Term
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Definition
| segment of DNA that is used to make a functional product, either RNA or polypeptide |
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Term
| 1st step to accessing information stored in gene? |
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Definition
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Term
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Definition
=act of making copy
-->the process of synthesizing RNA from a DNA sequence
-copy of DNA base sequence is made in form of RNA |
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Term
structural genes
-product after trascription? |
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Definition
=encode amino acid sequence of a polypeptide
-over 90% of genes
-mRNA is the first product after transcribed |
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Term
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Definition
| =temporary code of a gene that contains information to make a polypeptide (translation) |
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Term
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Definition
=process of polypeptide synthesis
-the sequence of nucleotides within the mRNA determines the sequence of amino acids in polypeptide |
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Term
| what determines and organism's traits? |
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Definition
| the synthesis of functional proteins |
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Term
| central dogma of genetics |
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Definition
| =flow of genetic information occurs from DNA -> mRNA -> polypeptide |
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Term
| what determine the beginning and ending of a gene & also help regulate level of RNA synthesis? |
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Definition
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Term
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Definition
=determine whether a gene is turned on or off
-the site of regulatory sequences for binding of regulatory proteins (which influence rate of transcription) |
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Term
gene expression
-defintion |
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Definition
=overall process by which the information within a gene is used to produce a functional product (polypeptide)
-determined by environment + molecular expression of gene |
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Term
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Definition
| -base sequence that provides a site to begin transcription |
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Term
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Definition
| -base sequence that specifies the end of transcription |
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Term
| what causes RNA synthesis to occur within a defined location? |
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Definition
promotor and terminator
-DNA transcribed into RNA from end of promoter->terminator |
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Term
| base sequence in RNA transcript will be complementary to the template strand of DNA. T/F |
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Definition
| True, opposite strand (RNA) is called nontemplate strand |
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Term
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Definition
aka nontemplate strand for structural genes
->its sequence is that same as the transcribed mRNA except that the DNA has Ts where mRNA had Us |
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Term
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Definition
=recognize base sequences in DNA & control transcription
-some may bind directly to promoter & facilitate transcription
-other tf may recognize regulatory sequences/elements. bind & increase rate of transcription |
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Term
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Definition
-short sequence within mRNA in bacteria
-provides location for ribosome to bind & begin translation
--recognizes site bc it's complementary to a sequence in ribosomal DNA |
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Term
| mRNAs contain a series of codons which are? |
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Definition
| read as groups of three nucleotides which contain info for polypeptide's sequence |
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Term
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Definition
-start: very close to ribosome-binding site. specifies first amino acid in a polypeptide sequences
stop: signals the end of translation- end of polypeptide synthesis |
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Term
| 3 stages of transcription? |
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Definition
1. Initiation
2. Elongation (synthesis of the RNA transcript)
3. Termination |
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Term
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Definition
synthesizes RNA
-binds to promoter sequences to begin initiation
-separates DNA strands as it slides along DNA, forming bubble-like structure (open complex)
-eventually RNA poly reaches terminator which causes RNA poly & newly made RNA transcript to dissociate from DNA |
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Term
| initiation stage of transcription? |
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Definition
-recognition step: seq of bases in promoter recognized by tfs.
--tf allow tfs & RNA polymerase to bind to promoter seqs identifies starting site for transcription |
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Term
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Definition
aka open promoter complex
=bubble like structure formed by RNA polymerase denaturing dsDNA |
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Term
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Definition
| -mRNA that can encode two or more polypeptides |
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Term
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Definition
-miRNAs
-involved in gene regulation of eukaryotes |
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Term
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Definition
-small cytoplasmic RNA
-found in cytoplasm or bac and euk
--in bac: protein secretion
--in euk: ex) 7S RNA: targeting protiens to ER. component of SRP |
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Term
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Definition
-transfer RNA
-necessary for translation of mRNA |
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Term
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Definition
-ribosomal RNA
-necessary for translation of mRNA
--ribosome: rRNA + protein subunits |
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Term
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Definition
-small nucleolar RNA
-processing of euk rRNA transcripts
-in euk: found in nucleolus, where rRNA processing & ribosome assembly occurs |
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Term
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Definition
-small nuclear RNA
-necessary in splicing of euk pre-mRNA
-components of spliceosome |
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Term
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Definition
-can be used as genome by viruses
-packaged within viral capsid |
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Term
| RNA contains __ instead of __ |
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Definition
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Term
| bases in promoter sequence are numbered in relation to? |
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Definition
the transcription start site (no zero)
-promoters are located upstream
-promoter would be negative number |
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Term
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Definition
| first base used as a template for RNA transcription |
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Term
| certain sequences of bases are necessary to create a functional promoter (2 sequence elements?) |
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Definition
located at -35 and -10 site in promoter region
-35: 5'-TTGACA-3'
-10: 5'-TATAAT-3'
-->aka Pribnow box (in E.coli & similar)
-varies among diff genes |
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Term
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Definition
=the most commonly occuring bases with a sequence element
-recognized by proteins that initiate transcription |
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Term
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Definition
| -composed of 5 subunits a2BB'w |
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Term
| core enzymes + sixth subunit (sigma factor)= |
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Definition
| RNA polymerase holoenzyme |
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Term
| role of subunits in RNA poly holoenzyme? |
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Definition
2 alpha: proper assembly of holoenzyme & in binding to DNA
beta/beta':binding to DNA & carry out catalytic synthesis of RNA
w(omega): prop assembly of core enzyme
sigma: recognize promotors by -35 & -10 regions. a tf. |
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Term
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Definition
sixth subunit of RNA poly holo
-recognize promotors by -35 & -10 regions
-a tf
-contains helix-turn-helix motif to bind to -35 & -10
--alpha helices fit into major groove & form H bonds with bases |
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Term
| marks transition to elongation phase of transcription? |
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Definition
| release of sigma factor (after short strand of RNA made within open complex) |
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Term
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Definition
=when sigma factor has bound to promoter region
-->then dsDNA unwound into open complex (begins at -10 bc only has AT bp- 2H). short strand RNA made then signma released |
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Term
| template strand used for RNA synthesis? |
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Definition
aka antisense strand
-opposite strand= coding =sense strand
--same seq except T=U in RNA |
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Term
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Definition
| 43 nucleotides per second |
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Term
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Definition
| =the complementary strand made by DNA template strand |
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Term
RNA polymerases
-moves?
-synthesizes? |
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Definition
-template strand read in 3->5 direction
-synthesizes in 5-3 direction |
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Term
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Definition
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Term
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Definition
RNA-DNA hybrid froced to separate
->releasing RNA poly & newly made RNA transcript |
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Term
| p(rho)-dependent termination |
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Definition
p (rho): RNA binding protein responsible for terminating transcription. functions as helicase (separates RNA-DNA hybrid.
1. rut site acts as recognition site for binding of rho. rho binds to RNA & moves in dir of RNA poly
2.DNA encodes RNA seq (GC pairs form stem-loop). RNA syn terminates several nucleotides beyond loop |
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Term
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Definition
aka hairpin
-can form complementary sequences within RNA
-forms immediatedly after RNA seq synthesized & binds to RNA poly
-->binding=conformation change causes RNA poly to pause in synthesis of RNA
--->pause allows rho to catch up in loop, pass, & break H bonds btwn DNA & RNA within open complex
----> completed RNA strand separated from DNA with RNA poly |
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Term
| p-independent termination |
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Definition
-no rho
-terminator composed of 2 adj nucleotides seq that function within RNA
--U-rich seq @ 3' end & 2nd seq adj to U-rich that promotes stem loop structure |
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Term
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Definition
| aka p-independent because does not require protein |
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Term
| Eukaryotes use which RNA polymerases to transcribe genes? |
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Definition
RNA poly I, II, & III
-all contain 2 large catalytic subunits (~B&B' of bac RNA poly) |
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Term
| what also has similar structures to eukaryotic's RNA polymerases |
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Definition
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Term
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Definition
| =core promotor + regulatory elements (enhancers & silencers) |
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Term
| Transcription of structural genes in eukaryotes require? |
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Definition
RNA polymerase II, 5 general tfs, & mediator
-open complex: 5 tfs + RNA polymerase |
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Term
| termination of transcription in RNA polymerase II occurs when? |
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Definition
| 3' end of transcript is processed |
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Term
| RNA transcripts can be modified by? (6 methods) |
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Definition
1. processing
2. splicing
3. 5' campping
4. 3' polyA tailing
5. RNA editing
6. base modification |
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Term
| what are processed to smaller, functional molecules via cleavage steps? |
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Definition
| certain RNA molecules (rRNAs & precursor tRNAs) |
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Term
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Definition
in a globin gene using microscopy
-leder |
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Term
| Group I & II introns removed by? |
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Definition
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Term
| pre-mRNA introns removed by? |
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Definition
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Term
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Definition
| =multicomponent structure that recognizes intron sequences & removes them from pre-mRNA |
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Term
| In eukaryotes, mRNA is give? |
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Definition
| methylguanosine cap at 5' end & polyA tail at 3' end |
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Term
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Definition
| -changes base sequence of an RNA after it has been synthesized |
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Term
| nonstructured genes encode ? |
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Definition
RNA that is never translated
-products (tRNA, rRNA, etc) |
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Term
| In eukaryotic transcription, RNA polymerase I transcribes? |
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Definition
all the genes that encode rRNAs
-EXCEPT 5S rRNA |
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Term
| In eukaryotic transcription, RNA polymerase II transcribes? |
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Definition
all structural genes
->responsible for synthesis of all mRNA & also transcribes certain snRNA (which are needed for pre-mRNA splicing) |
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Term
| In eukaryotic transcription, RNA polymerase III transcribes? |
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Definition
| all tRNA genes & 5S rRNA gene |
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Term
| Structure of eukaryotic RNA polymerase |
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Definition
-2 catalytic subunits (Mg2+ located here): where nucleotides are covalently attached to 3' end of RNA
-transcribed DNA is upstream; entering DNA is downstream
-dsDNA enters along bridge surface between jaw & clamp
-At wall, RNA-DNA hybrid makes right angle (enables nucleotides to bind to template strand)
- NTPs enter through a pore & bind to template
-rudder separates hybrid
-ssDNA exits under small lid |
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Term
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Definition
| rut(rho utilization site) |
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Term
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Definition
-protein bound to RNA polymerase
-promotes pausing at stem loop sequence during rho-independent termination |
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Term
| 3 features found in promotor of eukaryotic structural genes: |
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Definition
1. regulatory elements (short DNA seq that effect ability of RNA poly to recognize core promoter. recognized by tfs)
2. TATA box (25 bp upstream from start site)
3. transcriptional start site |
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Term
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Definition
=relatively short DNA sequence that is necessary for transcription
-consists of TATAAA sequence aka TATA box (impt for determing precise starting point of transcription) |
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Term
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Definition
| =low level of transcription produces by core promotor |
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Term
| 2 categories of regulatory elements: |
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Definition
1. enhancers (activating sequences)
- needed to stimulate transcription (most euk genes have low level of basal transcription)
2. silencers
-DNA seqs reconized by tfs that inhibit transcription |
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Term
| common location for regulatory elements? |
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Definition
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Term
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Definition
=TATA box, enhancers, & silencers exert their effect only over a particular gene
-cis= next to
- elements can be far from core promoter, but are found within same chromosome as the genes they regulate |
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Term
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Definition
-regulatory tfs that binds to regulatory element and maybe far away from genes they control.
--when gene encoding for trans factor is expressed, the tf protein that is made can diffuse throughout cell & bind to appropriate ci elements |
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Term
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Definition
| typical start site for promoter of structural genes recognized by RNA poly II in euk |
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Term
| needed for RNA polymerase II to initate transcription of structural genes? |
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Definition
5 GTFs (general transcription factors)
-TFIID, B, F, E, & H |
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Term
| what GTFs first binds to TATA box? |
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Definition
TFIID
-critical role in recognition of core promoter
-composed of several subunits (TATA-binding protein aka TBP & TBP-associated factors aka TAFs) |
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Term
| After TFIID binds to TATA box? |
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Definition
TFIID associates with TFIIB
-promostes binding of RNA poly II & TFIIF to core promoter |
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Term
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Definition
=assembly of proteins to form a closed complex
by D->B->F->E&H (dirty butt fell even harder) |
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Term
| acts as bridge to bind RNA poly II & TFIIF? |
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Definition
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Term
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Definition
-part of preinitiation complex
-acts as helicase to form open complex
--phosphorylates CTD domain of poly II.
-->CTD phos: breaks contact btwn B & polyII
---->B, E, H released= open complex |
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Term
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Definition
=carboxyl terminal domain
-phosphorylation: loss of BEH then poly II is free to proceed to elongation |
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Term
| In vitro, what are the components necessary to transcribe DNA to RNA? |
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Definition
D, B, F, E, H, poly II, TATA box & transcriptional start site
=basal transcription apparatus (in vitro) |
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Term
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Definition
-in living cells, helps regulate & proceed at reasonable rate
-mediates interactions between poly II & regulatory tfs that bind to enhancers or silencers
--may regulate H's ability to phos CTD |
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Term
| TATA, enhancers, & silencers exert effects only over 1 gene: |
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Definition
| they are examples of cis-acting elements |
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Term
| eukaryotic structural genes are not always colinear with their functional mRNAs. T/F? |
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Definition
True, (colinear=one-to-one correspondance between seq of codons in DNA coding strand & aa seq of polypeptide)
->coding seq are separated by DNA seq that are not translated into protein aka EXONS (within mature RNA) |
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Term
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Definition
introns (intervening sequences)
-as RNA matures, introns are removed & exons are connected (spliced) together |
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Term
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Definition
-comon in eukaryotic species
=introns are removed & exons are connected (spliced) together |
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Term
| for many nonstructural genes, RNA transcript is processed or cleaved into smaller pieces by? |
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Definition
-cleavage produces fragments (ex rRNA molecules)
ex) 45S -> 18S + 5.8S + 28S
-cleavage + assembly occur in nucleolus |
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Term
| production of tRNA requires? |
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Definition
processing via exonucleases & endonucleases
-2 endo, 1 exo
-precursor recognized by RNaseP (an endo that cuts precursor tRNA) |
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Term
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Definition
=type of enzyme that cleaves a covalent bond between 2 nucleotides at one end of strand.
-can digest strand, one nucleotide at a time
-can begin from 3' or 5' end |
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Term
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Definition
| =can cleave the bond between 2 adj nucleotides within a strand |
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Term
| require for accurate transcription? |
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Definition
regulatory information within DNA
proteins which bind the DNA
proteins which copy info from DNA |
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Term
| Helicase is included in the closed promoter complex? T/F |
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Definition
| False, closed promoter complex included promoter region of DNA, RNA polymerase, TFs |
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Term
| Which RNA molecule's primary function is modifying other RNA molecules? |
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Definition
RNA of RNaseP & snRNa
-required for splicing eukaryotic pre-mRNAs |
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Term
| If strain of bacteria produces nonfunctional sigma factor, what step of transcription would be affected? |
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Definition
| bacteria would be unable to identify and rightly bind promoter elements |
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Term
| conservative substitution effect on DNA binding by TFs? |
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Definition
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Term
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Definition
=RNA sequences that assist in termination of transcription
= does not require protein |
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Term
| nucleic acid synthesis is always in what directions of new strand? |
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Definition
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Term
| If mutation of RNA polymerase removed rudder? |
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Definition
DNA would not be released from template
-rudder acts to separate RNA-DNA hybrid |
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Term
| "removal of intervening sequences" |
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Definition
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Term
| When studying eukaryotic enzymes in relation to their prokaryotic counterparts, you discover that some eukaryotic enzymes seem to consist of several regions, each of which performs the function of a separate enzyme in bacteria. Which of the following explanations would you be most likely to accept? |
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Definition
| Several genes located near each other in bacteria became transcribed together and the intervening sequences spliced out. |
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Term
| to demonstrate mRNA contains introns |
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Definition
1. comparison of DNA and mRNA sequences
2. comparison of genomic DNA & cDNA sequences
3. hybridization between DNA & mRNA |
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Term
| Introns often have a specific function after they are removed via splicing? |
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Definition
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Term
| Some introns can splice themselves? |
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Definition
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Term
| Splicing is required for some tRNAS |
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Definition
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Term
| The final step of splicing is formation of a phosphodiester linkage |
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Definition
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Term
| If you took apart a spliceosome, you'd find? |
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Definition
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Term
| critical function of 5' cap of eukaryotic mRNAs? |
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Definition
| =recogniation of the 5' end of the transcript by ribosome |
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Term
| 5' cap facilitates splicing, particularly the most 5' intron? |
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Definition
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Term
| 3' splice site ends in what in order to makr the 3' end of the intron? |
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Definition
| AG (ends with AG, not begins) |
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Term
| 5' splice site: begins with? |
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Definition
begins with GU
-marks 5'end of intron |
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Term
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Definition
| A that binds U2; branch of lariat |
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Term
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Definition
U4/U6 & U5
-brings 5' splice site to branch site |
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Term
| from promoter of gene, coding strand would run? |
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Definition
5'->3'
has same essential sequence as mRNA including orientation. template strand expected to be orientated with 3' end toward promoter |
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Term
| Regulatory sequences are DNA sequences which encode TF? |
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Definition
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Term
| During transcription, RNA polymerase spends majority of time in open complex |
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Definition
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Term
| regulation of genes in euk and prok requires cis & trans acting factors? |
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Definition
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Term
| only proteins can be biological catalysts? |
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Definition
false, RNA can also have catalytic activity
->enzymes with catalytic RNA are called RIBOZYMES |
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Term
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Definition
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Term
| Can RNA editing alter base sequences of the mRNA after transcription? |
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Definition
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