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Final Exam Study Guide
This study guide is not exhaustive; anything from the course is fair game for the
cumulative final exam. Note that main ideas are included and you need to go back to
your notes, outlines, and worksheets to make sure you are familiar with the topics.
Chapter 1
Characteristics of living things
Hierarchical organization of living systems
Cell theory
Molecular basis of heredity
Relationship between structure and function
Evolution gives rise to diversity
Living systems use energy to exist in non-equilibrium states
Chapter 2
Matter
Element
Atoms
Protons
Neutrons
Electrons
Energy levels in atoms
Cations
Anions
Redox reactions
Oxidation
Reduction
Valence electrons
Octet rule
Chemical Bonds
Ionic bonds
Non-Polar covalent bonds
Polar covalent bonds
Hydrogen bonds
Chemical reactions alter bonds!
Properties of water
Chapter 3
Chemistry of carbon
6 elements make up macromolecules
Monomers
Polymers
Macromolecule
Dehydration synthesis
Hydrolysis
4 Groups of Macromolecules, structure, function, and examples
Carbohydrates
Nucleic Acids
Proteins
Lipids
Chapter 4
Cell Theory:
Cell size
Basic Requirements to be a cell
Prokaryotic Cells vs. Eukaryotic Cells
Examples of organisms
Characteristics of cells
Structures of cells
Eukaryotic cell
Nucleus
Ribosomes
Rough ER
Smooth ER
Golgi apparatus
Lysosomes
Peroxisomes
Vacuole
Mitochondria
Chloroplast
Endosymbiant Theory
Cytoskeleton
Extracellular Structures and Cell Movement
Cell-To-Cell Interactions
Adhesive junctions
Tight junctions
Gap (communication) junctions
Chapter 5
Structure of Membranes
phospholipids
proteins
cell surface markers
Passive Transport
Concentration gradient
Diffusion
Facilitated diffusion
Osmosis
Isotonic
Hypertonic
Hypotonic
Active Transport
Endocytosis
Exocytosis
Chapter 6
Flow of Energy in Living Systems
Potential energy
Kinetic energy
Chemical energy
Redox reactions
Laws of Thermodynamics and Free Energy
Endergonic reactions
Exergonic reactions
Activation energy and graphs
ATP – adenosine triphosphate
Enzymes
Induced fit model.
Enzymes affected by:
Temperature
pH
Inhibitors and activators
Metabolism – sum of all chemical reactions
Anabolic
Catabolic
Chapter 7
Cellular Respiration
Autotrophs
Heterotrophs
Aerobic
Anaerobic
Fermentation
ATP Prooduction
Substrate level phosphorylation
Oxidative phosphorylation
For each major phase of Cellular Respiration, you should know where it takes place, the
reactants, products, and biproducts.
Glycolysis
Oxidation of Pyruvate to Produce Acetyl-CoA
Kreb’s Cycle
Electron Transport Chain and Chemiosmosis
TOTAL NET YIELD FROM AEROBIC RESPIRATION:
Glycolysis 2ATP
Krebs 2 ATP
ETC 34 ATP
36-38 ATP
Anaerobic cellular respiration
Fermentation
Chapter 8
Anoxygenic photosynthesis
Oxygenic photosynthesis
THE KIND OF PHOTOSYNTHESIS DESCRIBED IS FOR C3 PLANTS;
EXCEPTIONS WILL BE NOTED AT THE END OF THE CHAPTER
Photosynthesis has 3 distinct phases
Capture of light energy
Production of energy (ATP and NADPH)
Synthesis of organic molecules
6CO2 + 12H2O + light  C6H12O6 + 6 H2O + 6O2
chloroplast
Thylkoid
Stroma
Cholorphyll
Light dependent reactions (LDR)
Photosystems II, ETC, and PS I roles and end products
Light independent reactions (LIR)
Calvin cycle, 3 phases, where it occurs, reactants and products, enzyme
Photorespiration
C3, C4, CAM
Chapter 10
Bacterial Cell Division
Eukaryotic chromosomes
Humans have 46 chromosomes (23 homologous pairs)
DNA Condensed structure
Haploid
Diploid
Homologous pairs
Cell Cycle; know the phases of I and M, and what happens in each
Interphase
Mitosis
Cytokinesis
3 major checkpoints:
G1/S primary checkpoint
G2/M
Spindle
Cancer
Proto-oncogenes
Tumor suppressor genes
Chapter 11
Sexual Reproduction Requires Meiosis
Meiosis occurs in gametes
Meiosis functions in the production of sex cells
4 genetically different haploid cells are produced
Know what goes on in phases of Meiosis, especially what makes it different from mitosis
Meiosis versus Mitosis
Chapter 12
Heredity
True-breeding
Hybrids
Gregor Mendel
Monohybrid cross
Principle of segregation
Pedigrees of dominant traits
Pedigrees of recessive traits
Di-hybrid crosses
Principle of independent
Testcross
Polygenic inheritance
Pleiotropy
Multiple alleles in a human population
Incomplete dominance
Co-dominance
Epistasis
Environmental effect on phenotype
Chapter 13
Chromosomal Theory of Inheritance
Sex Chromosomes and Sex Determination
Autosomes are homologous
Sex chromosomes are not
Female carries XX
Male carries XY
Sex Linkage; males and inheritance of sex linked recessive traits
Dosage compensation
In females one X chromosome is randomly selected for modification
Genetic Mapping
Frequency of recombination is related to relative gene loci.
Nondisjunction leads to aneuploidy
Monosomics
Trisomics
Nondisjunction of sex chromosomes
Chapter 14
Chromosomes are composed of DNA and protein: DNA carries genetic info
DNA Structure
3 components of a nucleotide
Purines & Pyrimidines
Chargaff’s Rule
Rosalind Franklin
Watson and Crick’s Double helix:
bonds between nucleotides vs nitrogen-bases
2 Anti-parallel strands one 5’3’ and the other 3’5’
Semi-conservative Model of DNA replication
Prokaryotic Replication: Single circular chromosome
Begins at A=T rich region (A=T only have 2 H-bonds) and proceeds bi-directionally
Know enzymes for DNA replication and their functions:
Helicase
SS binding proteins
DNA gyrase
Primase
DNA polymerase III( adds nucleotide in 5’ to 3’ direction)
DNA polymerase I
Ligase
Leading strand vs. Lagging strand Synthesis
Okazaki fragments
Eukaryotic Replication: Multiple linear chromosomes & Multiple origins of replication
Telomeres are replicated using telomerase
DNA Repair: DNA polymerase II
Chapter 15
One gene / one polypeptide hypothesis.
The central dogma of molecular biology
DNA –transcription RNA –translation proteins
Modified with discovery of reverse transcriptase (found in retroviruses)
DNA ↔ RNA  proteins
RNA’s and their functions:
mRNA, tRNA, rRNA, snRNA, SRP RNA, MicroRNA
Genetic Code: 64 codons & is degenerate
Stop codons: UAG, UAA, UGA
Start codon: AUG, (methionine) in prokaryotes codes for a slightly different
methionine
Wobble effect at third position
For both Prokaryotes and Eukaryotes know initiation, elongation, and termination for
transcription and translation
Prokaryotic Transcription
Initiation: Promoter – sequence within DNA
Elongation uses RNA polymerase to add ribonucleotides that are complementary to the
template strand of transcription unit
Most common mechanism for termination is the formation of a hairpin structure
In prokaryotes transcription and translation happen simultaneously.
Eukaryotic Transcription
Initiation: Promoter (differs for different polymerases) -10 sequence and TATA box
Elongation occurs in the same fashion, but eukaryotes have multiple RNA polymerases
Termination sites not well defined
Posttranscriptional mRNA processing
5’ cap allows for ribosome to bind
3’ poly A tail to protect the mRNA
Introns—interveneing sequence/ non-coding
Exons—expressed sequence only 1-1.5% of genome
Alternate splicing allows one transcript to code for multiple proteins
Process of Translation
Initiation
Initiation factors associate
Initiator tRNA enters ribosome
Small subunit of ribosome binds mRNA
Large subunit of ribosome binds small subunit
Elongation
tRNA with anticodon that can bind codon enters A site
peptide bond formed in P site
empty tRNA leaves ribosome
translocation
repeat
Termination
Stop codon is reached
Release factors enter ribosome and release, ribosome subunits and mRNA
Direction to roughER via SRP RNA
Mutations: Altered Genes
Point mutation – insertion, deletion, substitution
Chromosomal mutations: Deletions, Duplication, Inversions, Translocation
Chapter 16
Prokaryotes regulate gene expression in response to their environment
Eukaryotes regulate gene expression for development and maintenance of homeostasis
Use transcription factors to initiate transcription
Posttransciptional Regulation
Alternate splicing and mRNA editing
mRNA longevity
Transport out of the nucleus
Initiation of translation
Small RNAs and microRNAs cause RNA interferencce
Table 16.19
Controlled turnover of non-functional proteins
Chapter 17
Recombinant DNA—genetic information from two species
Restriction endonucleases (restriction enzymes)
Gel electrophoresis uses an electric current to separate DNA based on size.
(-) charge of DNA is attracted to the positive charge of the electric current.
PCR makes millions of copies of a sample of DNA
Then the DNA of interest can be sequenced to determine the order of nucleotides
DNA libraries contain entire genome of an organism contained in vectors
cDNA libraries contain the coding genome of an organism
Reverse transcriptase is used to make cDNA
cDNA (coding DNA) only includes exons for a certain polypeptide.
Southern blot detects DNA
Northern blot detects RNA
Western blot detects proteins
DNA fingerprinting uses restriction enzymes and gel electrophoresis
Chapter 18
Genetic maps show the location of genes on chromosomes
DNA Sequencing is the ultimate physical map is entire genomic sequence
Human Genome Project
25,000 genes in human genome
Protein coding genes have start codon, open reading frame, then stop
codon.
Types of Noncoding DNA in eukaryotes (makes up 99% of human DNA)
mRNA can be isolated and used to make cDNA
Only 25,000 genes, but 87,000 cDNAs (which code for proteins) made from
human cells!!!
Alternative splicing
Functional genomics
Proteomics
Transcriptomics
Chapter 19
Stem cells – capable of both continual division and differentiation
Totipotent
Pluripotent
Multipotent
Unipotent
Somatic cell nuclear transfer (Dolly)
Egg is enucleated, DNA from somatic cell added to egg, stimulate for cell division,
implant in surrogate mother.
Problems with this approach seem to stem from our inability to successfully rewind
molecular clocks, “the DNA of somatic cell is old”