Term
Composition of nucleotides.
Nucleotide vs. Nucleoside |
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Definition
Nitrogen-containing BASE, 5-carbon SUGAR, one or more phosphate groups.
Linked by Phosphodiester bond. Phosphate group on 5' C bonds to 3' carbon.
BASE + SUGAR + PHOSPHATE = Nucleotide
BASE + SUGAR = Nucleoside |
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Term
| Bases: pyrimidines or purines? |
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Definition
Pyrimidines: C, T, U
Purines: A, G |
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Term
| Differences between DNA and RNA |
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Definition
RNA: ribose (single stranded)
DNA: deoxyribose (double stranded)
- On 2' carbon, RNA has OH group (+O) and DNA has H group (-O)
RNA: Uracil replaces Thymine
- Local folding by base-pairing |
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Term
| DNA Double helix bonds/turns |
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Definition
A=T (DOUBLE BOND)
C=-G (TRIPLE BOND)
10 nucleotides = turn of helix |
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Term
| Composition of amino acids, linkage, chains |
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Definition
Amino group, carboxyl group, side chain (R-group)
Linked by peptide bonds.
Amino acid chains can form alpha helix or beta sheet |
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Term
| Amino Acid characteristics |
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Definition
Polar (hydrophilic) amino acids and Non-polar (hydrophobic) amino acids
Polar: Acidic or Basic
Lysine = K = basic/positively charged amino acid |
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Term
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Definition
STRONG (COVALENT)
Phosphodiester: DNA and RNA
Peptide: Amino acids
WEAK (NON-COVALENT)
Hydrogen base pairing
Covalent bonds group subunits into macromolecules, Non-covalent bonds group macromolecules into macromolecular complexes |
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Term
| What is chromatin? What is a nucleosome? |
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Definition
DNA + histones (protein) = chromatin
If genome were stretched out, it would be much much longer than the nucleus.
Nucleosome = each individual bead (DNA wrapped around 1 histone) |
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Term
| Types of histones (names) |
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Definition
Core histones (nucleosome): H2A, H2B, H3, H4
Linker histone: H1
Chromatin also has non-histone chromosomal proteins (HP1 = heterochromatin protein 1) |
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Term
| Describe Nucleosome assembly |
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Definition
- 8 subunits (octamer), 2 of each core histone
1) pairing:
H3 + H4 -> H3/4
H2A + H2B -> H2A/2B
2) H3/4 forms tetramer with H3/4 via interactions between H3
3) H3 recruits H2A/2B heterodimers (weakest interaction in complex, helped by high salt or DNA) |
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Term
| Describe nucleosome disassembly |
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Definition
Nucleosome has ~200 nucleotide pairs of DNA
1) Nuclease digests linker DNA
2) Released nucleosome core particle
3) Dissociation with high concentration of salt into histone core and 147 nucleotide-pair DNA double helix.
4) Histone dissociates into subunits (H2A, H2B, H3, H4) |
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Term
| Higher-order chromatin structure |
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Definition
H1 (linker histone) is involved in compaction.
30-nm chromatin fiber of packed nucleosomes |
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Term
| Multiple Mechanisms of Inheritance (Genetic vs. Epigenetic) |
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Definition
Genetic: coded within the nucleotide sequence of the genome, Mendelian inheritance of genes from parent to progeny.
Epigenetic: coded outside nucleotide sequence.
- DNA methylation: genes can be inherited with methyl
- Chromatin modification: histone marks can be inherited |
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Term
| Regulation of chromatin structure/function (2 methods) |
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Definition
- Potential forms of epigenetic inheritance
1) Histone modifying enzymes (covalent modification)
- Histone Acetyltransferase = HAT
- Histone Deacetylase = HDAC
- Histone Methyltransferase = HMT
- Histone Kinase (phosphorylates serine residues)
2) ATP-dependent remodeling machines (non-covalent modification)
- Chromatin Remodeling Complex (decondenses chromatin around nucleosome) |
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Term
| Histone modification areas |
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Definition
Histones are highly conserved and very basic. 10-16% K, 2-15% R.
1) N-terminal tail (Lysine = K)
- Acetyl group (A)
- Methyl group (M)
2) Globular core (Serine = S)
- Phosphate group (P) |
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Term
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Definition
- Difference in cytological staining and histone modifications
1) Euchromatin
- Associated with active genes
2) Heterochromatin (~10% of chromosome)
- More densely packed
- Concentrated around centromere, telomeres.
- Used to shut down or "silence" genes. (1 of 2 Female XX chromosomes is condensed and inactivated)
- Dynamic spreading of heterochromatin to "silence" genes |
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Term
| Centromere, Telomere, Replication Origin |
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Definition
Replication begins at REPLICATION ORIGIN, proceeds bidirectionally from origins.
In mitosis, CENTROMERE attaches duplicated chromosomes to mitotic spindle (and holds duplicated chromosomes together) so one copy is distributed to each daughter cell when cell divides.
TELOMERES form special caps at each chromosome end. |
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Term
| Combinations of histone modifications |
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Definition
1) Some amino acids can be modified in multiple ways. (Lysines can be modified with 1, 2, or 3 methyl groups)
2) Difference combinations of histone tail modifications have different meanings.
- Methyl group alone = heterochromatin formation, gene silencing
- Methyl group with Acetyl group to right = gene expression
- Phosphate group with Acetyl group to right = gene expression
Silencing gene is adjacent to heterochromatin, needs barrier between heterochromatin and gene in order to express gene. |
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Term
| Process of epigenetic inheritance through histone modification |
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Definition
- Parent nucleosome with modified histones
- Half of daughter nucleosomes have modified histones
- Parental pattern of histone modification re-established by reader-writer complexes that recognize the same modifications they catalyze |
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Term
| What does chromatin regulate? |
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Definition
Chromatin = genome
DNA replication, DNA repair, transcription, recombination |
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Term
| When does DNA replication occur? |
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Definition
S phase of cell cycle (DNA Synthesis)
Mitosis - compact chromosomes
Interphase - extended conformation |
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Term
| Describe process of DNA replication |
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Definition
1) DNA helicase opens DNA double helix at replication origins
2) Replication fork moves bidirectionally.
3) DNA polymerase adds nucleotides 5' to 3' direction (new strand forms 5' first, subunits added to 3' end). (1000 nucleotides/sec in prokaryotes, 100 nucleotides/sec in eukaryotes)
4) DNA proofreading occurs 3' to 5' (exonuclease activity) |
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Term
| Meselsohn and Stahl Experiment |
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Definition
Proof of semi-conservative replication
1) Bacteria grown in 14N (light) combined with bacteria grown in 15N (heavy)
2) Bacteria allowed to continue dividing, intermediate weight band produced (detected through centrifuge)
To determine if resulting strands were semiconservative or dispersive, Meselsohn and Stahl heated DNA to break H-bonds. Single strands resulted, strands were centrifuged, and they discovered one strand was heavy, other was light. |
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Term
| How did proofreading lead to 5' to 3' polymerase activity? |
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Definition
To add nucleotide subunit onto strand, one high-energy bond in nucleoside triphosphate (on 5' end) is hydrolyzed, fuels reaction linking subunit onto strand and releases pyrophosphate.
Hypothetical: If strand grew 3' -> 5', no high-energy bond is cleaved and subunit would not be able to attach onto strand. (5' end needs to be cleaved) |
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Term
| DNA replication on lagging strand (Okazaki fragments) |
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Definition
1) DNA PRIMASE synthesizes new RNA primer on old Okazaki fragment
2) DNA POLYMERASE adds to new RNA primer to start new Okazaki fragment, finishes fragment.
3) RNase (nuclease) erases old RNA primer, Repair DNA polymerase replaces with DNA
4) DNA LIGASE seals nick and joins new Okazaki fragment to strand. |
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Term
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Definition
| Protein keeping DNA polymerase firmly attached to template while synthesizing new strands of DNA. |
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Term
| What does telomerase do? Describe its process. What problem does it solve? |
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Definition
Telomerase adds DNA repeats to ends of chromosomes.
1) Telomerase binds to repetitive telomere sequence.
2) Telomerase adds additional repeats to template strand.
3) DNA polymerase completes lagging strand.
Solves end replication problem (prevents loss of DNA with replication) |
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Term
| Source and sites of DNA damage |
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Definition
Sources: DNA replication errors, radiation, environmental chemicals, reactive molecules
Sites:
- Germ cells = genetic diseases, inherited in all cells
- Somatic cells = sporadic disease, cancer (ex: colon cancer incidence increases with age due to multiple mutations)
DNA mismatch repair systems protect integrity of genome. |
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Term
| Effects of DNA mismatch repair on error rate |
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Definition
Without: 1 error/10^7 nucleotides
With repair: 1 error/10^9 nucleotides |
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Term
| Describe process of DNA mismatch repair. Which strand must DNA mismatch repair remove? |
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Definition
DNA mismatch repair must remove newly synthesized strand/error.
1) Recognition of error in newly synthesized top strand
2) Excision of damaged region
3) DNA polymerase makes new top strand
4) DNA ligase seals nick |
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Term
| Effect of UV radiation on DNA. What is the disease it causes? |
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Definition
UV radiation causes chemical lesions called THYMINE DIMERS that are repaired by nucleotide excision repair (NER) proteins.
Mutations in NER genes and proteins cause human genetic disease Xeroderma pigmentosum.
NER disruption leads to accumulation of thymine dimers. (Freckling, sun-sensitivity, melanoma) |
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Term
| How are double-stranded DNA breaks repaired? |
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Definition
Non-homologous end joining:
1) broken ends processed by nuclease
2) end-joining by DNA ligation
= break repaired with deletion of nucleotides at repair site
Homologous recombination: (has homologous DNA duplexes)
1) Nuclease digests 5' ends
2) Strand invasion into homologous pairs. BRANCH POINT = where 5' end meets homologous strand.
3) DNA synthesis and migration of branch point
4) Continued branch migration (down strand) and DNA synthesis
5) DNA ligation
= accurately repaired double strand break (no nucleotides deleted) (Wild type DNA needed) |
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