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Scientific Method
Lab write-up
Analyze:
o The quality of your experimental design.
o The quality of your write-up.
Make notes or comments in a different colored writing utensil.
Dont panic. You will have the opportunity to re-do.
What are the elements of a good Purpose?
o Detailed yet brief.
o Includes variables (What are you changing? What are you measuring?)
Independent variable: The variable that doesnt depend on other
variables and the one that you change during the experiment.
Dependent variable: What youre measuring. Its dependent on
the independent variable.
What are the elements of a good Hypothesis?
o Independent and dependent variables.
o Prediction of results.
o Justification for prediction (background information)
o Ifthenbecause format for hypothesis.
What are the elements of a good methods section?
o Detailed!
Step by step instructions
List all materials needed for the experiment to succeed
o Multiple trials
o
o
o
What
o
What
o
What
o
What
o
o
o
Control
Single variable being tested
Constants
is a control group?
The absence of the independent variable.
is an experimental group?
The group with the independent variable.
is a constant?
All the details that should stay the same throughout the entire
experiment in both the experimental and the control group.
Example: amount of soil, amount of water, etc.
makes a good conclusion?
Was your hypothesis supported or rejected?
Dont use the word prove
Explain your data.
Sources of Error vs. Whoopsies
Unit 1: Biochemistry
Chemistry Review
Chemical Bonds
Strong Bonds:
o Covalent Bonds share electrons
Polar Bonds share electrons unevenly
Ionic
Example: H2O
Non-Polar Bonds Share electrons evenly.
Example: Methane (CH4)
Bonds attraction between opposite ions
Example: Sodium Ion, Chloride Ion, Positive Sodium Ion,
Negative Sodium Ion.
Weak Bond:
o Hydrogen Bonds strong attraction, but a weak bond!
Hydrogen Bonds are the strongest kindergartners.
Properties of Water
Biochemistry
Macromolecules
Condensation Reactions
Hydrolysis
4 Main Macromolecules
o
o
Proteins
o Grouped according to their function.
o Skin, hair, muscle, blood, enzymes are made of proteins.
Structure:
o Tons of different types and shapes of proteins.
o Monomers are called amino acids.
Amino group NH2
Every single amino acid has NH2
All amino acids also have a Carboxylic acid group (C(O)OH)
The R group (side group) changes depending on what amino
acid it is.
There are 20 types of amino acids.
Arranging these in different combinations allows for a
huge diversity of proteins.
Analogy: Our 26 letter alphabet can be used to create millions of
different words.
o Peptide bonds:
Formed between 2 amino acids following a condensation
reaction (rxn) between the acidic group and the amino group.
Amino acids form H-bonds with each other to produce different
3D shapes.
Proteins: Energy and Enzymes
o Energy The ability to do work or cause change.
Potential Energy Energy of position.
Kinetic Energy Energy of movement.
Exothermic Energy Diagram (Energy that is released from the reaction)
Enzymes
o Proteins that speed up chemical reactions (AKA organic catalysts).
Enzyme Structure
Very specific 3-D shape.
Active Site Pocket of the enzyme that binds to the substrate
(reactant).
Each enzyme can only work with certain reactants
because of the specific shape.
Enzyme Function
1. Substrate binds to active site of the enzyme.
2. Enzyme lowers activation energy and reaction occurs faster.
3. Products are released.
Activation Energy
o The energy needed to start a chemical reaction.
Example
Salivary amylase
Enzyme in spit that breaks polysaccharide (starch) down
to the monosaccharide (glucose).
o If it ends with -ase, its most likely an enzyme.
Coenzymes
(AKA Cofactor) assist in enzyme action by being part of the
active site.
Example:
o Vitamins
Competitive Inhibitors
Bind to the active site but dont react; slow the reaction by
getting in the way.
Factors Affecting Enzymatic Speed
o Enzyme Concentration
Increase enzymes, increase enzyme activity.
Due to more collisions between substrate molecules and
the enzymes.
Will eventually level out.
o Substrate Concentration
Increase substrates, increase enzyme activity.
Due to more collisions between substrate molecules and
the enzymes.
Will eventually level out when the number of enzymes
and substrates even out.
o Temperature
Increase in temperature increases enzyme activity. (Up to a
certain point)
If the temperature is too high, enzyme activity levels out and
then declines rapidly because the enzyme gets denatured.
Denatured: A change in the shape of the enzyme where
its no longer functional.
The same thing happens if the temperature gets too cold.
o pH
Each enzyme has an optimal pH at which the rate of reaction is
highest.
Too drastic of a change in pH will also lead to denatured
enzymes.
o
Unit 2: Cells
Types of Microscopes
Compound Microscope
o Allows humans to see things so small that it cannot be seen with the
naked eye.
o Allows us to see individual cells.
Stereomicroscope
o Sees things in greater detail.
o Sometimes called a Dissecting scope.
Microscope Terms
10x magnification
Objective lenses
Scanning: 4x magnification
Low: 10x magnification
High: 40x magnification
o Total magnification
Scanning: 40x magnification
Low: 100x magnification
High: 400x magnification
Resolution: The ability of a microscope to distinguish two objects as
separate.
Field of View: Everything that can be seen through a microscope.
Depth of Field: Portion of field that appears sharp.
o Determined by adjusting the fine adjustment knob.
o
Cells
Cell size: Small cells are more efficient because of the high surface area to
volume ratio.
Animal Cells
Organelles
Plant Cells
o
o
Animal Cell
DNA inside
nucleus
Plant Cell
Prokaryotic Cells
Prokaryotic Cells
o Ex: Bacteria
o Smaller than eukaryotic cells.
o Contain no membrane bound organelles, only:
Cell membrane
Cytoplasm
Ribosomes
Ribosomes are pieces of RNA. RNA are pieces of rewritten
DNA.
Nuclear Material
DNA
RNA
Cell Wall
Cell Transport
Membrane Transport
Active Transport
o Transport of substance against the concentration gradient.
Molecules move from low concentration to high concentration.
Uses energy and a membrane protein.
Vesicular Transport
o Movement of large amounts of material using a vesicle.
Endocytosis: Moves substances into the cell.
Exocytosis: Moves substances out of the cell.
Unit 3: Energy (Cellular Respiration and Photosynthesis)
Types of Energy
Laws of Thermodynamics
Overview of Photosynthesis
Where does all the energy that supports life come from?
o The sun
Sunlight
o
o
o
Converts food energy into usable energy, called ATP, for the cell (+heat)
C6H12O6 + 6O2 6CO2 + 6H2O + ATP
Heterotrophs: Organisms that get their energy from another source.
o Example: animals, fungi, bacteria, protists.
Overview:
o 3 Methods to make ATP.
Phosphocreatine
Glycolysis and (Lactic Acid) Fermentation
(Aerobic) Cellular Respiration
o Track two things:
What energy transfers are occurring?
Where are the carbon atoms?
Phosphocreatine: Enzyme that adds Pi (Phosphate) directly onto ADP to make
more ATP.
o Used for quick energy.
o Anaerobic (doesnt use oxygen)
o Stored in muscles.
o Only works for ~30 seconds!
1. Glycolysis: The partial breakdown of glucose.
o Features:
Used for short term energy production.
Anaerobic
Occurs in the cytoplasm.
o Process:
Priming: ATP is used to add phosphates to glucose.
Cleavage: 6C unit split into 2 3C units.
Energy Recovery: Production of ATP and NADH.
Ends with 2 molecules of Pyruvate (AKA Pyruvic Acid).
Electron Carriers:
o NADH is formed to temporarily hang on to energy before making ATP.
Nicotinamine Adenine Dinucleotide.
o NAD+ and NADH are recycled over and over again!
Glycolysis Summary
o Inputs
Glucose
2 NAD+
2 ATP
4 ADP + 2 P
o Outputs
2 Pyruvate
2 NADH
2 ATP (NET gain)
After Glycolysis, the fate of Pyruvate depends
o Oxygen Absent
Fermentation
Oxygen Present
Cell Respiration
Energy in Heterotrophs
Fate of Pyruvate
o Oxygen absent
Fermentation (in cytoplasm)
o Oxygen present
Cellular Respiration (transition into mitochondria)
2. Transition Reaction
Whats involved?
o Electron carriers: NADH and FADH2 are temporarily storing energy.
o Electron transport proteins: Membrane proteins (part of the
mitochondrial membranes).
H+ Pumps: Membrane protein to pump a proton against
concentration gradient.
ATP Synthase: Protein that uses energy released by movement
of protons down concentration gradient to make ATP.
This process is called Chemiosmosis.
o Oxygen: An input and final electron acceptor of the process.
Catches electrons and binds to H+ to form water.
Process
o How many ATP does each NADH yield?
3 ATP
o How many ATP does each FADH2 yield?
2 ATP
Light Energy:
o Light is a wave.
Wavelength () Distance between two peaks.
2 Reactions
1. Light-dependent reactions
Occurs in Thylakoid membrane.
2. Light-independent Reactions (AKA Calvin Cycle)
Occurs in Stroma.
Also known as Carbon fixation.
Process
Light-dependent Reactions:
1. Sunlight excites e- in chlorophyll of photosystem II and
caught by an e- acceptor.
Cell Reproduction
Human (Eukaryotic) DNA
Storing DNA
o Nucleus:
Nuclear Envelope: Double membrane surrounding the nucleus.
Nuclear Pores: Small holes in the membrane.
o Packaging DNA
Chromatin Long, thin, uncoiled DNA.
Histone Proteins DNA wraps around to help coil.
Chromosomes DNA coiled, thick (stored this way for
replication).
Chromosome (cont.)
Replicated Chromosomes
Chromatin replicates itself into 2 identical pieces of
chromatin.
Chromatin condenses and forms 2 identical chromosomes.
Chromosomes connect together at a structure called
centromere. When they stick together at the centromere,
it creates one big chromosome made up of two identical
chromatids.
Quiz Time
Binary Fission:
o (Remember: no nucleus)
o Single piece of DNA (circular)
o Copies DNA
o DNA moves to opposite sides.
o Cell divides in half.
o Happens very fast.
Eukaryotic Cells
Interphase is the cell carrying out its normal life activities and chromosomes
become duplicated.
Prophase:
o Chromatin coils to form visible chromosomes.
o Nuclear membrane and nucleolus disappear.
o Spindle fibers form between Centrioles, which move to opposite ends
of cell.
Metaphase:
o Chromosomes meet in the middle.
o Each chromatid is attached to separate spindle fibers.
Anaphase:
o Centromeres split and sister chromatids separate as they are pulled
apart to opposite sides of cell.
Telophase:
o Nucleus and nucleolus reappear.
o Cells form two new daughter nuclei.
o Chromosomes begin to uncoil
o Cell begins to divide.
2n = 46 in humans.
Meiosis:
o Cell division that produces sex cells (sperm/egg).
o This is DIFFERENT from mitosis/the cell cycle (which is used for growth
and repair).
Meiosis
Two Divisions:
o Meiosis I:
Separates homologous chromosomes (the pairs).
Diploid haploid.
Total of 2 haploid cells at the end of division.
1 Diploid cell divides into 2 haploid cells.
o Meiosis II
Separates sister chromatids (the Xs).
Haploid haploid
Total of 4 haploid cells at the end of division.
2 Haploid cells divide into 4 haploid cells.
Fertilization
Errors in Meiosis
Asexual Reproduction A single parent passes copies of all its genes to each
of its offspring (a.k.a. clone)
o Clones may be produced by:
Binary fission
Mitosis
Fragmentation
Budding
Sexual Reproduction Two parents each form haploid gametes.
o Gametes fuse together to form a diploid zygote.
o Offspring have genetic variation due to the fusion of two different sets
of chromosomes.
o Occurs only in eukaryotes, including humans.
Cancer
Cancer Unregulated cell growth.
o Cell cycle continues uncontrollably.
o Keeps dividing and dividing doesnt stop.
Tumor: Cluster of cells from unregulated growth.
o Benign
Not dangerous
Not going to affect the body that much
o Malignant
Dangerous
Malicious
Metastasis
o Occurs in malignant tumors
o Cancerous cells spread to different parts of the body the through
bloodstream.
Risk factors
o Sun exposure (UV rays)
o Smoking
o Family history (genetics)
o Chemical exposure
o Radon
o Radiation
o Asbestos
Unit 5: Genetics
Gregor Mendel (1822-1884)
Austrian Monk
Developed Laws of Inheritance
Studied Pea plants (28,000)
Called the Father of Genetics
Mendel did not know that the physical traits inherited were actually
chromosomes and DNA.
Genetic Terminology
Pollination
o Pollen is male plant sperm.
o Plants have both male and female reproductive structures.
o Self-pollination:
Flowers are fertilized by own pollen.
o Cross-pollination:
Flowers fertilized by different flowers.
Mendel produced pure strains by allowing the plants to self-pollinate for
several generations.
Parental (P) generation: Purple x White
F1 Generation: All Purple
F1 Purple x F1 Purple
F2 Generation: 3:1 Ratio purple vs. white
Generations: P, F1, F2
More Terminology
Simple Probability
Product Rule (AKA AND rule) The probability that two events will both
happen; probability = product of their individual probabilities.
Sum Rule (AKA OR rule) Probability of an event that can happen in
multiple ways; probability = sum of their individual probabilities.
Pedigrees
DNA
DNA structure
Guanine
Pyrimidines
Cytosine
Thymine
Guanine will always pair with Cytosine
Adenine will always pair with Thymine
T will always pair with A
C will always pair with G
DNA Replication
Quick review
o Describe the structure of proteins
Amino Acids
o What cell structures build proteins
Ribosomes
o What do proteins do
Enzymes
Transport
Amino Acids
20 types of Amino Acids
Arranging these in different combinations HUGE
diversity of proteins.
DNA controls the cell by determining what proteins are made!
So how does it do that?
o In a 2 step process: Transcription and Translation.
Transcription
o Taking the information of DNA and transcribing (rewriting) it to RNA.
Translation
o RNA leaves the nucleus and is translated into a protein.
The process
o Transcription:
Genetic information is copied from DNA to RNA (Ribonucleic
Acid).
Re-writing of DNAs instructions in the form of RNA.
RNA structure
Single stranded
Ribose sugar
Uracil
mRNA, tRNA, rRNA
Occurs in the nucleus.
o
DNA Vs RNA
DNA
o
Sugar
Deoxyribose
o Nitrogen Base
[A, T,] [C, G]
o Function
Contains heredity information
2 strands
RNA (3 kinds)
o Sugar
Ribose
o Nitrogen Base
[A, U,] [C, G]
o Function
mRNA: Provides instruction (messenger RNA)
tRNA: Delivers amino acids (transfer RNA)
rRNA: Combines with proteins to form ribosomes (ribosomal
RNA)
1 strand
Whats involved?
o DNA (the gene)
Promoter Region where polymerase binds.
Termination signal Causes release of mRNA.
o RNA Polymerase: Forms complimentary base pairs between DNA strand
and RNA nucleotides.
o mRNA (messenger RNA) Molecules that will later be read to make
the protein.
Translation:
Process
o Translation: Assembling proteins from information encoded in the
mRNA.
o Occurs with the ribosomes, located in the cytoplasm/Rough ER.
Whats involved
o mRNA (messenger RNA):
Codons 3 bases of mRNA
o rRNA (ribosomal RNA): Ribosomes Creates the protein by reading
the mRNA.
o tRNA (transfer RNA): Matches mRNA with correct amino acid
Anticodons 3 bases on tRNA, complementary to mRNA.
Mutations
Types of Mutations
Silent mutation: The change in the base sequence does not change the
amino acids.
Missense mutation: The change in the base sequence causes a different
amino acid to be inserted into the protein.