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BIOL& 211, Levels of biological organization, pH scale, 2 H+, ADP,…
BIOL& 211
Chapter 12: The cell cycle
Mitosis
Somatic cells
2 identical daughter cells
Genetic material
Chromosomes
Sister chromatids
Centromere
Chromatin
Cell Division
Asexual reproduction
Growth & development
Tissue renewal
Phases of cell cycle
Interphase
Mitotic phase
Mitosis
Cytokinesis
Cleavage
Cleavage furrow
Prophase
Prometaphase
Metaphase
Anaphase
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Mitotic spindle
Kinetochore
metaphase plate
G1
S (DNA Synthesis
G2
Binary fission
Cell Cycle Control System
Checkpoints
G1 checkpoint
G2 checkpoint
M checkpoint
Cell cycle clock
Cyclins
Cyclin-Dependent Kinases
MPF
Stop and Go signs
G0 checkpoint
Factors that affect rate of cell division
Growth factors
PDGF
Density-dependent inhibition
Anchorage-dependent
Nutrition
Cancer cells
Tumor
Benign
Malignant
Metastasis
Chapter 18: Regulation of Gene Expression
Differential Gene
Cell Differentiation
Morphogenesis
Cytoplasmic determinants
Inductive signals
Induction
Pattern formation
Positional information
Bacteria
Operons
Repressible & Inducible operon
Inducer
Repressor
Regulatory gene
Operator
Genetic Analysis of Early development
Homeotic genes
Embryonic lethals
Axis Establishment
Maternal effect genes
Bicoid gene
Morphogens
Evolutionary Development Biology
Development
Egg
Epigenetics
Phenotype
Evolution
Mutation
Selection
Phenotype
Evo-Devo
Mutation
Egg
Epigenetics
Phenotype
Selection
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Noncoding RNAs
mRNA
miRNA
siRNA
RNA interference
piRNA
IncRNA
small ncRNA
CRISPR-Cas9
Gene regulation
Positive gene regulation
Cyclic AMP (cAMP)
Activator
Negative gene regulation
Gene expression
Differential gene expression
Degradation of mRNA
Degradation of protein
Ubiquitin + Proteasomes
Regulation of Chromatin structure
Histone acetylation
DNA methylation
Epigenetic Inheritance
Regulation of Transcription Initiation
Control elements
Transcription factors
General TF
TATA box
Enhancers & Specific TF
Proximal control elements
Distal control elements
Enhancers + activators
Repressors
Indirect activator & repressor actions
Cancer results from genetic changes that affect cell cycle control
Proto-oncogenes
Oncogenes
Tumor-suppressor genes
Interference with normal cell-signaling pathways
ras proto-oncogene
p53 gene
Cancer Development
Loss of tumor-suppressor gene APC
Activation of ras oncogene
Loss of tumor-suppressor gene SMAD4
Loss of tumor-suppressor gene p53
Additional mutations
Breast Cancer
Luminal A
Luminal B
Basal-like
Her2
Chapter 5: The structure and Function of Large Biological Molecules
Macromolecules
Polymers
Dehydration
Monomers
Hydrolysis
Monomers
Enzymes
Proteins
Catalysts
Polypeptide
Peptide bond
Amino acids
Blood
Functions of proteins
Enzymatic proteins
Storage proteins
Defensive proteins
Transport proteins
Hormonal proteins
Receptor proteins
Contractile & motor proteins
Structural proteins
Four levels of protein structure
primary
Change in primary structure
Sickle-cell disease
Secondary
Tertiary
Quaternary
Denaturation
Renaturation
Proteomics
Nucleic acids
DNA
RNA
Polynucleotides
Nucleotides
A, T, C,G
A, U, C, G
Carbohydrates
Polysaccharides
Starch
Glycogen
Cellulose
Chitin
Monosaccharides
Sugar
Glucose
Fructose
Sucrose
Disaccharide
Maltose
Lipids
Fats
Fatty acid
Saturated fatty acid
Unsaturated fatty acid
Trans fat
Phospholipid
Steroids
Cholestrol
Chapter 8: An introduction to Metabolism
Forms of Energy
Kinetic energy
Thermal energy
Potential energy
Chemical energy
Laws of Energy Transformation
First law of thermodynamics
Second law of thermodynamics
Entropy
Biological order and disorder
Metabolism
Metabolic pathways
Catabolic pathways
Anabolic pathways
Free Energy Change
System
Surrounding
Exergonic reaction
Energy released
Spontaneous
Endergonic reaction
Energy required
Nonspontaneous
ATP
Structure of ATP
Adenosine Triphosphate
3 phosphate groups
Hydrolysis of ATP
Adenosine diphosphate
Enzyme
Catalyst
Activation energy
Substrate
active site
Induced fit
Cofactors
Enzyme inhibitors
Competitive inhibitor
noncompetitive inhibitor
Allosteric regulation of enzymes
Allosteric activation
Stabilizes active form
Feedback inhibition
Allosteric inhibition
Stabilizes inactive form
Chapter 10: Photosynthesis
Heterotrophs
Chloroplasts
Mesophyll
Stroma
Thylakoids
Chlorophyll
Stages of photosynthesis
Light Reactions
PS II
Pq
Cytochrome complex
Pc
PS I
Fd
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ATP synthase
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Calvin cycle
Phase 1: Carbon fixation
Phase 2: Reduction
Phase 3: Regeneration of CO2 acceptor (RuBP)
glucose
Autotrophs
photoautotrophs
Light reactions
Electromagnetic spectrum
Wavelength
Visible light
Photons
Photosynthetic pigments
Spectrophotometer
Photorespiration
CAM
C4
Chapter 15: The chromosomal Basis of Inheritance
Alterations of Chromosome number and structure
Nondisjunction
Aneuploidy
Trisomic
Trisomy 21
Down syndrome
Monosomic
Polyploidy
Abnormal numbers of sex chromosomes do not usually affect survival
XXX (Klinefelter syndrome)
XYY
XXY
X0 Turner syndrome
Deletion
Duplication
Inversion
Translocation
Genomic imprinting
Crossing over produces new combination of alleles
Mutant
Recombination frequency
Geneticists use crossover data to map genes
Genetic map
Linkage map
Map units
Cytogenic map
Wild-type
Sex Chromosomes and Sex-Linked Genes
Autosomes
X-Linked gene
Duchenne muscular dystrophy
Hemophilia
Red-green color blindness
X Inactivation in Female
Barr body
Y-linked gene
SRY
Chromosomal basis of Mendel's laws
Law of Segregation
Law of independent assortment
Inheritance of Organelle Genes
Extranuclear genes
Mitochondrial gene defects
Genomic imprinting
Chapter 2: The chemical context of life
Molecular shape & Function
Hybridization of orbitals
Matter
Elements
Essential elements
O, C, H, N
Ca, P, K, S
Trace elements
Fe, I, F, B, Mn, Zn,
Isotopes
Radioactive isotopes
Radiometric dating
Half life
Compounds
Atom
Subatomic particles
Neutrons
Nucleus
Mass number
Protons
Atomic number
Electrons
Electron
Formation and Function of molecules depend on chemical bonding between atoms
Chemical bonds
Covalent bonding
Electronegativity
Nonpolar covalent bonding
Polar covalent bonding
Single bond
Double bond
Triple bond
Ionic bonding
Ions
Anion
Cations
ionic compounds
Hydrogen bonding
Van der Waals interaction
The energy levels of electrons
Energy
Potential energy
Kinetic energy
Electron shells
Valence electrons
Electron orbitals
Chemical reactions
Products
Reactants
Chemical equilibrium
Chapter 13: Meiosis and Sexual life cyces
Variations on a theme
Heredity
Genetics
Variation
Inheritance of Genes
Genes
Chromosomes
Karyotype
Homologous chromosomes
Sex chromosomes
Cell division
Asexual reproduction
clone
Parthenogenesis
Sexual reproduction
Diploid cell
Haploid cell
Life cycle
Human life cycle
Haploid gametes
Fertilization
Diploid zygote
Mitosis and development
Meiosis
Stages of Meiosis
Meiosis I
Meiosis II
Prophase II
Metaphase II
Anaphase II
Telophase II
Recombinant chromosomes
Prophase I
Metaphase I
Anaphase I
Telophase I
Independent Assortment
Random fertilization
Crossing over
Synaptonemal complex
Chiasmata
Chapter 17: Gene Expression: From Gene to Protein
Flow of Genetic Information
Gene expression
RNA processing
Split genes and RNA Splicing
5' Cap
Poly-A tail
Introns
Exons
Genes specify proteins via Transcription and Translation
Transcription
mRNA
Initiation
Promoter
Elongation
Termination
Transcription factors
TATA box
RNA polymerase
Translation
Ribosomes
rRNA
P site
A site
E site
Polypeptide
Elongation
Codon Recognization
Peptide bond formation
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SRP
tRNA
Anticodon
Aminoacyl-tRNA synthetases
Genetic code
Triplet code
Codons
Mutations
Substitution mutations
Frameshift mutations
Insertions/ Deletions
Point mutations
Silent
Missense
Nonsense
Mutagens
Carcinogens
CRISPR-Cas9
Gene editing
Chapter 19: Viruses
Bacterial defenses against phages
Restriction enzymes
CRISPR-Cas system
Replicative cycles of phages
Lytic cycle
Virulent phage
Lysogenic cycle
Prophages
Temperate phages
Replicative cycles of Animal viruses
RNA or DNA genome
dsDNA
ssDNA
ssRNA
Serve as template
for mRNA synthesis
for DNA synthesis
dsRNA
Presence or absence of membranous envelope
Viral envelopes
Viral genetic material
Retroviruses
Reverse transcriptase
Provirus
HIV
AIDS
Structure of Virus
Nucleic acid
Protein coat capsid
Membranous envelope
Viral diseases in plants
Prions
Chapter 9: Cellular Respiration and Fermentation
Redox reactions
Oxidation
Reducing agent
Reduction
Oxidizing agent
Electron transport chain
NAD+
NADH
Stages of Cellular respiration
stage 1: Glycolysis
Stage 2: Pyruvate oxidation
stage 3: Citric acid cycle (Kerb's Cycle)
Stage 4: Oxidative phosphorylation
Electron transport Chain
NADH
Complex I
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Chemiosmosis
ATP synthase
ATP
NADH
FADH2
Acetyl CoA
Glucose
Pyruvate
Catabolic pathways
Fermentation
Alcohol fermentation
Lactic acid fermentation
Aerobic respiration
Anaerobic respiration
Chapter 14: Mendel and the Gene Idea
MENDEL'S LAWS
There are alternative versions of genes that account for variations in inherited characters.
Alternative versions of genes are called
alleles
.
Pedigree
Many inherited traits in humans are controlled by a single gene
Recessive Disorders
Tay-Sachs Disease
Cystic fibrosis
Dominant Disorders
Disorders can be tested by
Fetal Testing
Newborn Screening
Genetic Testing
Fetal Imaging
Huntington's disease
Achondroplasia
For each character, an organism inherits two alleles of a gene, one from each parent.
An organism that has two identical alleles for a gene is called
homozygous
and an organism that has two different alleles for a gene is said to be
heterozygous
.
Locus
If the two alleles of an inherited pair differ, then one determines the organism's appearance and is called the
dominant allele
and the other has no noticeable effect on the organism's appearance and is called the
recessive allele
.
A sperm or egg carries only one allele for each inherited character because allele pairs separate from each other during the production of gametes. This statement is called the
law of segregation
.
Law of independent assortment
Monohybrid cross
Dihybrid cross
Punnet Square & Foil
Phenotypes
Genotypes
Finding unknown genotype by
Testcross
.
Homozygous
Heterozygous
True-breeding
P generation
Hybrids
F1 generation
Genetic Cross
F2 generation
Rules of probability
Rule of multiplication
"AND"
Rule of addition
"OR"
The science of genetics began in an abbey garden
Heredity:
The transmission of traits from one generation to the next
Genetics:
Scientific study of heredity
Character:
Heritable feature that varies among individuals
Trait:
Each variant for a character
Variations on Mendel's Laws
Complete Dominance
Incomplete Dominance
Codominant
ABO Blood group
Blood Type A
Carbohydrate A
Anti-B
Blood Type B
Carbohydrate B
Anti-A
Blood Type AB
Carbohydrate A and Carbohydrate B
No Antibodies present in blood
Blood Type O
No Carbohydrates present on Red Blood Cells
Anti-A and Anti-B
A single gene may affect many phenotypic characters
Pleiotropy
Sickle-cell Disease
Epistasis
A Single character may be influenced by many genes
Polygenic inheritance
The environment affects many characters
Nature vs. Nurture
The Chromosomal Basis of Inheritance
Chromosome theory of inheritance
Genes occupy specific loci (positions) on chromosomes.
Chromosomes undergo segregation and independent assortment during meiosis.
Pedigree Analysis
Violations of mendelian genetics
Linked genes
Chapter 3: Water and Life
Acidic and basic conditions affect living organisms
Acid
Hydrogen ion
Base
Hydroxide ion
Buffer
Four emergent properties of water
Cohesion of water molecules
Cohesion
Adhesion
Surface tension
Moderation of Temperature by Water
Temperature and Heat
Thermal energy
Heat
Temperature
Water's high specific heat
specific heat
Evaporative cooling
Heat of vaporization
Floating of Ice on Liquid Water
Water: The solvent of life
Solution
aqueous solution
Solvent
Solute
Hydrophilic
Hydrophobic
Polar covalent bonds in water molecules result in hydrogen bonding
Polar covalent bonds
Polar molecule
Chapter 4: Carbon and the molecular diversity of life
Organic chemistry
Compounds containing carbon
Carbon atoms can form diverse molecules by bonding to four other atoms
Hydrocarbons
Hydrogen
Carbons
Isomers
Structural isomers
Cis-Trans isomers
Enantiomers
Chemical groups
Functional groups
Hydroxyl groups
Carbonyl group
Carboxyl group
Amino group
Sulfhydrl group
Phosphate group
ATP
Methyl group
Chapter 6: A tour of the cell
Prokaryotic cell
DNA
Nucleoid
Eukaryotic cell
Organelles
Cytosol
Cytoplasm
Ribosomes
DNA
Plasma membrane
Animal cell
Endoplasmic Reticulum
Smooth ER
Rough ER
Cytoskeleton
Intermediate filaments
Microvilli
Peroxisome
Lysosome
Phagocytosis
Centrosome
Centriole
Vesicles
Transport vesicle
Vacuoles
Food vacuoles
Contractile vacuoles
Cell wall
Extracellular matrix (ECM)
Cell Junctions
Tight junctions
Desmosomes
Gap Junctions
Plant cell
Organelles
Cell membrane
Nucleus
Nuclear envelope
Nucleolus
Chromatin
Mitochondria
Endosymbiont Theory
Chemical energy
Cristae
mitochondrial matrix
Golgi apparatus
Cytoskeleton
Microfilaments
Actin
Protein
Myosin
Microtubules
Flagellum
Cilia
Ribosomes
Cell wall
Plasmodesmata
Chloroplasts
Thylakoids
Granum
Stroma
Central Vacuole
Microscopy
Light Microscope
Electron Microscope
Scanning Electron Microscope
Transmission Electron Microscope
Magnification
Contrast
Resolution
Chapter 1: Evolution, the Themes of Biology, and Scientific Inquiry
Properties of life
Order
Energy processing
Evolutionary adaptation
Regulation
Growth and development
Response to the environment
Reproduction
Five Unifying Themes
Information
DNA: The genetic material
Gene: A section of DNA of chromosome
Gene expression
Genome
Energy and Matter
Producers
Consumers
Interactions
Feedback regulation
Positive feedback
Negative feedback
Climate change
Evolution
Three domains of life
Domain Bacteria
Prokaryotic
Domain Archaea
Domain Eukarya
Kingdom Plantae
Eukaryotic
Kingdom Fungi
Kingdom Animalia
Protists
Charles Darwin and the Theory of Natural Selection
Population with varied inherited traits
Elimination of individuals with certain traits
Reproduction of survivors
Increased frequency of traits that enhance survival and reproductive success
Scientific Inquiry
Exploration and observation
Data
Inductive reasoning
Scientific process
Exploration and Discovery
Forming and Testing Hypotheses
Deductive reasoning
experiment
Community Analysis and Feedback
Societal benefits and outcomes
Experimental variables and controls
Controlled experiment
Independent variable
Dependent variable
Chapter 11: Cell communication
Apoptosis
Caenorbditis elegans
No death signal
Death signal
Stages of cell signaling
Reception
Transduction
Response
Nuclear & Cytoplasmic response
Regulation of Response
Signal amplification
Signaling efficiency
Scaffolding proteins
Signaling complexes
Termination of the signal
Signal transduction pathways
Protein phosphorylation & Dephosphorylation
Small molecules & Ions as Second messengers
Cyclic AMP
Calcium Ions and IP3
DAG
Receptors in plasma membrane
Receptor Tyrosine Kinase
Ion Channel receptor
G Protein-Coupled receptors
Intracellular receptors
Cellular messaging
Local signaling
Paracrine signaling
Synaptic signaling
Long distance signaling
Endocrine signaling
Chapter 16: The molecular basis of Inheritance
Many proteins work together in DNA replication and repair
Template stand
Dispersive model
Conservative model
Semi conservative model
DNA replication
Helicase
Topoisomerase
SSB
DNA polymerase
Ligase
Okazaki fragments
Leading strand
Lagging strand
Primase
DNA repairing
Mismatch repair
Nuclease
Nucleotide excision repair
Ends of DNA
Telomeres
DNA is genetic material
Evidence that viral DNA can program cells
Bacteriophages
Virus
Chromosome consists of DNA molecule packed together with proteins
DNA
Histones
Nucleosomes
30-nm fiber
Looped domains
Metaphase chromosome
Heterochromatin
Euchromatin
Chapter 7: Membrane Structure and Function
Cellular membranes
Fluid mosaic
Lipids
phospholipid
Proteins
Membrane proteins
Integral proteins
Peripheral proteins
Functions
Transport
Aquaporins
Passive transport
Diffusion
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Facilitated diffusion
Active Transport
Sodium-Potassium pump
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Osmosis
High concentration
Low concentration
Channel proteins
Ion channels
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Water Tonicity
Isotonic
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Hypotonic
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Hypertonic
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Bulk transport
Exocytosis
Endocytosis
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Enzymatic activity
Signal transduction
Cell-cell recognition
Glycolipids
Glycoproteins
Intercellular joining
Attachment to ECM and cytoskeleton
Chapter 20: DNA Tools and Biotechnology
Biotechnology
Techniques
DNA sequencing
Genetic engineering
DNA technology
Nucleic acid hybridization
Gene cloning
Plasmids
Restriction enzymes
Cloning vectors
Recombinant DNA molecule
Cloned organisms
Totipotent cell
Stem cell
Pluripotent cell
iPS
Nuclear transplantation
PCR amplification
DNA fragments
Gel electrophoresis
Denaturation
Annealing
Extension
Expressing genes
RNAi
Analyzing gene expression
RNA sequencing
nucleic acid probes
Reverse transcriptase and cDNA
Gene editing
CRISPR-Cas9
Applications
Agriculture
GMOs
Medicine
RNA seq and microarray assays
SNP detection kids
Pharmacogenetics
Forensics
STR
Ancestry
Environmental cleanup
Levels of biological organization
Biosphere
Ecosystem
Communities
Populations
Organisms
Organs
Tissues
Cells
Organelles
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Emergent properties
Structure and Function
The cell:
An organism's basic unit of structure and function
Eukaryotic cell:
Contains membrane-enclosed organelles.
Prokaryotic cell:
Lacks a nucleus or other membrane-enclosed organelles.
pH scale
Ocean acidification
2 H+
ADP
FADH2
Complex II