Term
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Definition
Purine - double ring structure, Adenine and Guanine
Pyrimidines - single ring structures, Cytosine, Uracil and Thymine |
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Term
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Definition
| Sugar (deoxyribose), base (purine or pyrimidine) and phosphate groups |
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Term
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Definition
| Adenine and Guanine, double ring structure |
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Term
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Definition
| Cytosine, Uracil and Thymine, single ring structure |
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Term
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Definition
| Polymer of nucleotide monomers |
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Term
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Definition
Nucleotides linked by a phosphodiester bridge between the 5' and 3' C's of adjacent sugar groups (forming sugar-phosphate backbone)
There is a 5' end and 3' end |
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Term
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Definition
Folding back where one double strand passes over another double strand
Regular DNA is relaxed |
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Term
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Definition
Enzymes that change DNA topology
Type I - Cleave 1 strand of DNA, swivel and reseal the DNA
Type II - Cleave both strands (generating a transient dbl strand break), pass a segment of DNA through the break and reseal the DNA |
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Term
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Definition
| Uses energy in the form of ATP to introduce negative supercoils into DNA to make it easier to separate strands of the double helix |
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Term
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Definition
Interfering with topoisomerase causes supercoils to build up downstream of the replication fork
Creates tension and stops replication, transcription or repair, anything that needs DNA unwinding |
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Term
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Definition
| Plant alkaloid that blocks intermediate formed by Topo I and used in treating various types of cancers |
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Term
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Definition
Hardest to separate
Supercoiled in a positive direction |
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Term
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Definition
Easiest to separate
Supercoiled in a negative direction
Favors transcription |
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Term
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Definition
H. Sapiens - 3 bil bps, 2.5 mil coding capacity, 25k genes
E. Coli - 4 mil bps, 3.4k coding capacity, 4 k genes |
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Term
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Definition
LINES/SINES for interspersed sequences of repetitive DNA
1.5% of DNA is exons that code for proteins |
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Term
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Definition
Indicates total length of different sequences present in a particular genome
More complex organisms have higher number of bps in general
However, some simple organisms have more DNA than humans but have more DNA than needed
Rel btwn complexity of an organism and number of bps becomes obscured as we move up evolutionary tree |
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Term
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Definition
Analysis using the kinetics of DNA hybridizationto study the sequences that are in the genome
Value is directly proportional to sequence complexity |
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Term
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Definition
| When heated the H bonds break, DNA becomes single stranded |
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Term
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Definition
1 - Shear DNA into few hundred fragments
2 - Melt DNA by boiling it near 90 degrees
3 - Incubate DNA 10-20 degrees below melting period to reform the double helix
4 - Can measure the rate of hybrid formation, which is depending on the concentration of complimentary strands |
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Term
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Definition
Major structural chrom. proteins
1 - small 118-236 AAs, 13-26 kDa
2 - rich in (+) charged basic AAs (Arg/Lys) that can interact w/polyanionic backbone of DNA
3 - 5 main Classes based on AA sequence: H4, H5, H2A, H2B and H1 in a 2:2:2:2:1 ratio
4 - Subject to numerous post-translational modifications - targets of regulatory pathways |
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Term
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Definition
Fundamental repeating unit of eukaryotic chromatin organization
Octamer containing |
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Term
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Definition
| 30-nm fiber composed of nucleosomes folded into a zig-zag/solenoid structure or a beads on a string form |
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Term
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Definition
| Contains genes, centromeres, telomeres and origins of DNA replication |
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Term
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Definition
Sequences that assure correct partitioning of chrom.s during mitosis
Interact w/proteins that segregate chrom.s
Roughly 1 mil bps in length, contain repetitive satellite DNA |
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Term
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Definition
| Repeated sequences at the end of chrom.s for protection |
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Term
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Definition
Tot # bps / (Avg AA per prot * 3)
Maximum number of avg-sized proteins that could be encoded by a genome |
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Term
| 3 Variables Determining DNA Melting Temp |
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Definition
Length - For sequences less than 100 bps the longer the length the more stable it is and has a higher melting point, after 100 bps length is negligible
Mismatches - In very short duplexes mismatches increase instability and lower the melting point
G+C content - GC rich DNA has a higher melting point because they contain 3 H bonds instead of 2 like AT bases |
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Term
| Kinetic Components of Eukaryotic Genomes |
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Definition
Non-repetitive - unique, coding sequences that have the highest Cot # b/c they're the most complex
Middle-repetitive - Has some repetitive sequences, Cot # falls in the middle
Highly-repetitive - Contains the most amount of repetitive DNA and has the lowest Cot # |
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Term
|
Definition
Building Blocks of Protein
20 kinds
Contain an amine/carboxylic group, H and a side chain
Have a chiral center (except Gly)
Optically active, in L formation |
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Term
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Definition
Smallest side chain (one H)
Extremely flexible
Found in flexible parts of proteins or in tight turns
Achiral |
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Term
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Definition
Side chain attaches to backbone to form ring
Extremely rigid and constrains flexibility of protein backbone
Found in tight turns |
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Term
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Definition
Ala - Leu - Ile - Val
Hydrophobic and found in the interior of proteins
Ile and Val are beta branched -> sterically hinders free rotation and imposes structural constraints on peptide backbone |
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Term
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Definition
Phe - Tyr - Trp
Bulky, planar and largely hydrophobic
Tyr and Trp amphiphilic and can make H bonds b/c O and N in reangs |
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Term
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Definition
Met - Cys
Largly hydrophobic, Cys is weakly acidic
Met initiates protein synthesis
Thiol on Cys can make disulfide bonds, which is important for tertiary and quaternary structural stabalization |
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Term
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Definition
Asp - Glu
End with carboxylic acid
Found on exterior of proteins
pKa around 4 in aqueous solutions
Negatively charged at neutral pH
Make good ionic bonds |
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Term
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Definition
Arg - Lys - His
N containing groups in side chains that can be protonated
Side chain pKa values vary
His side chain has a pKa around neutral level so it makes a good buffer and is ideal for enzymes that catalyze rxns with proton transfer steps
Arg and Lys are positively charged at a neutral pH and can make good ionic bonds |
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Term
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Definition
Asn - Gln - Ser - Thr
Hydrophilic uncharged side chains with terminal amines (Asn/Gln) or hydroxyls (Ser/Thr)
Involved in H bonding interactions |
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Term
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Definition
| 8 groups that the amino acids are divided into depending on the physical properties of their side chains |
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Term
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Definition
Formed by condensation rxns
Polymerization of amino acids
formed between the amine side of one amino acid and the carboxyl side of another amino acid |
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Term
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Definition
Six atoms closest to the peptide bond lying in the same plane
Includes: carbonyl carbon with its oxygen, two a-carbons and the amine nitrogen with its hydrogen
Together form a linked sequence to form the polypeptide backbone |
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Term
| Protein Primary Structure |
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Definition
| Just the sequence of amino acids without folding |
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Term
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Definition
Adjacent planar peptide groups can rotate around each a-carbon and alter backbone conformation
Primary - AA chain, no folding
Secondary - Beta sheets and alpha helices
Tertiary - Disulfide bonds
Quaternary - Joining of subunits |
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Term
| Protein Misfolding Disease |
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Definition
Mutations cause misfolding in proteins and this can cause diseases
Primary Amyloidosis
Alzheimer's Disease
Huntington's Disease |
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Term
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Definition
| Includes ionic, hydrogen and van der Waals bonding |
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Term
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Definition
Attraction of a cation to an anion
Seen between an acidic and basic amino acids
Small metal cations or inorganic anions interact with charged side chains to stabilize protein conformations |
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Term
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Definition
Equal or unequal sharing of a proton between a weakly acidic donor group and a weakly basic acceptor group that contains an electron lone-pair
Side chain hydroxide or amide could share a proton with a carbonyl oxygen
critical in secondary structure stabalization |
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Term
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Definition
Mutual attraction that two uncharged atoms feel when they approach each other
Caused by synchronization of electron clouds
Weakest but plays a role in packed interior of proteins where side-chains come into close proximity
Major type of binding observed between aliphatic side chains |
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Term
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Definition
Enormously important in stabilizing tertiary and quaternary structures
Tendency for hydrophobic molecules to minimize contact with water by packing together into oily globules |
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Term
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Definition
Covalent bond formed between terminal S between Cys-Cys
Oxidation reaction needing oxygen |
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Term
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Definition
| Adds base pairs to DNA in a 5'->3' direction and also has exonuclease functions |
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Term
| Exonucleolytic Proof Reading |
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Definition
Removes incorrect bases when they are improperly paired
Pol.s stall due to improper pairing and change shape so that the end of the growing strand is inserted into the active site and clips the incorrect base |
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Term
| Fidelity of DNA Replication |
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Definition
5'->3' polymerization (10^-5) - makes mistakes b/c variant forms of nucleotidesimproperly base pair and get incorporated
3'->5' Exonuclease (10^-2) -> When enzyme stalls b/c improper base pairing it fixes it
Mismatch repair (10^-2) -> Corrects most of mismatched base pairs not repaired by exonucleolytic proofreading
All repair processes bring total fidelity to 10^-9 |
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Term
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Definition
| RNA Polymerase that primes DNA synthesis by synthesizing a short complementary RNA strand |
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Term
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Definition
| Involved in unwinding the DNA by using ATP |
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Term
| Single Stranded DNA-binding Protein |
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Definition
| Specifically binds single-stranded DNA to stabilize the single strands and protect it from forming stem-loops or being degraded by nucleases |
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Term
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Definition
| Synthesized continuously by adding bases in a 5' to 3' direction |
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Term
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Definition
| Synthesized discontinuously with the generation of many small Okazaki fragments |
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Term
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Definition
Where replication begins
One in Prokaryotes
Multiple in Eukaryotes to decrease replication time |
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Term
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Definition
Creates DNA copy from RNA parent strand
Used by viruses that use RNA as the genetic material |
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Term
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Definition
Substitutions (transitions: pu->pu, py->py; transversions py->pu, pu->py)
Deletions of 1 or more bps
Insertions of 1 or more bps |
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Term
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Definition
1- Recognize damaged region by an endonuclease that makes an incision
2 - Exonuclease removes DNA adjacent to the damaged base on the damaged strand only
3 - Gap filled in by DNA polymerase
4 - Nick is sealed by DNA ligase |
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Term
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Definition
| Cyclobutyl linkage of adjacent thymines often resulting from UV damage |
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Term
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Definition
Occurs soon after DNA has been replication
Exonuclease that removes DNA recognizes new (unmethylated) DNA and removes newly synthesized DNA
Corrects mismatched bases incorporated during DNA replication |
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Term
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Definition
Example of a DNA repair deficiency
Results from an inability to remove and repair thymine:thymine dimers
Presents as dry skin in infancy, which atrophies, corneal ulcers, abnormal coloration of the skin and skin cancers
Tumors can appear and metastasize |
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Term
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Definition
Mutation in genes encoding the human counterparts of genes that are in the mismatch repair pathway
Causes a predisposition to colon cancer
Affects 1/200 people |
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Term
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Definition
Hereditary Nonpolyposis Colon Cancer - caused by DNA repair deficiency in humans
Also known as Lynch syndrome |
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Term
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Definition
Enzyme that participates in DNA replication
5'->3' DNA pol activity, adding bases
3'->5' exonuclease activity that mediates proofreading (reverse)
5'->3' exonuclease activity mediating nick translation during DNA repair (forward) |
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Term
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Definition
Does most of the work in new DNA polymerization
3'->5' exonuclease activity for editing during chromosomal replication |
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Term
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Definition
| Form of artificial DNA created by combining two or more sequences that would not normally occur together through gene splicing |
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Term
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Definition
Cleave "non-self" DNA at specific base sequences
Recognize palindromic sequences and cleave phosphodiester bonds in specific places |
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Term
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Definition
| Vehicle used to transfer genetic material to a target cell |
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Term
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Definition
| Small circular DNA molecules found in bacteria used for cloning with a defined set of restriction sites to allow them to be manipulated |
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Term
| Polymerase Chain Reaction |
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Definition
DNA sequence amplification using 2 oligonucleotide primers that flank fragment one would like to amplify
Use the 5' of the A end and the 5' of the B end |
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Term
| Oligonucleotide Hybridization |
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Definition
Can hybridize and form a stable duplex with complementary sequences
Measure melting curves, mismatches are less stable |
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Term
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Definition
Radioactive cloned DNA produced with dNTP and DNA pol
Labeled fragments used as probes to detect specific genes that have been electrophoresed and transferred to a filter |
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Term
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Definition
| Electrophoresing RNA using radiolabeled DNA "probe" |
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Term
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Definition
Different methods for determining order of the nucleotide bases in DNA
Use chain termination and amplification/cloning |
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Term
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Definition
Chips with thousands of oligonucleotides synthesized with photoactivated DNA synthetic rxns and photomasks
Chips used to analyze whether DNA forms stable DNA duplexes
Chips can be used to determine whether genes are expressed in cells or tissue using reverse transcriptase on mRNA and hybridizing it to the chip |
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Term
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Definition
Amplified population of DNA fragments to different locations of solid support
Use reversible fluorescent ddNTPs and fluorescent detectors to determine short segments
Can perform high-throughput sequencing so a high density of polonies can be sequenced and find the sequence to many different DNA fragments simultaneously |
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Term
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Definition
Local conformation of its backbone, or main chain
Helices and sheets |
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Term
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Definition
PP chain twisted by same amount about each of its alpha-C atoms and assumes a helical conformation
Counterclockwise w/3.6 residues/turn with a linear distance of 5.4 A
H bond forms between main chain carbonyl O of Nth helical residue and the main chain amine of the (N+4)th helical residue |
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Term
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Definition
All-trans peptide bondsadopt a rough planar geometry with H bonds forming between backbone carbonyls and backbone amines on adjacent strands
Neighboring hydrogen-bonded pp chains run in opposite directions
Have rippled or pleated appearance w/two residues repeating at a distance of 7A |
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Term
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Definition
Helices and sheets joined by nonrepetitive loop segments or coils
Not necessarily flexible as a random coil but instead are held rigidly in place as the backbone of an a-helix |
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Term
| Amphipathic Helix or Sheet |
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Definition
Helix - Has h+ and h- sides because side chains of the (n+3)th and (n+7)th chains stick out the same directions to make a unified side
Sheet - alternating h+/h- residues that form one side as h+ and the other side as h- |
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Term
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Definition
Certain combos of 2nd structural elements
Zn-finger: Beta-turn-helix structure, binds Zn through Cys and His side chains
EF-hand
Ankyrin-repeat
Beta-Barrels |
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Term
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Definition
Independently functional units of proteins that can serve their own purposes in the protein
Coiled-coil: forms basis of many structural proteins found in the cell, fibrous tissue and for functional proteins |
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Term
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Definition
| Spatial arrangement of many polypeptide chains in subunits in a single protein |
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Term
| Structure/function Relationship |
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Definition
| Example: Hb in a puckered form cannot bind oxygen but when it changes conformation to the planar structure it can bind oxygen better |
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Term
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Definition
| Transmembrane proteins that form ion conducting pores through lipid bilayer so that h+ ions can pass through the h- center of the bilayer |
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Term
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Definition
| Permits the flux of specific ions into or out of the cell based on structure of the channel |
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Term
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Definition
| Proteins have various levels of structure and motions depending on their environment and binding |
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Term
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Definition
Proteins not merely rigid bodies, can move
Atomic fluctuations - rapid vibrations
Collective Motions - breathing, coordinated vibrations of groups of covalently linked atoms
Triggered conformational changes - in response to ligand binding or other environmental change, can involve individual side chains to entire polypeptide subunits |
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Term
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Definition
| Structural changes because of the binding of a ligand at one site altering the binding of another ligand at a distant site |
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Term
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Definition
| Example: one Hb heme group binds one oxygen, conformation of the protein changes so that it's easier for the next oxygen to bind and then easier after that |
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Term
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Definition
| Proteins that undergo structural changes to convert between conducting and nonconducting conformations including activation, deactivation, inactivation and desensitization |
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Term
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Definition
| Energy stabilizing this tertiary/quaternary structure coming mainly from noncovalent interactions where the protein folds into rapidly after synthesis |
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Term
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Definition
| Unfolding of proteins due to heat, pH, detergents, miscible organic componds or salts/urea/guanidine |
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Term
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Definition
Maintained by polypeptide interactions started by primary structure of the amino acids
Can go awry with substitutions: h- for h+, Gly to non-Gly, Non-Pro to Pro or Glu to Arg |
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Term
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Definition
| Balance between protein synthesis and protein degradation |
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Term
| Dominant Negative Inhibition |
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Definition
| Ability of mutant proteins to adversely affect the activity of wild type proteins |
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Term
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Definition
Collection of mis-folded proteins
Responsible for many degenerative diseases
Basically amyloidosis |
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Term
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Definition
| Made of numerous closely packed B-sheets that make up amyloid deposits |
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Term
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Definition
| Deposits formed by proteins or protein fragments folded in a nonnative conformation that can be extracellular (plaques in Alzheimer's disease) or intracellular (Lewy bodies in Parkinson's disease) |
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Term
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Definition
| Process of copying DNA to RNA |
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Term
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Definition
Contains the same sequence as the new RNA strand
Contains the gene that will be synthesized
Not actually transcribed |
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Term
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Definition
Strand actually being transcribed
Serves as template for transcription |
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Term
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Definition
| DNA corresponding to protein sequence is coding region with an ORF |
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Term
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Definition
DNA sequence that directs RNA pol to starting point of a gene within 250 bps
Around 75 and 90 bps upstream are activating sequences (promoter elements) |
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Term
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Definition
DNA sequences that increase the activity of promoters
Can be found within proximal promotors or several kbps away
Cannot promote initiation alone |
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Term
| Transcriptional activator |
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Definition
| DNA-binding protein that regulates one or more gene by increasing rate of transcription |
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Term
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Definition
Core promotor element
Found around 30 Nuc.s upstream of the initiator |
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Term
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Definition
Thalassemis: group of hereditary anemias resulting from an imbalance in the synthesis of alpha/beta chains of hemoglobin
Caused by point mutations impairing synthesis of beta chain
Found between 90 and 31 bp within TATA box
Mutations reduce or eliminate binding of transcriptional activators or TBP and reduce mRNA synthesis
Not dom (-) because only reduces amount of Thalassemias, some still gets made |
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Term
| General Transcription Factor |
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Definition
| Protein transcription factors involved in formation of pre-initiation complex and bind with RNA pol II to single-stranded DNA gene template to read it |
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Term
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Definition
Protein that increases gene expression by binding to an activator that contains a DNA binding domain
Can't bind DNA alone |
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Term
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Definition
Decreases gene activity by binding to a transcription factor which contains a DNA binding domain
Can't bind DNA alone |
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Term
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Definition
Always bound by transcriptional activators
Promote genes that must be expressed in all cells at all times |
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Term
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Definition
Bound by transcriptional activators and activated in response to cellular conditions
Protein factors bind only under specific circumstances |
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Term
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Definition
Combination of DNA, histone and other proteins that make up chromosomes
Compacted form of DNA |
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Term
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Definition
Basic unit of DNA packaging
DNA wrapped twice around a histone octet |
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Term
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Definition
| Causes transcriptional activation by having causing the DNA strands to disassociate from the histones |
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Term
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Definition
| Protein domain containing at least one motif that recognizes double or single stranded DNA |
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Term
| Transcriptional Activation Domain |
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Definition
Domain of a protein that interact with transcriptional apparatus that activate transcription
May be glutamine rich, proline rich or acidic |
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Term
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Definition
| Proteins found within cells responsible for sensing steroid and thyroid hormones and work with other proteins to regulate the expression of specific genes |
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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
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Term
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Definition
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Term
| Intracellular Localization |
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Definition
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Definition
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Definition
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Definition
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Definition
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Definition
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Definition
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Term
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Definition
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Term
| 5' 7-Methyl Guanosine Cap |
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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
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Term
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Definition
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Term
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Definition
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Definition
| Regulates stability and translation of specific mRNAs |
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Definition
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Definition
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Definition
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Definition
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Definition
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Term
| HIV-1 Drug Resistance Mutation |
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Definition
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