ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
18 August 2022
Genetics: study of inherited traits and their variation; study of how
traits are transmitted; it is a life science along biology and others
Heredity: transmission of traits and biological info between
generations
Pedigree: used when tracing genetic info or traits from ancestors or
through generations; important when looking for disease
correlation especially genetic diseases
Genes: unit of heredity found in the long DNA sequence;
biochemical instructions that tell cells how to manufacture proteins;
sparsely located along the DNA (magkakalayo sila)
Genome: complete set of genetic instructions characteristic of an
organism (genes + other sequences)
*in research, Bioethics: confront concerns that arise from new
genetic technology (privacy, use of genetic info, and discrimination)
** can be used for bioterrorism
Nucleic Acids:
Deoxyribonucleic Acid (DNA): long molecule that transmits info in
its sequence of 4 types of building blocks, functioning like an
alphabet; blueprint of life; very long molecule (1 DNA =1 molecule)
Ex: if DNA is 100 cm long, the genes compose 2 to 5 cm only. only
1.5 to 2.5% are genes, the other 95 to 98.5% of the DNA is
composed of junk DNA, exons, repetitive and non-repetitive DNA
sequences, junk DNA useful during recombination and
transformation
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
DNA orientation: opposite strands, clockwise direction (twisted in
this direction), antiparallel; found inside the nucleus
DNA can roam around the cytoplasm when the nuclear membrane
is disintegrated; because of its size, DNA cannot pass through the
nuclear membrane pores, that’s why we create RNA, to carry the
DNA info through the nuclear pores
Ribonucleic Acid (RNA): carry DNA sequence info so it can be
utilized
4
a.
b.
c.
d.
bases of RNA
Adenine
Uracil
Cytosine
Guanine
3 main parts of both DNA and RNA
1. Pentose sugar
2. Phosphate
3. Nitrogenous Base: serves as the info, instructions on how to
create certain proteins, an alphabet; complementary to one
another, location where bonds are being created
Bases of DNA:
a. Adenine
b. Thymine
c. Cytosine
d. Guanine
Pairs: Apple Tree and Car Garage
Held together by H bonds
Bonds present in AT: 2
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Bonds present in AU: 2
human species that co-existed together: Homo Sapiens,
Neanderthals, )
Bonds present in TU: 2; if we are creating an RNA from the DNA
during transcription
**studies show that some Europeans’ genes show traces of
Neanderthals
Bonds present in CG: 3
Codon: Set of 3 nitrogenous bases (1 codon = 1 amino acid)
AUG: start codon: methionine: start amino acid
Sugar-phosphate backbone
DNA Replication: Creation of 2 new DNA from 1 parent DNA
Protein Synthesis: making of proteins
1. Transcription: copies the sequence of part of 1 strand of a
DNA molecule into a related molecule (mRNA); product is
mRNA; genes to RNA
2. Translation: alignment of amino acids link, forming a
protein; product is a polypeptide chain or protein; RNA to
protein or polypeptide
Amino acids are held together by peptide bonds creating the
chain of peptides called polypeptide or protein
Cell: basic building blocks of life
Mutation: Change in a gene that can cause a disease if it alters the
amino acid sequence of the specified protein; process of change
Evolution started as a mutation: acc. To The Evolution of Man by
Charles Darwin we came from cyanobacteria through
chemiluminescence: use chemicals for their biochemical processes
Cyanobacteria – plant life – water-dwelling animals – land-dwelling
animals – Australopithecus species – Homo sapiens sapiens (3
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Cystic Fibrosis: CFTR gene (Cystic Fibrosis Transmembrane
Conductance Regulator) mutation causes the protein’s inability to
open the cell’s surface = removing channels for certain salt
components leading to Cystic Fibrosis symptoms
Wild type CFTR
Variant type CFTR
*(Gly551Asp mutation)
DNA
CCA
CTA
RNA
GGU
GAU
Protein
Serine, Glycine,
Serine, Aspartic acid,
Glutamine
Glutamine
Channel
Open channel
Blocked channel
* On the 551st amino acid position, Glycine was replaced by Aspartic
acid
Wild type: common type of genes; present in a majority of the
population
Genome: complete set of the genetic instructions, characteristic of
an organism
Human Genome: 20, 325 protein-encoding genes (~1.5% of entire
genome)
-
-
Other parts of the genome are for assistance in protein
synthesis or turn protein-encoding genes on or off (switch
genes for gene regulation): Gene Regulation
Annotation: term used to understand what individual genes
do; to know the functions of certain genes
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Alleles: variation of genes (distinguishing sequences arise by
mutation) Ex: wild type CFTR gene and variant type (same gene but
w/ difference in some parts)
DNA to chromosome: they wrap around the protein called histones:
storage protein of nucleic acids
DNA + histone = nucleosome: will now wrap around together,
clump will clump together again, then clump again to form
chromosome
Chromosomes: 23 paired structures of the human genome;
condensed DNA; very densely packed
-
Somatic cell/body cells: 23 pairs of chromosomes (1-22
autosomes, Sex chromosome: 23rd (X: female or Y: male))
Female: XX
Male: XY
Karyotyping: charts that display the chromosome pairs from
largest to smallest
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Traits:
1. Mendelian Traits: caused primarily by a single gene
Ex: polydactyly: extra fingers/toes
2. Multifactorial Traits: determined by 1/more genes &
environmental factors
More factors contributing to traits or illness (may it be
inherited or environmental) = more difficult to predict risk
of occurrence
Ex: Osteoporosis: brittleness of the bones; factors like
genes, smoking, lack of weight-bearing exercise, calciumpoor diet (blood needs calcium, they extract calcium from
the bones leading to the weakening of the bone)
Hair color: caused by at least 3 genes plus environmental
effects such as bleaching effects of sun exposure
Human Body and the Genome
Consists of ~30 trillion cells
RBC’s or Erythrocytes: only cells without 2 copies of the genome
(RBC’s lack chromosome) because it has no nucleus: pyknotic cells
Each cell is differentiated in appearance and activities because they
use only some of their genes
-
Genes used by each cell depend upon environment
conditions inside and outside the body
Adipose cell is filled with fat, but not the contractile proteins
of muscle cells but both have 2 complete genomes
Tissues are aggregates of differentiated cells that assemble and
interact with each other and the nonliving materials that they
secrete
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Structural Levels of Organization
Atoms – molecules – cells – tissues -organs – organ systems –
organism
ELIC, MARIANA CLARIBEL R.
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DNA Profiling: compares DNA sequences among individuals to
establish or rule out identity

Stem cells can mature and differentiate, divide to yield another
stem cell and a cell that differentiates


Genetic Relationships
Genotype: underlying instructions (present alleles): our genes


Phenotype: visible traits, biochemical change, or effects on health
(expression of allele: different subsets of genes to manufacture
proteins drives specialization or differentiation)
Ex: skin color, use of sugar, proteins, how you consume fat, lipids,
diabetes, etc.
Genotype and phenotype relationship
1. Dominant allele: has an effect when present in just one
copy/chromosome
2. Recessive allele: must be present on both chromosomes of
a pair to be expressed
Populations to Evolution
Population definition


Biology: grp of individuals that can have healthy offspring
together
Genetics: large collection of alleles, distinguished by their
frequencies
Ex: Swedish people (biology): have a greater frequency of
alleles that specify light hair and skin than people from a
population in Nigeria (dark hair and skin)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)

Forensic Science: comparing DNA collected at crime scenes
to DNA in samples from suspects
Identity of victims of natural disasters
Assist adopted individual in locating blood relatives and
children of sperm donors in finding biological fathers and
half-siblings
Analyze food (foods have species-specific DNA sequences)
Rape cases: sperm cells remain viable in the vagina of the
victim for at least 3 days or few days
Scratch the skin of the suspect so it can be analyzed
forensically
Illuminating History: DNA Analysis
DNA analysis can connect past to present, determine family
relationships, establishing geographic origin of specific populations
Ex:
1. Thomas Jefferson and slave Sally Hemings: 9 children
together
- Male descendants of Sally Hemings share an unusual Y
chromosome sequence with the president’s male relatives
2. DNA analysis of mummy of King Tutankhamun (died 1323
BCE at age 19)
- Revealed DNA from the cause of Malaria (Plasmodium spp.)
- Tutankhamun died from complications of Malaria following
a leg fracture from weakened bones
o Support of the diagnosis: tomb included a cane and
drugs
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Precision Medicine
1. bacterium’s plasmid DNA + Human
cell’s DNA (human insulin-producing
gene)
2. DNA is cut with restriction enzymes;
bacterial DNA with human gene
inserted
3. Plasmid is reintroduced into
bacterium
4. Engineered bacteria multiply
People are having their genomes sequences to learn more about
health and disease: provide better healthcare and disease
monitoring
-
DNA contains info that can impact health: Environmental
exposures, exercise, diet, lifestyle, microbiome (EnExDiLiMi)
DNA info can select drugs that are most likely to work and
least likely to have side effects (Pharmacogenetics)
** Human microbiome: archaea, viruses, fungi, parasites,
bacteria
** responds to alternative medication, higher dose, lower
dose, normal dose
producing insulin
5. Insulin is separated and purified to produce human
insulin
6. Insulin injected into patient
We experience mutation every single day.
Genetic Modification: altering a gene or genome in a way that does
not occur in nature; manmade
Genome Editing: replace, remove, or add specific genes into
cells of any organism
Genetically Modified Organisms (GMO)



In healthcare: Bacteria bearing human genes for drugs
(insulin, clotting factors)
In agriculture: foods modified genetically to be more
nutritious, easier to cultivate, or able to grow in the
presence of herbicides and pests (USA, 90% of crops of
corn, soybeans, and cotton are GMO’s)
Traditional Agriculture and Animal Breeding not
considered GMO because in GMO, we select traits within
one species
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)


CRISPR: Clustered Regularly Interspaced Short Palindromic
Sequences
o Definition: repetitive DNA sequences observed in
bacteria used to detect and destroy DNA from
similar bacteriophages (virus that infects and
replicates within a bacteria) during infections
Two key molecules
o Enzyme: Cas9 or CRISPR-associated protein 9
(“Molecular Scissors” cut 2 strands of DNA at a
specific location in the genome so that bits of DNA
can then be added or removed)
ELIC, MARIANA CLARIBEL R.
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ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
Guide RNA (gRNA): Pre-designed RNA sequence
(~20 bases long) located within a longer RNA
scaffold. Built to find and bind to a specific
sequence in the DNA. Complementary to the target
DNA sequence in the genome
o
DNA target sequence
o
Guide RNA binds to target
sequence
o
Cas9 enzyme binds to guide
RNA
o
Cas9 enzyme cuts both
strands of DNA
o
The cut is repaired
introducing mutation
Exome Sequencing: determines the order of the DNA bases of all
parts of the genome that encode proteins (20,325 genes)
Info is compared to databases that list many gene variants (alleles)
and their association with specific phenotypes
Particularly valuable in identifying extremely rare diseases
Fragmentation of Genomic DNA (exon and
intron in double-stranded DNA)
Ligation of Adaptor
Hybridization on capture array for target
enrichment
Sequencing
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Metagenomics: Field that describes much of the invisible living
world by sequencing all the DNA in a habitat (soil, gut, garbage,
volume of captured air, etc.)



Can show how species interact; yields info useful in
developing new drugs or energy sources
Metagenomics researchers collect and sequence DNA, then
consult databases of known genomes to imagine what the
organisms might be like
First metagenomic project: exploration of the Sargasso Sea
(> 1 billion DNA molecules found from the depths: ~1, 800
microbial species from the previously thought life-lacking
sea due to a thick cover of seaweed)
25 August 2022
The Cell
The body >290 specialized/differentiated cells that aggregate and
interact to form the 4 basic tissue types: (ECoMuNe)
1. Epithelial: tight cell layers form linings that protect, secrete,
absorb, and excrete; covers the skin, the mouth, tongue, the
vagina
2. Connective: variety of cell types and surrounding materials
protect, support, bind to cells, and fill spaces throughout
the body; include cartilage, bone, blood, and fat
3. Muscle: cells contract, providing movement; skeletal,
cardiac, and smooth muscles
4. Nervous: neurons transmit info as electrochemical impulses
that coordinate movement, and also sense and respond to
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
environmental stimuli; neuroglia support and nourish
neurons; central and peripheral nervous system
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Cellular structures
1. Prokaryotic cell: anuclear
(no nucleus: archaea and
bacteria); has ribosomes
2. Eukaryotic cell: archaean +
bacterium fusion; has nucleus
(eukarya); has organelles; has
ribosomes
Somatic cells/body cells: contain 2 copies of the genome (diploid);
23 pairs of chromosomes
Germ cells/sperm cell and egg cell: contains 1 copy of the genome
(haploid); 23 chromosomes (1 of each 1-22 chromosomes + sex
chromosome)
Sperm cell + egg cell = diploid state
Stem cells: diploid cells that divide to give rise to differentiated cells
Taxonomical Domains
3 Major “domains of life”
1. Bacteria: no nucleus, mito, ER, Golgi app; single-celled;
2. Archaea
3. Eukaryota: single-celled or multi-celled; some parasites
single-celled or multi
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Chemical Constituents
4 Basic Macromolecules
1. Carbohydrates/Polysaccharides: sugars, starches, and
cellulose; provide energy (ATP) and contribute to cell
structure; must be converted back into glucose to be used
to produce energy, the form that allows it to be
immediately and directly consumed or absorbed by the cells
Monomer: monosaccharides
2. Lipids: fats, oils, steroids and cholesterols; form the basis of
hormones, form membranes, provide insulation, store
energy; most hormones have cholesterol (very useful in
creating hormones) in their structures; storage of energy;
kapag naubusan ng carbo and glycogen next is lipids and
protein: gluconeogenesis: formation of glucose from noncarbo sources
Monomer: fatty acids and glycerol
3. Proteins/polypeptides: enzymes, structural components;
human body is a walking protein; different types of
proteins; diverse functions:
enable blood to clot (fibrinogen)
ELIC, MARIANA CLARIBEL R.
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ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
form contractile fibers of muscle cells (actin)
form the bulk of the body’s connective tissues (collagen)
fight infections (immunoglobulins or antibodies)
Monomer: amino acids
Enzymes: facilitate or catalyze biochemical reactions so that
life can be sustained
4. Nucleic acids: DNA (genetic blueprint) and RNA (direct copy
of GENES found in the DNA); translate info from past
generations into specific collections of proteins that give a
cell its characteristics;
Monomer: nucleotides
Organelles of the Cell
Functions of Organelles: carry out the activities of life by dividing
the labor through partitioning off certain areas or serving specific
functions



Eliminates the need to maintain a high concentration of a
particular biochemical throughout the cell
Enable a cell to retain and use its genetic instructions to
secrete substances, dismantle debris and acquire energy
Saclike organelles sequester biochemicals that might harm
other cellular constituents: peroxisomes, lysosomes,
vacuoles
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
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

Organelles studded with enzymes embedded produce
molecules (such as mitochondrion)
In a cell the products are proteins
The Nucleus: largest organelle; contains nearly all the DNA; we have
nuclear DNA (from mother and father) and mitochondrial DNA
(mother only); an apparent amorphous mass enclosed by a nuclear
envelope
RNA synthesis: DNA can’t pass through nuclear pores, genes directly
copies to become RNA that may pass through the nuclear pores and
into the ribosomes: varies in shape; varies in number within a cell
Parts
1. Nuclear envelope: surrounds the nucleus; biochemicals can
exit and enter the nucleus through nuclear pores (rings of
proteins around an opening)
 Components:
o 2 parallel cellular membranes
 Perinuclear cisternae
 Barrier to ions, solutes, macromolecules
o Outer membrane
 Has ribosomes attached to it
 Continuous with Rough ER
o Inner membrane:
 meshwork of fibrous proteins with lamina
 nuclear lamina is a layer of fibrous material
located in the inner face of the nuclear
membrane; turns off the expression of
genes that contact from within; provides
mechanical support and holds the nuclear
pores in place
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Nuclear Pore Complex (NPC): pore with
glycoproteins; huge macromolecular complex;
nuclear pore + glycoproteins; 80 – 100 nm in
diameter; 3 ring-like arrays of protein; octagonal
symmetry = 8-fold repetition of subunits
2. Nucleolus: produces ribosomes; highly basophilic, spherical;
non-membrane bound structure/floats inside the nucleus;
active in protein synthesis
3. Nucleoplasm: fluid inside the nucleus
4. Contents of the nucleus: proteins form fibers giving a rough
spherical shape
 Abundance of RNA, enzymes, and proteins required to
synthesize DNA and RNA
o
The Cytoplasm: every part of the cell except the nucleus; plasma
membrane (a.k.a. cell membrane): outer boundary of the cell
Other cellular components: stored proteins, carbohydrates, lipids,
pigment molecules, and various other small chemicals
Cytosol: cytoplasm when other parts are removed
Three cellular functions:
1. Secretion: release of a substance from a cell
a. Start: body sends a biochemical msg to a cell to
begin production of a particular substance
b. Info in certain genes is copied into molecules of
mRNA which exits the nucleus
c. Cytoplasm: tRNA and ribosomes direct the
manufacture of proteins
Example: once the baby’s lips touch the nipple of the
mother (biochem msg), the mammary glands now secrete
milk
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
d. ER: maze of interconnected membranous tubules
and sacs where most protein synthesis occurs; acts
as a quality control center of the cell; degrades
protein with improper folding because it may cause
diseases; should be in 3D shape; enables the
forming protein to start folding into 3D shape
necessary for specific functions; misfolded proteins
pulled out of the ER and degraded
i. Rough ER: nearest the nucleus; flattened
and studded with ribosomes which make it
appear fuzzy when viewed; where protein
synthesis begins when mRNA attaches to
the ribosomes
ii. Smooth ER: ribosomes are fewer, tubules
widen; lipids are made and added to
protein; lipids + protein = lipoprotein
e. Vesicles: membrane-bound, sac-like organelles that
allow proteins to exit the ER; also important during
endocytosis: foreign materials entering the cells;
exocytosis is the process of materials going out of
the cell
i. Lipids: exported without vesicle because
vesicles are made of lipids
ii. DNA and RNA do not exit the cell
f. Golgi Apparatus: stack of pancakes; processing
center with a column of 4 to 6 interconnected flat,
membrane-enclosed sacs; processing center where
post-translational modification happens; proper and
final folding of protein occurs; activation of
proteins; where sugars are made; temporarily store
complex secretions
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
g. Exosomes: type of vesicle that transport molecules
from 1 cell to another or merge with, and empty its
contents to other cells; budding; 30 – 100 nm,
larger than vesicles; carry proteins, lipids, RNA;
remove debris, transport immune system
molecules, provide communication network among
cells
2. Digestion inside cells
a. Intracellular Digestion: Lysosomes: bodies that cut;
membrane-bounded sacs that contain enzymes that
dismantle bacterial remnants worn-out organelles
and other materials; break down digested nutrients
into forms that the cell can use; fuse with vesicles
carrying debris -> enzymes degrade the contents;
autophagy eating self, cell’s disposing of its own
trash, defective organelles and some debris;
maintain highly acidic environment w/out harming
other cell parts; differ in number per cell based on
their functions
i. Macrophages: for engulfment and
breakdown of bacteria
ii. Liver cells/hepatocytes: break down
cholesterol, toxins, and drugs
Contain all 43 types of enzymes; absence or
malfunction: lysosomal storage disease
Tay-sachs disease: 1 in 10, 000 people; deficient
enzyme breakdown of lipids in cells surrounding the
nerve cells (neurons), lack of enzymes
neuraminidase-A, accumulation of lipids that make
it look like foam cells
Endosome: ferries extra low-density lipoproteincholesterol to lysosomes, degrades it after
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
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b. Peroxisomes: sacs with single outer membranes
studded with proteins which houses enzymes;
catalyze breakdown of lipids and rare biochemicals;
synthesize bile acids (fat digestion); detoxify
compounds from oxygen-free radical exposure;
large and abundant in the liver and kidney cells
3. Energy Production
a. Mitochondria: powerhouse of the cell; provide
energy by breaking the chemical bonds that hold
together the nutrient molecules in the food; where
ATP is produced via glycolysis, gluconeogenesis
2 parts:
i. Outer membrane: similar to ER and GA;
protective membrane
ii. Inner membrane: with folds called cristae
that increases the surface area of the
mitochondria to hold more room for ATP
production; hold the enzymes that release
energy from nutrient molecules -> ATP
Holds mDNA (mitochondrial DNA)
Plasma membrane: phospholipid bilayer (fat molecule with
attached phosphate groups)
1. phosphate end: hydrophilic; heads
2. two chains of fatty acids: hydrophobic; fats hydrophobic in
nature; tails
Allows cell – to – cell communication
1. signal transduction: series of molecules that are part of the
plasma membrane form pathways that detect signal from
outside the cell and transmit inward
2. cellular adhesion: helps attach to certain other cells
ELIC, MARIANA CLARIBEL R.
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ELIC, MARIANA CLARIBEL R.
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Cytoskeleton: provides the framework of the cell, support the cell;
meshwork of protein rods and tubules that serve as the cell’s
architecture, to position organelles, to provide overall 3D shapes
motor molecules: part of it that powers the movement of
organelles along the rails as they convert chemical energy to
mechanical energy
3 major types
1. microtubules: 23 nm; dimers of tubulin assembled into a
hollow hole; important during cell div: fall apart into
individual tubulin dimers;
maintain cellular organization and enable transport of
substance within the cell
form cilia: motile cilia (movement) and primary cilia
(sensory function); filter or trap material
Motile cilia: Crowd surfing: coordinated movement that
generates a wave that moves the cell or propels substances
along its surface; specially in mucus membranes
*Pass inhaled particles up and out of respiratory tubules
*Move egg cells in the female reproductive tract
*Pseudostratified columnar epithelial cells or respiratory
cells
Bardet-Biedl Syndrome/sick cilia disease: causes obesity,
diabetes, cognitive impairment, and extra finger/toes
Primary cilia: do not move and serve as antennae: sense
signals to locations inside cells; stimulate cells to move;
absence can harm health (i.e., PKCD: Polycystic Kidney
Disease)
2. microfilaments: 7 nm; long, thin rods composed of many
proteins called Actin; more solid and narrower than
microtubules; enable cells to withstand stretching and
ELIC, MARIANA CLARIBEL R.
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ELIC, MARIANA CLARIBEL R.
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compression; help anchor one cell to another; specially in
muscle cells
absence or defect: genetic diseases occur: Alzheimer
disease: actin part of the cytoskeleton is abnormal
3. intermediate filaments: 10 nm; composed of different
types of proteins in different cell types; consist of proteins
entwined to form nested coiled rods; abundant in nerve and
skin cells
3 major types are distinguished by:
1. protein type
2. diameter
3. how they aggregate into larger structures
Cell Cycle: Somatic Cells
Describes sequence of activities as a cell prepares for and
undergoes division
2 major stages
1. Interphase (non-dividing phase)
2. Mitosis (dividing phase)
a. Cell duplicates its chromosomes
(final: 23 chromosome pairs)
b. Cytokinesis: cell apportions one set
of chromosomes and organelles into
each of two cells (daughter cell)
Interphase: 4 phases: G1, G2, S, and G0 phase
1. G0: resting phase: cells are alive and maintain their
specialized characteristics but does not replicate its
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
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DNA or divide; fate of the cell is decided: mitosis or
apoptosis (programmed cell death; occurs if DNA is
damaged such as in cancer); prevent mutations; cancer
cells don’t rest
2. G1: follows mitosis, cells resume synthesis of proteins,
lipids, and carbohydrates; cell enlarges
3. S phase: DNA replication phase, 8 – 10 hrs, 2 copies of
genome, synthesis of mitotic spindle: pulls the
chromosomes apart, formation of centrioles by
microtubules: join with other proteins, oriented at right
angles to each other forming paired oblong structures
called centrosomes (organize other microtubules into
the spindle)
4. G2: quiet phase; where energy is being stored up, more
protein synthesis in preparation for mitosis, after DNA
replication and before Mitosis;
Mitosis: chromosomes become condensed enough to become
visible when stained
Chromatids: long strands of chromosomal material in
replicated chromosomes (sister chromatids: 2 chromatids attached
at a centromere; a replicated chromosome)
Furrow: space between sister chromatids
1. Prophase: DNA coils tightly: shortens and thickens the
chromosomes for ease of separation; microtubules
assemble to form the spindles; nuclear membrane breaks
down to allow the chromosomes to be pulled away from
each other; nucleolus no longer visible
2. Metaphase: chromosomes attach to the spindle at their
centromeres and align along the center of the cell (equator
or metaphase line); metaphase chromosomes under great
ELIC, MARIANA CLARIBEL R.
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ELIC, MARIANA CLARIBEL R.
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tension but appear motionless due to equal force on both
sides
3. Anaphase: plasma membrane indents at the center; band of
microfilaments form on the inside face of the plasma
membrane to constrict the cell down in the middle;
centromeres part, releasing one chromatid to each of the
cell
4. Telophase: final stage, cell would now look like a dumbbell
because of the cleavage furrow, set of chromosomes are
already at each end; spindle falls apart, nucleoli, nuclear
membranes reform
Cytokinesis: microfilament band contract like a drawstring,
separating the newly formed cells
Apoptosis: programmed cell death; rapidly and neatly dismantles a
cell into membrane-enclosed pieces that a phagocyte can mop up;
continuous process, begins when a “death receptor” on the cell’s
plasma membrane receives a signal to die; cell’s way to prevent
mutations
Characteristics of an apoptotic cell:




Round in shape at first (contact with other cells are cut off)
Plasma membrane undulates, forming blebs
Cell shatter
Time to declutter fragmented cell: <1 hour
Cell -> chromatin condensation -> nuclear blebbing -> nuclear
collapse -> apoptotic body formation
Synchronicity between mitosis and apoptosis = maintenance of
tissue, keeps number of cells at bay
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
The Human Microbiome: living microorganisms within and on
human body
Biome: all the species
60% of cells in the human body are microorganisms
Different microbiome from everyone:



Circumcised penis vs. un
Vaginal microbiome of mothers vs. vaginal microbiome of
non-mothers
Microbiome changes with experience and environmental
exposures (streetfoods, vegan..)
Human gut microbiome: from mouth to rectum; 10 trillion bacteria


Mouth: 600 species of bacteria
Large intestine: 6, 800 species of bacteria
Probiotics: live microorganism when ingested confer a health
benefit; maintain the viability of our gut; breakdown different
cellular nutrients; aids even in diarrhea
Ex: Lactobacillus strains against Salmonella infections
Fecal transplantation: treatment based on altering the microbiome
that replaces hundreds of bacterial species at once; performed since
1958 in human; to make an individual’s microbiome better
Reproductive System
Zygote: when sperm cell and oocyte (egg) meet
Organization of the Reproductive organs
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
1. Gonads: paired structures where the sperm and oocytes are
manufactured
2. Tubular structures that transport these cells
3. Hormones and secretions that control reproduction
Male

Sperm cells
o Develop w/in a 125-m-long network of
seminiferous tubules
o Seminiferous tubules packed into paired, oval
organs called testes: outside the body or separated
because they need a cooler environment in order to
grow and develop; placed in a sac called scrotum
o Epididymis: for maturation and storage; tightly
coiled tube where the cells mature and are stored
o Ductus deferens: continuation of the epididymis
that bends behind the bladder and joins the urethra
o Urethra: tube that carries sperm and urine out of
the body through the penis
o Glands adding secretions to sperm
 Prostate gland: production of a thin, milky,
acidic fluid that activates the sperm to
swim; beneath the urinary bladder and
sigmoid colon;
 Seminal vesicles: secrete fructose (energyrich sugar) and hormone-like prostaglandins
(stimulate contractions in the female that
help sperm and oocyte meet)
 Bulbourethral gland (pea size): secrete an
alkaline mucus that coats the urethra
before sperm are released
o Produces seminal fluid (semen)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
o
o
Sexual Stimulation
Orgasm: pleasurable sensation at the peak of sexual
stimulation, accompanied by:
 Rhythmic muscular contractions ejecting
the sperm from each ductus deferens
 Ejaculation: discharge of sperm along with
other fluids from the penis (200-600 million
sperm cells)
 Semen analysis 2 or 3 to 5 days abstinence
from ejaculation to determine the accurate
sperm count in your submitted semen
testosterone
Female





Ovaries: female gonads where sex cells develop; each ovary
of a newborn girl: 1 million immature oocytes; each oocyte
nestles within nourishing follicle cells; after puberty: once a
month, 1 ovary releases the most mature oocyte
Cilia sweep mature oocyte into the finger-like projections of
one of two uterine tubes (Fallopian Tubes)
Uterine Tube/Fallopian Tube: carries the oocyte into the
uterus (womb), a muscular, saclike organ, expandable
Fertilization
o Oocyte released may encounter a sperm in the
uterine tube (usually)
o Ectopic pregnancy: when the fertilization occurs
outside the uterine/fallopian tube
o Sperm + oocyte =DNA merge into a new nucleus,
zygote
o If no fertilization: oocyte + uterine lining shed as the
menstrual flow
Opening
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)




Cervix: lower end of the uterus that leads to the vagina
Vagina: tubelike where the opening is protected on the
outside by two pairs of fleshy folds (like doors): (Labia
Minora and Labia Majora)
Clitoris: 2-cm long found at the upper juncture of both
pairs; anatomically like penis; rubbing the clitoris: female
orgasm
Control of oocyte maturation and preparation of uterus for
pregnancy controlled by hormones (estrogen, and
progesterone)
Meiosis: cell division of gametes that halves the chromosome
number
Maturation: further process that sculpts the distinctive
characteristics of sperm and oocyte
Gametes: contribute 23 different chromosomes; haploid
Homologous pairs (homologs): Chromosome pairs from
both mother and father; have the same genes in the same
order but may carry different alleles of the same gene;
“mixing” of chromosomes or genes
Polyploid: genetic overload IF NOT HAPLOID
2 main divisions of the genetic material
1. Meiosis I: Reduction Division: reduces the number of
replicated chromosomes from 46 to 23; 2 replicated
chromosomes
2. Meiosis II: Equational Division: produces four cells from the
two cells formed in the first division by splitting the
replicated chromosomes; unreplicated chromosome
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Independent Assortment of genes: fate of a gene
on one chromosome is not influenced by a gene on
a different chromosome
3. Anaphase I: Homologs separate
4. Telophase I: separate homologs move to opposite poles;
established a haploid set of still-replicated chromosomes at
each end of the stretched-out cell
o
Interphase II: Chromosomes unfold into thin threads;
manufacturing proteins, no DNA replication
Meiosis II:
Genetic recombination
Meiosis: occurs after an interphase period when DNA is replicated
(doubled)
After interphase: Meiosis I
1. Prophase I: replicated chromosomes condense and become
visible when stained; spindle forms
Synapsis: homologs line up next to one another, gene by
gene; chromosome pairs held together by a mixture of RNA
and protein
2. Metaphase I: homolog align down the center of the cell;
each homologous pair attaches to a spindle fiber at an
opposite pole: generates Genetic Diversity
The greater the number of chromosomes, the greater the
genetic diversity in Metaphase I.
o The 23 chromosome pairs can line up in 8, 388, 608
different ways (2^23)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
1. Prophase II: Start of the 2nd meiotic division; chromosomes
are condensed and visible
2. Metaphase II: replicated chromosomes align down the
center of the cell
3. Anaphase II: centromeres part; newly formed
chromosomes (unreplicated form) move to the opposite
poles
4. Telophase II: nuclear envelopes form around the four
nuclei, separating into individual cells
Net result of Meiosis: 4 haploid cells, new assortment of genes and
chromosomes that hold a single copy of the genome
Male begins manufacturing sperm AT PUBERTY and continues
throughout life.
Female begins meiosis AT FETAL STAGE and completes only if a
sperm fertilizes an oocyte.
Maturation of Gametes: Spermatogenesis: formation of sperm cells
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Spermatogonium: diploid stem cell; divides mitotically = 2 daughter
cells
1. First: continues to specialize into a mature sperm
2. Second: remains a stem cell (self-renew and continually
produce more sperm); reason why men continuously
produce sperm cells
Meiosis I (Reduction Division): Primary spermatocyte divides = 2
haploid cells (secondary spermatocytes containing replicated forms
of the chromosome)
Meiosis II (Equation Division): Secondary spermatocytes divide to 2
spermatids; spermatid develops flagellum; contain unreplicated
chromosomes
Sperm tail base contains many mitochondria: split ATP molecules to
release energy to propel sperm inside the female
Spermatid differentiation -> cytoplasm falls away -> mature,
tadpole-shaped spermatozoa
Size: 0.006 cm (0.0023 inch): travels 18 cm (7 inches) to reach an
oocyte; helps in their travel: prostaglandins in the semen, cilia of
women
Other parts of a Sperm Cell:
Acrosome: membrane covered area on the front end that contains
enzymes to help the sperm cell penetrate the protective layers
around an oocyte
Head: contains DNA wrapped around proteins inside its nucleus;
DNA: genetically inactive, don’t replicate, don’t produce proteins;
active only once it penetrates the oocyte
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Midpiece: contains lots of mitochondria; will immediately give
energy to the tail for propelling and locomotion
Female Meiosis: Oogenesis
Begins with an oogonium (diploid cell); not attached to each other,
instead follicle cells surround each oogonium
Oogonium – primary oocyte “arrested in prophase I until puberty” –
secondary oocyte and first polar body “meiotic arrest in Meiosis II
until fertilized” – fertilized – secondary oocyte
Meiosis I: primary oocyte divides into:
1. Polar body: small cell with very little cytoplasm (haploid)
2. Secondary oocyte (haploid)
Meiosis II:
A. first polar body may either:
1. Divide to yield 2 polar bodies of equal size (unreplicated
chromosomes)
2. Decompose
B. Secondary oocyte: divides unequally in Meiosis II to produce
another small polar body (unreplicated chromosomes) and
the mature egg (Ovum)
Only the ovum becomes the product
Polar bodies are absorbed, plays no further role in development
“Blighted Ovum”: miscarriage where the sperm fertilizes a polar
body; disorganized clump of cells that is not an embryo grows
for a few weeks, then leaves the woman’s body
Oogenesis
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Before birth: ~1 million oocytes arrested in Prophase I
Puberty: ~400, 000 oocytes remain, meiosis I continues in one
or several oocytes each month, but halts in metaphase II
Puberty to Menopause: ovulates about 400 oocytes
Prenatal Development
Embryo: prenatal human for the 1st 8 weeks; rudiments of all body
parts form
1st week: embryo is in a “preimplantation” stage, not yet
settled in the uterine lining
Fetal period: prenatal development after the 8th week; structures
grown and specialize
Fetus: 9th week until birth
Sperm and oocyte meeting at Fertilization
Sperm cell can survive in a woman’s body for up to 3 days
Oocyte can only be fertilized 12-24 hours after ovulation
Woman helps sperm reach an oocyte
o Capacitation: process in the female that chemically
activates sperm, and the oocyte secretes a chemical
that attracts sperm
o Contractions of female’s muscles and moving of
sperm tail propels the sperm
o Out of the 300 million sperm cells that are released
in one average ejaculation, only ~200 sperm get
near the oocyte
Once they meet, the sperm cell shall penetrate the egg cell;
this is the time when the acrosome will be at work
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Corona radiata: outermost layer, and covering of follicle
cells guarding the secondary oocyte where the sperm first
contacts with
Fertilization (conception): begins when outer membranes
of sperm and secondary oocyte met and a protein on the
sperm head contacts a different protein on the oocyte;
mitochondrial DNA can only be inherited from the mother
since the mitochondria of the sperm is in its midpiece and
the midpiece doesn’t enter the egg cell
o >1 sperm: too much genetic material for
development
12 hours after penetration of Sperm:
o Disassembly of ovum’s nuclear membrane
o Pronuclei (2 sets of chromosomes) approach one
another; within each pronucleus, DNA replicates
o Fertilization is complete: ZYGOTE is formed
Cleaving of Embryo and Implantation
o Cleavage: frequent cell division after fertilization
 Blastomeres: early cells from cleavage
 Morula: Latin for mulberry, when the
blastomeres form a solid ball of 16 or more
cells
 From here, cellular activity controlled by
secondary oocyte’s cytoplasm but some
genes from Embryo begin to function
 Blastocyst: blastomere hollows out and fills
its center with fluid
 Inner cell mass: clump of cells on
the inside lining of Blastocysts
 Formation is the 1st event
distinguishing cells from each other
by their relative positions
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)



Forms the embryo during
development
1 week after conception: Implantation:
blastocyst nestles, and is now safely
secured into the uterine lining
Outermost cells (Trophoblast) secrete
Human Chorionic Gonadotropin (hCG),
preventing menstruation; para hindi
malaglag yung bata; what we are testing or
detecting specifically the Beta subunit of
hCG on urine or serum of the woman
31 August 2022
Prenatal Development
Formation of Embryo: 2nd wk of development
Amniotic cavity formation between inner cell mass and
outer cells anchored to the uterine lining
o Gastrula/Primordial Embryo: inner cell mass
flattens into 2-layered embryonic disc, later
followed by a middle layer (layers are called
Primary Germ layers)
primary germ layer gives rise to certain structures
 Ectoderm: nearest to the amniotic cavity
 Endoderm: inner layer closer to blastocyst
cavity
 Mesoderm: last to develop, middle layer,
muscles
Supportive structures: chorionic villi, placenta, yolk sac,
allantois, umbilical cord, amniotic sac
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Chorionic villi: finger-like outgrowths that extend
from the area of the embryonic disc close to the
uterine wall; developed by 3rd wk
o Placenta: fully formed on 10th wk from the
Chorionic villi
 Links to the woman and fetus for the rest of
the pregnancy
 Secretes hormones to maintain pregnancy
and sends to the fetus
o Yolk sac: manufactures blood cells; shrinks at the
end of the embryonic period/after 8th wk because
replaced by the liver; primary function is to develop
blood vessels, hematopoietic organ, replaced by
liver, then bone marrow once born
o Allantois: membrane surrounding the embryo that
gives rise to umbilical blood vessels
o Umbilical cord: formed around the Allantois,
attaches to the center of the Placenta
o Amniotic sac: swells w/ fluid, cushioning the
embryo and maintains a constant temperature and
pressure
 Amniotic fluid: contains fetal urine and
fetal cells; acts as cushion for the baby
Multiples (twins or more): arise during the early stage in
development; Arise early in development
o Fraternal or Dizygotic twins (DZ)
 2 sperms fertilize 2 oocytes
 Happens if ovulation occurs in 2 ovaries in
the same month or if 2 oocytes leave the
same ovary and are both fertilized
o Identical or Monozygotic twins (MZ)
o
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Descends from a single fertilized ovum,
genetically identical (natural clones)
Conjoined or Siamese twins
 Named from Siam (Thailand), Chang and
Eng Bunker, born 1811 conjoined by a band
of tissue from the navel to the breastbone;
own separate organs
 Occurs in 1 in 50, 000 to 100, 000
pregnancies
 Embryo divides into twins after the point at
which groups of cells can develop as 2
individuals (between days 13 and 15)
Dicephalic or incomplete twins
 Dicephalic: 2 heads, one body
 Stoppage may be seen, because separation
occurred after day 9 but before day 14
 Shared organs have derivatives of
ectoderm, mesoderm, and endoderm (the 3
primary germ layers had not yet fully sorted
into 2 bodies)

o
o
Development of Embryo
rd
3 week: Primitive Streak (band) appears along the back of the
embryo
Some 14th day point beyond which research is banned on
the human embryo
1st sign of a nervous system, and the day when implantation
is completed
Reddish blue bulge appears containing the heart, heart
beats starting day 18, detectable by day 22
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
4th week: arms and legs begin to extend from small buds on the
torso
Blood cells form and fill primitive blood vessels
Immature lungs and kidneys begin to develop; pinakahuling
nadedevelop digestive and respiratory systems
5th and 6th wk
5th for sex determination for ethical purposes and avoid damage to
the embryo and 6th week
Embryo’s head appears too large for the rest of its body
Limbs end in platelike structures with tiny ridges
Apoptosis sculpts finger and toes
Eyes are open but still no lids or irises
7th and 8th week
Skeleton composed of cartilage forms, not yet calcified
Embryo about the length and weight of a paper clip
End of 8th week: prenatal human has tiny versions of all
structures that will be present at birth, now a FETUS
Fetus grows
Sex: determined at conception (x an y chromosomes); due
to chromosomal patterns
o XX: female
o XY: male
 SRY gene determines “maleness”
 Week 6: SRY gene expressed in males
anatomical differences between sexes
appear
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)

Male hormones stimulate male
reproductive organs and glands to
differentiate
Week 12
Fetus sucks its thumb, kicks, makes fists and faces,
beginnings of teeth (but underneath the gums)
Breathes amniotic fluid in and out, urinates and defecates
into it
End of 1st trimester
4th month
Fetus has hair, eyebrows, lashes, nipples, and nails
13th week: start of 2nd trimester
18th week: vocal cords have formed but fetus makes no sound
because it doesn’t breathe air; sound needs air to create sound
waves
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Final trimester
Fetal brain cells rapidly link into networks as organs
elaborate and grow
Layer of fat forms beneath the skin; not wrinkly anymore
Last to mature: digestive and respiratory systems
o Prematurely born: difficulty digesting milk and
breathing; with oxygen support; isolated and
monitored; placed in neonatal ICU (NICU)
~266 days after fertilization: a baby is ready to be born
Birth Defects
1st to 5th month: critical period of pregnancy
Critical period: time when genetic abnormalities, toxic
substances, or viruses can alter a specific structure
o 2/3 of all birth defects arise from a disruption
during the embryonic period
end of 5th month
Fetus curls into head-to-knees position (fetal position)
Weighs about 454 grams (1 pound)
6th month
Skin appears wrinkled (not much fat beneath), turns pink as
capillaries fill with blood; capillaries become bigger as the
fetus grows)
End of 2nd trimester
Fetus kicks and jabs, may even hiccup
Fetus about 23 centimeters (9inches long)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
o
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Disruption in 1st trimester: may cause intellectual
disability
Disruption in the 7th month: difficulty in learning to
read
o
Teratogens
most drugs are not teratogens
Some teratogens
o Accutane: Acne medication, may cause cleft palate
and eye, brain, and heart defects
o Diethylstilbestrol/DES: prevent miscarriage; can
cause vaginal cancer in “DES Daughters”
o Thalidomide: prevents morning sickness
 Mild tranquilizer used to alleviate nausea
early in pregnancy, during the critical period
for limb formation
 Caused Phocomelia-like illness between
1957 and 1961, lots of new born with
“phocomelia” which was doubting since it
was a rare genetic disorder
 “Thalidomide babies”, born with incomplete
or missing legs and arms
 Phocomelia: disease characterized by super
tiny or deformed limbs and babies
o Alcohol: one or two drinks per day or large amnt at
a single crucial time risks a fetal alcohol spectrum
disorder in the unborn child
 Fetal Alcohol Spectrum Disorder: small
heads, flat faces, thin upper lip
 Growth is slow before and after birth
 Teens and young adults: short and have
small heads
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
Nutrients
 Vitamin A excess: birth defects
 Isotretinoin or Accutane (Vit. A
derivative): treat acne, causes
spontaneous abortion and defects
of the heart, nervous system, and
face
 Acitretin (Vit. A derivative): treat
Psoriasis, also cause birth defects
Can’t donate blood because may affect the
fetus in pregnant woman
 Vitamin C
 Harms if large amounts are taken
 Baby may develop symptoms of Vit.
C deficiency (bruising, easily
infected) because “accustomed” to
high levels of Vit. C; tolerance
 Malnutrition
 Affects development of placenta
 Can cause low birth weight, short
stature, tooth decay, delayed sexual
development, and learning
disabilities
Viral Infections
 Viruses: small enough to cross placenta and
reach a fetus
 Zika virus: carried in semen; associated with a
dramatic increase of microcephaly in Brazil;
spread by mosquitoes
 HIV: Blood contact
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)

ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
that prevents itself from being phagocytized; 3rd rat
heat killed bacteria; mixed heat-killed bacteria and
nonvirulent bacteria – rat died = process called
transformation, nucleic acids from dead bacteria to
nonvirulent bacteria, and infected/mutated them)
German Measles (Rubella): well-known viral
teratogen; exposure during first trimester cause
cataracts, deafness, and heart defects; exposure
during 2nd or 3rd trimester cause learning
disabilities, speech and hearing problems, and
Type 1 DM
Post term delivery, lampas 10 months kaya lang placenta is not as
efficient as it’s supposed to be
Amniocentesis
Gestational diabetes may lead to diabetes type II
Masasakal ang baby ng umbilical cord so caesarean na, minsan
pwede pa ireposition
08 September 2022
History of DNA and RNA
Francis crick and James Watson: discovered the 3D structure of
DNA in 1953
DNA
o
o
o
Virulence factors: flagellum, enzymes, proteins, cell wall, plasmids;
anything that helps the bacteria to become more pathogenic
o
st
1871: 1 described by Friedrich Meischer (isolated
from WBC’s in pus on soiled bandages)
1902: Archibald Garrod 1st to link inherited disease
and “protein” (that time akala nil ana protein ang
carrier ng genetic information for inheritance;
1928: Frederick Griffith took 1st steps in identifying
DNA as the genetic material using rats (nonvirulent, negative control; positive control, virulent
factor = capsules – protective barrier of a bacteria
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
1909: Pheobus Levene identified the 5-Carbon
Ribose as part of some nucleic acids; pentose sugar;
2nd and 3rd C has Oxygen
 1929: Deoxyribose was discovered; removal
of O in the 2nd carbon of the pentose sugar
 Discovered that the 3 parts of a nucleic acid
are present in equal proportions
1950s: Erwin Chargaff showed that the DNA in
several species contain equal amounts of the bases
Adenine and Thymine, Guanine and Cytosine
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
o
Maurice Wilkins and Rosalind Franklin: bombarded
DNA with X-rays using X-ray diffraction to deduce
the overall structure of the DNA, 1st photo of the
nucleus taken by Rosalind Franklin
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Chemical Structure of the DNA: phosphate group, pentose sugar,
nitrogenous bases make up the nucleotide
Backbone: phosphate group and pentose sugar
DNA complementary because of the nitrogenous bases
*photo*
RNA: synth of proteins
DNA: carries all the genetic info needed for protein production
More stable because double stranded, better protection of nucleic
acid against degradation
More vulnerable: contains Thymine, can result to thymine
dimerization
Resistant because it has no Thymine
Virus: viral membrane inside there lies the nucleic acids of
the virus, ang napapasa lang talaga ay yung nucleic acids
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Components of Nucleic Acids
1. Pentose sugar: stability, conformational unity
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
a. Difference in the C 2 and number of OH: DNA stable
due to removal of Oxygen
2. Phosphate Group: allows the linking of nucleotides together
in a polymer chain; important because it will link them
together to form new polymer – polymer because
maraming chain
3. Nitrogenous Bases
a. DNA
i. Purine: Guanine, Adenine
ii. Pyrimidine: Cytosine, Thymine
b. RNA
i. Purine: Guanine, Adenine
ii. Pyrimidine: Cytosine, Uracil
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Complementary base pairs: H bonds
Nitrogenous base + pentose: glycosidic bonds between C-1’ of
sugar and Nitrogenous base; constant attachment to the pentose
sugar, 1st C lagi ang attachment; differ on the nitrogenous base
Purine base: N-9 atom, 2 rings, 1 hexagon, 1 pentose
Pyrimidine Base: N-1 atom, 1 ring
Pentose sugar + phosphate group = ester bond
Phosphodiester bond: dehydration reaction by linkage of
phosphoric acid and 2 sugars (2 ester bonds)
Polynucleotide Formation and Arrangement
Phosphate group of 1 nucleotide attaches to the C3 of another
nucleotide
Nucleotide Formation
Phosphate group + pentose sugar + Nitrogenous bases = nucleotide
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
ELIC, MARIANA CLARIBEL R.
Class Notes (unedited)
Formed: phosphate sugar backbone and Nitrogenous bases
5’ end: 5th Carbon attached ang Phosphate group, exposed because
wala nang naka-attach na ibang nucleotide
3’ end: 3rd C of pentose sugar, exposed (-OH)
Polynucleotide binding and arrangement
2 similar strands: 5’ to 3’ and 3’ to 5’; inverted or antiparallel
Bonded by H bonds
Important: Complementary Base Pairing: specific purine-pyrimidine
couples
Adenosine 5’ triphosphate
3’ -> 5’ or 5’ -> 3’?
Nucleotide Hydrolysis for DNA Synthesis
One end of the polynucleotide has a free 5’ Phosphate group: 5’ end
During DNA synthesis: betta and gamma phosphates are removed,
alpha are left
One end of the polynucleotide has a free 3’ – Hydroxyl group (OH):
3’ end
Produced are substrates: dATP, dTTP, dCTP, dGTP
When writing sequences of nucleic acids: 5’ to 3’ direction
*deoxy
Nucleotide Formation
*RNA no d
Triphosphate form: precursor molecule during nucleic acid
synthesis
D ATP and d TTP signify that this nucleotide is for RNA synthesis
Every addition of Phosphate -> release of one molecule of water
Nucleotide
Nucleoside: base and pentose sugar (glycosidic bond)
Monophosphate: only 1
Backbone: no base, phosphate and pentose only
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DNA
Polymer of nucleotides: A,T,C,G
Double helix associated with proteins
“backbone” deoxyribose-phosphate (ester bonds)
Strands are held together by H bonds between AT and CG
Strands: anti-parallel, opposing orientation of the 2
nucleotide chains in a DNA molecule
Exposed because it is where the Ester bonds are
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3 Major Forms of RNA
1. Messenger RNA (mRNA): nucleus, carries genetic material,
transformed back to DNA? Yes through reverse
transcription
2. Ribosomal RNA (rRNA): ribosomes (Ribosomal RNA and
proteins), structural component of ribosomes, transformed
back to DNA? No.
Large subunit, small subunit
3. Transport RNA (tRNA): ribosomes, cytoplasm, carries amino
acids to ribosomes, transformed back to DNA? No.
Central Dogma: flow of genetic info in cells is almost exclusively one
way: DNA -> RNA -> PROTEINS
DNA is copied by DNA polymerase
Transcriptions: DNA-directed RNA Polymerase; nucleus
In the 5’ -> 3’ direction, initiated by an RNA primer
Translation: Ribosomes; inside ribosomes
Leading strand: synthesized continuously
Lagging strand: synthesized discontinuously; Creates Okazaki
fragments
DNA
RNA Primers are removed, and Okazaki fragments joined by a DNA
polymerase and DNA ligase
Histones: proteins that the DNA coils to
DNA bead: nucleosome (8 histone proteins + 147
nucleotides of DNA entwined around) *147 nucleotides long
Chromatin: colored material of the chromosome substance
30% Histone + 30% scaffold proteins and other proteins +
30% DNA + 10% RNA
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replication: semiconservative
Each new DNA double helix conserves half of the original
2 identical double helices would form from one original,
parental double helix
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6. Lagging strand is synthesized discontinuously. RNA
polymerase synthesizes a short RNA which is then extended
by DNA polymerase
Summary:
1.
2.
3.
4.
5.
DNA Replication
Copying the DNA to form 2 daughter DNA strands
1. Enzymes unwind the parental DNA double helix to form a
linear strand, facilitated by the Topoisomerase or the DNA
gyrase; helicase acts as a zipper that unzips and removes
the H bonds between the nitrogenous bases
a. Tortional strain on the sides because of the failure
of the unwinding the dna
2. Proteins stabilize the unwound parental DNA (singlestranded binding proteins or SSB proteins)
a. Annealing when 2 DNA strands reconnect
3. Primase makes a short stretch of RNA on the DNA template;
add a primer
4. RNA primer start of the new strand
5. Leading strand is synthesized continuously by DNA
Polymerase; adds DNA nucleotides to the RNA primer
Recruitment of Helicase, unwinding of DNA
Rec of primase, primer synth
Rec of sliding clamp
Rec of DNA Polymerase, interaction with sliding clamp
Bidirectional fork movement, production of leading and
lagging strands
6. Ligation of DNA ligase
7. Termination
8. Successful replication
Important Enzymes
Okazaki fragments: short, newly synthesized DNA fragments on the
lagging strand
1000 to 2000 nucleotides long (prokaryotes)
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150 nucleotides long (eukaryotes)
Separated by ~10 nucleotide RNA primers
Connected by DNA ligase
Termination of DNA Replication
Occurs when 2 replication forks moving away from the single origin
of replication meet on the opposite side
Eukaryotic termination sequence: none
Prokaryotic termination sequence: ter site (~23 bp sequence)
-
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in the 5’ to 3’ direction; stops when it reaches when it reaches the
terminator sequence
Reads 3’ to 5’, meaning produces 5’ to 3’
Entire DNA is not transcribed. 3 reasons:
1. Some transcription units specify noncoding RNA; entire DNA
is composed only of 1.5% genes, not all are gene codes
2. The primary transcript units specifying mRNA is subject to
RNA processing
3. Only a central part of the mature mRNA is translated
Bp: base pairs
Tus – Helicase: while opening DNA can also sense the
sequences, in E. coli
Once Ter sites are reached, termination
Proteins: made of chains of amino acids, made in ribosomes
RNA
1. Messenger RNA: carries copies of instructions from DNA for
translation to proteins
2. Ribosomal RNA: major composition of ribosomes; 2 parts:
small and large subunits
3. Transport RNA: transfers amino acids to ribosomes during
protein synthesis
Transcription: DNA to RNA (mRNA)
DNA is transcribed to make RNA (m, r, t); begins when RNA
polymerase binds to the promoter sequence in the gene; proceeds
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Coding strand
Template strand: where the
Polymerization: dagdag ng rna nucleotides sa growing rna chain
3 steps:
I.
Initiation
1. Formation of a closed promoter complex: RNA
polymerase binds to the promoter sequence
becoming an open promoter sequence
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II.
III.
2. Conversion of the closed promoter complex to an
open promoter complex
3. Polymerization of nucleotides, adds 9 to 10
nucleotides as anchor para hindi mag-separate agad
yung RNA-DNA binding, gagalaw na si RNA
polymerase
4. Promoter clearance
Elongation
1. Sequential building of ribonucleotides to the
growing RNA chain
Termination: reached the terminator sequence, end of
transcription
1. Intrinsic termination (prokaryotes)
2. Rho (p)-dependent termination (transcription
termination factor) (eukaryotes)
Post transcriptional modification
Topoisomerase front: unwinds, back rewinds the DNA
RNA processing in Eukaryotes
Rna splicing
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Nitrogen 7th position of Guanine, 5’ end of mrna, put CH3 or methyl
group
Nuclease: enzymes that
degrade nucleotides
Exonuclease: out going in
Nonpolar: AlIsGlyLeMetPheProTVa
Polar: AsCysGluSeThreTy
Poly A Tail (Polyadenylate tail) many adenine
RNA Splicing only occurs in Eukaryotic cells
Exons: protein
coding
Introns:
important in
recombination,
nonprotein
coding,
removed
Exons are ligated together,
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Alpha carbon: central C
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Peptide bond between the amino group of 1 amino acid and
carboxyl group of another amino acid
Translation
Eukaryotes: a and p site only
CCA sequence: amino acid attachment site
Mrna is translated in codons (3nucleotides); begins at the start
codon, AUG (methionine: start amino acid of all proteins); ends at a
stop codon: UAA, UAG, UGA
Trna (transport RNA): start anticodon: UAC
Binds amino acids to trna,
Charged trna: has amino acid, brought to the large subunit
Translation: Wobble Effect
64 codons: 61 amino acids, 3 stop codons
45 trna molecules due to wobble effect
Wobble: relaxing of pairing between 3rd base of the codon
and anticodon
3rd base letter strict than 1st 2 bases: Wobble Base
Wobble rules
Uncharged trna: no amino acid
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“Foldings” of the proteins are what give them their functions
Complex: mrna, large and small sub unit of rrna, trna (later)
Movement is 5’ to 3’, rrna will move to the right
ER and Golgi Apparatus: post modification process
Peptide bond formation
Not yet a functional protein until it underwent the posttranslational
modification
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Passing scores
Mutagen: an agent that causes mutation
Quiz 2 25/35
Quiz 3 21/30
Mutations may:
-
Affect any part of the genomic sequences that encode
proteins
impair a function, have no effect, or can even be beneficial
o deleterious mutations can stop or slow production
of proteins, overproduce, or impair the protein’s
functions
2 types:
1. “Gain of Function”: Gene’s activity changes, “toxic”
products
2. “Loss of Function”: Gene’s product is reduced or absent
Polymorphism: many forms (under ng mutation)
06 October 2022
Single nucleotide Polymorphisms (SNPs): single base change
Does not harm health but only slightly elevates risk of illness
May also be beneficial if prevalent in a population or even
beneficial when prevalent in a population
Mutation: change in a DNA sequence that is rare in population and
typically affects the phenotype
-
-
Refers to the genotype
(change at the DNA or
chromosome level)
Mutate: process of
altering a DNA
sequence
-
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A person with a somatic mutation has somatic mosaicism
(hindi pare-parehas ang genes, chromosomes na present sa
body; iba ay mutated, iba ay normal)
Germline and Somatic Mutations
Germline Mutation: change occurs during the DNA replication that
precede meiosis. (sex cells)
Transmitted to the next generation of individuals
All cells of the indiv’s body are affected
Somatic Mutation: happens during DNA replication before mitosis
(cell that is part of the person’s body)
Passed on the next gen of cells but not to all the cells of the
indiv’s body
Occurs in cells that divide often (skin, blood cells, etc.)
Normally happens in DNA replication for every 300 mitotic
cell divisions
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Allelic Disease: different phenotypes but caused by 1 mutation;
different clinical phenotypes caused by mutations in the same gene
Arise from a mutation that affects a protein that is used in
different tissues
Causes of Mutation
1. Spontaneous Mutation: originates as an error in DNA
replication
a. May happen due to the tendency of free DNA bases
to exist in 2 slightly different chemical structures
(tautomers)
a. If unstable base is inserted into newly
forming DNA -> error will be generated; can
insert non-complementary base; 1 of the
daughter cells has a diff base pair, this will
create an altered and unaltered DNA
b. Gonadal mosaicism: a parent has a mutation in
some sperm or oocytes
a. Spontaneous mutation occurred in the
developing testis or ovary and was
transmitted only to the cells descended
from the original cell bearing the mutation
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b. Suspect gonadal mosaicism when more
than one child in a family has a genetic
condition but both parents do not have the
mutation
c. Fairly common
a. Mitochondrial genes mutate at a higher
rate than nuclear genes because Mito
cannot repair the DNA
b. Each person has about 175 spontaneously
mutated alleles
d. Hot spots: regions of the DNA where the sequences
are repetitive
a. Mutations are more likely to occur
b. Molecules that guide and carry out
replication become “confused” by short
repetitive sequences
2. Induced Mutation
a. Intentional use of Mutagens
a. Chemicals or Radiation
1. Alkylating agents: chemicals that
remove a DNA base and replaced by
any of the 4 bases (3 of w/c are a
mismatch against the
complementary strand, only 1 is a
correct match)
2. Acridines: dyes that add or remove
a single DNA base
3. Common products that contain
mutagens: hair dye, smoked meat,
flame retardants used in children’s
sleepwear, food additives
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b. Ames Test: assess how likely a substance is
to harm the DNA of rapidly producing
bacteria
1. Ex: strain of Salmonella that cannot
grow when amino acid Histidine is
absent from the medium
a. If this Salmonella strain
grows on the deficient
medium -> gene is mutated
that allows growth
c. Limitation of Mutagens: cannot cause a
specific mutation
1. Site directed mutagens: change a
gene in a desired way; more
accurate/precise
a. Gene is mass produced, but
the copies include an
intentionally substituted
one
3. Accidental Exposure to Mutagens
a. Workplace contact, industrial accidents,
medical treatments (chemotherapy and
radiation), exposure to radioactive
weapons, and from natural disasters that
damage radiation-emitting equipment
b. Chernobyl accident (April 25, 1986, Ukraine)
1. Evidence of mutagenic effect:
children who were living near
Chernobyl Plant has a 10-fold
increase rate of thyroid cancer
2. Tracking of mutation rates done
through comparing minisatellite
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sequences: length of short DNA
repeats
4. Natural exposure to Mutagens
a. Natural resources account for 81% of our exposure
(cosmic rays, sunlight, radioactive substances in the
Earth’s crust)
b. Medical x-rays and occupational radiation hazards
add risk
a. Major source of exposure to human-made
radiation: x-rays
1. Less energy, do not penetrate the
body to the extend of Gamma rays
c. Ionizing radiation has sufficient energy to remove
electrons from atoms
a. Breaks the DNA’s sugar-phosphate
backbone
b. 3 types:
1. Alpha Radiation: least energetic,
short-lived, skin absorbs most of it;
tend to harm health but it can do
damage if inhaled or eaten (ex:
Uranium and Radium,)
2. Beta Radiation: can penetrate the
body; tend to harm health but it can
do damage if inhaled or eaten (ex:
Tritium: A form of Hydrogen,
Carbon-14, Strontium-70)
3. Gamma rays: can penetrate the
body and damage tissues; used to
kill cancer cells (Ex: Plutonium and
Cesium isotopes)
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Fidelity of DNA replication: way that enzymes involved in DNA
replication can maintain the accuracy of replication itself
1 enzyme involved in the fidelity of DNA replication: DNA
polymerase
DNA Polymerase: main function is to add nucleotides in the growing
nucleotide chain
1. Proof reading mechanism
a. 3’ -> 5’ exonuclease activity can remove incorrect
nucleotides
b. Error: 1 in every 10^9 – 10^10 base after proof
reading
2. Polymerase exonuclease activity
a. DNA Polymerase I 5’ -> 3’
Exonuclease domain: removes mismatched pair
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Nonsense-mediated decay: response of cells to
shortened proteins that destroys mrnas with
premature stop codons
 Protective response because some
shortened proteins cause a gain-function
and damage the cell
Splice-Site mutations
o A type of point mutation that affects a gene’s
product if it alters the site where introns are
normally removed from the mrna
o Can affect the phenotype if:
 An intron is translated into amino acids
 Exon is skipped instead of being translated
(protein is shortened)
o Exon skipping: created when a missense mutation
creates an intron splicing site where there should
not be one
 An entire Exon is “skipped”
o
Mutation and Damage
Base Pair Mutations (Point Mutations)
Point Mutation: change in a single DNA base
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o
Exon skipping is:
 DELETION at the mrna level
 POINT MUTATION at the DNA level
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Tandem Mutation: two complete copies of a gene next to
each other
Pseudogene: results when a duplicate of a gene mutates;
may disrupt chromosome pairing causing mutations
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Have a direct effect by inserting into a protein-coding gene
and offsetting its reading frame
Have an indirect effect by destabilizing surrounding
sequences
Common among people who have behavioral disorder
(ADHD, autism, schizophrenia)
Expanding repeats: genes that grow as a small part of the DNA
sequence is copied and added
1. Triplet repeat diseases (trinucleotides), once translated, can
harm cells by:
Binding to parts of transcription factors that have stretches
of amino acid repeats similar to or matching the expanded
repeat
Block proteosomes, enabling misfolded proteins to persist
Trigger apoptosis
2. Triplet repeat disease cause “dominant toxic gain-offunction”
many triple repeat disease are “ polyglutamine diseases”:
repeats of the mrna codon CAG, encoding for Glutamine
3. Copy number variant: specific DNA sequence that varies in
number of copies from person to person
Have no effect on the phenotype or may disrupt a gene
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Tautomeric Shifts
Tautomer: diff forms of bases that differ on a single proton shift in
the molecule; isang molecule sa structure ng nucleotide na
nagchange or shifted from 1 location to another
Increases the chance of mispairing during DNA Replication
The shift changes the bonding structure of the molecule and allow
the H bonding with non-complementary bases
DNA Damage: chemical alteration to DNA which can be introduced
by many ways
Left unrepaired: Mutation
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Different ways:
1. Base analogs (base modifications): substitute
purines/pyrimidines during nucleic acid biosynthesis;
creates new binding sites that make the DNA unstable
2. Alkylating agents: causes electrophiles to attack negatively
charged DNA molecules and add carbon-containing alkyl
groups, like CH3, can cause DNA rep to stall, once ma-halt, it
will kill the cell; however stalled reps can sometimes be
resumed without repairing the damage = mutation
3. UV radiation: cross-linking of adjacent Pyrimidines on the
same DNA strand: pyrimidine dimers; formation of Thymine
dimers or pyrimidine rings. Connection of 2 thymine
adjacent to each other, this connection is called cyclobutyl
ring
4. Ionizing radiation: can cause damage by ionizing the
molecules in molecules surrounding the DNA specially
water; form free radicals that are extremely reactive with
DNA, can attack neighboring molecules,
5. Byproduct damage: produce chemical modifications in DNA
(loss of base and single-strand breaks) due to reactive
Oxygen species, hydroxyl radicals, and Hydrogen peroxide;
they are genotoxic due to the loss of bases, can also cause
the formation of single stranded DNA
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Example: G6PD Deficiency (Avoid eating Fava beans or
taking anti malarial drugs to prevent life-threatening
Hemolytic Anemia)
Stem cells offer protection
The oldest DNA strands segregate with the stem cells and the most
recently replicated DNA strands go to the more specialized daughter
cells
Skewed distribution of chromosomes sends the DNA containing
mutations into cells that will soon shed, while keeping mutations
away from stem cells
Factors that Lessen the effects of Mutation
Conditional Mutation: affects the phenotype only under certain
circumstance
Protective if an individual avoids the exposures that triggers
symptoms
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Repair of Mutations
DNA Replication: 1 to 100 million or so bases is incorrectly
incorporated
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DNA replicates approximately 10^6 times during an ave
human lifetime
DNA polymerase and DNA damage response: oversee the
accuracy of replication
DNA repair: cell detects the damage and then signaling in the cell
respond by repairing the damage or will signal apoptosis
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1. Single-strand damage repair: one of those 2 strands breaks
a. Direct reversal
b. Excision repair
2. Double strand break repair: both strands break
a. Homologous recombination
b. Nonhomologous end joining
Mismatch Repair
Mismatch: escaped the exonuclease activities of DNA Polymerase I
and III
To correct: DNA Methylation (Prokaryotes)
Parental: methylated
Daughter strand: non-methylated; the one na sisisrain para
i-repair ang mismatch)
Goal of Mismatch repair: identify the strand with a methylated
adenine in the GATC sequence of the parent strand
Damage Repairs: Single and Double strand damage repair
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SOS: induces repair and mutagenesis; entire cell cycle stops; multifaceted cellular response; >40 pyrimidine dimers
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Nonpolyposis: cancer may occur even without the
presence of polyps
Xeroderma Pigmentosum (XP)
o Autosomal recessive, caused by mutations
 Can reflect malfunction of nucleotide
excision repair or deficient “sloppy” DNA
Polymerase -> Allow Thymine Dimers to
stay and block replication
o Briefest exposures to sunlight cause painful blisters
o Have a 1,000-fold increased risk of developing
cancer
Ataxia Telangiectasia (AT)
o Result of a defect in a kinase that functions as a cell
cycle checkpoint
o Cells produced through the cell cycle without
pausing after replication to inspect the new DNA
and repair any mispaired bases (cells undergo
apoptosis if damage is too great to repair)
o Symptoms: poor balance and coordination (Ataxia),
red marks on the face (Telangiectasia), delayed
sexual maturation, high risk of infection and DM
o
Non-homologous end joining: rejoining of broken DNA parts; prone
to error because it doesn’t use a template
DNA Repair Disorder
DNA Repair Disorders: chromosome breakage persists
Trichothiodystrophy
o Causes dwarfism, intellectual disability, brittle hair
and scaly skin (Low sulfur content)
o Child may appear to be normal for a year or two but
will show dramatical slowing of development
o Premature aging signs begin, life ends early
o Hearing and vision may fail
Inherited Colon Cancer (Hereditary Nonpolyposis Colon
Cancer or HNPCC)
o Aka Lynch Syndrome: Group of 7 disorders linked to
DNA repair defect with different-length short
repeated sequences of DNA
o Colorectal cancer
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The Chromosomes
Characteristic x-shape due to the fact that they are attached at the
centromere or kinetochore; contain all genetic material compacted
or compressed to one another
But in a normal situation, without the mitosis/meiosis (cell division),
the genes/DNA are surrounding or all throughout the nucleus
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Structure that contains the DNA and the storage protein called
histones
Genetic Variation: differences bet members of the same species
Allelic variations: due to mutations in particular genes (ex:
ABO blood group)
Chromosomal aberrations/damage: substantial changes in
chromosome structure
o Typically affect more than 1 gene
o Also called chromosomal mutations
 Sets of chromosomes
22 pairs of chromosomes: somatic
chromosomes (all cells, mostly for protein
synthesis)
1 pair of chromosomes: sex chromosome
 Numbers of individual chromosomes in a
set
Specific chromosome becomes mutated (ex.
Chromosome 21 becomes triplicated: Doan
syndrome)
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1. They can have major effects on the phenotype of an
organism (depends on the composition of the codons,
insertions, deletion, frameshift mutation, missense…
protein expression is changed)
2. They can have major effects on the phenotype of the
offspring of an organism
3. They have been an important force in the evolution of
species
Chromosomes: tail end of each chromosome is called telomere
Center: centromere
Middle: euchromatin: where the protein-coding regions (genes) are
mostly located
Chromo: means color
Soma: means body
Chromosomes: body of color; high affinity to basic dyes; rod-shaped
filamentous bodies that present in the nucleus; carriers of the gene
or unit of heredity; not visible in active nucleus (because not yet
Cytogenetics: field of genetics that involves the microscopic
examination of chromosomes, physical features, microbiota,
illnesses
Cytogeneticist: typically examines the chromosomal composition of
a particular cell or organism; works or specializes in cytogenetics
Allows the detection of individuals with abnormal
chromosome number or structure; provides a way to distinguish
between species
Variation in Chromosomal Structure: study of chromosomal
variation is important for several reasons
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compressed) due to their high-water content but are clearly seen
during cell division (because of their size)
Chromosomes formation
1st described by Strasburger (1875) , and Term chromosome:
Waldeyer (1888)
Chromatin: nucleosomes complex (nucleosome: DNA + Histones);
“beads on a string”; nucleosome core: (histone proteins + 147 bp of
DNA)
Compressed form of DNA, occurs during metaphase stage into the
compressed x-shape
DNA (string) is double stranded, helical, 2 nm wide, rotating in a
clockwise direction
22 pairs homologous, 2 sex chromosomes
Histones (beads): proteins where DNA will wrap around for 1.65
times; 1 full rotation plus 1.65 times; contain/host of 8 proteins per
histone
Size:
smallest human chromosome: ~4.6 x 10^7 bp (base pairs) of
DNA (1.4 cm of extended DNA)
most condensed: ~ 2 micrometers long; (super compressed)
linear: attachment only
during cell division,
individually they are
linear
Nucleosome: 7 proteins without the H1 Histone; DNA plus 7 histone
proteins
Chromatosome: nucleosome + H1 histone
Multiple chromosomes
in 1 cell
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After the rotation of the DNA around histone proteins, these
nucleosomes will fold/coil to create the 30 nm fiber.
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Nucleotide sequence content of the human genome
The 30 nm fiber turns loops approximately 300 nm long
(approximately). These will compress into 250 nm wide fibers that
are then tightly coiled into the chromatid of a (1, 400 nm wide)
chromosome.
Chromosome formation
1. Divide into 2 important sequences: repeated and unique
sequences
a. Repeated sequences: paulit-ulit ang sequence; ex:
telomeres, repeated 6 nucleotide long repetition of
sequences TTA GGG, TTA GGG all throughout
i. Transposons: transposable elements whose
transposition does not require an RNA
intermediate
*DNA-only transposon “fossils”: ancient
*Retroviral-like elements
*LINEs: Lone Interspersed Nuclear Elements
*SINEs: Short Interspersed Nuclear
Elements
LINEs and SINEs are called junk DNA; they
replicate but has no contribution to the dev
of a person, around 33 % of genome
ii. Single sequence repeats
iii. Segmental duplication
b. Unique sequences: non-repetitive sequences; no
patterns; another 50%
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i. Non-repetitive DNA that is neither in
introns nor codons: around 28%
ii. Genes: approx.. 21-22% of the entire
genome
*introns: 20 %; some junk, some for
translocation and recombination; facilitate
recombination of genes during fertilization
*protein-coding regions: 2% only
Parts of a Gene
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Product of transcription: pre-mrna (containing exons: proteincoding, and introns: non-protein coding) that must undergo RNA
splicing.
Post-transcriptional modification must be performed before it goes
out of the nucleus: introns are removed. Exons are ligated to each
other to form the mature mrna. 5’ cap and poly-A tail are added.
Mrna can now exit the nucleus into the ribosomes for translation
Features of Genomic Sequences
NON-REPETITIVE DNA: unique, only 1 copy per haploid; proteincoding genes; size is proportional to the overall genome size (higher
eukaryotes: increase in genome size -> increase in amount and
proportion of non-repetitive DNA)
Higher eukaryotes: humans, animals, multi-cellular, can be fungi
(can be multi or single-cellular)
Not equal genome size: the more complex the organism is, the
higher the genome size
RNA Polymerase will attach at the promoter sequence creating
short nucleotide chain (8 - 10 nucleotides long), then move forward
in 3’ to 5’ direction to create a 5’ to 3’ mrna until terminator
sequence is reached. That’s the time when the RNA polymerase will
dissociate.
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Features of
Genomic
Sequences:
moderatelyrepetitive
sequences
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Interspersed
Elements AKA
Selfish/Junk
DNA because
they undergo
replication, but
they do not
contribute to
the organism’s
development
and function
Tandem Repeat DNA: also repetitive sequences but they are used
well
1. Microsatellites or short tandem Repeats (STRs)
Array: collection of genes’ specific nucleic acids defines by
our cells
2. Minisatellites or Viable Number Tandem Repeats (VNTRs)
DNA fingerprinting: unique in each individual; not literally
the prints on our fingers
The number of TRs of each seq at each loc, varies from 1
indiv. To another
HIGHLY-REPETITIVE SEQUENCES
Satellite DNA (satDNA): short sequences repeated many times;
(Adenine and Thymine) AT-rich repat unit, arrays up to 100 mb –
megabase pairs, big, for protection of our chromosomes and
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attachment; located in heterochromatic regions (Centromeres,
subtelomeres)
Role: Formation and maintenance of heterochromatin
Parts of a Chromosome: 2 essential features of all eukaryotic
chromosomes
1. Centromeres: middle of the chromosome
2. Telomeres: tail-end of the chromosomes
Each provide a unique function i.e., absolutely necessary for the
stability of the chromosome
1. Centromeres: largest constriction of the chromosome and
where the spindle fibers attach (to the kinetochore of the
centromere)
: bases that form the centromere are repeats of a 171-base
DNA sequence
: replicated at the end of S – phase
: facilitated by centromere protein A
: CENP-A is passed to next generation; crucial to centromere
function
: example of an epigenetic change (do not change the DNA
sequence but can change how body reacts or reads a DNA
sequence)
2. Subtelomeres: chromosome region between the
centromere and telomeres
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: consists of 8, 000 to 300, 000 bases
: near telomere the repeats are similar to the telomere
sequence
: contains at least 500 protein-encoding genes (most in
euchromatin but not all because some are in the
subtelomeres)
: about 50% are multigene families that include
pseudogenes (nonfunctional DNA segments that resemble
functional genes)
: TAG sequence but not same, different in the number of
TAG present in the 6-base sequence
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3. Telomeres: provide stability and protection; protect against
endonucleases that degrade nucleic acids, and exonucleases
Before DNA replication, formation of replication bubble. This
replication bubble means that the origin of replication found in the
DNA is being opened up. This is the region that does not contain
genes.
Kinetochores are disc-shaped protein structures associated with
replicated chromatids where spindle fibers attach
Telomeres can still be extended, however a lot are still being
removed. DNA break or double-stranded break. If the telomere
length reaches 0, it will be very difficult for the cells to divide
successfully. Telomeres are biological ________
Written AFTER the chromosome number
Short arm: p
Long arm: q
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Numbers on the right are bonds, and denote the location in the
chromosome
Position of the
Centromere:
chromosomes may
differ in the position
of the centromere,
the place on the
chromosome where
the spindle fibers are attached during cell division.
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Humans: all except telocentric
4 types of chromosomes based on the position of the centromere
1. Telocentric:” no short (p) arm, centromere at the very end
of the chromosomes; found normally in house mouse
2. Acrocentric: very small, short (p) arms, centromere at very
nearly end
3. Submetacentric: short (p) arm is just a little smaller than q
arm; centromere in middle (off middle)
4. Metacentric: p and q arms are exactly the same in length;
centromere in exact middle of chromosome
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Chromosomal Bands
Chromosomes may be identified by regions that stain in a particular
manner when treated with various chemicals.
Several different chemical
techniques are used to identify
certain chromosomal regions by
staining then so that they form
chromosomal bands.
The position of the dark-staining
region or heterochromatin.
Light staining are euchromatic
region or euchromatin.
Based on the staining characteristics of the band.
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Methylated: although they have genes, they are silenced (noncoding)
Stains darker because they are more condensed
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Euchromatin loosely packed: for protein
encoding; RNA polymerase can easily
manage its way onto the chromosome
during protein synthesis
Heterochromatin tightly packed:
purpose/function is for protection
Genes: protein coding regions of the DNA,
~2% of the entire DNA sequence
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Heterochromatin is classified into 2 groups:
1. Constitutive: remains permanently in the heterochromatic
stage, i.e., it does not revert to the euchromatic stage;
structural function/integrity
2. Facultative: consists of euchromatin that takes on the
staining and compactness characteristics of
heterochromatin during some phase of development
C bands: centromere bands
Number of Chromosomes
Presence of a whole set of chromosomes is called euploidy
Gametes normally contain only one set of chromosomes:
this number is haploid (half)
Somatic cells usually contain 2 sets of chromosomes (2n):
Diploid
The condition in w/c the chromosome sets are present in a
multiples of “n” is polyploidy (3n: triploid, 4n: tetraploid)
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Polyploidy: affects
the number of
chromosomes
present in a cell
n: number of
chromosomes
XX – female; XY – male
Turner syndrome (45X) : 1 of the X chromosome of a female is
missing
Aneuploidy: when a change in a chromosome number does not
involve entire sets of chromosomes, but only a few of the
chromosomes
Monosomics (2n-1)
Trisomics (2n+1)
Nullisomics )2n-2)
Tetrasomics (2n+2)
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Chromosome size
In contrast to other cell organelles, the size of chromosomes shows
a remarkable variation depending upon the stages of cell division.
1. Interphase: chromosome are longest & thinnest
2. Prophase: there is a progressive decrease in their length
accompanied with n increase in thickness
3. Anaphase: chromosomes are smallest
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4. Metaphase: Chromosomes are the most easily observed
and studied during metaphase when they are very thick,
quite short, and well spread in the cell.Therefore,
chromosomes measurements are generally taken during
mitotic metaphase.
Detecting Chromosomes
Cytogeneticists use 3 main features to identify and classify
chromosomes (size, location of centromere, banding patterns).
These features are all seen in a karyotype.
Karyotype:
In order to understand chromosomes and their function, we need to
be able to discriminate among different chromosomes.
In a species Karyotype, a pictorial or photographic representation of
all the different chromosomes in a cell of an individual,
chromosomes are usually ordered by size and numbered from
largest to smallest.
All except the sex chromosomes. 1-22, largest to smallest. Current
studies, chromosome 22 is larger than 21.
Karyotype: accurate organization (matching and alignment) of the
chromosomal content of any given cell type.
Chromosomes are arranged and numbered by size, largest to
smallest.
Karyotype is the general morphology of the somatic chromosome.
Generally, represent by arranging in the descending order of size
keeping their centromeres in a straight line.
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Idiotypoe: the karyotype of a species may be represented
diagrammatically, showing all te morphological features oif the
chromosome; sizes of each chromosome
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Karyotyping is useful at several levels:
1. Confirm a diagnosis
2. Reveal effects of environmental toxins
3. Clarify evolutionary relationships
Marrowed blood: almost all cells are nucleated; precursor cells
1. get marrow blood
2. culture in a cell, contains phytohemoglobulin that will
encourage the cell cycle to continue, and fastens it
3. incubate it at37 degrees Celsius at 5% CO2
4. arrest the metaphase of the cell with Colcemid, arrests only
at metaphase stage within 1 -2 hrs
5. hypotonic treatment (sline solution), very low salt content,
will destroy rbc, increase the size of lymphocytes to be able
to further check chrom in those
6. fix it to maintain the arresting of the metaphase atge and
prevent biochem reactions to occur
7. polace in a slide, spread, stain
8. do karyotyping
Genetic abbreviations
The good thing about karyotyping is that first chromosomal
abnormalities can be detected already.
3 copies of chromosome 21, trisomy 21
Copies of chromosome 18: Edward syndrome
3 copies of chromosome 13: Patau syndrome
Centromeres can be drawn with slant lines (1 straight line)
+
dil
der
dup
Gain
Loss
Dilution
derivative
duplication
r
t
tel
Ring chromosomes
translocation
telomere
13, 14, 15: acrocentric
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Direct visualization of chromosomes
1. amniocentesis
2. chorionic villi sampling
3. FISH (Fluorescent… Hybridization)
Tissue is obtained from person
Chromosomes are extracted.
Then stained with a combination of dyes and DNA probes.
1. Fetal tissue
a. Amniocentesis
b. Chorionic villi sampling
c. Fetal cell sorting
d. Chromosome microarray analysis
2. Adult tissue
a. White blood cells
b. Skin-like cells from cheek swab: tongue depressor
or applicator stick, scrape the swab or stick a little
on the inner cheek, then spread on a slide
Use a microscope to locate the cell, develop a print, cut it out, then
the individual chromosomes will be arranged based on the sizes on
the charts
Now: comp will scan the ruptured cells
For detailed identification of, chromosomes are treated with stains
to produce characteristic banding patterns
Example: G-banding
Chromosomes are exposed to the dye Giemsa
Some regions bind the dye heavily: dark bands
(heterochromatin)
Some regions do not bind the stain well: light bands
In humans: 300 G bands are seen in metaphase, 2000 G bands in
prophase
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The banding pattern is useful in several ways:
Distinguishes indiv chromosomes from each other
Detects changes in chromosome structure
Reveals evolutionary relationships among the chromosomes
of closely-related species
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Colcomid: to arrest it on the metaphase stage
Band 11, sub-band 21
Indirect visualization of chromosomes
1.
2.
3.
4.
5.
Beta human chorionic gonadotropin
Inhibin A
Estradiol
Alpha fetoprotein
Pregnancy-associated plasma protein
Semicolon: to separate 2 regions from each other
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