©FYNDLAY EXAM SOLUTIONS 2024/2025
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Advanced Biochemistry Exam 3 Questions
And Answers (Guaranteed A+)
All RNAs are synthesized from DNA templates by __? - answer✔DNA-dependent RNA
polymerases
__ direct the synthesis of proteins. - answer✔mRNAs
RNA polymerases link __ in the order specified by base pairing with a DNA template. -
answer✔NTPs
RNA polymerase moves along the template strand in the __ direction, and the RNA chain grows
in the __ direction. - answer✔3' --> 5'; 5' --> 3'
__ of Ppi to inorganic phosphate by __ makes the polymerase reaction thermodynamically
favorable. - answer✔hydrolysis; pyrophosphatases
Transcription is initiated in prokaryotes by __. - answer✔RNA polymerase holoenzyme
Subunits of RNA polymerase holoenzyme. - answer✔alpha x 2, beta, beta-prime, sigma
Function of alpha subunit of RNA polymerase holoenzyme in prokaryotes. - answer✔scaffold
and regulation; dimerize
Function of beta subunit of RNA polymearse holoenzyme in prokaryotes. - answer✔Part of
polymerase active site
Function of beta prime subunit of RNA polymerase holoenzyme in prokaryotes. - answer✔binds
to and unwinds DNA
Function of sigma subunit of RNA polymerase holoenzyme in prokaryotes - answer✔
Core polymerase structure - answer✔alpha x 2, beta, beta-prime
Core polymerase can transcribe DNA into RNA, but cannot __. - answer✔recognize promoters
and initiate transcription
1|Page
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Binding of __ subunit allows polymerase to recognize __. - answer✔sigma; different DNA
sequences that act as promoters
Promoters - answer✔nucleotide sequences that identify the location of transcription start sites
RNA polymerases (do/do not) require a primer. - answer✔do not
Four stages of transcription - answer✔1. Binding of RNA pol holoenzyme to template DNA at
promoter sites; 2. initiation of polymerization; 3. chain elongation; 4. chain termination
RNA pol holoenzyme binds __ to DNA with __ affinity and migrates __ looking for a sigma
promoter region. - answer✔nonspecifically; low; downstream
Holoenzyme + promoter - answer✔closed promoter complex
open promoter complex - answer✔polymerase unwinds 12 base pairs in the -9 to +3 region
Operon: Promoter - answer✔DNA sequence which identifies and binds to the primary
transcription site where transcription begins
Prokaryotic Promoters - answer✔TATA box at -10 region; -35 region TTGACA
Operon: Operators - answer✔sequence near the promoter which regulates the transcription
start
Operon: Structural Genes - answer✔a gene that codes for any RNA or protein product other
than a regulatory factor
Lac Operon - answer✔consists of 3 structural genes (LacZ, LacY, LacA), promoter, terminator,
regulator, and operator
Lac Operon Structural Genes - answer✔LacZ - encodes beta-galactosidase
LacY
LacA
Beta-galactosidase - answer✔intracellular enzyme that cleaves the disaccharide lactose into
glucose and galactose
Chromatin Remodeling - answer✔the dynamic modification of chromatin architecture to allow
access of condensed genomic DNA to the regulatory transcription machinery proteins, and
thereby control gene expression
Nucleosome-Histone Interactions - answer✔move, restructure, or eject the nucleosome to
allow for the interaction with transcription factors
2|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
Acetylation - answer✔reduces the binding affinity and loosens the bond between chromatin
and histones, thereby exposing DNA
DNA Start Sequences: Promoters: Consensus Sequences - answer✔TATA box
INR box
BRE
CCAAT-box
GC-box
DNA Start Sequences: Enhancers - answer✔a short region of DNA that can be bound by
proteins (activators) to increase the likelihood that transcription of a particular gene will occur
DNA Start Sequences: Silencers - answer✔DNA sequence capable of binding transcription
regulation factors (repressors); prevents RNA pol from transcribing DNA into RNA
prevent genes from being expressed as proteins
DNA Start Sequences: Response Elements - answer✔short sequences of DNA within a gene
promoter region that are able to bind specific transcription factors and regulate transcription of
genes
Mediators - answer✔multiprotein complex that functions as a transcriptional coactivator by
interacting with transcription factors and RNA pol II in which it transmits signals from the
transcription factor to polymerase
Role of RNA pol I - answer✔transcribe rRNA genes
Role of RNA pol II - answer✔transcribe mRNA, miRNA, snRNA, and snoRNA genes
Role of RNA pol III - answer✔transcribe tRNA and 5S rRNA genes
Roles of CDT Regions - answer✔(C-terminal domain)
exists only in RNA pol II and stretches from the core to the exit channel
involved in initiation of transcription, capping of RNA transcript, and attachment to the
spliceosomes
Role of General Transcription Factors in Initiation - answer✔bind to promoter region of gene to
form the pre-initiation complex
3|Page
ALL RIGHTS RESERVED.
Advanced Biochemistry Exam 3 Questions
And Answers (Guaranteed A+)
All RNAs are synthesized from DNA templates by __? - answer✔DNA-dependent RNA
polymerases
__ direct the synthesis of proteins. - answer✔mRNAs
RNA polymerases link __ in the order specified by base pairing with a DNA template. -
answer✔NTPs
RNA polymerase moves along the template strand in the __ direction, and the RNA chain grows
in the __ direction. - answer✔3' --> 5'; 5' --> 3'
__ of Ppi to inorganic phosphate by __ makes the polymerase reaction thermodynamically
favorable. - answer✔hydrolysis; pyrophosphatases
Transcription is initiated in prokaryotes by __. - answer✔RNA polymerase holoenzyme
Subunits of RNA polymerase holoenzyme. - answer✔alpha x 2, beta, beta-prime, sigma
Function of alpha subunit of RNA polymerase holoenzyme in prokaryotes. - answer✔scaffold
and regulation; dimerize
Function of beta subunit of RNA polymearse holoenzyme in prokaryotes. - answer✔Part of
polymerase active site
Function of beta prime subunit of RNA polymerase holoenzyme in prokaryotes. - answer✔binds
to and unwinds DNA
Function of sigma subunit of RNA polymerase holoenzyme in prokaryotes - answer✔
Core polymerase structure - answer✔alpha x 2, beta, beta-prime
Core polymerase can transcribe DNA into RNA, but cannot __. - answer✔recognize promoters
and initiate transcription
1|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
Binding of __ subunit allows polymerase to recognize __. - answer✔sigma; different DNA
sequences that act as promoters
Promoters - answer✔nucleotide sequences that identify the location of transcription start sites
RNA polymerases (do/do not) require a primer. - answer✔do not
Four stages of transcription - answer✔1. Binding of RNA pol holoenzyme to template DNA at
promoter sites; 2. initiation of polymerization; 3. chain elongation; 4. chain termination
RNA pol holoenzyme binds __ to DNA with __ affinity and migrates __ looking for a sigma
promoter region. - answer✔nonspecifically; low; downstream
Holoenzyme + promoter - answer✔closed promoter complex
open promoter complex - answer✔polymerase unwinds 12 base pairs in the -9 to +3 region
Operon: Promoter - answer✔DNA sequence which identifies and binds to the primary
transcription site where transcription begins
Prokaryotic Promoters - answer✔TATA box at -10 region; -35 region TTGACA
Operon: Operators - answer✔sequence near the promoter which regulates the transcription
start
Operon: Structural Genes - answer✔a gene that codes for any RNA or protein product other
than a regulatory factor
Lac Operon - answer✔consists of 3 structural genes (LacZ, LacY, LacA), promoter, terminator,
regulator, and operator
Lac Operon Structural Genes - answer✔LacZ - encodes beta-galactosidase
LacY
LacA
Beta-galactosidase - answer✔intracellular enzyme that cleaves the disaccharide lactose into
glucose and galactose
Chromatin Remodeling - answer✔the dynamic modification of chromatin architecture to allow
access of condensed genomic DNA to the regulatory transcription machinery proteins, and
thereby control gene expression
Nucleosome-Histone Interactions - answer✔move, restructure, or eject the nucleosome to
allow for the interaction with transcription factors
2|Page
, ©FYNDLAY EXAM SOLUTIONS 2024/2025
ALL RIGHTS RESERVED.
Acetylation - answer✔reduces the binding affinity and loosens the bond between chromatin
and histones, thereby exposing DNA
DNA Start Sequences: Promoters: Consensus Sequences - answer✔TATA box
INR box
BRE
CCAAT-box
GC-box
DNA Start Sequences: Enhancers - answer✔a short region of DNA that can be bound by
proteins (activators) to increase the likelihood that transcription of a particular gene will occur
DNA Start Sequences: Silencers - answer✔DNA sequence capable of binding transcription
regulation factors (repressors); prevents RNA pol from transcribing DNA into RNA
prevent genes from being expressed as proteins
DNA Start Sequences: Response Elements - answer✔short sequences of DNA within a gene
promoter region that are able to bind specific transcription factors and regulate transcription of
genes
Mediators - answer✔multiprotein complex that functions as a transcriptional coactivator by
interacting with transcription factors and RNA pol II in which it transmits signals from the
transcription factor to polymerase
Role of RNA pol I - answer✔transcribe rRNA genes
Role of RNA pol II - answer✔transcribe mRNA, miRNA, snRNA, and snoRNA genes
Role of RNA pol III - answer✔transcribe tRNA and 5S rRNA genes
Roles of CDT Regions - answer✔(C-terminal domain)
exists only in RNA pol II and stretches from the core to the exit channel
involved in initiation of transcription, capping of RNA transcript, and attachment to the
spliceosomes
Role of General Transcription Factors in Initiation - answer✔bind to promoter region of gene to
form the pre-initiation complex
3|Page
