Download Workshop: Biology 3 Final Ray Chen Lilit Haroyan

Workshop: Biology 3 Final
Ray Chen
Lilit Haroyan
Special Thanks to Dr. Elkerdany for kindly
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providing his material and support.
Ion, atom, isotope
• Atoms – smallest units that make up the matter
– Hydrogen = H
– Sodium = Na
– Chloride = Cl
• Ions – can form when atoms lose or gain electrons
– Positive and negative ions are attracted to one another and
bond together in ionic bonds
– Ex: Na+, Cl• Isotopes – which have the same numbers of protons and electrons
but different numbers of neutron
– Ex: C-12, C-13, C-14
Atoms
• Protons -- (+) charge
• Electron -- (-) charge
• Neutron -- No charge
• Nucleus consists of protons and neutrons
• Atomic number = # of proton
• Mass number = # of proton+ # of neutrons
• # of protons = # of neutrons
• # of protons = # of electrons
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Example: Carbon
# of proton= 6
# of nutron= 6
# of electron= 6
Atomic number= # of proton= 6
Mass number = 6+6=12
Mass number
Atomic number
Copyright © 2009 Pearson Education, Inc.
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C
Chemical symbol
Let’s Practice
• Given atom Oxygen:
# of proton:__
# of electron:__
# of neutron:__
Atomic number:__
Mass number:__
5
Ionic, covalent, hydrogen bond
• Ionic bond: occurs when electron transfer
from one to the other. One is losing and
one is gaining. (NaCl)
• Covalent bond: occurs when two atoms
share electron (
• Hydrogen bond: Polar water molecules
are attracted to one another and can form
H-bond.
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Transfer of
electron
Na
Sodium atom
Cl
Chlorine atom
+
–
Na+
Sodium ion
Cl–
Chloride ion
Sodium chloride (NaCl)
Na+
Cl–
Types of Chemical Bonds
• A covalent bond results when two atoms share electrons, thereby
completing their valence shells
(–)
(–)
O
H
(+)
H
(+)
Hydrogen bond
Acid, base, buffer, pH
• Acid -- Substance that can release H+ ions
- HCl: HCl-->H+ + Cl• Base -- Substance that can release OHions
- NaOH: NaOH--> Na+ + OH• Buffer -- is a chemical or combination of
chemicals that keeps a pH within a given
range
• pH -- is a mathematical way of indicating
11
+
pH scale
0
1
Acidic solution
Increasingly ACIDIC
(Higher concentration of H+)
Battery acid
2 Lemon juice, gastric juice
3 Grapefruit juice, soft drink,
vinegar, beer
4 Tomato juice
5
Rain water
6
Human urine
Saliva
NEUTRAL
[H+]=OH–]
7 Pure water
Human blood,
tears
8
Seawater
Increasingly BASIC
(Lower concentration of H+)
Neutral solution
9
10
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
Basic solution
14
Organic Molecules
• Inorganic chemistry - chemistry of the nonliving world
• Organic chemistry - chemistry of the living world
– Carbon-based molecules are called organic compounds
– By sharing electrons (what type of bond?), carbon can bond to
four other atoms
– By doing so, it can branch in up to four directions
• CH4 – most simple organic compound
Isomers, hydrocarbon, function
group
• Hydrocarbon -- Compounds composed of
only carbon and hydrogen
• Isomer -- different compounds with the
same molecular formula can be produced
• Functional group --
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Propane
Ethane
Length.
Carbon skeletons vary in length.
Isobutane
Butane
Branching. Skeletons may be unbranched or branched.
2-Butene
1-Butene
Double bonds.
Skeletons may have double bonds,
which can vary in location.
Cyclohexane
Rings.
Benzene
Skeletons may be arranged in rings.
Hydrophobic vs. hydrophilic
• Hydrophobic – afraid of water (hydrocarbons)
• Compounds containing functional groups are
hydrophilic (water-loving)
– carboxyl (COOH), alcohol (-OH), amino (-NH2)
Monomers, polymers
• Polymer: Macromolecule
-
Carbohydrates (Monomer: small sugar)
-
Lipids (Monomer: fatty acid)
-
Proteins (Monomer: Amino acid)
-
Nucleic acids (Monomer: nucleotides)
• Monomer: Building block of
macromolecule
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Short polymer
Dehydration
reaction
Longer polymer
Unlinked
monomer
Hydrolysis
Mono-and-poly saccharides
• Monosaccharides are carbohydrates with a single sugar
molecule
- Glucose, Deoxyribose, ribose
• Polysaccharides are polymers of monosaccharide
- Starch, glycogen, cellulose and chitin
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Monosaccharides: Ready Energy
Polysaccharides as Energy
Storage Molecules
Fatty Acids
• Two types:
– Saturated fatty acids - no double bonds between
carbon atoms
– Unsaturated fatty acids - at least one double bond
between carbon atoms
• Oils tend to contain unsaturated fatty acids
• Fats like butter tend to contain saturated fatty acids
Fatty Acids
Fatty Acids
Hydrophilic
heads
Water
Hydrophobic
tails
Water
Four Levels of Protein Structure
Primary structure
Amino acids
Hydrogen
bond
Secondary structure
Alpha helix
Tertiary structure
Quaternary structure
Polypeptide
(single subunit
of transthyretin)
Transthyretin, with
four identical
polypeptide subunits
Pleated sheet
The Effect of Osmosis on Cells
Isotonic solution
Hypotonic solution
Hypertonic solution
(A) Normal
(B) Lysed
(C) Shriveled
Animal
cell
Plasma
membrane
Plant
cell
(D) Flaccid
(E) Turgid
(F) Shriveled
(plasmolyzed)
NUCLEUS:
Nuclear envelope
Smooth endoplasmic
reticulum
Chromosomes
Nucleolus
Rough
endoplasmic
reticulum
Lysosome
Centriole
Ribosomes
Peroxisome
CYTOSKELETON:
Microtubule
Intermediate
filament
Microfilament
Golgi
apparatus
Plasma membrane
Mitochondrion
NUCLEUS:
Rough endoplasmic
reticulum
Nuclear envelope
Chromosome
Ribosomes
Nucleolus
Smooth
endoplasmic
reticulum
Golgi
apparatus
CYTOSKELETON:
Central vacuole
Microtubule
Chloroplast
Cell wall
Intermediate
filament
Plasmodesmata
Microfilament
Mitochondrion
Peroxisome
Plasma membrane
Cell wall of
adjacent cell
3 components of cytoskeleton
• Microfilaments
• Intermediate filaments
• Microtubules
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1 Enzyme available
with empty active
site
Active site
Glucose
Substrate
(sucrose)
2 Substrate binds
to enzyme with
induced fit
Enzyme
(sucrase)
Fructose
4 Products are
released
3 Substrate is
converted to
products
Energy of Activation
Reaction
without
enzyme
EA without
enzyme
EA with
enzyme
Reactants
Net
change
in energy
(the same)
Reaction with
enzyme
Products
Progress of the reaction
Lock and Key Model
• Enzyme represented rigid
• Substrate fits perfectly in the active site region; if doesn’t
fit perfectly it will not react
Induced-fit Model
• Enzyme structure flexible
• Enzyme and active site adjust shape to bind substrate
 increases range of substrate specificity
3 types of cell transport
•
•
•
-
Passive transport
Requires no energy
Simple diffusion/Osmosis (diffusion of water)
always from high conc to low conc
always involve small/nonpolar molecules
Active transport
Require energy and membrane protein
always go against its concentration
Bulk transport
Require energy
Endocytosis, Exocytosis
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Cellular Respiration
– Glucose loses its hydrogen atoms and is ultimately
converted to CO2
– At the same time, O2 gains hydrogen atoms and is
converted to H2O
– Loss of electrons is called oxidation
– Gain of electrons is called reduction
oxidation
C6H12O6 + 6 O2
6 CO2 + 6 H2O + energy
reduction
Glucose Breakdown
NADH
Mitochondrion
High-energy electrons
carried by NADH
NADH
FADH2
and
OXIDATIVE
PHOSPHORYLATION
(Electron Transport
and Chemiosmosis)
GLYCOLYSIS
Glucose
CITRIC ACID
CYCLE
Pyruvate
Cytoplasm
Inner
mitochondrial
membrane
CO2
CO2
ATP
ATP
Substrate-level
phosphorylation
Substrate-level
phosphorylation
ATP
Oxidative
phosphorylation
Energy Currency
• NADH=3ATP
• FADH2=2ATP
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• Glycolysis takes place in cytoplasm
• Krebbs cycle takes place in the matrix of
mitochondria.
• Electron transport chain takes place in the
inner membrane of mitochondria
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• Anaerobic -- no oxygen
• Aerobic -- have oxygen
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2 ADP
+2P
2 ATP
GLYCOLYSIS
Glucose
2 NAD+
2 NADH
2 Pyruvate
2 NADH
2 CO2
released
2 NAD+
2 Ethanol
Alcohol fermentation
Mitosis
Prophase
Chromosomes condense, nuclear
membrane, centriole separate,
spindle apparatus forms
Metaphase
forming the metaphase plate
Anaphase
Sister chromatid separation
Telophase
Cytokinesis(cytoplasm separate),
spindle disappear, nuclear
membrane forms
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•
•
-
Mitosis: final result: Dipolid (2N)
Somatic cells (body cells)
Meiosis: final result: Hapolid (N)
Egg cells or sperm cells
• # of chromosome in human body cell= 46
• # chromosome in human sperm or egg
cell = 23
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Abnormal sex chromosomes
number
• Down syndrome is trisomy for chromosome 21
• A Turner syndrome female has monosomy for the sex
chromosomes (XO)
• A person with Klinefelter syndrome is an XXY male
Light
energy
6 CO2 + 6
H2O
Carbon dioxide Water
C6H12O6
Photosynthesis
+ 6
O2
Glucose Oxygen gas
Reduction
6 CO2 + 6 H2O
C6H12O6 + 6 O2
Oxidation
CO2
H2O
Chloroplast
Light
NADP+
ADP
+ P
LIGHT
REACTIONS
CALVIN
CYCLE
(in stroma)
(in thylakoids)
ATP
NADPH
O2
Sugar
• PS I: Split of H2O by solar energy
• PSII: NADP+ is reduced to NADPH
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Photon
Photosystem II
Stroma
Electron transport chain
Provides energy for
synthesis of ATP
by chemiosmosis
NADP+ + H+
Photon
Photosystem I
1
Primary
acceptor
Primary
acceptor
2
e–
e–
Thylakoid
membrane
4
P700
P680
Thylakoid
space
3
H2O
1
2
5
O2 + 2 H+
6
NADPH
Chargaff rule
• A-T
• C-G
• DNA replication: occur in the nucleus
• Transcription: occur in the nucleus
• Translation: cytoplasm
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http://www.dnai.org/lesson/go/19436/15510
Next amino acid
to be added to
polypeptide
Growing
polypeptide
tRNA
mRNA
Codons
Third base
First base
Second base
• PCR: is a method of amplifying a specific
segment of a DNA molecule
• Restriction Enzyme: is an enzyme that
cuts double-stranded or single stranded
DNA at specific recognition nucleotide
sequences known as restriction sites.
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Cycle 1
yields 2 molecules
Genomic
DNA
3
1
3
5
3
Target
sequence
5
5
5
3
Cycle 2
yields 4 molecules
3
5
5
2 Cool to allow
3
Heat to
primers to form
separate
DNA strands hydrogen bonds
with ends of
target sequences
5
3
5
3
Primer
5
DNA
polymerase adds
nucleotides
to the 3 end
of each primer
5
3
New DNA
Cycle 3
yields 8 molecules
Genes and Gene Mutations
• A mutation is a change in the nucleotide sequence of
DNA
– Mutations in DNA are rare (one in 100 million cell divisions)
– Base substitutions: replacement of one nucleotide with another
– Deletions or insertions
• Mutations can be caused by
– mutagens
• Radiation (radioactivity, X-rays, UV light)
• Chemicals (pesticides, cigarette chemicals)
– Spontaneous
• Errors in DNA replication
• Phloem: is the living tissue in vascular
plants carries organic nutrients (glucose)
to where needed.
• Xylem is the transport tissue in vascular
plants carries water and minerals from
roots throughout the plant
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•
•
•
•
•
•
•
•
•
•
•
Truebreeding: AA x aa
Monohybrid cross: Single character (tall x short)
Dihybrid cross: Two character (round/tall x wrinkle/short)
Incomplete dominance: Red, pink, white flower
Codominace: AB blood type
Pleiotropy: One gene influencing many characteristics
X-linked gene: Colorblindness/hemophilia
Genotype: gene makeup (AA, Aa, aa)
Phenotype: trait ( have the disease or not)
homozygous: AA or aa
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heterozygous: Aa
Lamarck vs. Darwin
• Jean-Baptiste de Lamarck
– According to Lamarck, individuals passed on to offspring body and
behavior changes acquired during their lives
– Adaptation occurs because of the use or disuse of a structure (Use it or
lose it), an element of the theory of acquired characteristics (wrong)
– Use and dis-use theory (true)
•
Darwin
- Theory of natural selection
- Variation among the population
- limited resources
- Fittest survive, and pass their gene to the next gene
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•
Microevolution involves the evolutionary changes within a
population
• Microevolution involves changes on the small scale
at the level of gene pool alleles
• Causes:
– Mutations introduce new variation into a population
– Gene flow when breeding members of a population leave a population
or new members enter
– Nonrandom mating – selection of specific mates
– Genetic drift – change in allele frequency of a gene pool due to chance
(small population – 50 people or less- maybe one specimen doesn’t
mate)
Two small population can differ strongly
- founder effect occurs when one of a few individuals migrate and
become the founders of a new, isolated population at some distance
from their place of origin
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– bottleneck effect occurs when a population is drastically reduced in
61
Two Types of Succession
• There are two types of succession.
– Primary succession occurs where soil has not
formed.
– Secondary succession occurs on a disturbed
site with soil (such as an old agricultural field)
that returns to a natural pattern of community
change.
Interactions in Communities
• The species in a community can interact in a
variety of ways.
– Competition occurs when species compete for the
same resource.
– In predation, one species preys upon another.
– In parasitism(+/-), one species is a parasite on
another.
– In commensalism(+/-), one in which the interaction
benefits one species, but the other is not affected.
– In mutualism (+/+), the interaction benefits both
species.
Ecology of Ecosystems
• The populations of an ecosystem are
described in terms of their food source.
• Autotrophs, also called producers,
produce their own food.
– Photoautotrophs use the sun to make their
own food.
– Chemoautotrophs obtain energy to make food
by oxidizing inorganic compounds.
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Superior
vena cava
Capillaries of
head, chest, and
arms
Pulmonary
artery
Pulmonary
artery
Capillaries
of right lung
9
Capillaries
of left lung
Aorta
2
7
2
3
3
4
5
10
4
Pulmonary
vein
Right atrium
6
1
9
Pulmonary
vein
Left atrium
Left ventricle
Right ventricle
Inferior
vena cava
Aorta
8
Capillaries of
abdominal region
and legs
Closed Circulatory Systems
• Arteries carry blood away from the heart; elastic walls (why?); high
pressure
• Veins return blood to the heart; thinner walls; unidirectional valves;
larger diameter; low pressure (why?)
• Capillaries - fine network of vessels involved in exchange of oxygen
and food between blood and body’s cells; narrow and thin
Flow of blood through
veins
Comparison of Circulatory Pathways
• All other vertebrates have a double circulatory system
– The systemic circuit includes the blood vessels that carry blood
to the body
– The pulmonary circuit includes the blood vessels that send
blood to the lungs
• The double circulatory system helps terrestrial organisms breathe
air (use lungs)
Right
atrium
To lung
To lung
Left atrium
From lung
From lung
Semilunar
valve
Semilunar
valve
Atrioventricular
(AV) valve
Atrioventricular
(AV) valve
Right
ventricle
Left
ventricle
Gland
Secreted
Digest
Pancreas
Amylase,
chemotrypsin, lipase,
nucleases
Carbohydrate, protein,
fat
Salivary gland
Amylase
Starch to Disaccharide
Large intestine
None
Absorb H2O+Salt