Designer Genes SCIOLY

DNA

molecule for genetic instructions.
uses deoxyribose sugar
A:T
C:G

RNA

molecule for genetic instructions
acts as a messenger
uses ribose sugar
A:U
C:G

Mitosis

Growth, Repair, Asexual Reproduction.
Produces two identical diploid cells, used for body cells (somatic cells)

Prophase: Chromosomes become visible, nuclear envelope breaks down, the mitotic spindle (microtubules) forms

Metaphase: Chromosomes line up at the cell's equator (metaphase plate). 

Anaphase: Sister chromatids separate and are pulled to opposite poles by the spindle fibers. 

Telophase: New nuclear membranes form around the separated chromosomes, which begin to unwind. 

Cytokinesis: The cytoplasm divides, completing the formation of two separate cells (often overlaps with telophase)

Meiosis

Se*ual Reproduction.
Produces gametes (sex cells)
Interphase: DNA replication occurs, duplicating chromosomes. 
Meiosis I (Reduction Division): Homologous chromosomes separate. 

Prophase I: Chromosomes condense, pair up, and exchange genetic material (crossing over). 

Metaphase I: Homologous pairs line up at the cell's center. 

Anaphase I: Homologous chromosomes separate and move to opposite poles. 

Telophase I & Cytokinesis: Two haploid cells form, each with duplicated chromosomes. 

Meiosis II (Equatorial Division): Sister chromatids separate. 

Prophase II, Metaphase II, Anaphase II, Telophase II & Cytokinesis: Similar to mitosis, sister chromatids (now individual chromosomes) separate, resulting in four unique haploid cells. 

Direct reversal

DNA REPAIR.
consecutive pyrimidine bases become fused together when they are exposed to UV light, forming pyrimidine dimers.
Photoreactivation reverses this process, using an enzyme, “photolyase",” that reacts directly to exposure to blue/UV light. Photolyase no longer functions in humans, but can be found in bacteria, fungi and some animals.
Humans use a process known as nucleotide excision repair to repair damage done by UV light.

Excision repair

DNA REPAIR.
When one strand of a double helix is damaged, the other strand is used to identify the missing/incorrect bases. Excision repair mechanisms remove damaged nucleotide and replace it with the correct undamaged nucleotide.

Base excision repair (BER) repairs damage to a single base using glycosylases. These enzymes remove the specific affected base, and DNA polymerase correctly synthesizes the new strand.

Nucleotide excision repair (NER) is less specific, and is typically used in cases where a large portion of the helix is distorted. Damaged regions are removed in a three step process with the recognition of the damage, excision of the damaged area, and resynthesis of the removed region. NER occurs in almost every organism.

Postreplication repair

Postreplication repair (also known as translesion synthesis) occurs when the replication process is allowed to replicate past DNA lesions. A gap is left at the damaged site when the Okazaki fragments are synthesized, filled in later by either recombination repair or error-prone repair. Recombination repair uses the sequence from a sister chromosome to repair the damaged DNA, and error-prone repair uses the damaged strand as a sequence template. Error-prone repair is typically inaccurate, and commonly results in mutations.

Phylogenetics

the study of evolutionary relationships

phylogenetic tree displays these relationships based upon their similarities and differences. Rooted trees have a common ancestor, and in some cases the length of a line can indicate time estimates. Unrooted trees only show the relationship between a couple of organisms and do not require an ancestral root. Phylogenetic trees are based on speculation and do not show exact evolutionary history, but they can still display how animals could have possibly evolved.

Gene expression

fundamental process where the instructions in DNA are used to create functional products like proteins or RNA, essentially turning a gene "on" to build the cell's machinery and perform tasks, a tightly regulated system that allows cells to specialize and respond to their environment.

1. Transcription: A specific gene sequence on the DNA is copied into a messenger RNA (mRNA) molecule.

2. RNA processing & Transport: The mRNA is modified and exported from the nucleus to the cytoplasm.

3. Translation: The mRNA sequence is read in codons (three-nucleotide units) to assemble a chain of amino acids, forming a protein.

4. Protein Function: The amino acid chain folds into a functional protein that carries out specific jobs, from fighting disease to absorbing nutrients. 
   Why it's important

   • Cell Specialization: All cells have the same DNA, but gene expression dictates which genes are active, creating different cell types (like nerve cells or liver cells) with unique functions.

   • Regulation: It acts like a switch and dimmer, allowing cells to control protein production in response to needs, developmental stages, or environmental changes, as seen with melanin for hair color or enzymes for detoxification.

   • Phenotype: The pattern of gene expression results in observable traits (phenotypes) and biological functions. 

Down Syndrome

Trisomy 21
Extra copy of chromosome 21
intellectual disabilities, developmental delays, and distinctive facial features like upward slanting eyes, a flattened nose bridge, and small ears, along with increased risks for heart defects, hearing/vision problems, and other health issues.

Translocation Down syndrome

an extra piece of chromosome 21 attaches to another chromosome, rather than there being a full extra copy of chromosome 21
causes the developmental and physical characteristics of Down syndrome, such as intellectual disability, distinct facial features (like flattened face, almond-shaped eyes), and hypotonia (poor muscle tone)

Mosaic Down Syndrome

only some cells have an extra copy of chromosome 21, leading to a mix of normal and trisomic cells

milder or fewer Down syndrome features, but symptoms vary greatly depending on the percentage and location of affected cells, including developmental delays, speech issues, and learning challenges, though many individuals thrive with therapy and support. 

Monosomy 21

most or all of chromosome 21 is missing
severe intellectual disability, developmental delays, birth defects, and distinctive facial features

Turner’s syndrome

genetic condition in females where one X chromosome is missing or altered
short stature, underdeveloped ovaries (leading to infertility and lack of puberty), heart defects, kidney problems, and a webbed neck

trisomy X

genetic condition where females have an extra X chromosome
often undiagnosed due to mild or absent symptoms
can sometimes cause developmental delays (speech, motor), learning disabilities, taller stature, and potential mood or anxiety issues

Klinefelter's syndrome

genetic condition in males with an extra X chromosome (47, XXY)
varied symptoms like infertility, delayed development, weaker muscles, learning difficulties, and reduced testosterone, leading to small testes, breast growth (gynecomastia), and less body hair
often goes undiagnosed

Jacobs syndrome

genetic condition in males with an extra Y chromosome, resulting in 47 chromosomes instead of 46
increased height, learning challenges, and potential developmental delays, though many individuals have few symptoms and normal lives

Tetrasomy X

rare chromosomal disorder in females with four X chromosomes instead of the usual two
mild to moderate developmental delays, learning difficulties, speech problems, and distinctive facial features like upslanting eyes

XXXY syndrome

rare chromosomal disorder in males, caused by an extra X chromosome
developmental delays, intellectual disability, distinctive physical features like hypogonadism and short stature, and infertility
generally more severe than Klinefelter's syndrome

Frameshift mutation

genetic error from inserting or deleting DNA bases (not in multiples of three) that shifts the gene's reading frame, scrambling the amino acid sequence and usually creating a nonfunctional, truncated protein, leading to severe consequences like genetic diseases. It disrupts the triplet codons (groups of three bases) that specify amino acids, altering the entire protein structure from the mutation site onward

Deletion mutation

genetic mutation where one or more nucleotides (DNA building blocks) are removed from a DNA sequence, ranging from a single base to entire chromosomes

Nonsense mutation

DNA change creating a premature stop codon, halting protein production early, resulting in a shortened, often nonfunctional protein
Common cause of genetic diseases like cystic fibrosis or Duchenne muscular dystrophy, treatable in some cases by promoting "readthrough" to bypass the stop signal. 

Missense mutation

change in a single DNA building block (nucleotide) that results in a different amino acid being coded for in a protein
can be harmless (benign), beneficial, or cause disease like sickle-cell anemia by changing protein function, as seen with the hemoglobin gene, leading to varied outcomes from no effect to severe illness. 

Huntington’s Chorea

caused by a specific genetic mutation on chromosome 4, involving an expansion of the CAG (cytosine-adenine-guanine) DNA segment in the HTT gene

fatal, inherited brain disorder causing progressive breakdown of nerve cells, leading to motor issues like uncontrolled body movements, as well as severe cognitive decline (memory, judgment) and psychiatric problems (depression, irritability)

Hardy-Weinberg Equilibrium

common population model used in genetics
states that a population will maintain the exact allele and genotype frequencies over each generation unless five specific influences are introduced into the population.
to be in Hardy-Weinberg equilibrium, it must meet all of the 5 conditions listed below:

1. No mutations: Mutations introduce new alleles into the population.

2. No gene flow: Like mutations, immigration or emigration can introduce new alleles (or bolster/diminish existing alleles)

3. Very large population: Genetic drift is likely to occur in a smaller population. Hardy-Weinberg equilibrium can only occur in a population approaching infinity.

4. No natural selection: If some traits are discriminated for/against by environmental conditions, the genotype frequencies will not be in equilibrium over the generations.

5. Random mating: Like natural selection, sexual selection involved in non-random mating could discriminate for/against traits.

Hardy-Weinberg Equilibrium equations

two equations used in the Hardy-Weinberg Law:
p² + 2pq + q² = 1
p + q = 1
p= the frequency of the (homozygous) dominant allele in the population, as a percentage
q= the frequency of the (homozygous) recessive allele in the population, as a percentage
p² = the percentage of the homozygous dominant individuals
2pq = the percentage of the heterozygous individuals
q² is the percentage of the homozygous recessive individuals.

Epistasis

genetic phenomenon where one gene modifies or masks the expression of another gene

Exon

segment of a gene that contains the code for building a protein and remains in the mature messenger RNA (mRNA) after non-coding sections, called introns, are removed during RNA splicing

Cross-over

during meiosis where homologous chromosomes exchange segments of their DNA, creating new combinations of genes (recombination) and significantly increasing genetic diversity in offspring

Operon

functional unit of DNA in prokaryotes (like bacteria) where a group of related genes, along with their shared promoter and operator, are transcribed together as a single mRNA molecule

Promotor

region of DNA where transcription of a gene is initiated

Sigma factor

crucial bacterial protein subunit that directs the RNA Polymerase (RNAP) to specific gene promoters

Exome

collection of all protein-coding regions (exons) within an organism's DNA

Haplotype

set of DNA variations (like SNPs) or alleles that are inherited together from one parent on a single chromosome, forming a distinct segment of genetic material, used to study disease links, ancestry, and evolution because these segments tend to stay linked unless broken by recombination

Phenocopy

organism develops a trait (phenotype) that looks like a genetically determined condition, but it's actually caused by environmental factors

Pleiotropy

genetic phenomenon where one gene influences multiple, seemingly unrelated phenotypic traits