| Term | Definition |
| similarities between bacterial and viral chromosomes | · single nucleic acid molecule
· few associated proteins
· smaller and less genetic info than eukaryotic chromosomes |
| characteristics of viral chromosomes | · DNA or RNA, single or double stranded
· circular or linear
· genetic material inert until released into host cell
· can package long DNA into small volume like eukaryotes |
| characteristics of bacterial chromosomes | · circular, double stranded, DNA, compacted into nucleoid region
· associated with small proteins: HU and H-NS, other binding proteins made of many (+) charged amino acids
· self-replicated and transcribed readily |
| supercoiled DNA | · closed-circular molecules found in eukaryotes
· more compact and sedimentates more rapidly than linear DNA
· used for gene therapy and DNA vaccines: delivers more DNA per dose, harder to destroy |
| topoisomerases | · enzymes that cut DNA strands and wind/unwind the helical structure
· found in eukaryotes |
| polytene chromosomes | · paired homologs, unusual for eukaryotes
· visualized by light microscopy of nuclei of interphase cells - usually from salivary, rectal, midgut, excretory tissues
· undergo replication with no strand separation or cell division |
| puff regions in polytene chromosomes | · bulges where DNA has uncoiled for easy access - represents high level gene activity
· determined with radioactively labeled RNAs |
| lampbrush chromosomes | · large with extensive DNA looping, found in vertebrate oocytes and some insect spermatocytes
· isolated from oocytes in diplotene stage of prophase I (meiosis)
· similar to polytene puff regions - high gene activity |
| chromatin | · eukaryotic chromosomes uncoiled and decondensed
· dispersed thru nucleus in interphase - chromosomes not visible, transcriptionally active
· condenses into visible chromosomes for division - almost 0 transcriptional activity |
| histones | · positively charged proteins associated with eukaryotic chromosomes
· contains large amounts of lysine and arginine
· electrostatically bonds to negatively charged phosphate groups in DNA
· H1, H2A, H2B, H3, H4 |
| nucleosomes | · spherical particles that resemble beads on a string
· DNA wraps around them, associate with H1 histone, and condenses several times to form intact chromatids |
| chromatin remodelling | · chromatin structure must change to accommodate DNA-protein interactions and allow for replication and gene expression
· chromatin must relax, expose regions of DNA to regulatory proteins, and have a reversal mechanism for inactivity |
| superhelix | · principal packaging unit of DNA in eukaryotic nucleus
· twists and turns of the superhelix encircle a group of histones
· histone tails are unstructured and are not folded into histone domains within the nucleosome (no secondary structure) |
| chemical modifications | · important to genetic function - histone tails provide potential targets for changes
· acetylation, methylation (activates on histones and inactivates on DNA), phosphorylation all lead to gene activation |
| acetylation | · histone acetyltransferase (HAT)
· adds acetyl group to (+) charged amino group on side chain (lysine) -> net charge of protein is now neutral
· increases areas of gene activity |
| methylation | · methyltransferase
· adds methyl groups to arginine and lysine residues in histones
· increases gene activity |
| phosphorylation | · kinase
· adds phosphate groups to hydroxyl groups of serine and histidine in histone |
| methylation of DNA instead of histone | · methylation of cytosine in polynucleotide chain of DNA forms 5-methyl cytosine, which decreases gene activity
· PSEN1 gene methylation in peripheral blood may be an early marker for Alzheimer's |
| CpG island | · region of DNA where many cytosine-guanine dinucleotides are present |
| euchromatin | · uncoiled and active
· appears unstained during interphase |
| heterochromatin | · condensed and mostly inactive - lacks genes or contains repressed genes
· appears stained during interphase, replicates later in S phase than euchromatin
· telomere maintains integrity and centromere allows movement |
| repetitive DNA sequences | · repeated many times in eukaryotic chromosomes
· many categories - main ones are highly repetitive or middle repetitive |
| satellite DNA | · highly repetitive
· short repeated sequences that make up a variable portion of total DNA
· found in heterochromic centromeric regions of eukaryotic chromosomes |
| centromere | · enables separation of homologs
· primary constriction along eukaryotic chromosomes |
| kinetochore proteins | · region that binds to spindle fiber microtubules during cell division |
| types of moderately repetitive DNA | · variable number tandem repeats (VNTRs): 15-100bp, found with and between genes
· minisatellites
· microsatellites (short tandem repeats, STRs): tandemly repeated, dispersed thru genome |
| short interspersed elements (SINES) and long interspersed elements (LINES) | · transposable sequences that are mobile and can relocate within genome
· dispersed throughout genome rather than being tandemly repeated
· 1/3 of human genome |
| retrotransposons | · transposable elements generated via RNA intermediate (LINES) |
| pseudogenes | · only 2-10% of eukaryotic genome is protein-encoding genes
· there is a large number of single-copy noncoding pseudogenes: represent evolutionary vestiges, have undergone significant mutation, and are not transcribes |
| general features of the genetic code | · written in linear form using ribonucleotide bases (RNA)
· codon: every three ribonucleotides
· unambiguous: each codon specifies only one amino acid
· degenerate: 18 of 20 amino acids can be specified by more than one codon |
| mRNA | · serves as intermediate in transferring genetic info from DNA to proteins
· genetic info stored in DNA but translated to protein with RNA |
| triplet code | · provides 64 codons for 20 amino acids |
| reading frame | · contiguous sequence of nucleotides
· insertions and deletions cause a frameshift mutation -> triplet code revealed |
| triplet binding assay | · Nirenberg and Leder developed this to determine some specific codon assignments
· ribosomes bind to single codon of three nucleotides so the complementary amino acid-charged tRNA can bind |
| amino acids encoded by only one codon | · tryptophan (UGG) and methionine (AUG, start) |
| wobble hypothesis | · initial two ribonucleotides are more critical than the third
· third position is less spatially constrained and doesn't need to adhere as strictly to base-pairing rules |
| methionine in bacteria | · modified form: N-formylmethionine (fmet) |
| stop codons | · UAG, UAA, UGA
· do not code for any amino acid, not recognized by tRNA, simply terminates translation |
| nonsense mutations | · produce a stop codon early
· translate is terminated and partial polypeptide is produced |
| mitochondrial DNA | · reveals exceptions to the universal genetic code
· UGA codes for tryptophan instead of termination
· AUA codes for methionine instead of isoleucine |
| overlapping genes | · single mRNA with multiple initiation
· creates different reading frames and specifies more than one polypeptide
· mose viruses use this to compensate for small genome |
| open reading frame of overlapping genes | · initiation at different AUG positions out of frame with another lead to distinct polypeptides |
| codon vs. anti-codon | · mRNA contains the codon in triplet code
· tRNA contains the anti-codon |
| RNA polymerase | · does not require a primer for initiation - can be used to repair telomeres |
| transcription start site | · RNA polymerase binds to promoter region (omega subunit) - specific DNA sequence upstream of transcription start site |
| consensus sequences | · DNA sequences that are homologous in different genes of same organism
· ex. E. coli promotors have two of these - TTGACA and TATAAT - Pribnow box |
| transcription termination in bacteria | · termination transcribed into RNA causes newly formed transcript to fold back on itself (hairpin) |
| transcription in eukaryotes | · occurs in nucleus but mRNA leaves nucleus for translation
· chromatin must uncoil (remodeling) to make DNA accessible to RNA polymerases
· RNA pol. rely on transcription factors to scan/bind DNA
· enhancers and silencers regulate transcription |
| differences in RNA polymerases (eukaryotic) | · I -> rRNA
· II -> mRNA, snRNA
· III -> 5SrRNA, tRNA |
| RNA polymerase II (eukaryotic) | · transcribes wide range of genes
· activity dependent on cis-acting elements and trans-acting transcription factors
· core promotor determines where it binds to DNA |
| TATA box | · core promotor element
· binds TATA-binding protein of transcription factor to determine transcription start site |
| enhancers and silencers | · found upstream of, within, or downstream of a gene
· enhancers increase and silencers decrease transcription levels, modulating from a distance
· change transcription levels in response to cell's requirement for gene product |
| posttranscriptional modifications of mRNA | · addition of 5' cap (7-mG cap)
· addition of 3' tail (poly-A tail)
· excision of introns |
| introns | · regions of initial RNA transcript not expressed in final amino acid sequence
· DNA sequences not represented in final mRNA product
· removed by splicing
· not found in prokaryotes |
| self-splicing RNAs | · self-excision group I introns
· occurs in bacteria, lower eukaryotes, and higher plants |
| spliceosome | · pre-mRNA introns spliced out by spliceosome
· involves formation of lariat structure, splice donor and acceptor sites, branch point sequence |
| translation of mRNA | · requires amino acids, mRNA, ribosomes, tRNA |
| tRNAS | · adapt genetic info from mRNA codons -> amino acids
· tRNA is anticodon and carries corresponding amino acid |
| ribosomes | · essential role in expression of genetic information
· consist of large and small subunit
· prokaryotes' are 70s and eukaryotes' are 80s |
| rDNA | · rRNA genes
· moderately repetitive DNA fraction present in clusters at various chromosomal sites
· contains tandem repeats separated by noncoding spacer DNA |
| tRNAs | · small and very stable, cloverleaf structure
· 75-90 nucleotides
· transcribed from DNA
· contain post-transcriptionally modified bases |
| aminoacylation ("tRNA charging") | · aminoacyl tRNA synthetase catalyzes aminoacylation - tRNA chemically linked to respective amino acid
· 20 different synthetases, one for each amino acid |
| initiation of translation | · requires: small and large ribosomal subunits, mRNA molecule, GTP, charged initiator tRNA, initiation factors, Mg2+ |
| Shine-Dalgarno sequence (bacterial) | · precedes AUG start codon
· base-pairs with region on small ribsosomal subunit, facilitating initiation |
| polysomes/polyribosomes | · mRNAs with several ribosomes translating at once |
| eukaryotic translation | · ribsosomes larger and longer lived
· transcription in nucleus and translation in cytoplasm - in prokaryotes, both simultaneous in cytoplasm
· needs more factors for initiation, elongation, and termination
· ribsomes not free-floating but bound to ER |
| Kozak sequence (eukaryotic) | · purine (A/G) three bases upstream from AUG start codon, followed by G
· A/GNNAUGG
· thought to increase efficiency of translation by interacting with initiator tRNA |
| closed loop translation | · mRNA cap and tail brought together to form loop
· Poly-A-binding proteins bind to cap-binding protein to form loop
· saves energy by eliminating translation on incomplete mRNA |
| peptide bonds | · dehydration reaction facilitates bond between carboxyl group of one amino acid and amino group of another
· two amino acids linked are dipeptide, three = tripeptide, etc... ten+ = polypeptide |
| four levels of protein structure | · primary: sequence of amino acids
· secondary: alpha-helix and beta-pleated sheets
· tertiary: three-dimensional conformation
· quaternary: composed of more than one polypeptide chain |
| posttranslational modifications | · n-terminus amino acid removed or modified
· individual amino acid residues modified
· carbohydrate side chains sometimes attached (glycosylation)
· chains may be trimmed, often complexed with metals
· signal sequences removed for secreted proteins |
| protein folding | · not spontaneous - dependent on chaperones: proteins that mediate folding process
· diseases of protein folding: prion diseases |
| classifications of mutations | · point mutation/base subsitution
· missense: different amino acid - gain/loss of function or neutral
· nonsense: early stop codon prematurely terminates translation
· silent mutation: new triplet code but same amino acid (degeneracy) |
| base substitution types | · transition: pyrimidine replaces pyrimidine (A/G) or puring replaces purine (C/T/U)
· transversion: pyrimidine swapped for purine/vice versa |
| frameshift mutation | · result from insertion or deletion of base pair
· frame of reading for triplet code is altered |
| Marfan syndrome | · dominant mutation
· loss of one copy of FBN1 allele |
| mutations classified by phenotypic effect | · loss-of-function: reduces/eliminates function of product
· null: complete loss of function
· dominant: results in mutant phenotype
· gain-of-function: gene has enhanced, negative, or new function
· lethal: death
· conditional: ex. temp-sensitive |
| mutations classified by location | · somatic: not heritable, in any cell except germ cells (tumor formation)
· germ-line: heritable, in gametes (trisomy 21)
· autosomal: in autosomes (trisomy 21)
· X- and Y-linked (color blindness, hemophilia) |
| induced mutations | · result from influence of extraneous factors, natural or artificial
· radiation, UV light (melanoma), natural and synthetic chemicals |
| replication slippage | · loop in template strand during replication -> DNA polymerase misses looped out nucleotides -> insertions and deletions
· more common in repeat sequences (hot spots) - contribute to hereditary diseases (Fragile-X, Huntington) |
| tautomers | · alternate chemical forms of purines and pyrimidines - increased chance of mispairing during replication
· tautomeric shifts can change binding structure to allow for noncomplementary base pairing (may be a permanent mutation) |
| DNA base damage | · common causes of spontaneous mutation which can lead to new base pairing
· depurination: loss of purines (A/G) within a site
· deamination: amino group in C/A -> U, A -> hypoxanthine |
| oxidative damage to DNA | · due to by-products of cellular processes or exposure to high-energy radiation - need antioxidants in diet to prevent
· superoxides: O2-
· hydroxyl radicals: OH
· hydrogen peroxide: H2O2 |
| transposable genetic elements | · DNA elements that move with or between genomes of all organisms
· can act as naturally occurring mutagens
· create chromosomal damage thru inversions, translocations, double-stranded breaks |
| types of mutagens | · fungal (aflatoxins)
· cosmic rays
· UV light
· industrial pollutants
· medical x-rays
· chemicals in tobacco smoke or vape products
· micro and nanoplastics |
| alkylating agents | · donate alkyl group (CH3 or CH3CH3) to amino or keto groups in nucleotides
· alter base-pairing affinity and result in transition mutations
· ex. mustard gas (lethal to mammals) |
| intercalating agents | · chemicals that wedge between DNA base pairs -> distortions and unwinding
· ex. ethidium bromide |
| adduct-forming agents | · covalently binds to DNA, altering conformation and interfering with replication and repair
· ex. acetaldehyde (cigarette smoke) and heterocyclic amines (HCAs, from cooking meats) |
| free radicals | · stable molecules transformed into free radicals (has one or more unpaired electrons) by radiation
· alter purines and pyrimidines, break phosphodiester bonds, produce deletions, translocations, and fragmentation (all may be permanent) |
| beta-Thalassemia | · inherited autosomal recessive blood disorder
· most common single-gene disease, results from reduction or absence of hemoglobin |
| DNA strand discrimination | · based on methylation: newly synthesized strand remains unmethylated
· mismatch repair recognizes unmethylated strand and looks for sites to repair |
| postreplication repair | · responds after damaged DNA has escaped repair and has failed complete replication
· recA protein directs recombination exchange with region on undamaged parent strand (donor DNA)
· gap filled in by repair synthesis |
| photoreactivation repair | · enzyme absorbs photon of light to cleave thymine dimer, reverses effect of UV radiation on DNA
· humans and other organisms lack photoreactivation repair |
| xeroderma pigmentosum | · rare genetic disorder caused by defects in nucleotide excision repair pathways
· skin abnormalities and cancers, developmental and neurological effects
· individuals have 2000-fold higher rate of cancer |
| diseases caused by defect in NER pathway | · besides XP: cockayne syndrome and trichothiodystrophy |
| double-strand break repair | · DSBs are incredibly dangerous - chromosomal rearrangements, cancer, cell death
· can be repaired by either homologous recombination repair or nonhomologous end joining |
| Ames test | · detects chemicals that may cause cancer after metabolic activation |
| transposons | · genes that can move with and between chromosomes
· insert themselves into various locations within the genome
· found in all organisms, unknown function
· in bacteria, these may confer resistances to antibiotics or heavy metals |
| bacterial transposons | · insertion sequences: cause mutations if inserted into gene or regulatory region
· bacterial transposons: larger than IS elements, can move between plasmids and chromosomes to spread resistances thru strains |
| transposable elements in the human genome | · LINEs: 1-6kb long, 850k copies in genome, 21% of total genome
· SINEs: 100-500bp, 1.5mil copies, 13% of genome
· LTR elements: <5kb, 443k copes, 8% of genome
· DNA transposons: 80-300bp, 294k copies, 3% of genome |
| bacterial enzymes involved in gene regulation | · inducible enzymes: produced only when specific substrates are present to help bacteria adapt to environment
· constitutive enzymes: continuously produced regardless of chemical makeup of environment |
| positive vs. negative control | · negative: genetic expression occurs unless shut off by regulator molecule
· positive: transcription occurs only when regulator molecule directly stimulates RNA production |
| prokaryotic lactose metabolism | · gene activity repressed when lactose absent and induced when available to produce enzyme to metabolize it
· lactose is the inducer |
| bacterial Lac operon | · three structural genes code for enzyme structure to digest lactose: lac2, lac4, lacA
· upstream regulatory region consisting of operator and promotor
· gene cluster functions to provide rapid response to presence/absence of lactose |
| bacterial trp operon | · repressible gene system
· when tryptophan present, enzymes necessary for its synthesis are not produced |
