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Intro to Biology: Themes of Life

7/5/16 1:57 PM

Themes of Life
• From organizational hierarchy emerges functional properties
• Organisms interact with the environment
o Unity
o Diversity
o Evolution mediated by Natural Selection
o Life emerges at the level of the cell
Microscopic Tier
• Molecules – clusters of atoms
• Organelles – membrane-bound molecular structures with specific
functions (ex: mitochondria)
Cells – living entities distinguished from their environment by a
molecular membrane
o Not a cell without a membrane!
Organelles contain molecules, which are clusters of atoms held together
Macroscopic Tier
Organism, a living individual, composed of:
• Tissues – groups of similar cells
• Organs – sets of specific tissues that work together to perform function
for organism
• Organ systems – organs that function together for a broader role
• Individual organism
A cell is a unit of living matter separated from its environment b a boundary
called a membrane
Each tissue has a specific function and is made of a group of similar
cells
Each organ is made up of several different tissues
Global tier
Global perspective of life
• Population – individuals of a species within a specific area
• Community – array of organisms living in a particular ecosystem
• Ecosystem – all biotic and abiotic components of a particular area (ex
abiotic: weather)
• Biosphere – all environments on earth that support life
Emergent properties: the whole is greater than the sum of its parts
With the addition of each new level, new properties emerge
•

Biotic and Abiotic Components of Ecosystems:
• Life: interactions between biotic (living) and abiotic (nonliving)
components
• Biotic:
o Producers – photosynthetic organisms provide food (plants)
o Consumers – eat plans (or animals that profit from plants)
o Decomposers – bacteria, fungi, and small animals in the soil
decompose remains of dead organisms
• Abiotic: chemical nutrients required for life
A successful ecosystem must:
• Recycle chemicals necessary for life
•

Move energy through ecosystem
o Energy enters as light and exits as heat

Unity of Life
• All forms of life have common features
o Cellular basis of life
o DNA
• Cellular basis of life
o Structural and functional units of life
o Cells can
§ Regulate internal environment
§ Take in and use energy
§ Respond to environment
§ Give rise to new cells
§ Units that comprise multi-cellular organisms
§ DNA is the genetic (hereditary) material of all cells
All forms of life have common properties
• Reproduction
• Death
• Use energy from their environment
The Unity of Life: All forms of life have common properties:
• Order – the complex organization of living things
• Regulation – an ability to maintain an internal environment consistent
with life

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Growth and development – growth and development controlled by
DNA
Energy processing – acquiring energy and transforming it to a form
useful for the organism
Response to the environment – an ability to respond to environmental
stimuli
Reproduction – the ability to perpetuate the species
Evolutionary adaptation – acquisition of traits that best suit the
organism to its environment

Diversity
There is a vast diversity of life
Life is very diverse
So far about 1
...
004% of body mass
§ Energy processing
§ Oxygen transport
• Iodine (I) is required only by certain species
o 0
...
e
...
1
• Polar covalent – between 0
...
1
• Non-polar covalent – less than 0
...
Compounds
• Molecules: H2 and O2 (NOT compounds, atoms of only a single
element)
• Molecules and compounds: methane (CH4)
Organic Molecules
• A cell is mostly water
• Rest of cell: carbon-based molecules
• Carbon: versatile atom
o Four electrons in outer shell that holds eight
o Carbon can share to form four covalent bonds
o Carbon can use its bonds to
§ Attach to other carbons
§ Form an endless diversity of carbon skeletons
•

Sharing: Polarity, Electronegativity
• Atoms in covalent bond in a constant tug-of-war for the shared
electrons
• Atom’s attraction for electrons, including shared electrons à
electronegativity
o The more electronegative an atom, the more strongly it pulls
electrons toward its nucleus
o How good is an element at pulling an electron
• Unequal electron sharing creates polar molecules
• A water molecule (H2O) has 2 hydrogen atoms covalently bonded to
1 oxygen atom
If two atoms are identical, atoms exert an equal pull on electrons
Two nuclei pulling equally: nonpolar because electrons are shared
equally between atoms
Organic Molecules: Hydrocarbons with functional groups
• Hydroxyl – alcohols and sugars
• Amino – from protein breakdown
• Carboxyl – fatty acids, vitamins, and amino acids
• Carbonyl – sugars
Smaller building blocks à Giant molecules
• Macromolecules: DNA, carbohydrates, proteins, lipids
o Most macromolecules are polymers
o Polymers: smaller molecules (monomers) linked together
o Cells link monomers by dehydration reactions
Giant molecules à Smaller building blocks
• Organisms break down macromolecules
o Cells break up monomers into monomers by hydrolysis reactions
Linking Monomers
• Cells Link monomers together by dehydration reactions
Carbohydrates
• Carbohydrates = sugars for energy and structure
• Sugar = Saccharide = monomer
• Glucose: C6H12O6
Monosaccharides
• Simple sugars
o Glucose is found in sports drinks
•
•

o Fructose is found in fruit
• Honey: glucose + fructose
• In aqueous solutions, monosaccharides form rings
• Monosaccharides: main fuel for cellular work
Disaccharide Synthesis
• Two monosaccharides à disaccharide (dehydration reaction)
• As H2O forms, an oxygen atom is left, linking
Polysaccharides
• Complex carbohydrates: polysaccharides, long chains of
monosaccharides
o Starch: digestible to produce monosaccharides for energy
§ Form of polysaccharides for plant energy storage
§ Potatoes and grains
o Glycogen: digestible to produce monosaccharides for energy
§ Form of polysaccharide for animal energy storage
§ Liver, muscle
o Cellulose: not digestible
§ Most abundant organic molecule on Earth
§ Cable-like fibrils in plant walls
§ Major component of wood
§ Dietary fiber
Polysaccharides: Glycogen
• Glycogen is more highly branched than starch
• Stored in granules in liver and muscle cells
• Hydrolyzed to release glucose when needed
Polysaccharides: Cellulose
• Structural compound
• Parallel cellulose molecules are joined by hydrogen bonds forming part
of a fibril
• Cellulose cannot be hydrolyzed by most animals
• Not a human nutrient
• “insoluble fiber”
• in fresh fruits, vegetables and grains
• ruminants, termites obtain energy from cellulose via gut inhabitants
• carbohydrates: hydrophilic (water-loving)
Carbohydrates

Simple sugars
o Table sugar, tree sap (syrup) (sucrose)
o Fruit (fructose)
o Milk (lactose)
• Polymerized carbohydrate
o Starch
o Glycogen
o Cellulose
• Readily available source of energy
Lipids are Hydrophobic (not miscible with water)
• Groups of lipids:
•

o Fats and Oils
§ Energy storage
§ Cushioning
§ Insulation
o Phospholipids
§ Cell membranes
o Steroids
§ Sex and stress hormones
Lipids: Fats
• Dietary fat: triglyceride
o = glycerol + three fatty acids
• Unsaturated fatty acids
o Less than maximum number of hydrogens bonded to carbons
• Saturated fatty acids
o Maximum number of hydrogens bonded to carbons
Good vs
...
Saturated Fat
• Most plant fats are unsaturated oils
• Most animal fats are saturated
• Saturated fats and trans fats may contribute to cardiovascular
(atherosclerosis)
• Lipid-containing deposits (plaques) build up within the walls of blood
vessels, reducing blood flow
Fats and Oils:
Free fatty acids

Phospholipid = glycerol + 2 fatty acids + phosphate group
• Membrane: Phospholipid Bilayer
o Membrane is fluid; objects will move through it
• Molecule is polar
• Non-Polar Part + Polar Part = Amphipathic
Lipids: Steroids
• Cholesterol: membrane constituent and building block of steroids
Steroid Hormones:
• Synthetic anabolic steroids: variants of testosterone
• Anabolic steroids build muscles quickly
o Serious health risks
Proteins
• Protein: polymer of amino acid monomers
• Proteins perform most of the tasks the body needs to function
Amino Acids
• All proteins are constructed from a common set of 20 kinds of amino
acids
• Each amino acid consists of
o A central carbon atom bonded to four covalent partners
o A side group that is variable among all 20
Polypeptides: protein polymers
• Amino acids link together by dehydration reactions
• Tens of thousands
Up to 4 levels of protein structure
• Primary: sequence of amino acids (determined by genes in DNA)
• Secondary: H-bonds can form between polar regions of peptide
bonds = helix or pleated sheet
• Tertiary: folding based on R (functional) groups
• Quaternary: polypeptides can associate

Chapter 3: Cells

7/5/16 1:57 PM

Chapter 3: Cells
• Prokaryotic and Eukaryotic Cells
• Eukaryotic Cells
o Membranes, cytoskeleton
o Making proteins with information in DNA
o Endomembrane system
o Energy organelles
Cell junctions between animal cells
• Tight junctions – bind cells very tightly together, forming a leak-proof
sheet
• Anchoring junctions – rivet cells together with cytoskeletal fibers,
forming strong sheets, (tissues subject to stretching or mechanical
stress)
• Gap junctions – (plasmodesmata of plants) allow flow of ions and small
molecules through adjacent cells
Genetic Control of the Cell: Nucleus
• Nucleus contains DNA
o Information passed on to next generation
o Controls cellular activities by directing protein synthesis
o Forms long fibers of chromatin that fold and loop into
chromosomes
• Nuclear envelope separates nucleoplasm from cytoplasm
• Nuclear pores control flow of materials in and out
Genetic Control: Making Cell Proteins
• Nucleic acids are information storage molecules
o Directions for building proteins
• Two types of nucleic acids
o DNA: deoxyribonucleic acid
o RNA: ribonucleic acid
• Genetic instructions in DNA translated from “nucleic acid language” to
“protein language”
Genetic Control of the Cell: Ribosomes and DNA
• Synthesis of mRNA in the nucleus
• Movement of mRNA into cytoplasm via nuclear [ore
• Synthesis of protein in the cytoplasm
Endomembrane System: Manufacturing and Distributing Cellular Products

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Overview: organelles are connected through the endomembrane
system
Some are physically connected; others are related by the transfer of
membrane segments by tiny vesicles (sacs made of membrane)
Endomembrane system is a collection of membranous organelles
Damaged organelles, bacteria or small amounts of cell fluid become
enclosed in a membrane vesicle
Fuses with lysosome
Contents digested to components for reuse
Lysosomes enable cell to continually self-renew

Chapter 4: Energy
Energy converting organelles
• Mitochondria: site of cellular respiration
o Conversion of chemical energy in foods to chemical energy in
ATP (adenosine triphosphate)
• Chloroplasts: site of photosynthesis
o Conversion of light energy to chemical energy of sugar
molecules
Focus on the energy component
• ATP – Adenosine Triphosphate
• ADP – Adenosine Diphosphate
• AMP – Adenosine Monophosphate
ATP for What?
Cellular and organismal work
• Building macromolecules
• Nervous signals
• Digestion
• Transport of molecules
• Movement of muscles (voluntary of involuntary)
• Cellular and organismal reproduction
Energy Flow in Ecosystems
• From a seed to a tree: where does the mass come from?
Energy flow and chemical cycling in the biosphere
Producers and consumers
• Autotrophs = producers: photosynthesizers

Heterotrophs = consumers
o Herbivores
o Carnivores
o Detritivores
Autotrophs: “Producers” of biosphere
• Make own food
• Who are the producers in the biosphere?
Photosynthetic Power
• Photosynthetic organisms make about 176 billion tons of carbohydrates
per year
• All foods from photosynthetic organisms: direct or indirect
•

• Burning plant material a major source of heat, light, and cooking fuel
• Increasing demand and burning of fossil fuel
• à increasing production of polluting greenhouse gases (CO2)
cellular respiration: process of oxidizing glucose to CO2 and H2O
Breathing (respiration): exchanges CO2 and O2 gases between the blood and
outside air
• Sugar = Saccharide: CH2O
• Glucose: C6H12O6
Summary Equation for Cellular Respiration
• Cellular respiration fuel is glucose
• Cellular respiration banks energy in ATP molecules
• Glucose + Oxygen à Carbon Dioxide + Water + Energy
Energy converting organelles: Mitochondria
• Site of cellular respiration
• Intermembrane space
• Cristae: inner membrane folds
o Enclose mitochondrial matrix
o Increased surface area for enzymes that make ATP

Midterm 2
Chloroplasts
• Green parts of plant have chloroplasts for photosynthesis

Highest chloroplast density (half a million per square millimeter or leaf
surface)
• Leaves’ green color from chlorophyll, light-absorbing pigment
o Key to conversion of solar energy to chemical energy
Plant Parts
• Stoma = small opening, orifice
• Stroma = bed covering
o Thick fluid, site of sugar synthesis
• Mesophyll = “middle” and “leaf”
• Granum = grain, unit
• Thylakoid = pouch
•

o System of interconnected membranes in stroma
• Chloroplast = green and form
• Grana = Stacks of thylakoids
• Thylakoid membranes = contain chlorophyll pigments and ATP
synthase
Sunlight: Electromagnetic Energy
• Electromagnetic Energy: travels through space as waves
• Wavelength (frequency): distance between the crests of two adjacent
waves
• Electromagnetic Spectrum: very short gamma rays (high energy) à
very long radio waves (low energy)
Electromagnetic Spectrum
• Visible light: radiation your eyes see as different colors
• Visible: 380nm to about 750nm
• Short = high energy: can damage organic molecules (DNA, proteins)
Pigments like Chlorophyll absorb light
• Chloroplasts contain several pigments
• Chlorophyll pigments transmit and reflect green light
The Process of Photosynthesis
Photosynthesis occurs in two stages:
• Light reaction: Light energy captured by chlorophyll molecules in
chloroplast provides boost for electrons à ATP and NADPH

Chapter 5

7/5/16 1:57 PM

Chapter 5: DNA, Gene Expression, and Biotechnology
• Hydrogen bond: non-covalent attractive interaction of a hydrogen
atom with an electronegative atom, like nitrogen, oxygen or fluorine
...
Does it by wrapping around
DNA, ripping it open, and takes the RNA nucleotides and fits them
where it can
DNA made up of introns and exons
Eukaryotic RNA processed in nucleus
o 5’ cap: single guanine nucleotide
o 3’ tall: poly-a tail of 50-250 adenines
o RNA splicing: removal of introns and joining of exons
o à mRNA
Translation à protein
• Occurs in the cytoplasm
• Requires:
o Amino acids
o Energy (ATP)
o Messenger RNA (mRNA, made during transcription)
o Ribosomes (rRNA and ribosomal proteins)
o Transfer RNAs (tRNA)
• Ribosome
o rRNA
o Ribosomal protein
o Large subunit and small subunit (involved more in dealing with
the nucelotides)
• Transfer RNA (tRNA)
o Carries amino acids
o Matches its anticodon with codon on mRNA
o Freely flow in the cytoplasm
o Each is associated to an amino acid
• tRNA must be changed with amino acids
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•

•

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o 1) amino acids and tRNAs float freely in the cytoplasm
o 2)
Specific charged tRNAs join growing protein based on
codon/anticodon complementary
o 3) a tRNA will dock if the complementary RNA codon is present
on the ribosome
o 4) the amino acids join together to form a polypeptide
Protein chain grows, adding new amino acids and making peptide
bonds
o 5) the ribosome moves on to the next codon to receive the next
tRNA

o 6) when the ribosome reaches the stop codon, no tRNA can
base-pair with the codon on the mRNA
...
Microtubules form and
begin to migrate toward the poles of the cell, where they are
anchored by centrioles
...

Metaphase
o Chromosomes align at the middle of the cell, between the
poles
...
During cytokinesis in an animal cell,
a band of filaments contracts around
...

Nuclear envelopes reform
• Prophase II – Microtubules lengthen
• Metaphase II – chromosomes alig at middle of cell
• Anaphase II – Sister chromatids are seprated by shortening of
microtubules
• Telophase II – Four haploid daughter cells result
...
characters
First experiment – Monohybrid Cross
• Single-factor cross (only different in one character)
• Mendel followed his experiment for 2 generations
o Parental and Filial
o F1
o F2
• Definitions:
o True breeding: repeated generations have consistent traits
o Hybrid: offspring of two different true-breeding varieties
Mendel’s Laws
From his experiments with pea plants he made several seminal
determinations
o Genes and alleles
o Different genes independently assort
o Dominant and recessive traits
o Segregation of alleles
Four hypotheses from monohybrid cross
• Alternative versions of genes: alleles

For each character, an organism inherits two alleles, one from each
parent
o Homozygous for character if alleles are identical
o Heterozygous for character if the alleles are different
• If two alleles of an inherited pair differ (heterozygous)
o Dominant allele: determines the organism’s appearance
o Recessive allele: has no noticeable effect on appearance
• Gametes carry only one allele for each character
o Law of segregation: allele pair segregate (separate) from each
other during the production of gametes
Types of Alleles:
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•
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Recessive (trait or allele): phenotype observed when two copies of
allele are required to express trait (homozygous)
Dominant (trait or allele): phenotype observed when homozygous or
heterozygous

Chapter 21: Circulation and Respiration

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Lungs
• Massive surface area for gas (O2 and CO2) exchange
• 300 million alveoli create respiratory surface
The lungs are mostly open space
Alveoli
• Sacs of tissue to create massive surface area
• Each alveolus surrounded by a net of capillaries
Gas exchange in lung
• O2 from environment is exchanged for CO2 from the body
• Simple diffusion between the alveoli and capillaries
Hemoglobin carries O2
• Hemoglobin: respiratory pigment, binds to oxygen
• Changes color when it binds with O2
• Hemoglobin has 4 protein chains, each with iron atom (binds O2)
• Rbc: 250 million hemoglobin molecules à 1 billion O2 molecules
Effects of Smoke on the Respiratory System
• ETS: Environmental Tobacco Smoke = “secondhand smoke”
• Inhaled passively (passive smokers) if in same environment as smokers
(active smoker)
• ETS contains:
o Carbon monoxide (CO)
o Particulates (tar)
• ETS damages lungs, but chemicals can also pass into bloodstream
CO binds hemoglobin better than O2
• Small amounts of carbon monoxide can bind a lot of hemoglobin
• Carbon monoxide causes oxygen shortages in tissues
• Carbon monoxide is especially damaging to fetuses and embryos
• Lower than average birth weight associated with smoking mothers are
due to oxygen deprivation
Impact of Smoke Particles
• Exacerbation of bronchitis and asthma
Smoking Causes Bronchitis
• Particles interfere with lung’s defense ssytems
• Cough: first response to lung irritants
o Small particles become trapped in mucus lining
o Cilis move trapped particles to nose and mouth

o Particles increase mucus production, but damage cilia à
bronchitis
Smoking exacerbates asthma
• Asthma: allergic reaction; bronchioles constrict
Smoke causes Emphysema
• Alveoli can become damaged and merge into fewer and larger sacs
o Drastically reduces surface area
o Permanent
Smoking causes lung cancer
• Smoke particulates contain carcinogens
o Particulates stay on lung surfaces for long periods of time
o Risk of mutation remains long after cigarette has been smoked

Extra Credit Opportunity:
Find 3 news articles (2013-present) that connect course material to
social, cultural, economic or political topics
...
Read, understand, and
associate the issues with the course Materials
o EX: Psychology in relation to bio
• Study the figures
...
If they don’t, draw some! They can be theoretical
models to show an idea, but make sure you label each axis! Each
article must have a figure associated with it, personally drawn or
otherwise
• Assimilate the information
...
g
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Backflow of blood is prevented
Blood consists of red and white blood cells suspended in plasma
• Plasma: 90% water
• Rest of plasma:
o Inorganic ions
o Proteins
Blood cells suspended in plasma
• Platelets for clotting
• White blood cells (leukocytes)
o Function inside and outside the circulatory system
Regulation of red blood cell production
• Hormone erythropoietin (EPO)

Some athletes inject themselves with EPO to improve oxygenation of
tissues, but can lead to:
o Clotting
o Stroke
o Heart failure
o Death
Blockage in a blood vessel: prevents blood flow (ischemia)
• Heart attack: damage/death of cardiac muscle cells usually from a
blocked coronary artery
• Stroke: damage/death of brain tissue from blocked arteries in brain
• Erectile Dysfunction: loss of blood flow to penis
•

Blockage: Atherosclerosis
• Plaques develop inside inner walls of blood vessels
• Plaques narrow blood vessels
• Blood flow is reduced
Hypertension
• Consistent pressures above either
o 140 systolic
o 90 diastolic
• Hypertension causes
o Heart to work harder, weakening heart over time
o Increased plaque formation from tiny ruptures
o Increase risk of blood clot formation
• Hypertension can cause
o Heart attacks
o Strokes
o Kidney failure
Other issues of the circulatory system
• Blood disorders
• Vessel disorders
• Abnormal heart rhythms
• Heart failure
• Valve defects (murmurs)
• Aneurysms
• Cerebral vascular diseases

Chapter 22: Nutrition and Digestion

7/5/16 1:57 PM

Why do organisms eat?
Processing food
Human digestive system
Nourishment
Why do we eat?
• Fuel to power the body
o Proteins, carbohydrates, and fats are oxidized inside cells to
make ATP
o ATP is “currency” cell uses to do cellular work
• Organic molecules to build macromolecules
• Essential nutrients
Essential Nutrients
• Cannot be made from any raw material
• Malnourishment: missing essential nutrients
• Undernourishment: insufficient calories
• Overnourishment: too many unhealthy calories consumed
Essential Vitamins and Minerals
• Required in small amounts
• Vitamins: organic (with carbon)
o Water-soluble
o Fat-soluble
• Minerals: inorganic (no carbon)
Ingestion
• Entry and pre-processing
o Initial item capture and manipulation
o Mechanical with minor chemical action
Digestion
• Processing
o Mechanical and chemical action
o Prepares nutrients for absorption
Absorption and transportation
• Shipping
o Absorbs nutrients into body fluids
o Nutrients are delivered to necessary systems
Elimination
• Waste removal

o Potentially hazardous or excess materials removed from body
Digestion
• Mechanical digestion à smaller pieces
o Easier to swallow
o More surface area exposed to digestive fluids
• Chemical digestion: macromolecules à monomers
o Hydrolysis
Herbivores have gut specializations that promote growth of cellulose-digesting
microbes
Path of food
• Oral cavity
• Pharynx
• Esophagus
• Stomach
• Small intestine (SI)
• Large intestine (colon)
• Rectum
• Anus
Path of food: Digestion begins in oral cavity
• Teeth break up food, saliva moistens it
o Salivary enzymes begin starch hydrolysis
o Buffers neutralize acids
o Antibacterial agents kills some bacteria ingested with food
• Tongue tastes, shapes bolus of food, and moves it toward pharynx
Oral cavity to pharynx to esophagus
Swallowing reflex
• Food moves from pharynx into esophagus
• Swallowing reflex prevents food from entering
When food reaches the stomach, its referred to as chyme
Stomach Chemicals and Activities
• Acid
o Parietal cells secrete hydrogen and chloride ions
§ à HCl à pH2
o Acid kills most bacteria and breaks apart cells in food
• Pepsinogen and HCl à pepsin
o Activates more pepsinogen production – positive feedback

o Pepsin digests proteins
• Acid chyme: acidic gastric juices mixed with food
Common Digestive Ailments
• Acid reflux into esophagus—heartburn and GERD
• Bacterial infections (Helicobacter pylori) in the stomach and
duodenum can produce ulcers
• Vomiting—the forceful ejection of stomach and intestinal contents
(chyme) from the mouth
Small intestine: major organ of chemical digestion and nutrient absorption
• Small intestine: small diameter, 6 meters long
• Alkaline pancreatic juice (digestive enzymes)
o Neutralizes acid chyme
o Enzymes digest food
• Bile
o Made in liver (stored in gall bladder)
o Emulsifies fat for digestion by pancreatic enzymes
• Massively increased surface area
Lots of Surface Area in Small intestine: Nutrient Absorption
• Surface area for absorption is increased by
o Long length of small intestine
o Circular folds of the intestinal lining
o Macroscopic fingerlike villi
o Microscopic microvilli on cell surface
• Nutrients pass small intestine epithelium into blood
Role of Liver
• Blood from the digestive tract drains to the liver
• Role of liver:
o Blood glucose conversion to glycogen and storage
o Metabolism of toxins to less toxic forms
o Production of bile
o Synthesis of many proteins



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