Term
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Definition
| study of DNA,RNA, proteins and the biological pathways between them |
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Term
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Definition
1. understand processes to pass genetic info from one generation to next,
2. understand processes to transfer info from DNA-->RNA->PROTEIN |
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Term
| what else can we learn from mbio? |
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Definition
| information encoded in genetic material links all organisms to each other and provides record of evolution |
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Term
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Definition
1. discovery: physiological and disease processes (cancer), neurobiology and aging
2. Biotechnology and drug development (Venter-synthetic,and paleoanthropy )
3. Medicine Diagnostics (prenatal, disease prediction and diagnosis)
4. legal- forensics |
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Term
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Definition
| a chemical system capable of Darwinian evolution |
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Term
| how does life differ from non life? (7 ways) |
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Definition
1. adaptation
2. Complexity and organization
3. Growth, development and death
4. energy acquisition
5. transmission of genetic information between generations
6. Homeostasis
7. Interactions |
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Term
| what are the key requirements for life? |
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Definition
| 1. raw materials 2. energy 3. envelope 4. catalysis 5. Biological information 6. capacity to evolve |
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Term
| when were earth and plants formed |
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Definition
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Term
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Definition
| hundred of millions of years of contact energy from solar radiation,volcanism ect. the molecular constituents of earth early atmosphere were converted into range of complex organic molecules and polymers |
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Term
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Definition
-over millions of years the accumulation of reaction products yielded a soup of molecules and polymers
-polymers acquired the capacity to duplicate
-first life:self replicating polymer with 1. catalysis and 2. biological information |
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Term
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Definition
| 1. catalysis and 2. biological information |
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Term
| 4 lines of evidence of RNA (ie what discoveries suggest a protein world arose from an RNA world?) |
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Definition
1. ribozymes
2. artificially constructed RNA molecules can catalyze rxns
3. RNA is the active catalysis component of ribosomes
4. RNA sequences can self replicate |
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Term
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Definition
| A proposal that provides a reasonable explanation for observations, but has not yet been substantiated by sufficient experimental evidence to stand up to rigorous critical examination. |
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Term
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Definition
| Refers to the only assumption made by scientists—that basic forces and laws in the universe are not subject to change. They can thus be studied and defined by scientific inquiry. The term was coined by Jacques Monod. |
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Term
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Definition
| Hypothesis that in an early stage of evolution, a living system was based on RNA. In this system, RNA enzymes could catalyze the synthesis of all the molecules required for life from simpler molecules available in the environment. |
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Term
| how do we know adenine was there? |
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Definition
| it can be synthesized with probiotic chemistry from HCN |
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Term
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Definition
| how life emerged from non life (molecules could contain information and a template) |
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Term
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Definition
| simple molecules assemble |
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Term
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Definition
evaporation of primordial puddles concentrates raw materials and leads to polymer formation (note: input of energy from the SUN not from the cell)
i) polynucleotides
ii) polypeptides |
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Term
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Definition
polynucleotides can be replicated based on the fact that they self template (base pair)
-geochemical conditions and thermal gradients provide: catalytic environments and energy input to assits with information and enzyme polymer formation (like a PCR machine and protein free) |
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Term
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Definition
-prebiotic evolution
-interconnected compartments: hatchery for origin of life |
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Term
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Definition
| polymerizes nucleotides (~40) |
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Term
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Definition
1. subtraction: take away as many coding regions are you can and still have it survive and replicate
2. Commonalities: compare genomes, universal sequence |
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Term
| discoveries that lead to DNA as repository of biological information |
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Definition
1.Fredrerick Griffith found heritable changes transmitted from "transforming factor" chemical extract
2. Avery showed transforming factor was DNA
3. Hershey Chase showed radio-labeled DNA (not labeled protein) enters host cells and propagates to progeny phage
4. Chargaff showed ACGT ratios are the same in different tissues of same organism
5. Watson/Crick/Franklin showed double helix (replication&function of genes and no constraints on linear order)
6. Kornberg showed DNA synthesis in cell free extracts can ink nucleotides when template is present (pol1) |
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Term
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Definition
1. metabolism
2. RNA genetic material + code
3. ribosome and protein biosynthetic app
4. transcription machinery |
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Term
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Definition
| provides an explanation for a series of experimental observations, providing a basis for more rigorous examination |
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Term
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Definition
| what is it? how does it work? |
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Term
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Definition
hypothesis or discovery base
analytical, descriptive of mechanistic |
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Term
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Definition
| discover new facts, revisions of hypothesis |
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Term
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Definition
| availability of reagents, equipment, expertise, feasibility |
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Term
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Definition
| development of scientific th |
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Term
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Definition
| have questions been properly addressed? something discovered? |
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Term
| scientific approach to discovery (3 main characteristics) |
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Definition
1. focuses on natural universe
2. relies on ideas that can be tested by experiments and on observations that can be reproduced
3. occurs, not within a vacuum,but within an ever expanding web of scientific theories |
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Term
| places to report scientific findings |
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Definition
1. peer refereed scientific journals
2. non refereed journals, reports, conference presentations, invited seminars |
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Term
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Definition
| aim: to solve the riddle of the RNA structure and understand how it built proteins |
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Term
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Definition
-Russian physicist George Gamow proposed that double-stranded DNA acted directly as a template for assembling amino acids into proteins
-the various combinations of bases along one of the groove in the double helix could form distinctively shaped cavities into which the side chains of the amino acids might fit
-when all the amino acids were lined up in the correct order along the groove, an enzyme would come along to polymerize them |
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Term
| problems with diamond code |
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Definition
a) didn’t realize DNA and protein never actually see each-other
b) the sequence of the 4 bases would determine the orientation of the amino acids, and
c) a mutation would affect all amino acids |
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Term
Later Hypothesis: that RNA molecules might direct protein synthesis by folding structures that formed specific pockets for individual amino acid binding.
-RNA strand could make pockets that gave different amino acids based on shape
PROBLEM? |
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Definition
| this was not feasible because of the chemical incapability of DNA/RNA bases and many amino acid side groups (charges) |
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Term
| tRNA attaches _______ to amino acids to direct protein synthesis |
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Definition
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Term
| key flaw(s) with rRNA as template for ordering amino acids |
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Definition
1. non specificity of rRNA
-all rRNA chains are of similar lengths in large and small ribos
-rRNA base compositions across different organisms is largely the same despite variations in AT/VG ratios in DNA or these organisms |
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Term
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Definition
carries the specific instructions for building a specific protein
-transcient product |
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Term
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Definition
serves to transfer individual amino acid molecules from cytoplasm to their appropriate location in a growing polypeptide chain during protein synthesis
-non specific, end products of protein synthesis |
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Term
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Definition
| required for building ribosomes, which are structures necessary for protein synthesis. |
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Term
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Definition
| : the propensity of an atom within a molecule to attract electrons to itself |
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Term
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Definition
| Connect protein and nucleic acid subunits |
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Term
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Definition
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Term
| true or false: the polarity of biomolecules governs their locations within cells and their interactions with other molecules |
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Definition
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Term
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Definition
-double helix of DNA is due to weak bonds
-underlie most interactions between DNA, RNA, proteins and small molecules
-allow DNA replication, repair and recombination
-RNA and protein synthesis
-Chemical signaling, |
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Term
| base pairing is ____ bond |
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Definition
| Two nucleotides in nucleic acid chains that are paired by hydrogen bonding |
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Term
| stabilize protein-protein i.e. antibody antigen reactions use shape |
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Definition
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Term
| bonds b/n backbone carbonyl and imino groups to stabilize a helices and B sheets |
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Definition
| H bonds in terms of secondary protein structure |
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Term
| complementary nucleotides forms double helix (which bond) |
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Definition
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Term
| Proteins recognize shape of bases in groove without separating |
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Definition
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Term
| Shaping proteins (what bond?) |
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Definition
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Term
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Definition
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Term
| what contibutes to base stacking (forms double helix) |
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Definition
| hydrophobic (little vanderwaals) |
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Term
| .protein folding and stabilization |
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Definition
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Term
| .protein folding and stabilization (bond) |
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Definition
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Term
| protein folding and stabilization |
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Definition
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Term
| Protein insertion into membranes |
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Definition
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Term
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Definition
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Term
| Binding of nucleic acids/proteins to other molecules |
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Definition
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Term
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Definition
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Term
| Having a molecular surface with chemical groups arranged to interact specifically with chemical groups on another molecule |
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Definition
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Term
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Definition
| An RNA molecule that is a functional end product, as distinct from messenger RNA (mRNA), which serves as a transient intermediary between DNA and a protein product it encodes. |
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Term
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Definition
| the study of the structure and function of genes at the molecular level. |
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Term
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Definition
| A nucleoside phosphorylated at one of its pentose hydroxyl groups. |
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Term
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Definition
| A class of RNA molecules (Mr 25,000 to 30,000), each of which combines covalently with a specific amino acid for use in protein synthesis. |
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Term
| why is the major groove information rich? |
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Definition
| 1. The major groove is sized to fit protein α-helices. 2. The edges of base pairs in the major grove are more exposed than in the minor groove. 3.The identities of the edges of the base pairs in the major groove are more information rich than those of the minor groove becasue the H bond donors and acceptors are unique on each side. |
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Term
| true or false: the amino acids in humans are different from bacteria |
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Definition
| false. they use the same 20 |
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Term
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Definition
make up Hydrogen bonding interactions with H20 and other side chains
- 2 cysteins can form a disulphide bond |
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Term
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Definition
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Term
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Definition
| SH group, donor (and disulphide covalent interaction with another cysteine ) |
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Term
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Definition
| amide group, donor or acceptor |
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Term
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Definition
-primary and secondary amines and carboxylates
-make primarily ionic and H-bonding interactions |
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Term
| polar positively charged at pH=7 |
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Definition
BASIC
proteins slide along negatively charged DNA backbone using charged residues to make ionic interactions with backbone |
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Term
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Definition
side chain amino group
hydrophobic chain and charge group protrudes on surface |
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Term
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Definition
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Term
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Definition
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Term
| polar, negatively charged at pH=7 |
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Definition
ACIDIC
-more often on surface of proteins because they can form H bonds
-often comprise an active site for reaction chemistry |
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Term
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Definition
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Term
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Definition
-side chains are hydrophobic
-aromatic chains absorb UV light strongly (useful for quantitating proteins in soln) |
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Term
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Definition
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Term
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Definition
| OH can form H bonds (imparts polarity) |
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Term
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Definition
| nitrogen can form H bonds (imparts polarity) |
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Term
| non polar, aliphatic R groups |
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Definition
-HYDROPHOBIC interactions
-can NOT donate or accept with other amino acids
-internal (cluster in proteins)
-hydrophobic, helps stabilize 3D folding |
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Term
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Definition
| nonpolar, but single H in side chains so contributes little to hydrophobic interactions |
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Term
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Definition
| aliphatic side chain, rigid cyclic structure limits conformations |
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Term
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Definition
3 bonds that separate the sequential alpha carbons in polypeptide chain
lie in plane |
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Term
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Definition
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Term
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Definition
| the tendency for an acid to loose its proton (lower pka is stronger acid) |
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Term
| why do the atoms of a peptide bond lie in one plane? |
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Definition
| partial double bond between carbonyl and amide groups |
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Term
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Definition
| pI the pH at which the amino acid/polypeptide IS IONIZED and yet has no net electric charge (or where it stops migrating on gel) |
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Term
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Definition
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Term
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Definition
| linear sequence of amino acids |
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Term
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Definition
nearby residues, mainly backbone interactions
"alpha/beta" |
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Term
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Definition
packing or folding of secondary structures of one chain
"folded polypeptide chain" |
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Term
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Definition
complexes of multiple polypeptide subunits
"assembled subunits" |
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Term
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Definition
| proof that amino acid sequence determines 3D structure |
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Term
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Definition
| primary structure determines tertiary and quaternary structures |
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Term
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Definition
pancreatic ribonuclease that cleaves ss RNA
when folded correctly into its active conformation its forms 4 specific disulfide bonds |
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Term
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Definition
| a reducing agent that disrupts disulphide bonds |
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Term
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Definition
| denaturing agent that disrupts non covalent bonds within proteins that stabilize the native tertiary and quarternary structure |
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Term
| what did the anfinsen experiment show? |
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Definition
-loss of native 3D structure inactivated RNase A, but the refolded enzyme regained activity
-thus all that was needed to generate active 3D structure was primary sequence of amino acids |
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Term
| additional notes on anfinsen experiment |
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Definition
-function is dependant upon refolding into correct tertiary structure
-proper refolding is dependant on formation of weak, non covalent interactions (no merely disulphide bond formation)
-disulphide bonds can form spontaneously with wrong combinations of Cys residues if protein in improperly folded |
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Term
| true or false: proteins randomly search all possible conformations until they arrive at the most stable (lowest deltaG) structure |
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Definition
| FALSE! they fold on a defined pathway |
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Term
| diseases caused by protein misfolding |
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Definition
1. parkinsons
2. cycstic fibrosis
3. alzymers
4. creutzfeild jakob
5. mad cow |
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Term
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Definition
-most stable
-right handed helix
-repeats every 5.4 A
-favorable phi and psi angel accomodate regular pattern of H bonding between carbonly(oxygen) and imino (NH) groups on the same strand |
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Term
| protein structure concepts (3) |
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Definition
1. proteins fold spontaneously under physiological conditions as they are biosynthesized, primary structure determines 3/4
2.proteins can be denatured and sometimes refold, they fold on a defined pathway
3. proper folding means attaining right combinations of phi and psi |
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Term
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Definition
| refold proteins to keep them on correct folding pathway |
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Term
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Definition
-second most stable arrangement of polypeptide backbone
-highly extended
-H bonding b/n adjacent chains
-stabilization comes from alignment of carbonyl groups of one strand against NH groups of adjacent
-typically involves 4-6 strands |
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Term
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Definition
"helix breaker"
too restrictive to allow to make a coil
terminates alpha helixes |
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Term
| why is proline a helix breaker (specific) |
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Definition
-Proline’s side chain exists as a cyclic structure.
-places restrictions on rotation within its polypeptide backbone, which is a requirement for achieving the correct geometry in a protein α-helix.
-Specifically, proline locks its φ backbone dihedral angle at approximately −75°, giving proline an exceptional conformational rigidity compared to other amino acids. Also, because proline lacks a hydrogen on the amide group, it cannot act as a hydrogen bond donor, as is required to achieve the interactions involved in stabilizing the helix. Instead, it can only act as a hydrogen bond acceptor. |
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Term
| how to alpha helices and beta sheets differ in proteins? |
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Definition
1.α-helices form right-handed coiled structures, while β-sheets are extended structures.
2. α-helices are stabilized by H-bonding interactions between backbone atoms from amino acids close to one anther on the same section of a polypeptide strand, while β-sheets are stabilized by H-bonding interactions between backbone atoms from amino acids found on different (distant sections) polypeptide strands. |
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Term
| protein tertiary structure (explanation) |
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Definition
| -loops and turns connect secondary structures together -tertiary structure in a protein involves compromises between tendency of backbones to form regular helices and sheets and the tendency of side groups to twist the backbone into less regular configurations that maximize their weak bonding interactions with the protein |
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Term
| a fold is determined from: |
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Definition
| number, arrangement and connectivity (topology) of secondary structure elements |
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Term
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Definition
-single proteins larger than 20,000 Daltons (150-200 residues) often fold into two or more separate folding domains
-domains can typically involve a continuous part of the amino acid sequence
-each domain can have a unique functional role |
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Term
| quaternary structure basics |
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Definition
| -proteins can complex with identical or different polypeptide subunits (2-hundreds) |
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Term
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Definition
=multimer
complex of multiple polypeptide chains |
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Term
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Definition
=subunits
individual polypeptide chains in a multimer complex |
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Term
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Definition
| oligomer with identical subunits |
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Term
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Definition
| oligomer with non-identical subunits |
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Term
| identical subunits are generally arranged in ______ |
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Definition
| symmetric pattern (helical or rotational) |
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Term
multimers with non identical subunits can be ____ and _____
(example?) |
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Definition
| complex! and lack symmetry |
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Term
| GrEL chaperonin is an example of |
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Definition
| a large, machine-like oligomer with multiple identical and non identical subunits assembled into repeating groups with some symmetrical properties |
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Term
interactions of subunits can be influcenced by ____
and can have _________ or ______ functions |
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Definition
small molecules!
identical or different (ie catalysis,regulation,scaffolding/structural roles) |
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Term
| is protein association promiscuous? |
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Definition
|
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Term
| what is the basis for high specificity in proteins? |
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Definition
|
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Term
| name 3 types of complementarity |
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Definition
1. ionic (salt bridges)
2. H-bonding
3. steric (vanderwaals) |
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Term
| left handed protein protein interaction |
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Definition
| two alpha helices packed against eachother at an angle of 18 degrees and gently twisted |
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Term
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Definition
two alpha helices interact through hydrophobic contacts
-amphipatic (burry hydrophobic interactions) |
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Term
| the primary "protein protein bond" in all proteins associations is _____ and _______ |
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Definition
non covalent
and freely reversible |
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Term
| protein protein bond formation reaction can be characterized by 1. 2. |
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Definition
| 1. equilibrium constant (ka) 2. associated free energy (delta G) |
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Term
| coiled coils are found in (4) |
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Definition
1.skin - keratin
2. motor proteins -kinesin, dynein, myosin
3. DNA binding proteins - GCN4 leucine zipper
4. blood blotting proteins- fibrinogen |
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Term
| Conformation specific (2 exs) |
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Definition
1.DNA damage recognition& repair proteins
2.Single stranded DNA binding proteins (SSBs) |
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Term
| Sequence specific ( 2 exs) |
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Definition
| Lambda repressor, restriction enzymes |
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Term
| Most common mechanism by which proteins recognize specific DNA is (why?) |
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Definition
involves insertion of α-helix into major groove (helix-turn-helix motif)
why?
-width and depth of major groove match the dimensions of the α-helix
-major groove is rich in H bond acceptors and donors on edges of bases, and pattern is distinct for each base pair |
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Term
| how do proteins recognize their preferred binding site? |
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Definition
-extensive DNA backbone contacts made by patches of (+) charged amino acids found at sites close to those that recognize specific base pairs
-because of non specific electrostatic interactions even highly sequence specific protein have some affinity for non specific DNA as well |
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Term
| why do non specific back bone contacts do? |
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Definition
1. accelerate the rate at which a protein finds the appropriate target site
2. constrain the protein DNA interaction, causing linear diffusion of the protein along DNA (allows DNA-bding proteins to sample sites and random in their search for a specific binding site) |
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Term
| what do proteins involved in DNA replication, recombination and repair do that is interesting in terms of locating preferred binding site? |
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Definition
1. dont diffuse but actively track along DNA using directed movement
2. movement is dependant on ATP hydrolysis |
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Term
| why do oligomers form multiple subunits rather than producing large multi domain polypeptide chain? (5) |
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Definition
| 1. folding 2. energy investment 3. denaturation 4. translation 5. DNA code: multiple copies of same subunits (less DNA) |
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Term
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Definition
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Term
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Definition
|
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Term
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Definition
base on known vanderwaals radii and bond angles
-characteristic of 2ndary structure |
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Term
| DNA binding sites in proteins are often |
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Definition
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Term
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Definition
|
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Term
| protein domains are formed from distant sections on polypeptide amino acid sequence (T or F) |
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Definition
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Term
| True or false: non specific interactions between proteins dna the backbone of DNA are hydrophobic in nature |
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Definition
|
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Term
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Definition
| provide information about where in the cell or whole organism the protein functions and how it is regulated |
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Term
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Definition
| purified protein to understand how they look and function (e.g. enzyme kinetics, catalytic mechanism, affinity for substrates and 3D structure) |
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Term
| how can you detect protein once you've purified it? |
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Definition
biological activity
spectroscopy
PAGE and staining
PAGE and immunoblotting |
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Term
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Definition
-double helix of DNA is due to weak bonds
-underlie most interactions between DNA, RNA, proteins and small molecules
-allow DNA replication, repair and recombination
-RNA and protein synthesis
-Chemical signaling, |
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Term
| explain the differences and similarities between left handed supercoil and coiled coil |
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Definition
differnces : left handed super coil: HYDROGEN BONDS ( 2 alpha helices at angel of 18 degrees twisted around eachother)
coiled-coil: HYDROPHOBIC contact (2 alpha helices interact) --> amphipathic
simmiliarites: both involve 2 alpha helices |
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