Biology

-CH1: The Cell

 Cell Theory:
 All living things are made of cells
 The cell is the most basic unit of life
 Cells only arise from preexisting cells
 Cells carry genetic information in the form of DNA. This genetic material is passed from parent
to daughter cell
 Eukaryotic cells have a nucleus. Prokaryotic cells do not.
 Cytosol – allows for diffusion of molecules throughout the cell
 Nucleus – genetic material is encoded in DNA, which is organized into chromosomes
 Surrounded by a nuclear membrane/envelope ( - a double membrane that contains a nuclear
environment separate and distinct from the cytoplasm)
 Nucleolus – subsection of the nucleus where rRNA is synthesized
 Mitosis – how eukaryotic cells reproduce. Forms 2 daughter cells
 Genes – Coding regions in DNA
 Histones – Organizing proteins that is wound by linear DNA
 Mitochondria – organelle for ATP synthesis
 2 layers:
 Outer membrane: barrier btw the cytosol & inner environment of the mitochondria
 Inner membrane:
 contains cristae (-numerous infoldings)
 contains molecules & enzymes necessary for ETC
 Intermembrane space – the space btw the inner and outer membrane
 Matrix – the space inside the inner membrane
 Mitochondrias are paradigmatic exs. of cytoplasmic/extrranuclear inheritance (- the
transmission of DNA independent of the nucleus)
 Can trigger apoptosis (- programmed cell death) thru release of enzymes from the ETC
 Lysosomes – organelle containing hydrolytic enzymes that are capable of breaking down many diff
substrates, ex: cellular waste products & substances ingested by endocytosis
 Release of hydrolytic enzymes triggers autolysis (- leads to apoptosis. But thru the degradation
of cellular components)
 Endoplasmic reticulum (ER) – a series of interconnected membranes that are contiguous w/ nuclear
envelope.
 Two types:
 Rough ER (RER): studded w/ribosomes for translation of proteins
 Smooth ER (SER): lacks ribosomes. Mainly used for lipid synthesis & detoxification of
certain drugs & poisons. Also transports proteins from RER to the Golgi apparatus.
 Golgi Apparatus - consists of stacked membrane-bound sacs. Receives materials from the ER. Once in
the golgi apparatus, the products may be modified by the addition of various groups, including carbs,
phosphates, & sulfates.
 may also modify cellular products thru the intro of signal seq, which direct delivery of the
substance.
 exocytosis - the secretory vesicle merges w/ the cellular membrane & its contents for release
 Peroxisomes – contain H2O2.
 Breaks down very long fatty acid chains via Beta-oxidation
 Participates in the synthesis of phospholipids
 contain some of the enzymes for the pentose phosphate pathway
 Cytoskeleton – provides structure to the cell & helps it to maintain shape
 Provides a conduit for the transport of materials around the cell
 Made of 3 things:
 Microfilaments – made of actin (- provide protection for the cell & use ATP to generate
force to movement by acting with)
 Play a role in cytokinesis (- division of materials btw daughter cells) w/ the
cleavage furrow (- a ring at the site of division btw the 2 new daughter cells). As
the actin filaments within the ring contract, the ring becomes smaller till it
pinches off the connection btw the 2 daughter cells
 Microtubules – made of tubulin. Radiates throughout cell.
 2 motor proteins:
o Kinesin
o Dynein
 Components of:
o Cilia – projections from a cell that are primarily involved in movement of
materials along the surface of cell
o Flagella – structures involved in movement of the cell
o Both flagella & cilia have the same structure, called the 9+2 structure (- 9
pairs of microtubules to form outer ring & 2 microtubules in the center)
 Centrioles – organizing centers for microtubules. Found in centrosomes
o Play a role in mitosis by organizing mitotic spindle
o Microtubules emanating from the centrioles attach to the chromosomes
via kinetochores
 Intermediate filaments – diverse grp of filamentous proteins, including keratin, desmin,
vimentin, & lamins.
 Involved in cell-cell adhesion & anchor organelles maintenance of the overall
integrity of the cytoskeleton.
 4 tissue types:
 Muscle
 Nervous
 Connective
 Epithelial
 Connective: supports the body and provides framework for epithelial cells to carry out functions
 Main contributors to the stroma
 Stroma – support bone structure
 Ex: bone cartilage, tendons, ligaments
 Produce and secret materials like collagen and elastin to form the extracellular matrix
 Epithelial: Covers the body & lines its cavities, providing protection against pathogen invasion &
desiccation. Are often polarized, having one side facing the lumen and the other interacts with blood
vessels & structural cells
 In certain cells, its involved in absorption, secretion, and sensation
 Basement Membrane – underlying layer of connective tissue made of tightly bound epithelial
cells
 Parenchyma – functional parts of the organ
 Epithelial cells make up the parenchyma
 Shape classification:
 Layers:
 Simple Epithelia – one layer
 Stratified epithelia – multiple layers
 Pseudostratified epithelia – appear to have multiple layers due to differences in
cell height, but is actually only one layer
 Shape:
 Cuboidal – cube shaped
 Columnar – long and thin
 Squamous – flat and scale-like
 Prokaryotes have a nucleoid region (- area where a single circular molecule of concentrated DNA is)
 3 domains of life:
 Archaea
 Bacteria
 Eukarya
 2 Prokaryotic Domains:
 Archaea: more similar to euks than proks, so possibly share common origin with euks.
 Archaea & Eukarya Similarities:
 Start translation w/ METhionine
 Contain similar RNA polymerases

Associate DNA w/ histones
 Archaea & Eukarya Differences:

Archaea have:
o a single circular chromosome
o divide by binary fission/budding
o share a similar structure to bacteria.
 Bacteria: All contain a cell membrane & cytoplasm. Some have flagella/fimbriae.
  Some are mutually symbiotic w/ humans
 Some are pathogens/parasites.
 3 shapes of bacteria:
 Cocci: spherical shape
 Bacilli: Rod shaped
 Spirilli: spiral shaped
 Aerobes – bacteria that require oxygen for metabolism
 Anaerobes – bacteria that do not need oxygen for metabolism
 Obligate anaerobes – bacteria that cant survive in oxygen environments
 Facultative anaerobes – bacteria that can toggle btw aerobic metabolism and anaerobic
metabolism
 Aerotolerant anaerobes – bacteria unable to use oxygen for metabolism but is not harmed by
oxygen’s presence
 Prokaryotic cell structure:
 Cell wall: forms outer barrier of the cell
 2 types of cell walls:
 Gram (+): appears purple in gram staining. Has a thick layer of peptidoglycan (- a
polymeric substance made from amino acids & sugars). Also contains lipoteichoic
acid
 Gram (-): appears pink in gram staining. Has a thin layer of peptidoglycan. Have
outer membranes containing phospholipids and lipopolysaccharides (- triggers
an immune sys response in humans. Causes inflammation response).
 Cell membrane: made of phospholipids
 Envelope: cell wall + cell membrane
 Flagella: bacteria can have 1+ flagella
 Flagella composed of:
 Filament: a hollow helical structure composed of flagellin
 basal body: a complex structure that anchors the flagellum to the cytoplasmic
membrane and is also the motor.
 Hook: connects the filament & the basal body
 Chemotaxis – Ability of a cell to detect chemical stimuli & move forward/away from it
 Plasmids – Circular structure that carry DNA. Carry antibiotic resistant genes, virulence factors
(- traits that increase how pathogenic a bacterium is, ie toxin production)
 Episomes – a subset of plasmids that are capable of integrating into the genome of the
bacterium
 Cell membrane is used for ETC & generation of ATP
 Ribosome size for bacteria are 30s & 50s (euk ribosomes are 40s & 60s)
 Binary Fission – asexual reproduction seen in prokaryotes. Proceeds more rapidly than mitosis.
 Bacterial genetic recombination:
 Transformation: results from the integration of foreign genetic material into the host
genome; Usually comes from other bacteria. Many gram (-) are able to carry this out.
  Conjugation: bacterial form of mating. Involves two cells forming a conjugation bridge (-
allows for transfer of genetic material. Made of sex pilli, which is found on the male.)
Transfer is unidirectional, from male (+) to female (-). Bacteria must contain plasmid sex
factors (- a plasmid. But thru transformation processes, it can be integrated into the
host genome. Referred to as an Hfr (high frequency of recombination)) to form the
pilus. Best studied sex factor is the F (Fertility) factor in E. Coli. Those with the F factor
can transfer it to bacteria without an F factor during conjugation.
 Transduction: The only recombination that requires a vector (- a virus that carries
genetic material from one bacterium to another). Viruses are obligate intracellular
pathogens (aka cant reproduce outside of a host cell)
 Bacteriophages – viruses that infect bacteria. Can lead to accidentally
transferred host DNA during transfer of viral DNA to another host.
 Transposons – genetic elements capable of inserting and removing themselves
from the genome.
 Growth phases:
 1. Lag Phase – bacteria adapting to new local conditions
2. Exponential phase/log phase – growth increases exponentially
3. Stationary phase – slowing reproduction due to the decrease of resources
4. Death Phase – occurs as the resources completely deplete
 Viral Structure:
 Composed of genetic material, a capsid (- a protein coat), and sometimes an envelope
containing lipids.
 If an envelope is present, it will envelop the capsid. But it is sensitive to heat, detergents, and
desiccation. So enveloped viruses easier to kill
 If envelope absent, then the virus will be more resistant to sterilization and are likely to persist
on surfaces for an ext period of time
 Viruses are obligate intracellular parasites. Viruses must express & replicate genetic info within
a host cell because they lack ribosomes to carry out protein synth. After hijacking a cell’s
machinery, a virus will replicate & prod virions (-viral progeny. Can be released to infect
additional cells)
 Bacteriophages do not enter bacteria, they inject their genetic material. In addition to a capsid,
bacteriophages have a tail sheath (- acts like a syringe, injecting genetic material into a
bacterium) & tail fibers (- spooder legs. help the bacteriophage to recognize & connect to the
correct host cell).
 Viral Genomes:
 Genetic info may be circular, linear, singular or double stranded, and composed of either RNA
or DNA
 Single stranded RNA viruses may be (+) sense strand (- the genome may be directly translated
to func proteins by the ribosomes of the host cell, just like mRNA) or (-) sense strand (- viruses
that require the synthesis of an RNA strand complementary to the (-) sense strand, which can
be used as a template for protein synth. (-) sense RNA viruses MUST carry an RNA replicase in
the virion to ensure that the complementary strand is synthesized)
 Retroviruses – enveloped, single stranded RNA viruses. Usually the virion contains 2 identical
RNA molecules. Each virus contains enzyme reverse transcriptase, which synthesizes DNA from
RNA. This is then integrated into the host cell genome where it is replicated & transcribed as if
 it were the host’s DNA. The only way to cure the infected cell is to kill the cell itself. HIV utilizes
this life cycle.
 Viral Life Cycle:
 1. Infection:
 Virus binds to specific receptors to target cell(s). Once bound, the virus & the cell are
brought into close enough proximity for interactions. Enveloped viruses fuse with the
plasma membrane of a cell, allowing entry of the virion into the host cell. Sometimes
the host cell may mistaken the binding of a virus as nutrients and willingly brings the
virus in via endocytosis. Bacteriophage’s tail fiber may have some enzymatic activity,
allowing for both penetration of the cell wall & the formation of pores in the cell
membrane.
 2. Translation & Progeny Assembly:
 Translation of viral genetic material must occur in order for the virus to reproduce. This
requires translocation of the genetic material to the correct location in the cell. Most
DNA viruses go to nucleus to be transcribed to mRNA. The mRNA goes to the cytoplasm,
where it is translated into proteins.
Genetic material from (+) sense RNA viruses stays in the cytoplasm, where it is
translated into proteins by host cell ribosomes.
(-) sense RNA viruses req synth of a complementary RNA strand via RNA replicase, which
is translated to proteins.
Using the ribosomes, tRNA, amino acids, & enzymes of the host cell, the viral RNA is
translated into protein. Many of these proteins are structural capsid proteins for making
new virions. Once the viral genome has been replicated, its packaged with a capsid. Viral
genome muse be returned to its original form before packaging.
 3. Progeny Release:
 There are multiple ways of release:
 Cell death: Viral invasion may initiate cell death. Results in spilling of viral
progeny
 Lyse: Host cell may lyse as a result of being filled with too many virions
o Lysing is actually a disadvantage to the for the virus b/c the virus can no
longer use the cell to carry out its life cycle
 Extrusion: Virus leaves the cell by fusing with its plasma membrane (basically
budding off). Allows for survival of host cell, and continued use of the host cell by
the virus. A virus in this state is said to be in a productive cycle
 4. Lytic & Lysogenic Cycles:
 Depending on growth conditions & the specific virus, bacteriophages may enter a lytic
or lysogenic life cycle. These 2 phases are similar to the lysis and productive cycle
methods of progeny.
 Lytic Cycle: the bacteriophage makes maximal use of the cell’s machinery with little
regard for the survival of the host cell. Once the host is swollen with new virions, the cell
lyses and the other bacteria can be infected. Bacteria in the lytic phase are termed
Virulent.
 Lysogenic profile: when virus doesn’t lyse the bacterium, it may integrate into the host
genome as a provirus/prophage. In this case the virus will be replicated as the bacterium
reproduces b/c it is now a part of the hosts genome. Although the virus may remain
 integrated into the host genome indefinitely, environ factors will cause the provirus to
leave the genome & revert to a lytic cycle at some point. This causes the trapping of
segments of bacterial genome. Infection with one strain of phage generally makes the
bacterium less susceptible to superinfection (- simultaneous infection with other
phages).
 Prions & Viroids:
 Prions and viriods are very small particles that can cause disease under certain circumstances
 Prions: Infection proteins that are nonliving things. Causes diseases by triggering misfolding of
other proteins, usually involving the conversion of a protein from an (alpha)-helical structure to
a (Beta)-pleated sheet. This drastically decreases the solubility of the protein, as well as the
ability of the cell to degrade the misfolded protein. Known to cause mad cow disease,
creutzfelft-Jakob disease, etc
 Viroids: small pathogens consisting of a very short circular single-stranded RNA that mainly
infect plants (There are a few human viriods, ex Hep D virus. Alone, Hep D is innocuous, but
when co-infected with Hep B virus, Hep D can exert silencing function on human hepatocytes).
Viroids can bind to a large number of RNA sequences & will silence genes in the plant genome.
This prevents synthesis of necessary proteins & can cause metabolic & structural derangements
in the plant cell.

-CH2: Reproduction:
 Diploid (2n) – contain 2 copies of each chromosome. Autosomal cells are Diploid. Humans have 46
 Haploid (n) – contain one copy of each chromosome. Germ cells are Haploid. Humans have 23
 Cell cycle – Specific series of phases during which a cell grows, synthesizes DNA, and divides.
Derangements of the cell cycle can lead to cancer.
 Cell Cycle:
o 4 stages:
 G1, S, G2, and M
 Interphase – Consists of G1, S, G2. Longest part of the cell cycle. Genetic material
is in chromatin form, so its less condensed. Needs to be so its available to RNA
polymerase for transcription.
 G0 stage - is within G1 stage. Cell is simply living and serving its function. No prep
for division.
o G1 stage: cells create organelles for energy & protein production, while also increasing cell size.
Passage into the S (Synthesis) stage is governed by the restriction point (- certain criteria that
needs to be met. Ie containing the proper complement of DNA)
o S Stage: cell replicates its genetic material so that each daughter cell will have identical copies.
After replication, each chromosome consist of 2 identical chromatids, bound at the centromere.
Cells entering the G2 have twice as much DNA as cells in G1.
o G2 Stage: Cell passes thru another quality control checkpoint. Cell checks to ensure theres
enough organelles & cytoplasm to divide btw 2 daughter cells. Cell also checks on the DNA
replication process to make sure errors are not replicated to the daughter cells.
o M Stage: consists of mitosis & cytokinesis. 4 phases: prophase, metaphase, anaphase,
telophase (PMAT). Cytokinesis is the splitting of the cytoplasm & organelles into 2 daughter
cells
  Control of the Cell Cycle:
o Cell cycle is controlled by restriction points G1 -> S, G2 -> M
 G1 --> S restriction points determine if the DNA is in good enough condition for
synthesis. If theres DNA damage, the cell cycle stops until the DNA has been repaired.
P53 protein is in control of this.
 G2 --> M restriction point is mainly concerned w/ adequate cell size and correct
organelle replication to support 2 daughter cells

CHAPTER EMBRYO
Section 1.1