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PTYS 214 – Fall 2019
Midterm 1 graded!
Office hours: T,Th 2:30--3:30 SS 423a
Announcements
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Midterm #1
Total Students: 14
Class Average: 72
Low: 22
High: 97
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If you have questions see me!
Do your Homework and make sure you understand it!
Remember: 3 midterms are dropped!
Atoms
• Protons, electrons, neutrons; charge, mass
Chemical Bonds
• Ionic, Covalent, Hydrogen
Carbon and Polymerization
Organic vs. Inorganic Compounds
Alternatives to Carbon
Organic Molecules / Building Blocks of Life
• Lipids, Carbohydrates, Proteins, Nucleic Acids
Last Time
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Chains of nucleotides linked together by dehydration reactions between the phosphate group of one and the sugar residue of the next
Example: RNA Bases used:
- Guanine - Cytosine - Adenine - Uracil
Polynucleotides
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Deoxyribonucleic Acid (DNA)
Stores the genetic code
Two polynucleotide strands held together by hydrogen bonds between adjacent bases:
- Guanine - Cytosine - Adenine - Thymine
The two DNA strands are complementary
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DNA vs. RNA ?
1.Choice of sugar
2. Choice of bases
3. Structure: Double vs. single strand
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The language of DNA / RNADNA can be thought of as a string of letters (the bases of the nucleotides):
English Language DNA Language
Letters 26: A -- Z 4: A, G, C, T(U)
Units Words (different lengths) Codons (3 “letters” )
Language Ordered succession Ordered succession of words of codons
What do you think this language describes?
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Each codon represents an amino acid!
43= 64 “words” representing 20 amino acids plus one start and 3 end signals
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Three major functions of DNA/RNA
DNA mRNA ProteinTranscription Translation
Replication
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Three major functions of DNA/RNA
DNA mRNA ProteinTranscription Translation
Replication
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Replication: DNA → DNA (Templated Polymerization)
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Note: polymerase, helicase, primase are enzymes (proteins)!
Explanation of Darwin’s theory
Even though DNA replication proceeds with incredible accuracy, errors do occur (< 1 error per billion bases copied) – mutations
If the organism survives the mutation, the mutation will be copied every time DNA is replicated
Mutations cause diversity within species
Some mutations have no effect, most are detrimental, and in very rare occasions mutations are useful – basis for evolution via natural selection
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Three major functions of DNA/RNA
DNA mRNA ProteinTranscription Translation
Replication Transcription
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Transcription: DNA → mRNA
mRNA carries the information on how to build proteins
Like DNA replication, but only a section (gene) of one DNA strand is duplicated
mRNA messenger RNA
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Three major functions of DNA/RNA
DNA mRNA ProteinTranscription Translation
ReplicationTranslation
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Each type of tRNA can attach a specific amino acid at one end, and at its other end displays a specific sequence of three nucleotides (anticodon)
Transfer RNA (tRNA)
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Translation: RNA → Protein
Note: RNA can be a catalyst!
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RNA typesmRNA = messenger RNA (mRNA)
RNA molecule that transcribes a piece of DNA to specify the amino acid sequence of protein(s)
tRNA = transfer RNA (tRNA) Set of small RNA molecules used in protein synthesis as an interface (adaptor) between messenger RNA and amino acids
rRNA = ribosomal RNA (rRNA) Any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins
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Why proteins? Proteins have the diversity to allow them to perform the various functions necessary to maintain a living organism
Structures: hairs, horns, eye lenses Molecular recognition and signaling Catalysis (enzymes) Molecular transport: e.g., hemoglobin binds with O
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Mechanical actions: generate forces and torques
Replication / Protein Factory
Replication Transcription Transport Translation
Where is all of this happening?
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The Cell
Smallest unit of any living organism that can:• Gather raw materials from the environment• Construct out of them a new cell with a new copy
of the hereditary information
Think of it as a small bag of macromolecules that is separated from the outside world by a membrane (cell wall)
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Common features of all Cells
All Cells store their hereditary information in DNA
All Cells replicate their hereditary information by templated polymerization
All Cells transcribe portions of their hereditary information into the same intermediary form (RNA)
All Cells use proteins as catalysts
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Cells can be very diverse but they are classified by whether or not they have a cell nucleus that walls off genetic material from the rest of the cell
Eukaryotic Cells have a cell nucleus
Prokaryotic Cells no cell nucleus
Cell Types
These two types of cells identify the main domains of life:
prokaryotes and eukaryotes23
ProkaryotesSingle-celled organisms
Some have photosynthetic pigments (cyanobacteria)
Some have external whip-like flagella for locomotion or hair like pili for adhesion
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Eukaryotes They may be either single-celled or
multicellular organisms
Amoeba Plant cell Animal cell
There are many different types of eukaryotic cells - Plant cells are quite different from animal cells - There are approximately 210 distinct cell types in the adult human body
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Eukaryotes vs. Prokaryotes
Which came first?
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How does life begin?
We know that: a) Life requires carbon-based macromolecules – lipids,
proteins, carbohydrates, nucleic acids
b) The smallest living units of life are cells
There are two approaches for investigating the origin of life:
“Biological” – Top-down approach “Chemical” – Bottom-up approach
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“Top-down” approachLook at the present day biology and
extrapolate back towards the simplest living entities
“Bottom-up” approach Make the complex building blocks of
life (organic macromolecules) and put them together
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Top-down approach
Is there a minimum requirement for the number of genes (DNA information)?
The minimum number of genes for a viable cell in today's environments is thought to be no less than 200–300
– Mycoplasma genitalium (parasite in mammals) has the smallest known genome of free-living organisms, with about 480 protein-coding genes and over 582,000 nucleotide pairs
– Carsonella rudii (endosymbiotic bacterium in small insects) has the smallest known genome of any living organisms, with 182 genes and about 160,000 nucleotide pairs (probably missing genes essential for life)
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Corresponding segments of the gene for 16S rRNA (~1500 nucleotides, coding for ribosome) for different organisms:
an archaean (Methanococcus jannaschii) a eubacterium (Escherichia coli) a eucaryote (Homo sapiens)
Sites where the nucleotides are identical between species are indicated by a vertical line
Genetic information conserved since the beginnings of life
How do the genomes (order of nucleotides) of Eukaryotes and Prokaryotes compare?
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Top-down approachThe Tree of Life
By looking at the differences in 16S rRNA we can identify three domains of life Bacteria, Archaea, and Eucaryotes
Pro
kary
otes
Single cell organisms
Single- and multi-cell
organisms
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Problems with initiating the DNA/RNA/protein system
DNA has information to reproduce itself but needs proteins to catalyze the reaction
Proteins can catalyze reactions but need DNA to “reproduce”
It is very unlikely that all DNA/RNA/proteins components would form spontaneously at the same time
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The RNA World Hypothesis
RNA is an information carrier (like DNA) RNA can self-replicate RNA molecules can act as catalysts (unlike DNA)
DNA/protein world may have evolved from RNA world.
RNA worldDNA/protein
world
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Two Problems
How can RNA-type nucleotides be produced without life?
Difficult, based on laboratory work major problem
How do RNA-type nucleotides find each other so as to combine into the first RNA-type molecule that can replicate?
Dilution problemless major problem
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The “Metabolism”-first Hypothesis Before RNA could form, simple molecules started to form from simpler metabolically active entities via autocatalytic cycles; e.g.:
Once a primitive metabolic cycle is established, it begins to grow exponentially
These entities could be subject to a primitive form of selection, eventually giving rise to RNA
Metabolic entities
RNA worldDNA/protein
world35
A + B → 2B
C + A + B → 2B + C
Homework #4 available shortly on the web site
Homework
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Next time: Organic synthesis (bottom-up approach)!
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