral staircase.
Each sidepiece is a backbone of alternating phosphate groups and deoxyribose.
Step-like connections between the backbones are made by base pairs unified by hydrogen bonds.
Base Pairing: Purines pair with pyrimidines:
A pairs with T using 2 hydrogen bonds.
G pairs with C using 3 hydrogen bonds.
Law of Complementary Base Pairing: The sequence of one strand dictates the sequence of the other.
DNA Structure and Function 4
Function of DNA:
The primary function of DNA is to carry genetic instructions (genes) for protein synthesis.
Gene Definition: A segment of DNA coding for a specific protein.
Humans possess about 20,000 genes, accounting for approximately 2% of total DNA.
The remaining 98% is noncoding DNA which plays roles in chromosome structure and regulation of gene activity.
Chromatin and Chromosomes 1
DNA Organization:
DNA organizes itself with proteins into chromatin, which is a fine filamentous material complexed with histones.
Exists as 46 chromosomes in most cells, resulting in a 6 feet long thread packed into the cell nucleus of about 5 μm in diameter.
In non-dividing cells, chromatin is slender enough to be undetectable under a light microscope.
Forms complex loops and coils, appearing 150 times thicker and 1,000 times shorter than naked DNA.
Each chromosome occupies its own region of the nucleus known as a chromosome territory, permeated with channels for regulatory chemicals to access genes.
Chromatin and Chromosomes 3
Chromosome Preparation for Division:
Prior to cell division, the cell duplicates all nuclear DNA.
Each chromosome then consists of two identical DNA strands, referred to as sister chromatids, joined at the constricted centromere.
4.1c RNA Structure and Function
Ribonucleic Acids (RNAs):
RNAs exist in different forms, each serving various functions.
General RNA Structure:
Contains the sugar ribose.
Bases include A, U, G, C; with uracil (U) replacing thymine found in DNA.
Composed of a single nucleotide chain (except in short regions).
Smaller than DNA, with lengths varying from less than 100 to just over 10,000 bases per molecule.
Functions mainly in cytoplasm.
Three important types of RNA for protein synthesis:
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
4.2 Genes and Their Action 1
Expected Learning Outcomes:
Provide a working definition of a gene and discuss how recent discoveries in genetics have modified our concept of genes.
Explain the human genome and its implications for health sciences.
Define genetic code and elucidate how DNA codes for protein structure.
4.2 Genes and Their Action 2
Expected Learning Outcomes Continued:
Describe the process of assembling amino acids to form proteins.
Explain the fate of a protein after its amino acid sequence has been synthesized.
Discuss mechanisms by which genes can be activated (turned on) or inactivated (turned off).
Explain how DNA regulates nonprotein molecule synthesis indirectly.
What Is a Gene? 1
Previous Definition: A gene is defined as a segment of DNA coding for a specific protein. However, the body has millions of proteins but only about 20,000 genes.
Current Definition: A gene is an information-containing segment of DNA that codes for the production of RNA, which often plays a role in synthesizing one or more proteins.
The amino acid sequence of a protein is determined by the nucleotide sequence in DNA.
What Is a Gene? 2
Human Chromosomes:
Humans have 46 chromosomes arranged in two sets of 23, one from each parent.
Genome: All the DNA contained within one set of 23 chromosomes.
There are 3.1 billion nucleotide pairs in the human genome.
Individual genetic variation arises from single-nucleotide polymorphisms.
Genomics: The study of the entire genome; genes and noncoding DNA interact, affecting the structure and function of an organism.
Genomic Medicine: The application of genomic knowledge for predicting, diagnosing, and treating diseases (examples include cancer, Alzheimer's disease, schizophrenia, obesity, AIDS, tuberulosis).
4.2b The Genetic Code
Proteome Evolution: The human body can generate millions of unique proteins (the proteome) from just 20 amino acids encoded by genes composed of merely four nucleotides (A, T, C, G).
Genetic Code: A system that allows these four nucleotides to codify for the amino acid sequences of all proteins.
Base Triplet: A sequence of three DNA nucleotides representing one amino acid.
Codon: A three-base sequence in mRNA.
There are 64 possible codons representing 20 amino acids, with 61 coding for amino acids and 3 serving as stop codons.
Start Codon: The codon AUG which codes for methionine and initiates the amino acid sequence of a protein.
Stop Codons: UAG, UGA, and UAA are signals indicating "end of message," akin to a period at the end of a sentence.
4.2c Protein Synthesis 1
Cellular Identity: All body cells, except sex cells and some immune cells, contain identical genes; however, cells differ because they activate and utilize different genes.
Any specific cell uses about one-third to two-thirds of its genes, while the remainder remain inactive.
Upon activation of a gene, mRNA (messenger RNA) is synthesized as a code for a specific protein.
Central Dogma of Molecular Biology:
DNA → RNA → Protein
The process from DNA to mRNA occurs through transcription in the nucleus.
The conversion from mRNA to protein occurs through translation in the cytoplasm.
Transcription 1
Transcription: The process of copying genetic instructions from DNA to mRNA.
It employs the enzyme RNA polymerase, which binds to starting sequences in DNA and unwinds the helix.
RNA polymerase reads bases from one strand of DNA to build a complementary mRNA strand:
For DNA bases:
C → G
G → C
T → A
A → U
Terminator: A stop sequence found at the end of a gene.
Pre-mRNA is the immature RNA created during transcription and later processed to remove introns around splicing exons together.
Alternative Splicing: Variations in splicing exons allow for the production of various proteins from a single gene, illustrating that one gene can encode more than one protein.
Alternative Splicing of mRNA
Transcription:
Gene (DNA) → Intron/(Pre-mRNA) → Exon
Splicing:
mRNA can form multiple versions due to alternative splicing allowing different mRNA products from a single gene.
This leads to various proteins being synthesized (Protein 1, Protein 2, Protein 3).
Translation 1
Translation: The process in which the nucleotide language of mRNA is interpreted into the amino acid language.
A ribosome reads the mRNA code to construct a protein.
There are three main participants in translation:
Messenger RNA (mRNA): Carries the code from the nucleus to the cytoplasm and has a protein cap serving as a recognition site for ribosomes.
Transfer RNA (tRNA): Delivers a single amino acid to the ribosome; contains an anticodon, a series of three nucleotides that complement the mRNA codon.
Ribosomes: Organelles that interpret the message and synthesize a peptide chain; consists of a large and small subunit, present free in cytosol, on rough ER, and on the nuclear envelope.
The ribosome has three sites involved in the translation process: E (exit), P (peptidyl), and A (aminoacyl) sites.
Translation 2
Three Steps of Translation:
Initiation:
The ribosome assembles with mRNA in the cytosol; the small subunit binds with the leader sequence of mRNA, the large subunit joins, and protein synthesis commences at the AUG codon, with tRNA delivering the initial amino acid, methionine.
Elongation:
The next tRNA with an amino acid arrives, binding to the A site.
The ribosome forms a peptide bond between the first and second amino acids, and the ribosome then shifts down the mRNA by one codon, with the growing peptide now attached to tRNA in the P site.
Termination:
The ribosome arrives at a stop codon, and the A site binds a release factor protein, causing ribosomal disassembly and dissociation from mRNA.
Translation of mRNA1
Figure 4.8:
Illustrates the process including components such as nuclear pore, protein cap, ribosomal subunits, tRNA, and protein synthesis pathway utilizing free amino acids and ATP.
Translation of mRNA 2
Polyribosomes:
Multiple ribosomes can translate the same mRNA molecule simultaneously, forming clusters called polyribosomes.
Protein Modification:
Proteins destined for lysosomes/excretion undergo modification by the endoplasmic reticulum (ER); the ribosome docks on the ER synthesizing the protein into ER cistern, with modification and packaging into transport vesicles.
Relationship of a DNA Base Sequence to Peptide Structure
Figure 4.9:
Shows the DNA double helix, base triplets on the template strand, corresponding mRNA codons, tRNA anticodons binding to mRNA codons, and linked amino acids forming a peptide chain.
4.2d Protein Processing and Secretion 1
Post-Synthesis Protein Processing:
Protein synthesis is incomplete when the amino acid sequence (primary structure) is assembled.
Proteins must undergo proper folding into secondary and tertiary structures to function.
Chaperone Proteins: Assist in protein folding, help prevent misfolding/misassociation between distinct proteins, often referred to as stress or heat shock proteins produced in response to heat/stress, assisting in correcting misfolded proteins.
Protein Processing and Secretion 2
Protein Processing and Secretion Mechanism for Secretory Proteins:
Proteins formed by ribosomes on rough ER.
Proteins are packaged into transport vesicles, which bud from the ER.
Transport vesicles fuse into clusters to form a new cis cistern.
Golgi complex modifies the protein structure.
The trans cistern breaks up into cargo-laden vesicles.
Secretory vesicles release proteins by exocytosis.
Protein Processing and Secretion 3
Detailed steps involved in the secretion pathway from the rough ER to the Golgi, to the final exocytosis that releases proteins into the cellular environment.
4.2e Gene Regulation 1
Gene Activation:
Genes can be turned on and off; cells may permanently deactivate some genes (e.g., liver cells turning off hemoglobin genes).
Genes can be activated as needed; expression levels may fluctuate over time, influenced by chemical messengers such as hormones.
Example: Mammary gland cells activate casein gene production in response to prolactin only during lactation.
Gene Regulation 2
Casein Synthesis and Secretion by Mammary Gland Secretory Cells:
Process of activation involving prolactin, transcription activation by regulatory protein, and the downstream production of mRNA for casein leading to secretion.
4.2f Synthesizing Compounds Other Than Proteins
Cellular Synthesis:
Cells synthesize various compounds (glycogen, fats, steroids, phospholipids, pigments) under indirect genetic control.
Synthesized through enzymatic reactions, wherein enzymes as proteins are encoded by genes (e.g., testosterone production).
4.3 DNA Replication and the Cell Cycle 1
Expected Learning Outcomes:
Describe how DNA is replicated, consequences of replication errors, life history of a cell, events in mitosis, and regulation of cell division timing.
4.3 DNA Replication and the Cell Cycle 2
DNA Duplication:
Prior to cell division, it is essential for a cell to duplicate its DNA to provide complete genetic copies to each daughter cell.
Since DNA regulates all cellular functions, this replication must occur accurately.
The Law of Complementary Base Pairing assists in anticipating one strand's sequence if the complementary strand is known.
4.3a DNA Replication 1
Four Steps of DNA Replication:
Unwinding the Helix:
Histones are released to allow access to the DNA strand.
Unzipping the Helix:
A segment of the helix is unwound by the enzyme DNA helicase, creating a replication fork.
Synthesis of Complementary Strands:
The enzyme DNA polymerase navigates each strand, reading exposed bases and synthesizing their complementary strands.
New, but discontinuous strands are connected by DNA ligase.
Semiconservative Replication:
Each new DNA molecule consists of one old (parental) strand and one new (daughter) strand.
Newly synthesized histones are used to bundle new DNA strands into nucleosomes.
4.3b Errors and Mutations
Replication Errors:
DNA polymerase can make errors during replication.
DNA Damage Response (DDR):
Mechanisms in place for rectifying these errors.
DNA polymerase checks base pairs and tends to replace incorrect, unstable pairs with stable, accurate options, estimated as 1 error per billion bases replicated.
Mutations:
Alterations in DNA structure resulting from replication mistakes or environmental impacts (radiation, viruses, chemicals).
Mutations can have varying effects: some cause no harm, others can be lethal, induce cancer, or result in genetic defects in future generations.
4.3c The Cell Cycle 1
Components of the Cell Cycle:
The cell cycle includes interphase and mitosis.
Interphase includes:
First Gap Phase (G1):
The interval between cell division and DNA replication; during which normal cell functions, protein synthesis occur.
Synthesis Phase (S):
The period where all nuclear DNA and centrioles are replicated.
Second Gap Phase (G2):
The interval between DNA replication and cell division; where DNA repair and additional growth occurs.
Mitosis consists of:
Prophase, Metaphase, Anaphase, Telophase, and Cytokinesis.
The Cell Cycle 3
Interphase Specifics:
G1 Phase: Initial phase with normal cells functions and preparations for division.
S Phase: Concentrates on DNA replication along with centriole duplication.
G2 Phase: Cells focus on fixing any DNA errors and get ready for mitosis.
G0 Phase: Non-dividing state, cells that leave the cycle for extensive periods can enter this phase.
Duration of the cell cycle can vary across different cell types.
4.3d Mitosis 1
Mitosis Overview:
Cell division yielding two genetically identical daughter cells.
Functions of Mitosis:
Development from a single fertilized egg to a vast number of cells (~50 trillion).
Growth of tissues and organs post-birth.
Replacement of deceased cells.
Repair of cellular damage.
Four phases of mitosis: Prophase, Metaphase, Anaphase, and Telophase.
Mitosis 2
Phases of Mitosis:
Prophase:
Genetic material compacts into chromosomes for easier distribution.
Nuclear envelope breaks down; spindle fibers emerge from centrioles, which help pull apart the chromosome pairs by anchoring to kinetochores of centromeres.
Metaphase:
Chromosomes are aligned on the equator of the cell, forming a structured mitotic spindle.
Anaphase:
Sister chromatids are separated, with single-stranded daughter chromosomes migrating toward opposing cell poles.
Telophase:
Chromosomes cluster on either side of the cell, acquire new nuclear envelopes, and revert to chromatin form as the mitotic spindle dissolves.
Mitosis 5
Cytokinesis:
Involves the division of cytoplasm into two distinct cells.
While telophase concludes nuclear division, it coincides with cytokinesis, which is enabled by myosin pulling on actin in the cytoskeleton's terminal web, producing a cleavage furrow around the cell’s equator.
4.3e Regulation of Cell Division 1
Cells typically divide under the following conditions:
Sufficient cytoplasm for two daughter cells.
Completion of DNA replication.
Adequate nutrient supply.
Growth factors (chemical signals) stimulating division. - Cell death by neighboring cells allowing for space.
Cessation of Division:
Cells stop dividing under nutrient or growth factor deprivation or through contact inhibition in response to neighboring cell contact.
Regulation of Cell Division 2
Cell Cycle Control:
Governed by a molecular timer and checkpoints.
Molecular Timer: Composed of proteins:
Cyclins: Levels fluctuate throughout the cell cycle.
Cyclin-dependent Kinases (Cdks): Activated by cyclins for phosphorylating target proteins.
Hematics Under Cyclin–Cdk Complex:
It directs DNA replication, chromsome composition, nuclear envelope breakdown, mitotic spindle formation, and chromatid separation during respective phases.
Regulation of Cell Division 3
Checkpoints in the Cell Cycle:
Managed by Cyclin–Cdk complexes for:
Start or G1 Checkpoint: Determines if the cell can transition into S phase or revert to the noncyclic G0 phase.
G2/M Checkpoint: Late in G2, verifies if the cell is ready for mitosis.
A checkpoint transitions from metaphase to anaphase verifies readiness for chromatid separation.
4.4 Chromosomes and Heredity
Expected Learning Outcomes:
Describe chromosomes' paired arrangement in the human karyotype.
Define allele and discuss its influence on traits in an individual.
4.4a The Karyotype
Heredity: The process of transferring genetic traits from parent to offspring.
Karyotype: A visual representation of all 46 chromosomes arranged by size in pairs:
Homologous Chromosomes:
One chromosome from each pair inherited from each parent; comprise 23 pairs of homologous chromosomes.
Autosomes: 22 pairs that are congruent and carry the same genes.
Sex Chromosomes: 1 pair; females possess a homologous X chromosome pair, while males have one X and a notably smaller Y chromosome.
The Normal Human Karyotype
Figure 4.16: Illustrates normal karyotype structure.
4.4b Genes and Alleles 1
Gene Characteristics:
Genes vary but locate at the same position (locus) on chromosomes.
Locus: Indicates the precise position of a gene on a chromosome.
Alleles: Different variants of a gene, existing at the same locus on homologous chromosomes.
Alleles can be:
Dominant: Typically expressed in phenotype if present; masks recessive effects.
Recessive: Not expressed unless present on both chromosomes; often linked to nonfunctional variants.
4.4b Genes and Alleles 2
Genotype vs Phenotype:
Genotype: The specific alleles an individual has for a particular gene.
Homozygous individuals: possess identical alleles.
Heterozygous individuals: have differing alleles.
Phenotype: The observable trait of an individual influenced by one or multiple genes.
Example: Sickle-cell disease results from homozygous recessive alleles; carriers with one allele exhibit the sickle-cell trait.
4.4e Sex Linkage
Sex-Linked Traits: Carried on X or Y chromosomes, which often results in different inheritance patterns between sexes.
Example: The recessive color blindness allele is found on the X chromosome without a corresponding locus on the Y chromosome, making color blindness more frequent in males (with female carriers illustrated in Figure 4.20).
4.4h Epigenetics
Epigenetic Effects: Gene expression modifications that occur without altering base sequences, which can still be inherited, referred to as epigenetic inheritance.
Mechanisms of Epigenetic Changes:
DNA methylation: The addition of methyl groups (—CH3) to the DNA structure.
Variations in chromatin packaging.
Gene silencing via noncoding RNA (ncRNA).
Health Implications: These epigenetic changes may be typical, but some could lead to diseases, such as cancer.