Term
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Definition
Are genes made of DNA or protein?
E. Coli leave protein coat outside of bacterium and inject DNA into bacterium |
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Term
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Definition
enzyme that catalyzes DNA synthesis
reads 3' to 5'
produces DNA 5' to 3' |
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Definition
| catalyzes breaking of H-bonds between two DNA strands to separate them |
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Term
| single-strand DNA-binding proteins (SSBPs) |
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Definition
| attach to separated strands to prevent them from closing |
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Definition
| enzyme that cuts and rejoins DNA downstream of replication fork to relieve tension |
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Definition
| a few nucleotides bonded to template strand that provide a free 3' OH that can combine with an incoming dNTP to form a PDE bond |
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Term
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Definition
type of RNA pol
synthesizes a short RNA segment that serves as primer for DNA synthesis
does not require a free 3' OH |
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Term
| leading (continuous) strand |
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Definition
| synthesized towards replication fork in 5' to 3' direction |
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Term
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Definition
| holds DNA Pol in place to increase its efficiency |
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Definition
| adds bases to 3' end of primer in lagging strand synthesis |
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Definition
| short discontinuous DNA fragments in lagging strand |
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Definition
| removes RNA primer at beginning of each Okazaki fragment and fills in gaps |
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Term
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Definition
| joins Okazaki fragments to form a continuous DNA strand |
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Definition
| most of enzymes responsible for DNA synthesis around replication fork |
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Term
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Definition
| regions at ends of eukaryotic chromosomes |
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Term
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Definition
section on lagging strand where there is not available 3' OH for DNA synthesis and primer is removed
eventually degraded, resulting in shortening of chromosome |
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Term
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Definition
enzyme that adds more bases to end of lagging strand, catalyzing synthesis of DNA across from and RNA template that it carries with it
primase makes an RNA primer, which DNA Pol (euk) uses to synthesize strand (then ligase) |
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Term
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Definition
normal in somatic cells
limits amount of time cells are actively growing
promotes cell entry into G0
uncontrolled growth in cancer cells |
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Term
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Definition
| one part of DNA Pol III that removes deoxyribonucleotides from DNA |
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Term
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Definition
mismatched bases are corrected after DNA synthesis is complete
enzymes recognize, remove, and refill |
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Term
| nucleotide excision repair system |
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Definition
recognizes damaged bases
enzymes remove ssDNA in damaged section |
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Definition
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Term
| important properties of genetic code |
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Definition
redundant
unambiguous
nearly universal
conservative |
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Term
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Definition
result from a simple base change due to either
DNA Pol inserting incorrect base
unrepaired DNA damage |
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Term
| chromosome-level mutations |
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Definition
| much larger in scale, resulting from addition or deletion of chromosomes from individual's karyotype |
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Term
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Definition
| change in nucleotide that does not change amino acid specified by codon |
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Term
| missense (replacement) mutation |
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Definition
| change in nucleotide that changes amino acid specified by codon |
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Term
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Definition
| change in nucleotide that results in early stop codon |
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Term
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Definition
| addition or deletion of a nucleotide |
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Term
| three categories of mutations |
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Definition
beneficial
neutral
deleterious
(most are neutral or slightly deleterious) |
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Term
| single nucleotide polymorphisms (SNPs) |
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Definition
| single base changes (within genome) |
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Term
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Definition
synthesizes RNA in 5' to 3' direction
does not require a primer to begin transcription
one type in bacteria, several in eukaryotes |
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Term
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Definition
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Term
| (transcription in bacteria) initiation |
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Definition
sigma protein subunit binds to RNA Pol (to form holoenzyme)
sigma acts as a regulatory factor, guiding RNA Pol to specific promoter sequences on DNA template strand |
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Term
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Definition
-10 box
-35 box
transcription start site = +1 site |
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Term
| (transcription in bacteria) start |
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Definition
sigma binds to -35 and -10 boxes
sigma makes initial contact with DNA that starts transcription
most bacteria have several types of sigma proteins (for different promoter -> gene types) |
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Term
| (transcription in bacteria) inside enzyme |
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Definition
sigma opens DNA double helix and template strand is threaded through RNA Pol active site
incoming ribonucleoside triphosphat (NTP) pairs with complementary base on DNA
digma dissociates from core enzyme once initiation phase is complete |
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Term
| (transcription in bacteria) elongation and termination |
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Definition
RNA Pol moves along DNA template strand
encounters a termination signal in DNA template
signal codes for RNA segment that has enough complementarity for a hairpin 2o structure, which causes RNA Pol to separate from transcript |
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Term
| (transcription) initiation in eukaryotes |
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Definition
much more diverse and complex set of promoters
TATA box (~30 bp upstream)
instead of sigma factor, large group of proteins called basal transcription factors bind to promoter to initiate transcription (no holoenzyme) |
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Term
| RNA processing in eukaryotes |
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Definition
bacteria- DNA -> mRNA
eukaryotes- pre-mRNA
eukaryotic genes are much larger than their corresponding mature mRNA
addition of a 5' cap and a poly(A) tail- protect mRNAs from degradation by RNAses and enhance translation efficiency |
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Term
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Definition
| protein-coding regions of eukaryotic genes |
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Term
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Definition
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Term
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Definition
aminoacyl tRNA synthetases charge tRNA by catalyzing covalent addition of aa to tRNA
for each of 20 aa's, there are 1 or more aminoacyl tRNA syntheses and 1 or more tRNAs
tRNA covalently linked to aa is called an aminoacyl tRNA (aa-tRNA) |
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Term
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Definition
sequence at 3' end for aa binding
triplet on opposite loop is anticodon
L-shaped 3o structure
all tRNAs have same shape but vary at anticodon and attached aa |
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Term
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Definition
61 codons but 40 tRNAs
anticodon of tRNAs can still bind successfully to a codon whose 3rd position requires a nonstandard base pairing
one tRNA is able to base pair with more than one sequence of codon |
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Term
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Definition
A- acceptor site for an aa-tRNA
P- where peptide bond forms that adds aa to growing chain
E- where tRNAs no longer bound to an aa exit |
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Term
| (translation in bacteria) initiation |
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Definition
ribosome small subunit binds mRNA at binding site
initiator aa-tRNA bearing a modified methionine (f-met) binds to start codon (modification only in prokaryotes)
large ribosomal subunit binds, completing complex |
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Term
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Definition
arrival of aa-tRNA
peptide bond formation
translocation |
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Term
| (translation) termination |
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Definition
stops when A site encounters a stop codon
protein called a release factor enters site (resembles tRNA but does not have an aa)
catalyzes hydrolysis of bond linking tRNA in P site with polypeptide chain |
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Term
| post-translational modifications |
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Definition
enzymes may add or remove a phosphate group
covalent addition of sugar groups (glycosylation)
protein ubiquitin (ubiquitination)
protein SUMO (SUMOylation)
and many other types |
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Term
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Definition
chaperone proteins help with folding
protein function is determined by
aa sequence
post-translational modifications
later addition/removal of modifications
localization signals for where protein should go
modifications that influence stability |
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Term
| gene regulation (3 levels in bacteria and eukaryotes) |
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Definition
transcriptional = prevent RNA Pol from binding to promoter
translational = prevent translation of existing mRNA
posttranslational = prevent modification/addition of existing protein |
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Term
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Definition
| molecule that stimulates expression of a specific gene (lactose) |
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Term
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Definition
| lack functional B-galactosidase |
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Term
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Definition
| lack membrane protein galactoside perm ease and so cannot transport lactose into cell |
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Term
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Definition
| constitutive- produce B-gal and galactoside permease even when lactose is absent |
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Term
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Definition
| occurs when a regulatory protein binds to DNA and shuts down transcription |
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Term
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Definition
| occurs when a regulatory protein binds to DNA and triggers transcription |
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Term
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Definition
| set of coordinately regulated bacterial genes that are transcribed together into one mRNA |
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Term
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Definition
| set of coordinately regulated bacterial genes that are transcribed together into one mRNA |
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Term
| lac operon three hypotheses |
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Definition
lacZ, lacY, and lacA genes are transcribed together -> coordinately regulated
lacI protein is a repressor that prevents transcription of lac operon by binding to a site called operator in absence of lactose
lactose, inducer, binds directly to lacI repressor, causing it to release from operator -> presence of lactose ends negative control of operon |
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Term
| advantage of coordinate regulation |
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Definition
| efficiency- gene products needed at same time and in same amounts |
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Term
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Definition
| a product molecule (=catabolite) represses production of enzyme(s) responsible for that reaction |
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Term
| lac operon positive control |
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Definition
absence of glucose -> high cAMP
catabolite activator protein (CAP) binds CAP binding site near lac promoter -> triggers transcription
CAP can only bound to DNA when bound to cAMP
adenylyl cyclase (produces cAMP) is inhibited by extracellular glucose |
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Term
| differential gene expression |
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Definition
| responsible for creating different cell types, arranging them into tissues, and coordinating their activity (in multicellular eukaryotes) |
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Term
| additional mechanisms of gene regulation |
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Definition
chromatin remodeling
RNA processing
regulation of mRNA life span or stability |
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Term
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Definition
| repeating, beadlike structures that form basis for orderly packing of DNA |
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Term
| histone acetyl transferases (HATs) |
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Definition
add acetyl groups to positively charged side chains in histones
reduces histone positive charge -> decondenses chromatin
histone deacetylases (HDACs) can reverse this |
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Term
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Definition
| precise patterns of chemical modifications of histones contain information that influences whether or not a particular gene is expressed |
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Term
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Definition
daughter cells can inherit patterns of histone modification, and thus patterns of gene expression, from parent cells
patterns of inheritance that are not due to differences in DNA sequence |
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Term
| promoter-proximal elements |
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Definition
| located just upstream of promoter and transcription start site, and have sequences that are unique to specific genes that are needed, providing a mechanism for eukaryotic cells to exert precise control over transcription |
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Term
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Definition
can be more than 10,000 bp away from promoter
can also be located in introns or untranscribed sequences
can work even if normal orientation is flipped or if they are moved to a new location on same chromosome |
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Term
| basal transcription factors |
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Definition
interact with promoter and are not restricted to particular cell types
required for transcription, but do not regulate gene expression |
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Term
| different cell types express different genes because |
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Definition
they have different histone modifications
contain different regulatory proteins -> certain proteins produced only in certain types of cells and at specific times |
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Term
| post-transcriptional control |
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Definition
splicing mRNA in various ways
altering rate at which translation is initiated
modifying life span of mRNAs and proteins after translation has occurred |
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Term
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Definition
bind to a protein complex RISC and to complementary sequences in mRNA
(cut) mRNA -> dsRNA -> proteins degrade it or prevent it from being translated |
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