Genetics in Nutrition: Nucleotide Chemistry

• Course: Genetics in Nutrition (BDTS 417)
• Lecturer: Peter Nuro-Ameyaw

Course Objectives

• Understand the genetic basis of the disease
• Explain basic genetics concepts, including the gene, mutations, their impact on phenotype, and modes of inheritance
• Analyze how a person's genetic trait affects their metabolic and physiological function
• Assess how bioactive components in food can modulate gene expression
• Explain the basic concept of the metabolome in relation to nutrient intake

Course Outline

• Week 1: Nucleotide Chemistry
• Content includes the double helix and nucleotide components
• Weeks 2-3: The Flow of Genetic Information
• Content includes DNA replication, transcription, translation, how antibiotics affect gene expression, DNA repair, and mutagenic agents
• Week 4: Genome and Chromosome Mutations
• Content includes mechanisms and effects of numerical and structural chromosomal aberrations
• Week 5: Mendelian Defects and Single Gene Defects with Non-Classic Inheritance
• Content includes mechanisms, effects, and modes of inheritance
• Weeks 6-7: Antioxidant
• Content includes the antioxidant enzyme system, nutrient antioxidants, importance of antioxidants, free radicals, sources of free radicals

Basic Terminologies

• Genetics: The study of genes, heredity, and variation in living organisms
• Heredity: Transmitting genetic information from parents to offspring which keeps species consistent from generation to generation
• Variation: Differences in genetic traits among individuals caused by genetic mutations, recombination, and environmental factors
• Gene: A fundamental unit of heredity made up of DNA sequence of nucleotides on a chromosome that encodes a specific function
• Chromosome: A self-replicating genetic structure of cells containing DNA in its nucleotide sequence as a linear array of genes
• Chromosomes are composed of coiled DNA
• DNA is organized into a double helix structure and carries the genetic code
• Histones help package and organize the DNA, around which DNA wraps to form chromatin
• DNA (Deoxyribonucleic Acid): A molecule that carries genetic information, organized into chromosomes
• Each organism has a unique DNA, like a fingerprint

Nucleotide Chemistry

• DNA is found in cells of most living things and contains the genetic material to differentiate one organism from another
• Some viruses have RNA as the genetic material
• Viruses which contain RNA as genetic material are called retroviruses
• Most DNA molecules are double-stranded helices
• Eukaryotes like human DNA are double stranded
• Some viruses have single-stranded DNA like Papillomaviruses
• Double-stranded DNA molecules consist of two biopolymers made of simpler units called nucleotides
• Each nucleotide is composed of a nucleobase, recorded with letters G, A, T, and C
• Nucleotides are the monomeric unit of DNA
• DNA is the hereditary material in humans and nearly all other organisms
• Red blood cells do not contain DNA
• Lens fibre cells do not contain DNA
• Mature keratinocytes in the epidermis do not contain DNA
• DNA is mainly located in the nucleus
• Mitochondria have DNA called mitochondrial DNA (mtDNA)

History of DNA

• Friedrich Miescher isolated "nuclein" (DNA) from pus cells in 1869, which became known as nucleic acid after 1874
• Phoebus Levene discovered that DNA is made up of nucleotides and proposed the tetranucleotide hypothesis
• Rosalind Franklin used X-ray crystallography to help visualize the structure of DNA
• James D. Watson and Francis Crick are the originators of the double helix model

DNA structure

• DNA and RNA contain deoxyribose and ribose sugars, respectively
• The nitrogenous bases come in two groups: pyrimidines and purines
• Pyrimidines (one 6-member ring) include thymine and cytosine
• Purines (a 6-member ring, fused to a 5-member ring) include adenine and guanine
• Uracil is found in ribonucleic acids alone
• Each spiral strands has sugar phosphate backbone with attached nitrogen containing bases connected by complementary strand
• Bases are paired with covalent bonding
• Adenine is paired with thymine
• Guanine is paired with cytosine
• Two chains do not have the same composition
• Chains are complimentary
• The more GC bonds, the stronger the bond between strands
• DNA melting temperature (Tm) is the temperature at which 50% of double-stranded DNA separates into single strands

General DNA Structure

• Consists of a double helix in a twisted ladder-like structure formed from two strands of nucleotides
• DNA has about 10 nucleotide pairs per helical turn
• DNA strands are anti-parallel, running opposite of each other, along the length of the double helix

DNA replication

• DNA replication: The production of identical copies of DNA
• DNA replication is essential for cell division
• DNA makes copies of itself during cell division, ensuring that genetic information is passed to new cells
• The enzyme DNA polymerase helps achieve this replication task
• Replication involves multiple steps: initiation, elongation, and termination

Initiation of DNA Replication

• Begins at a site of DNA known as origin of replication (Ori)
• Eukaryotic DNA has multiple origins of replication to accelerate the process
• “Ori” are rich strands
• Helicases unwind and separate double-stranded DNA at “Ori”, forming replication bubbles with replication forks

Elongation of DNA Replication

• Enzyme "primase" attaches (anneals) the RNA primer to a specific location to start replication
• A Primer ~20 bases serves as starting synthesis
• DNA polymerase requires Primer for replication
• DNA polymerase (DNA Pol III) catalyzes synthesis of new DNA strands using original DNA as templates
• DNA polymerases adds nucleotides to growing new strands in 5' to 3' direction, complementary to templates
• Leading strand: RNA Primers are first synthesized by Primase
• The leading strand is continuously synthesized by DNA polymerase in the 5’ to 3’ direction as replication fork opens
• Lagging strand: DNA is discontinuously synthesized in short 100-200 nucleotide fragments called RNA Primers (Okazaki fragments)
• Okazaki fragments are synthesized by Primase and joined by DNA polymerase

Termination phase of DNA Replication.

• Exonucleases removes the RNA primers from both strands
• During the termination phase, DNA polymerase fills the gaps with DNA DNA ligase seals the fragments of DNA to form a continuous double strand

General facts on DNA replication

• Semi-conservative: Made up of one old conserve strand and one new stand

Gene expression

• Different organisms produce different proteins
• Gene expression: The information coded in a gene is used to produce a functional product like a protein or RNA molecule.
• It is essential for regulation of cellular functions

Gene Structure

• A chromosome contains genes and each gene contains DNA, thus genes contain the start and finish points of the DNA coding
• One gene contains the promoter, coding region, and termination sequence. All of the regions of the gene are used in the process of coding and protein synthesis

Gene Expression

• Gene expression: Central Dogma of Molecular Biology
• Describes the flow of genetic information inside biological systems
• It was proposed by Francis Crick in 1958 and it states that information flows one way

Central Dogma

• DNA -> RNA -> Protein via transcription and translation
• Replication of DNA generates a DNA copy of itself

Transcription

• A specific gene in DNA is copied into messenger RNA (mRNA)
• Occurs in the nucleus (eukaryotes)
• Carried out by an enzyme called RNA polymerase
• RNA polymerase binds DNA and synthesizees MRNA
• Protein molecules called transcription factors also binds to DNA
• They regulate gene expression
• The first step of gene expression
• Complementary base pairing as in DNA synthesis with Uracil replacing Thymine in RMA
• MRNA synthesized on antisense strand OR non coding strand OR template OR Minus strand
• DNA strand that is not part of RNA synthesis is coding strand OR non templating strand OR plus strand

RNA processing

• Newly synthesizes mRNA undergoes:
• Capping: Addition of a “5’ cap”.
• Protecting from degradation. Facilitating export out of nucleus.
• Splicing: the cutting out of sections of genetic material, and subsequent re-attachment to the coding sections
• Polyadenylation: Addition of a string of adenine to a “Poly-A tail”. Protecting from degradation. mRNA stability and translation.
• Types of RNA produced
• Messenger RNA (mRNA): Carries instructions
• Transfer RNA (tRNA): Helps protein synthesis.
• Ribosomal RNA (rRNA): Forms ribosomes.

Translation

• MRNA has sections called RNA triplets
• Each MRNA is read to assemble amino acids (subunits of proteins)
• RNA three section nucleotide sequences called CODONS direct the type, selection and placement of the amino acid Key players in the process are: Ribosomes, transfer RNA (tRNA) and amino acids.
• Transfer RNA units bind to mRNA by anticodon
• Codon triplet sequences are read to assemble amino acids in a string
• The series of amino acids determines the proteins final structure, shape conformation.
• Translation occurs in cytoplasm MRNA interacts w Ribosomes

Main roles of tRNA

• Genetic information encoded in mRNA is decoded and translated for assembly
• Transfer RNA (TRNA) molecules bring specific amino acids to the ribosome
• Amino acids assemble to polypeptide chain in code or sequence
• The anticodon codes in tRNA ensure the correct assembly of amino acids at each step

Post-translational modification

• Newly synthesized polypeptide chains may undergo further modifications to become functional proteins
• These modifications include:
• Folding into a three-dimensional structure.
• Cleavage of amino acid sequences.
• Additions like phosphorylation.
• The coming together of subunits of associated protein sequences