Week 3 General principles Flashcards
What are the key steps of Central Dogma (3 steps)
- Replication (DNA > DNA)
- DNA serves as a template to make an identical copy of itself
- This process ensure that genetic information is passed from one cell to another during cell division
Enzyme involved: DNA polymerase - Transcription (DNA > RNA)
-A specific segment of DNA is copied into messenger RNA (mRNA).
- This occurs in the nucleus (for eukaryotes) or cytoplasm (for prokaryotes)
Enzymes involved: RNA polymerase - Translation (RNA > Protein)
- The mRNA travels to the ribosomes, where it directs protein synthesis
-Transfer RNA (tRNA) brings amino acids to the ribosomes, assembling them into a protein based on the mRNA sequence
Key molecules involved: Ribosomes, tRNA and amino acids
Explain the central Dogma of Genetics
Central dogma of genetics describes the flow of genetic information within a biological system. It was first proposed by Francis Crick in 1958.
Central dogma outlines how genetic information stored in DNA is used to synthesize proeines which carry out cellular functions
What are the exceptions to the central dogma (3)
Whilst central dogma described the general flow of genetic information, there are some limitations
- Reverse transcriptions: RNA>DNA certain virus like retroviruses (HIB) uses reverses transcriptase to convert RNA to DNA
- RNA replications: some RNA viruses replicate their RNA without a DNA intermediate
- Epigenetics: Modifications like DNA methylation and histone modification can effect gene expression without altering the DNA sequences
Explain the Genetic code
The genetic code is a set of rules by which genetic information in messenger RNA (mRNA) is translated into proteins.
It defines how sequences of nucleotide bases (adenine (A), bracil (U) cystonie (C) and guanine (G) are ready to specify amino acids during protein synthesis
What are the key features of the Genetic Codes (5)
- Triplet code: Each amino acids is encoded by a sequence of three nucleptode bases called a codon
- Degenerate (redundant): Multiple codon can code for the same amino acids e.g UCU, UCC, UCA and UCG all codes for serine
- None-overlapping: Codons are ready one after another without overlapping
- Universal: The genetic code is nearly universal across all living organisms with a few exceptions (e.g Mitochondria and some microbes have a slight variations)
- Unambiguous: Each codes for only one specific amino acids or a stop signal
What are the types of Codons in proteins translation (3)
- Start codon (initial)
AUG (methionine), it signals the start of protein synthesis, in prokaryotes, AUG codes for formyl-methionine fMet) at the beginning of translation - Sense Codons
(Amino acid codons)
61/64 codons encode 20 amino acids, some amino acids have multiple codons due to teh degeneracy of the genetic code - Stop codons (termination codons)
UAA (ochre, UAG (amber) and UGA (opal) do NOT code any amino acids, signal the end of translations and the release of the newly formed protein from the ribosome
What is the process of protein translation (3)
Initiation:
Ribosomes assembles around the mRNA and finds the AUG start codon, the first tRNA carrying methionine (MET) binds to the start codon
Elongation:
Ribosomes moves along the mRNA, reading each codon, tRNA molecules bring corresponding amino acids, which are linked together to form a polypeptide chain
Termination:
When a stop codon (UAA, UAG, UGA) is reached, release factors bind to the ribosome, the polypeptide is release and the ribosomes disassembles
Explain point Mutations (3)
A single nucleotide is changed, inserted or deleted
Silent mutation: no change in the amino acid sequence due to the redundancy of the genetic code, so protein functions remains unaffected.
Missense mutation: a single nucleotide change results in a different amino acid, which can alter protein function potentially causing disease like sickle cell anemia
Nonsense mutation: A nucleotide change creates a premature stop codon, leading to a truncated, usually nonfunctional protein, as seen in some genetic disorders like DUchenne muscular dystrophy
Explain Frameshift mutations
Frameshift mutation:
Insertion of deletion of nucleotides (not in multiple of 3) shifting the reading frame. This changes all downstream codons, often resulting in a completely nonfunctional protein. Cystic fibrosis can be causes by such mutations.
Explain Splice site mutations
Splice site mutations affect RNA splicing by altering intron-exon boundaries leading to incorrect mRNA processing and defective proteins
What are Expanding repeat mutations
Short nucleotide sequences repeat abnormally, potentially affecting protein functions such as Huntingtons disease caused by excessive CAG repeats
What are the types of mutations on protein synthesis?
- Point mutation
- Frameshift mutations
- Splice site mutations
- Expanding repeat mutations
Overall mutations can result in proteins with altered structure and functions. Leading to disease or developmental disorders. However, some mutations maybe neutral or even beneficial, contributing to genetic variations and evolution
Describe trinucleotide repeat disorders (3)
- Repeat expansion: the number of repeats increase from generation to generation a phenomenon called anticipation leading to earlier onset and increase severity in successive generations
- Threshold effect: A small number of repeats is normal but when the repeat number exceeds a critical threshold it causes disease
- Types of repeat sequences: Different disorders involve different trinucleotide sequences such as CAG, CGG, GAA, CTG
What are the types of Trinucleotide repeat disorders (2 types)
- Polyglutamine (PolyQ) disorders: caused by CAG (cystosine-adenine-guanine) repeats which code for glutamine (Q) leading to protein aggregation and neurodegeneration.
Examples: Huntingtons disease (HD) - CAG expansion in the HTT gene causes progressive brain cell death, motor dysfunctions, cognitive decline and MH
- Non-polyglutamine disorders: repeats occur in the non- coding regions, affecting gene regulation or RNA processing.
Examples: Fragile X syndrome (FXS) CGG expansion in the FMR1 gene leads to intellectual disability and autism related traits
Myotonic dystrophy (DM1 & DM2): CTG or CCTG repeats in DMPK or CNBP genes causing muscle weakness, CVD and cognitive impairment
Friedreich’s Ataxia (FRDA) GAA repeats in the FXN gene leading to progressive nerve damage and movement disorders
What are the effects of Trinucleotide repeat expansions
Loss of protien functions: excessive repeats can silence genes, preventing proper protein production e.g Fragile X syndrome
Toxic gain functions: Abnormal proteins accumulate and interfere with cellular functions e.g Huntingtons disease
RNA toxicity: Expanded repeats in mRNA can trap essential proteins disrupting normal cellular processes (Myotonic Dystrophy)
Summary: Trinucleotides repeat disorders are progressive and often inherited in a dominant manner due to anticipation, symptoms worsen with each generation.
Define Anticipation and the mechanism
Anticipation is a genetic phenomenon in which the symptoms of a hereditary disorder appear earlier and with increasing severity in successive generations. this is due to progressive expansion of trinucleotide repeats in the affected genes. The longer the repeat expansion the more severe the disease and the earlier the onset.
A specific trinucleotide repeats sequence (CAG, CTG, CGG, GAA) they become unstable and expands as its passed from parent to child. Larger repeat expansions lead to more severe protein dysfunction RNA toxicity or gene silencing.
Expansion often occurs more dramatically when inherited from a specific parent such as fragile X syndrome from the mother, Huntingtons disease from father
What are some diseases showing Anticipation (4 types)
- Huntington’s disease (HD): caused by CAG repeat expansion in the HTT gene, more repeats lead to earlier onset and severe neurodegeneration. Symptoms: involuntary movements, cognitive decline, psychiatric disturbances.
- Myotonic Dystrophy (DM1 & DM2) causes by CTG (DM1) or CCTG (DM2) repeat expansion in teh DMPK or CNBP genes. Symptoms: worsen in younger generations with congenital forms in severe cases, muscle weakness, heart issues, cataracts and cognitive impairment.
- Fragile X syndrome (FXS) caused by CGG repeat expansion in the FMR1 gene, leading to gene silencing, more severe intellectual disability like autism like traits in later generations
- Friedrecih’s Ataxia (FRDA) caused by GAA repeat expansion in the FXN gene, progressive worsening of movement disorders, speech impairment and CVD
Define the terms: Gene, Locus, Allele, Genotype, Phenotype, Homozygous, Heterozygous, Dominant and Recessive
Gene: Segment of DNA that encodes a specific protein or functional RNA
Locus: specific locations of a gene on a chromosome
Allele: a variant form of a gene found at a particular locus
Genotypes: Genetic makeup of an organism representing the combinations of alleles
Phenotypes: observable traits of an organisms influence by genotypes and environment
Homozygous: Having two identical alleles for a gene e.g (AA or aa)
Heterozygous: having two different alleles for a gene Aa
Recessive: allele that expresses its trait only when two copies are present e.g aa
Compare Autosomal dominant vs Autosomal recessive with examples of conditions
Autosomal dominant; affected individuals have at least one copy of mutant allele Aa or AA, 50% recurrence risk if one parent is affected (Aa x aa), 75% recurrence risk if both patents are affected (Aa x Aa), equal occurrence in males and females no skipping generation (vertical transmissions)
Examples: Huntington’s disease, Marfan’s syndrome, Achondroplasia
Autosomal recessive inheritance: Affected individuals inherit TWO copies of the mutant allele (aa) 25% recurrence risk if both parents are carriers (Aa x Aa), 50% being a carrier and 25% chance of being unaffected, equal occurnece in males and females, can skip a generations (horoziontal transmission)
Examples: Cystic fibrosis, sickle cell anemia, phenylketonuria (PKU)
Compare X- Linked dominant vs X- Linked recessive inheritance
X-Linked dominant
Females (xx): affected with one mutant allele (XaX or XaXa)
Males: (XY) Affected with one mutant X chromosome (XaY) often more severe
- Affected fathers pass the trait to all daughters but NO sons
- Affected mothers have a 50% recurrence risk for both sons and daughters
Examples: Rett syndrome, Fragile X syndrome, Hypophosphatemic Rickets
X- Linked recessive inheritance:
-Males: (XY) Affected with one mutant X chromosome (XrY) since the lack a second X
-Females (XX): Affects only if they inherit 2 mutant alleles (XrXr) otherwise they are carriers (XrX).
-carrier mothers have a 50% recurrence risk of passing the mutation to sons (affected) and daughter (carriers)
- Affected fathers pass the gene to ALL DAUGHTERS (carriers) but NO SONS
Examples: Hemophilia A, Duchenne Muscular Dystrophy, Red- Green colorblindness.
Describe Mitochondrial inheritance
Maternal inheritance: only inherited from the mother, as mitochondria in sperm at typically discarded at fertilization
- Affects both sexes male and females can be effects but only females transmit the disorder
-variable expressivity: due to heteroplasmy (a mix of normal and mutated mitochondria in cells) symptoms severity varies among individuals
_ Variable expressivity: Due to heteroplasmy (mix of normal and mutated mitochondria in cells) symptoms varies among individuals
- High energy demand organs affects: Disorders primarily impact organs requiring high energy such as muscles, nerves and the heart
What are some examples of mitochondrial disorders (3)
-Leber’s hereditary optic neuropathy (LHON) causes vision loss
- Mitochondrial Encephalomyopathy Lactic acidosis and stroke like episodes (MELAS) affects brain and muscle function
-Myoclonic epilepsy with ragged red fibers (MERRF)- Causes muscle weakness and seizures
Define incomplete penetrance and pleiotropy
Incomplete penetrance: A genetic condition where individuals with a disease causing mutations do not always show symptoms. E.g BRAC1 mutations increase cancer risk but not all carries develop cancer
Pleiotropy: A single gene mutation affecting multiple, seemingly unrelated traits or organs.
Examples: Marfan’s syndrome caused by FBN1 gene mutations, affects the heart, eyes and skeleton
Describe genetic imprinting and uniparental disomy with the examples of Prada willi and Angelman syndromes
GENETIC IMPRINTING
-Genetic imprinting: Is only when one allele of a gene is expressed, depending on whether it is inherited from the mother or father. The other allele is silenced through epigenetic modifications (DNA methylation)
-Imprinted genes: typically involved in growth, development and brain function
UNIPARENTAL DISOMY (UPD)
-Genetic disomy: Occurs when both copies of a chromosome or part of a chromosome are inherited from one parents leading to an imbalance in gene expression.
Prada-willi syndrome: Caused by deletions of segment on chromosome 15 inherited from the father or maternal uniparental disomy (both copies of chromosome 15 from the mother)
Symptomes: Hypotonia, obesity, intellectual disability and insatiable appetite.
Angelman syndrome: Caused by deletion of the same region chromosome 15 but inherited from the mother or paternal uniparental disomy (both copies from father)
Symptoms: severe intellectual disability, seizures, and happy demeanor
Describe factors responsible for genetic variations in populations
- Mutation: Changes in the DNA sequence that introduce new genetic variants. These are
the primary source of new alleles. - Gene Flow (Migration): The movement of individuals or their genetic material between
populations, introducing new alleles and increasing genetic diversity. - Genetic Drift: Random fluctuations in allele frequencies due to chance events, especially
in small populations. This can lead to the loss or fixation of alleles over time. - Sexual Reproduction: The recombination of genes during meiosis (crossing over) and
the random assortment of chromosomes, leading to unique genetic combinations in
offspring. - Natural Selection: The differential survival and reproduction of individuals based on
their genetic traits. This can increase the frequency of advantageous alleles and decrease
the frequency of harmful alleles. - Non-Random Mating: When individuals preferentially mate with others based on
specific traits, such as inbreeding or assortative mating, it can affect allele frequencies.
Discuss Autosomal aneuploidy (trisomy 21, 18 and 13) and sex chromosomes (XXY,X0)
Aneuploidy: refers to abnormal number of chromosomes, either an extra chromosome (trisomy) or missing one (monosomy). These abnormalities can affect autosomes (non-sex chromosomes) or sex chromosomes.
Trisomy 21 (down syndrome)
Causes: extra copy of chromosome 21
Symptoms: intellectual disability, characteristic facial features, heart defects and increase risk of leukemia and Alzheimer’s disease
Karyotype: 47, XX +21 or 47,XY +21
Trisomy 18 (Edwards syndrome)
Extra copy of chromosome 18
Symptoms: Severe developmental delay, heart defects, clenched hands, low birth weight, rocker feets, short life expectancy
Trisomy 13 (Patau syndrome)
Cause extra copy of chromosome 13
Symptoms: Severe intellectual disability, cled lip/palate, heart defects and typically death within first year.
Karyotype 47 xx +13 or 47XY +13
Sex chromosome aneuploidy
Klinefelter syndrome (XXY):
Causes: males with an extra X chromosomes,
Symptoms: hypohonadism, infertility, taller stature and mild developmental delay
Karyotype: 47 XXY
Turner syndrome (X0)
Causes: Females with only 1 X chromosome (monosomy X)
Symptoms: short stature, infertility, heart defects, lack of secondary sexual characteristics and puberty.
Karyotypes 45,X
Describe structural chromosomal abnormalities
Translocation
Definition: A segment of one chromosome is transferred to another chromosome.
o Types:
Reciprocal Translocation: Two chromosomes exchange segments.
Robertsonian Translocation: Fusion of two acrocentric chromosomes (common
in Down syndrome).
Example: Chronic Myelogenous Leukemia (CML), caused by a Philadelphia
chromosome (t(9;22)).
- Deletion
Definition: A segment of a chromosome is lost.
Result: Loss of genetic material, leading to disorders.
Example: Cri-du-chat syndrome, caused by a deletion on chromosome 5 (46,XX,5p-).
Inversion
Definition: A chromosome segment is reversed end to end.
Result: No loss of genetic material, but it can affect gene function or result in problems
during meiosis.
Example: Pericentric inversion of chromosome 9 can be benign or lead to fertility
issues.
- Ring Chromosomes
Definition: A chromosome forms a ring structure due to the deletion of the ends of the
chromosome, followed by the fusion of the broken ends.
Result: Loss of genetic material at the ends and potential gene imbalances.
Example: Ring chromosome 14 causes severe developmental delay and other health
issues.
Discuss multifactorial inheritance factors (3) and examples (4)
Multifactorial inheritance refers to traits or diseases caused by the combined influence of
multiple genes and environmental factors. Unlike Mendelian inheritance, where one or two
genes dictate the outcome, multifactorial traits are influenced by a range of genetic and
environmental interactions.
Influential Factors
1. Multiple Genes: Several genes contribute to the trait or disease, each having a small effect.
2. Environmental Factors: Lifestyle, diet, exposure to toxins, and other environmental factors can
modify the expression of the genetic predisposition.
3. Gene-Environment Interaction: The interaction between genetic predisposition and
environmental influences can increase or decrease the risk of developing a disease.
Examples of Multifactorial Inheritance Diseases
1. Heart Disease: Caused by a combination of genetic susceptibility (e.g., cholesterol metabolism
genes) and environmental factors (e.g., diet, exercise).
2. Type 2 Diabetes: Genetic factors (insulin resistance genes) combined with environmental
factors (obesity, sedentary lifestyle).
3. Cleft Lip and Palate: A complex condition with genetic and environmental risk factors (e.g.,
maternal smoking).
4. Hypertension: Both genetic predisposition and environmental factors like salt intake and stress
contribute to the condition.
Key Points
Polygenic: Multifactorial traits often involve multiple genes.
Risk Prediction: The risk of inheriting multifactorial diseases is higher when close relatives are
affected, but inheritance patterns are less predictable than Mendelian traits.
Describe Genetic analysis and different methods used in analysis
- Polymerase Chain Reaction (PCR)
Purpose: Amplifies specific DNA sequences to detect mutations or genetic variants.
Use: Diagnosis of genetic disorders, detecting infectious agents, and genetic
fingerprinting. - Gel Electrophoresis
Purpose: Separates DNA, RNA, or proteins based on size and charge.
Use: Identifying genetic mutations, checking DNA purity, and allele analysis. - DNA Sequencing
Purpose: Determines the exact sequence of nucleotides in a DNA sample.
Use: Identifying genetic mutations, studying genetic variation, and gene mapping.
Techniques: Sanger sequencing (traditional) and next-generation sequencing (NGS, high
throughput). - Chromosome Analysis (Karyotyping)
Purpose: Visualizes chromosomes to detect large-scale chromosomal abnormalities
(e.g., trisomies, deletions, translocations).
Use: Diagnosis of chromosomal disorders like Down syndrome and Turner syndrome. - Fluorescence In Situ Hybridization (FISH)
Purpose: Uses fluorescent probes to bind specific DNA sequences on chromosomes.
Use: Detecting chromosomal abnormalities and gene localization. - Microarray Analysis
Purpose: Detects the expression of thousands of genes simultaneously or identifies copy
number variations.
Use: Studying gene expression profiles and identifying genetic mutations linked to
diseases. - Genomic Profiling
Purpose: Analyzes an individual's entire genome using various techniques like NGS.
Use: Personalized medicine, disease risk assessment, and identifying gene-environment
interactions.
Conclusion
Genetic analysis involves various methods that help in identifying mutations, understanding
inheritance patterns, and diagnosing genetic conditions. These tools are essential in research,
clinical diagnostics, and personalised medicine.
Describe different blotting techniques and their implications in diagnosis
Blotting Techniques
Blotting techniques are used to transfer and detect specific molecules (DNA, RNA, or proteins)
from a sample to a membrane, followed by visualisation using specific probes or antibodies.
They are commonly used in research and diagnostics to identify genetic mutations, gene
expression patterns, or protein markers.
Types of Blotting Techniques
1. Southern Blotting (DNA)
Purpose: Detects specific DNA sequences.
Method: DNA is digested, separated by gel electrophoresis, transferred to a membrane,
and hybridized with a labeled probe.
Use: Diagnosing genetic diseases (e.g., detecting gene deletions, mutations) and
identifying specific genetic markers.
- Northern Blotting (RNA)
Purpose: Detects specific RNA sequences and measures gene expression.
Method: RNA is separated by gel electrophoresis, transferred to a membrane, and
hybridized with a labeled probe.
Use: Analyzing gene expression in diseases like cancer, studying gene regulation, and
detecting RNA mutations. - Western Blotting (Protein)
Purpose: Detects specific proteins.
Method: Proteins are separated by gel electrophoresis, transferred to a membrane, and
detected using antibodies specific to the target protein.
Use: Diagnosing diseases with protein markers (e.g., HIV detection, autoimmune
disorders, and cancer diagnosis). - Eastern Blotting (Post-translational Modifications)
Purpose: Detects post-translational modifications of proteins, such as glycosylation.
Method: Similar to Western blotting, but focuses on detecting modified proteins using
specific probes or antibodies.
Use: Studying protein modifications in diseases like cancer, diabetes, and
neurodegenerative conditions.
Implications in Diagnosis
-Genetic Disorders: Southern and Northern blotting help detect mutations or abnormal gene
expression patterns associated with genetic diseases (e.g., sickle cell anemia, cystic fibrosis).
-Cancer: Western blotting detects cancer-associated proteins (e.g., p53 mutation detection).
-Infectious Diseases: Western blotting is used for detecting HIV antibodies, confirming other viral
infections, or identifying bacterial proteins in diagnostic tests.
-Autoimmune Diseases: Western blotting helps detect autoantibodies, used in diagnosing
conditions like lupus or rheumatoid arthritis.
Conclusion
Blotting techniques are powerful tools in molecular diagnostics, enabling the detection of genetic
mutations, disease markers, and protein expression. They have wide applications in research and clinical diagnostics for a variety of genetic, infectious, and autoimmune diseases.
Genetic screening in the fetus and newborn
- Chromosomal Abnormalities:
-Down Syndrome (Trisomy 21): Screened through non-invasive prenatal testing (NIPT),
maternal serum screening, and ultrasound.
-Trisomy 18 (Edwards Syndrome)
- Trisomy 13 (Patau Syndrome): Also detected
through NIPT, combined first-trimester screening, and second-trimester screening (e.g.,
quadruple screen). - Neural Tube Defects:
o Spina Bifida and Anencephaly: Detected through maternal serum screening (elevated
alpha-fetoprotein levels) and ultrasound. - Cystic Fibrosis:
-Carrier screening for CFTR mutations is offered to high-risk populations (family history,
ethnicity).
Newborn Screening
1. Metabolic Disorders:
-Phenylketonuria (PKU): A condition where the body cannot metabolize phenylalanine,
leading to intellectual disability.
-Congenital Hypothyroidism: Causes developmental delays and growth problems if
untreated.
-Galactosemia: A disorder affecting the metabolism of galactose, leading to liver damage, cataracts, and intellectual disability.
-Maple Syrup Urine Disease: A disorder where the body cannot process certain amino
acids, leading to brain damage.
- Hemoglobinopathies:
-Sickle Cell Disease and Thalassemia: Identified through blood tests for abnormal
hemoglobin or carrier status. - Cystic Fibrosis:
-CFTR mutations are screened to detect cystic fibrosis, which affects the lungs and
digestive system. - Inborn Errors of Metabolism:
-Disorders like Medium-chain acyl-CoA dehydrogenase deficiency (MCAD) and Organic
acidemia that disrupt energy metabolism. - Congenital Adrenal Hyperplasia (CAH):
-A genetic disorder affecting hormone production, leading to salt imbalances and sexual
development issues.
Describe the polymerase chain reaction (PCR) and the 3 steps involved and its use in genetics (5)
Polymerase Chain Reaction (PCR) is a molecular technique used to amplify a specific segment
of DNA, creating millions of copies from a small initial sample. PCR is based on the repetitive
cycling of DNA denaturation, annealing, and extension, which allows the targeted DNA region
to be exponentially replicated.
Steps of PCR
- Denaturation: The DNA sample is heated to around 94–98°C, causing the double-stranded DNA
to separate into two single strands. - Annealing: The temperature is lowered to 50–65°C, allowing short DNA primers to bind to the
complementary sequences on the single-stranded DNA. - Extension: The temperature is raised to 75–80°C, where a DNA polymerase enzyme extends the
primers, synthesizing new DNA strands. - Amplification: These steps are repeated for 20-40 cycles, resulting in millions of copies of the
target DNA segment.
Uses in Genetic Analysis - Mutation Detection: PCR amplifies specific DNA regions for analysis, helping detect mutations in
genes (e.g., for cystic fibrosis or sickle cell anemia). - Genetic Profiling: PCR is used in DNA fingerprinting for forensic analysis, paternity testing, and
ancestry studies. - Gene Expression: PCR (often quantitative, qPCR) is used to measure mRNA levels, helping assess
gene expression in different conditions, such as in cancer research or infectious disease
detection. - Pathogen Detection: PCR is used to detect pathogens like viruses and bacteria by amplifying
their genetic material (e.g., HIV, COVID-19, TB). - Cloning and Gene Therapy: PCR amplifies genes of interest for cloning into vectors or for
therapeutic purposes, such as gene editing and gene therapy.
