The document provides information on cell biology. It describes the anatomy of the cell including organelles like the nucleus, mitochondria, endoplasmic reticulum, and Golgi apparatus. It also summarizes macromolecules like carbohydrates, lipids, proteins, and nucleic acids. Additional topics covered include DNA, chromosomes, genes, transcription, translation, the cell cycle, cellular respiration, photosynthesis, and cell communication.

1. Biology

2. Anatomy of the Cell
Nucleus: Contains DNA
Nucleolus: contains DNA
Ribosomes: Proteins to make amino
acids for the cell
Golgi Apparatus: Packages & modifies
Mitochondria: power house “ATP”
Smooth ER: synthesize lipids
Rough ER: contains rough ribosomes
Cytoplasm: The jell inside
Microtubules: Used fro replication
Centrioles: used for replication

3. Macromolecules
Carbohydrates
Monomer: Monosaccharides
Function: Energy, Glycoproteins, Glycolipids, at the membrane, protein recognition, cellulose (plant cells)
Energy Level: Primary source
Examples: Glucose, fructose, lactose, maltose, sucrose
Biological proceses: Cellular respiration
Lipids
Monomer: Monoglycerols, Free fatty acids, Cholesterol, Triglycerides. LDL & HDL
Function: membranes, steroid hormones, energy, lipoprotein, fat soluble vitamins
Energy level: Secondary
Examples: oils, fats, cholesterol, phospholipid, glycolipids
Biological process: Beta oxidation into acetyl coA
Nucleic Acids
Monomer: Nucleotides
Functions: Inheritable component of Gene, transmission, transcription & translation, all cell have the same gene in 1 organism
Energy: Not used for energy
Example: ATCG
Biological process: DNA replication for mitosis & meiosis & RNA synthesis for translation into primary polypeptide protein
Proteins
Monomer: Amino Acids
Function: Enzymes, transporters, channels, antibodies, microtubules, muscles tissue, energy source
Energy Level: Tertiary
Examples: histadine, Methionine, valine, proline, peptides & polypeptides
Vitamins & Minerals
Vitamins A, D, E, K [Fat Soluble]
A,B,C,D,E, K+, Fe+, Ca+, Na+

4. DNA, Chromosomes & Genes
DNA is all the genetic makeup
that makes YOU as YOU
Chromosomes [23 pairs] we
have are large structures of
DNA that Contain genes “small
snipits”. The chromosomes are
wrapped around histones &
can be unwrapped through a
process called acetylation

5. DNA ingredients
Pentose
Phosphate group
Nitrogenous Base:
2 Bonds
[2 rings Purine] Adenine
[1 ring Pyrimidine] Thymine (Uracil in RNA)
3 bonds
[2 rings Purine] Gaunine
[1 ring Pyrimidine] Cytosine

6. Transcription
RNA processing
(Spliced)
mRNA leave
nucleus & attach
to a ribosome
Activates Amino
acyl charged
tRNA
Translation
Transcription &
Translation

7. Initiation, Elongation & Termination
1.Initiation: After RNA polymerase binds to the promoter, the
DNA strands unwind and the polymerase initiates RNA synthesis
at the start point on the template strand
1.Elongation: The Polymerase moves downstream unwinding the
DNA and elongating the RNA transcription 5’ 3’ in the wake
of transcription the DNA strands re-form a double Helix
1.Termination: Eventually the Rna transcript is released and the
polymerase detaches from DNA
Begins with Tata box
[several transcription factors]
transcription initiation complex

8. RNA processing [Modified & Spliced]
1.Introns are removed
2.Introns are included in
mRNA
3.RNA splicing & includes a
Poly A tail & Cap
Introns are
removedExon 1 Exon 2
Intron
Pre-mRNA  RNA

9. Protein Synthesis
mRNA is transcribed either on free ribosomes
in the Cytoplasm or on the endoplasmic
reticulum. The tRNA reads the codon which
are on the mRNA strand consisting of Adenine,
Guanine, Cytosine & Uracil. Three of these
chemicals together are a codon representing
an amino acid. The transfer RNA reads the
codon on the Mrna and creats a chain of
amino acids that are necessary ingredients for
cell to function.

10. Cell Cycle
G1
Phase
S phase
G2
Phase
M
phase
G1, S, G2: Interphase
M Phase: Mitosis & Meiosis

11. S Phase: Replication of Semi Conservative DNA
 Topoisomerase: CUT it, release it & join it again
 Helicase: unwind parental double helix at the forks
 Single stranded binding protein: helps keep fork open
 Primase: starts a complementary RNA chain, Primer starts at 3’ end of DNA
 DNA pol III: adding nucleotides
 DNA pol I: change RNA to DNA
 DNA ligase: Joining sugar phosphate backbones of all okazaki fragments into continuous DNA
Leading Strand
1. After RNA primer is made DNA pol III starts to synthesize the leading strand
2. The leading strand is elongated continuously in the 5’  3’ direction as the forks progress
Lagging strand
1. Primase joins RNA nucleotides into RNA Primer
2. DNA pol III adds DNA nucleotides to the primer forming okazaki fragments
3. After reaching the next RNA primer to the right DNA pol III detaches
4. Fragment 2 is primed then DNA pol III add DNA nucleotides detaching when it reaches fragment 1
primer
5. DNA pol II replaces the RNA with DNA adding to the 3’ end of fragment 2
6. DNA ligase forms a bond between the newest DNA and the DNA fragment I
7. The lagging strand in this region is now complete

12. Mitosis
46
Meiosis
46
46
46
46 46
23 23 23 23
Prophase: Chromosomes condense &
nuclear
membrane disappear
Metaphase: the paired chromosomes
line up in the middle
Anataphase: The chromosomes separate
Telephase : The chromosomes arrive at
each opposite end.
Cytokinesis: the cytoplasm completely
separates becoming
meiosis results in Genetic Varition …The
first time in prophase 1 the sister
chromatids perform crossing over for
genetic variation. The first time through
in anaphase the homologous
chromosomes separate. Durning the
seond round the individual sister
chromatids separate resulting in 4
haploid cells

13. Cell cycle
DNA Repair
Cell cycle restart
Apoptosis
Death &
elimination of
damaged cells
Checkpoint in Cell cycle
P53 was the first cell cycle checkpoint gene to be discovered
in humans “the guardian of the genome” “guardian angel
gene” “master watchmen” many anti- cancer mechanisms
[tumor suppressor gene]
mdm2 p53 p53
Inactive Active
Cellular & Genetic
stability
DNA damage cell
cycle [ex. Hypoxia]

14. Tumor
metasosis
Cancer
Human body composed of 200 different
cell types that are required to
accomplish a specific function
Cancer is class of disease in which a
group of cells display uncontrolled
growth and exhibit reduced
performance of specialized function
while reproducing without limit
If enough cell become cancerous the
organism dies
Normal
Cells
Tumor
Growth
Tumor
Cells
transformation
proliferation
invasion

15. Taxonomy Domain
Kingdom
Phylum
Class
Order
family
Genus
Species
Prokaryote, Eukaryote, Archaea
Animal, Plant, Fungi,Monera, Protista
Chordata-Presence of spinal chord or not
Mammalia
Carnivora
Common members
Types
Specific Organism [Ex. Homo Sapiens]

16. Natural Selection & Adaptation
Charles Darwin
• Animals Adapt [Adaptation]
• Environment Selects[Natural selection]

17. Mendel Law (Punnet Square)
Gregor
Mendel
“Genetic
Variation”

18. Genotype & Phenotype
Genotype is the
organisms individual
DNA [Ex. Homogenous
for Green eyes]
Phenotype is what you
can see with the naked
eye [EX. Green Eyes]

19. Photosynthesis
Sun + H2O + CO2  C6H12O6 + O2
Oxidized:
Loss H+
Reduced:
Gain H+

20. Cellular Respiration
C6H12O6 + O2 CO2 + H2O + ATP

21. Metabolism
1.Glyoclysis
2.Kreb Cycle
3.Electron Transport Chain

22. Cellular
Respiration
Pathway ATP
produced
ATP
Used
NADH
produced
FADH2
Glycolysis 4 2 2 0
Synthesis of
Acetyl-CoA &
Krebs Cycle
2 0 8 2
Electron
Transport
Chain
34 0 0 0
Total 40 2
Net Total 38
Alternative
Pathways
ATP
produc
ed
Electron
Carriers
Products
Pentose
Phosphate
1 ATP 2 NADPH 5 Carbon Precursor
metabolites
Entner-
Doudoroff
1 ATP 2 NADPH Other precursor
metabolites
Alternate pathway’s

23. Kreb Cycle
Cellular Respiration
Glucose
C02
Pyruvic
Acid
Acetyl
CoA
Glycolysis
2
2
2
2
2
NADHFADH2
C02
Electron
Transport
Chain
4
62
2
Ubiquinone's
Cytochromes
Metal containing Proteins
Flavinones
e-
Proton Gradient
ATP
synthase 34
Final
Electron
Acceptor
Fumarate
Nitrate
Sulfate
Oxygen
Fermentation
NADH
NAD
+
Ethanol
C02
+
Lactic
Acid
Acetic
Acid
Decarboxylation
Goes TO
oxidized
Main PURPOSE
Anaerobic
Aerobic
H+
Energy From e-
Transfer Pumps &
H+ across
Membrane
Protons re-enter
through channel

24. 5. DHAP rearrange to form
G3P
Energy Investment Stage
C C C C C C
Glucose
C C C C C C
Glucose 6- Phosphate
P
CP PC C C C C
Fructose 1, 6- Bisphosphate
ADP
ADP
Lysis Stage
Fructose 1, 6- Bisphosphate
P PC C C C C C
CCC
Dihydroxyacetone Phosphate
(DHAP)
P
1. Glucose (Substrate- Level
Phosphorylation)
2. Glucose Molecules Rearranged
for form fructose 6 phosphate
3. Fructose 6 phosphate
Phosphorylated to form Fructose 1,
6-Biphosphate
4 . Fructose 1, 6-Biphosphate
splits to form (DHAP & G3P)
Glyceraldehyde 3 Phosphate (G3P)
C C CP C C CP

25. Energy Conserving Stage
Glyceraldehyde 3 Phosphate (G3P)
C CCP P C CC
P2
NAD
+
2
NADH2
C CCCCCP P P P
STEP 6: 2 Inorganic
phosphates are added to
(G3P) & 2 NAD+ are
reduced to NADH
Two 1, Phosphoglyceric Acid
ADP
2
2
Two 3 Phosphoglyceric Acid
CCC P C C C P
STEP 7: 2 ATP are
phosphorylated by substrate
level to form 2 ATP
H20
2
C C C C C C
PP
Two Phosphoenolpyruvic Acid (PEP)
STEP 8 & 9: Remaining
Phosphates moved to middle
carbon & water removed from
each substrate
ADP
2
2
C C C C C C
STEP 10: 2 ATP are
phosphorylated by substrate
level to form 2 ATP
Two Pyruvic Acid

26. Formation of Acetyl-CoA
C
C
C
Pyruvic
Acid
OOH
C02
C
C H
Acetate
NADHNAD
+
CoA
Acetyl-CoA
Decarboxylation
C
C
CoA
Fermentation
C
C
C
C02
Pyruvic
Acid
Lactic
Acid
NAD
+
NADH
Acetaldehyde
NADH NAD
+
Ethanol

27. Krebs
Cycle
Acetyl-CoA
CoA
C
C
C
C
C
CC
C
C
OOH
OOH
OOH
Citric Acid
1 2
CoA
C
C
C
C OOH
OOH
OOH
C
IsoCitric Acid
NADH
NAD
+
C02+3
C
C
C
C
C
OOH
OOH
α-ketoglutaric Acid
NADH C02+
C
C
C
C
CoA
Succinyl-CoA
OOH
ADP
GDP
Acetyl-CoA
CoA
CoA
FAD
+
4
5
C
C
C
C OOH
OOH
Succinic Acid
6
C
C
C
CHOO
OOH
Fumaric
Acid
FADH2
7
H20
8
C
C
C
C
Malic
Acid
OOH
OOH
C
C
C
C
OOH
OOH
Oxaloacetic Acid
NADH
Start
Here

28. H20
Electron Transport Chain
Flavoproteins Ubiquinone
Cytochromes (b) Cytochromes (c)
NAD
+
NADH
FADH2
FAD
+
H+
+
+
H+
H+
e- e-
e-e-
e-
e-
H+
H+
H+
H+
H+H+
H+
H+
+
+
+
+ +
+
+
+
+
-
-
-
-
- -
-
-
-
-
𝟏
𝟐
o
e- e-
ATP
synthase
ADP
P+
H+
H+
H+ H+
1
2
4
3

29. Cell Communication
Signal Transduction
pathway
Signal transduction
pathway is a series of
steps by which a signal
on a cells surface is
converted into a
specific cellular
response

30. Local & Distance Signaling
Cells in multicellular organisms communicate by chemical
messengers. Animal & plant cells have cell junctions that directly
connect the cytoplasm of adjacent cells.
In local signaling animal cells may communicate by direct contact
or cel to cell recognition in many other cases animal cells
communicate using local regulators, messenger molecules that
travel only short distances. In long distances signaling plants &
animals use chemical messengers called hormones
Methods of cell communication
1. Gap Junctions
2. Cell-cell recognition use glycoproteins
3. Paracrine signaling secrete signals to nearby cells by
discharging molecuels of local regulator
4. Sypnaptic signaling [ex. Nerve cell]
5. Endocrine signaling secrete horomones into the blood
stream

31. Stages of cell signaling
Earl W. Sutherland
discovered how the hormone
acts on cells
Sutherland suggested that
cells receiving signals went
through 3 processes:
1.Reception
2.Transduction
3.Response

32. Plasma Membrane Receptors: “water soluble”
G protein coupled receptor, Receptor Tyrosine kinase, ligand Gated ion channel
G protein: Is a plasma membrane receptor that
works with the help of the G protein
The G protein act as an on/off switch: If GDP is
bound to the G protein the G protein is inactive
Tyrosine Kinase: Is a plasma membrane
receptor that attach phosphates to tyrosine's. A
receptor tyrosine kinase can trigger multiple signal
transduction at once.
Ligand gate ion channel: Is a Receptor
that acts as a gate when the receptor changes shape.
When signal molecule binds as a ligand to the
receptor the gate allows specific ions such as Na+
or Ca2+ through a channel in the receptor.
Second messengers:
cyclic cAMP &
calcium ion
channels… to further
the signal to a
response

33. Intracellular Receptors: “Lipid Soluble”
Hormone, Steroid or thyroid
The chemical signal is
able to enter the cell &
has ability to turn on/off
genes

34. How to amplify a chemical
signal response
Transduction pathways are a cascade of
molecular interactions that relay signals
from receptors to target molecule's in the
cell. Examples is protein kinases &
protein phosphatases. This pathway is
transmitted by a cascade of protein
phosphorylation. Protein kinase transfers
phosphates from ATP to protein a process
called phosphorylation. Protein
phosphatases removes the phosphate
from proteins a process called
dephosphorylation. This system acts as a
molecular switch. Because a one
molecules can activate many molecules
this response can be amplified a million
fold within an organism. Scaffolding is
another efficient method.

35. Responses can be
located in the
nucleus or
cytoplasm

36. Apoptosis

37. Metabolism
Anabolism: metabolic
pathways that
consume energy to
build compounds
Catabolism: Metabolic
pathways that release
Energy by breaking
down compounds

38. Energy
Kinetic energy: energy of motion
Potential energy: stored energy (not moving object still has energy)
Chemical energy: the potential energy available for release in a chemical
Organisms are open systems: the absorb & release energy

39. Laws of
thermodynamics
1st Law: Energy can be
transferred &
transformed but it
cannot be created or
destroyed
2nd Law: Energy transfer
or transformation
increases the entropy
(disorder or randomness)
of the universe

40. Free Energy
Gibbs formula
▲G= ▲H- T▲s▲G: Change in free (available energy)
▲H: enthalpy (change in total energy)
T: Temperature in Kelvin
▲s: Change in entropy (disorder)
Chemical reactions that..
 Loose free energy are spontaneous or exergonic (catabolism) ▲G < 0 spontaneous
 Absorb free energy are endergonic (anabolism) ▲G>nonspontaneous
 Equilibrium: state of maximum stability ▲G=Equilibrium

41. Exergonic &
Endergonic
Energy
Absorbed
Energy
Released

42. ATP & Cellular Work
ATP “adenosine Triphosphate”
 Immediate source for energy
 Common to ALL living things
 Responsible for mediating most
energy coupling reactions (use of
exergonic reactions to drive
endergonic reactions)
 Composed of ribose (sugar),
adenine (nitrogenous base) and 3
phosphate groups. One ATP
molecule has a ▲G= -7.3Kcal/mol
3 types of Cell Work
Mechanical [ex. Beating of cilia,
muscle contraction, movement of
chromosome during division]
Transport [ex. Active transport]
Chemical [Ex. Respiration Reactions]

43. Hydrolysis
The bond between the 2nd & 3rd
phosphate group breaks. The phosphate
group is transferred to another molecule
(phosphorylation)

44. Enzymes
Cells use enzymes (catalytic proteins) to speed up reactions [LOWER
activation Energy]. Enzymes show specificity the active site of an
enzyme has a specific shape that is specific to the shape of the substrate
that bind to it
Induced fit hypothesis: Substrate induces a change in the shape f the
active site to create a snug fit

45. Enzymes can be
effected by..
pH & Temperature
Optimal Human Temperature: 37ºC
Optimal Thermophilic Bacteria: 77ºC
Optimal pH of pepsin [stomach enzyme]: 2
Optimal Trypsin [intestinal enzyme]: 8

46. Cofactors, Enzyme
inhibitors & Regulation of
Enzyme activity
Cofactors
 Many enzymes require non-protein helpers called cofactors to be active
 May be permanent fixture or bind reversibly along w/substrate
 May be inorganic metals: zinc, iron, copper
 May be organic (coenzymes): vitamins
Enzyme Inhibitors:
Competitive: Mimic the substrate; bind to & block the active site
Noncompetitive: bind away from the active site, cause the enzyme to change shape which changes the shape of the active site.
Regulation of enzyme activity:
Allosteric regulation: binding of an activator or inhibitor molecule to a regulator site on a enzyme which stabilizes the functional or inactive form of the enzyme [ADP acts as activator & ATP
acts as an inhibitor]
Cooperativity: one substrate binds to an enzyme & primes the enzyme to accept additional substrates
Feeback inhibition: product of a metabolic pathway binds to & inhibits an enzyme that acts early in the pathway
-the end product of a metabolic pathway shuts down the pathway
-prevents a cell from wasting chemical resource by synthesizing more product than is needed