Biology1A03: Theme 5 Module 1

11/26/25, 6:45 PM Biology1A03: Theme 5 Module 1 2025. 11. 25. 16:48 Biology 1A03 Unit 1: Genetic variation Genome variation and repeated sequences Human genome = the complete set of instructions that codes for life Exons and regulatory elements make up a small portion of eukaryotic genome Rest, there are noncoding and repeated sequences with their own functions among protein-coding genes Genome contains various repeated nucleotide sequences, including: Tandem repeats Up to thousands of nucleotides; multiple identical or near-identical copies Example: ACGTTGACGTTGACGTTGA … Simple-sequence repeats As short as 2 nucleotides, repeated many times Example: CACACACACACACACA… These sequences distributed throughout the genome create genetic variation Variation occurs within individuals and across organisms Not all variations in DNA sequence will have an ​observable effect Especially in non-protein-coding regions Among variations that do affect the organism: Some are less serious Some can be beneficial Outcome of a variation depends on: Nature of the change Location in the genome Consider: What would be the effect of a change in a noncoding region vs a coding or regulatory region? 11/26/25, 6:45 PM Genome mapping & DNA polymorphisms One primary goal of genome sequence projects is to map each chromosome with high resolution High resolution: determining the underlying DNA sequences and annotating coding and non-coding regions This is important for understanding: Inherited diseases Genetic variability DNA polymorphisms = two or more alternative forms (alleles) at a chromosomal region (locus) Polymorphisms differ by: Single nucleotide base Example: A → G Variable numbers of tandem nucleotide repeats Example: (CA) repeat Someone 10 repeat Someone 15 repeat Sequencing projects show a large number of DNA polymorphisms across genomes Most polymorphisms reside in non-coding regions Polymorphisms are useful by allowing creation of high-density genetic maps These are often called DNA markers DNA markers can be detected using: Microarray analysis PCR Southern blot DNA sequencing DNA markers can be used to ​identify individuals​and determine relatedness e.g., DNA fingerprinting 11/26/25, 6:45 PM Unit 2: Detecting Variation SNPs (Single Nucleotide Polymorphisms)​ Although 99.9% of human DNA is the same genetic variations → differences between individuals Single nucleotide polymorphism (SNP) Most common variations Arise from single nucleotide base changes or substitutions in the DNA sequence Occur in lot of portion of the population ​​ throughout the genome Found in both noncoding and coding regions Occur with high frequency: about 1 in every 350 bp This means there are millions of SNPs in each human genome Most SNPs occur in noncoding regions If an SNP is located near a gene → it can be used as a DNA marker​for that gene If linked closely enough to a gene → the SNP is passed from parent to child along with that gene A widely used technique for detecting SNP genotypes is DNA microarray analysis On a microarray chip: Oligonucleotides that match the common allele and all variant SNP alleles are attached to microarray glass Millions of ​short, single-stranded oligonucleotides of known sequence are printed on the chip with the SNP-complementary base in the center 3/12 11/26/25, 6:45 PM Fragments of single-stranded fluorescently labeled DNA from the individuals being tested are hybridized to the microarray chip Because the positions of all oligonucleotide probes are known Fluorescent pattern reveals which SNP each individual has The fluorescence shows whether an individual is homozygous or heterozygous for each SNP Example, two SNP alleles are being detected: C – G allele A – T allele Each SNP genotype produces a distinct fluorescence pattern The microarray pattern indicates whether an individual is: C–G allele: Homozygous C–G / A–T alleles: Heterozygous T–A allele: Homozygous Probing SNPs across the human genome reveals many variations​​within a population Each individual has unique SNP profile These variations do not necessarily affect gene function or cause disease SNPs are often used simply as markers to identify genomic feature 11/26/25, 6:45 PM VNTRs (Variable Number of Tandem Repeats) All mammals have essentially the same set of genes Many differences is from variations in short DNA sequences repeated in tandem These repeats are called variable number of tandem repeats (VNTRs) Tandem repeats = patterns of 1 or more nucleotides repeated directly adjacent to each other Example: CACACACACACACACA AGATAGATAGATAGAT VNTRs vary greatly in number​among individuals Lengths can differ across individuals and populations Can be identified using PCR and gel electrophoresis Sequence-specific primers target the flanking regions ​() of the variable repeats Amplified fragments are then separated and detected via gel electrophoresis VNTR VNTR VNTRs and DNA fingerprinting Detection of VNTRs with variable lengths used to identify individuals based on their DNA profiles This process is DNA fingerprinting VNTRs are great for distinguishing between different people 11/26/25, 6:45 PM VNTRs are useful because locations (loci) are similar among closely related individuals (family) But variable enough that unrelated individuals are extremely unlikely to share the same VNTR pattern Detection of VNTRs + other polymorphisms = Personal genetic profile Used to determine: Genetic family relationships Forensic identification in crime scene investigations Compared across individuals for identification Each individual has a unique combination of markers Unit 3: Variation and Disease Variations, phenotypes & sickle cell anemia Most variations in the human genome have no known effect Because they occur mostly in noncoding regions Detectable by molecular techniques(PCR, sequencing) Called silent variations Variations in protein-coding or regulatory regions can be harmful Harmful variations result in an altered gene product () Can lead to detrimental effects in the organism Sickle cell anemia is an example of an inherited genetic disease Characteristic variations (alleles) are passed from parent to child Genotype = the pair of alleles a person carries Example: HbA/HbA, HbA/HbS, HbS/HbS 11/26/25, 6:45 PM Phenotype = the cell’s or body’s interpretation ()​ of the genotype In sickle cell disease: Red blood cells contain a variant hemoglobin protein Cellular Phenotype Cells assume a sickled shape instead of a normal round biconcave shape Physiological phenotype: Reduced oxygen transport Blocked capillaries Anemia Acute pain Key question: What variation in the human genome causes sickle cell anemia? A single nucleotide substitution in the β-globin gene (GAG → GTG), causing glutamate → valine Inheritance of the β-globin gene Gene for the Beta-globin protein lies on an autosome (chromosome 11) Autosome = Means every person carries TWO alleles for the gene One inherited from the mother One inherited from the father In most people, both alleles are HbA alleles HbA alleles code for the functional Beta-globin protein homozygous for the HbA allele Since two alleles are same With two HbA alleles, individuals have a normal cellular phenotype (겉모양) Red blood cells are smooth Biconcave shape Able to glide through blood vessels Next idea: Consider the inheritance of alternate alleles for the beta-globin gene that can lead to sickle cell anemia 11/26/25, 6:45 PM The HbS genotype and sickle cell disease HbS (sickle cell) genotype is caused by a mutation Single nucleotide polymorphism (SNP) in the protein-coding sequence of the βhemoglobin gene With two HbS alleles is homozygous (allels same = homozygous) These individuals cannot produce functional β-globin proteins The SNP causes: Glutamate → valine substitution GAG → GTG Hydrophillic → Hydrophobic Changes the three-dimensional (tertiary) structure of hemoglobin Valine wants to go inside the protein Harmful variation because: Hemoglobin has decreased ability to bind and transport oxygen The amino acid substitution causes abnormal hemoglobin aggregation (응집) Aggregated β-hemoglobin forms ​long rod-like structures in red blood cells​ These rods force cells to assume a sickle shape The sickle-shaped cellular phenotype leads to: Blocked capillaries Anemia Acute pain Damage to vital organs and tissues Heterozygotes (HbA/HbS) and sickle-cell trait 11/26/25, 6:45 PM Individuals who inherit HbA from both parents are homozygous for HbA Individuals who inherit HbS from both parents are homozygous for HbS What happens when a person inherits HbA from one parent and HbS from the other? Is heterozygous (HbA/HbS) Results in the sickle-cell trait In heterozygotes: Some hemoglobin will be sickle-cell β-hemoglobin under certain conditions Rest will be ​normal β-hemoglobin Heterozygotes usually show no symptoms​of sickle-cell anemia Since HbA/HbS individuals produce enough normal hemoglobin to overcome the effect of the abnormal hemoglobin When will be sickle-cell? Genotype Alleles HbA / HbA HbS / HbS HbA / HbS Hemoglobin Cellular Phenotype Type Symptoms Notes X non-carrier Sickle Cell Disease Sickle Cell sickle β-Hb Trait (Carrier) Unit 4: Variation in population DNA polymorphisms, population variation & malaria advantage Many DNA polymorphisms → no humans have exactly the same genome​ DNA fingerprinting enables large-scale population studies Used to analyze genetic variability across populations and ethnic groups 11/26/25, 6:45 PM Regarding sickle cell disease, global epidemiology shows: HbS mutant allele may give heterozygous individuals a selective advantage Heterozygotes show resistance to malaria In regions with endemic malaria Plasmodium( Even though the sickle cell mutation is harmful at the cellular level, it can be advantageous in malaria-prone regions Provides evidence of balancing selection Sickle cell mutation is found in many populations with different alleles (haplotypes) Haplotypes: These haplotypes appear to have emerged independently across populations Among nations with high sickle cell prevalence, up to 5 distinct β-globin haplotypes exist Each haplotype correlates with regional distribution of specific HbS SNPs Haplotypes can be: Widely distributed across several nations Multiple haplotypes within a single nation Each color in the figure corresponds to the relative frequency of each haplotype in that region In these regions, heterozygotes (HbA/HbS) show resistance to malaria infection Copy Number Variations (CNVs) SNPs and VNTRs are examples of polymorphisms that create genetic variation SNP (Single Nucleotide Polymorphism) 10/12 11/26/25, 6:45 PM VNTR / Tandem Repeats Copy number variations (CNVs) contribute to genetic differences between individuals CNVs can occur in: Noncoding DNA regions No affect As many tandem copies of a coding region along a chromosome A region normally present in one copy per chromosome may become: Duplicated or Deleted CNVs can be detected using DNA microarray analysis Detection is based on relative fluorescence intensities More copies of a chromosome sequence → ​higher fluorescence signal on the microarray chip Gene duplications & AMY1 copy number variation When gene duplications occur, they are usually found adjacent to each other on the chromosome Human ​AMY1 gene shows detectable copy number differences on chromosome 1 AMY1 gene codes for amylase, a starch-digesting enzyme Differences appear across groups with different ancestral diets: Societies with historically low-starch diets → ​fewer AMY1 copies Societies with long histories of high-starch diets → more AMY1 copies Hypothesis: AMY1 copy number variation reflects selective pressures Extra gene copies in high-starch diet societies likely confer a digestive advantage Overall: DNA polymorphisms can cause both harmful and beneficial effects They contribute significantly to genetic variation within and across populations Variation Type SNP (Single Nucleotide Polymorphism) Definition Size / Length 1 bp VNTR (Variable Number of Tandem Repeats) CNV Cause Substitution Detection Method Biological Impact Microarray, Sequencing Tandem repeat PCR + Gel count variation electrophoresis Deletion / Duplication Microarray intensity (fluorescence) Population Type AMY1 Copy Number Low-starch diet High-starch diet Genotype fingerprinting), Evolutionary Interpretation Microarray Fluorescence Pattern Interpretation AA A spot only Homozygous (A) GG G spot only Homozygous (G) AG A + G both spot Heterozygous 12/12