Chapter 7: From DNA to Protein Flashcards
A series of 3 nucleotides for a specific amino acid
Codon
Enzyme that synthesizes DNA, using an existing strand as a template to make a complementary strand
DNA polymerase
Functional unit of the genome; it encodes a product , most often a protein
Gene
Complete set of genetic information in a cell or virus
Genome
Type of RNA molecule translated during protein synthesis
Mrna
Nucleotide sequence to which RNA polymerase binds to start transcription
Promoter
Structure that facilitates the joining of amino acids during transcription; composed of ribosomal RNA and protein
Ribosome
Enzyme that synthesizes RNA using 1 strand of DNA as a template
RNA polymerase
Process by which information encoded in DNA is copied into RNA
Transcription
Type of RNA molecule involved in interpretating the genetic code; each_____ molecule carries a specific amino acid
tRNA
The process by which the information carried by mRNA is used to synthesize the encoded protein
Translation
Functional unit of the genome; it encodes a product, most often a protein
Gene
Study and analysis of genome
Genomics
Gene expression is these 2 processes
Transcription & Translation
2 tasks cells must do to multiply
DNA replication
(Gene Expression)
Translation & Transcription
Flow of information from DNA –> RNA is called?
The central dogma
DNA has a _____ backbone
Sugar-phosphate
2 strand of DNA are ______ but _______and held together by ________ bonds between the nucleobases
Complimentary / antiparallel
Hydrogen
Bonding of A-T and G-C is called
Base-pairing
How many hydrogen bonds between G-C base pair
Between A-T
3 / 2
DNA is oriented in 3’ to 5’ and 5’ to 3’ direction what do these numbers stand for?
The carbon molecule
By regulating the synthesis of _______, a cell can quickly change levels of protein production
mRNA
Distinct region of DNA at which replication is initiated
Origin of replication
In which direction does DNA Replication go? In Prokaryotic cells
Bidirectional both ways
In DNA synthesis the site at which the double helix is being unwound to expose the single strands that can function as a template for DNA synthesis
Replication fork
Nucleic acid replication that results in each of the two double-stranded molecules containing one of the original strands(template) strand and one newly synthesized
Semiconservative replication
The process that starts DNA replication is called…
Initiation
Enzyme that helps relieve the tension in DNA caused by unwinding of the 2 strands of the DNA helix during DNA replication
DNA gyrase
Enzyme that unwinds the DNA near the replication fork
Helicase
Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis during DNA replication
Primase
Once replication is initiated, enzymes called _______ synthesize DNA in the 5’ to 3’ direction
DNA polymerase
A complex of enzymes and other proteins that cells use to replicate DNA
Replisome
In DNA replication, the DNA strand that is synthesized as a continus fragment
Leading strand
In DNA replication, the strand that is synthesized as a series of fragements
Lagging strand
Nucleic acid fragment synthesized as a result of the discontinuous replication of the lagging strand of DNA
Okazaki fragments
Enzyme that forms covalent bonds between adjacent fragments of DNA
DNA ligase
What keeps the strand seperated after helicase unzips them
Single strand binding proteins
Polymerase makes DNA in which direction 5 to 3 or 3 to 5
5 to 3
In transcription the enzyme ______ synthesizes single-stranded RNA using ______ as a template.
RNA polymerase/ DNA
In transcription a DNA sequence to which RNA polymerase can bind and start transcription is called _____ and the one that stops the process is called ____
Promoter / Terminator
Does RNA polymerase need a primer for transcription
No
A promoter is ______ of the gene it controls, a terminator is ______ of the promoter
Upstream/ Downstream
In translation the “template DNA strand is called _____”
While it’s complement is called
Minus strand
Plus strand
The DNA strand used as a template for RNA synthesis
Minus strand
The DNA strand complementary to the strand used as a template for RNA synthesis
Plus strand
A transcript that carries one gene is called?
One that carries for multiple genes is called
Monocistromic
Polycistronic
Transcription is started when _______ binds to _______
RNA polymerase/ promoter
Component of RNA polymerase that recognizes and binds to promoter
Sigma factor
3 phases of transcription
- Initiation
- Elongation
- Termination
Translation requires 3 major structures
mRNA, rRNA, and tRNA
Code that correlates a codon to one amino acid
Genetic code
How many different combinations of codons
64
_____ strings amino acids together to make a polypeptide
Ribosome
AUG is what
Start codon
This phase of translation creates a full length peptide
Elongation
Where do tRNA and mRNA meet. Which structure?
In the ribosomes
What does the e site in a ribosome do
Exit where the deacylated tRNA leaves the ribosome
What does the p site do in a ribosome
Holds the peptide chain
What does the a site do in a ribosome
Accepts the tRNA
Ribosome advancing one codon during Elongation this process is called.
Translocation
Protein that helps other protiens fold properly
Molecular chaperone
Which have pre-mRNA
Eukaryotic cells
In Eukaryotic gene expression adding a series of adenine derivates to the 3’ end of an mRNA transcript is called
Polyadenylation
In Eukaryotic gene expression adding methylated guanine derivatives to the 5’ end of mRNA is called
Capping
Eukaryotic transcript that has not yet had its introns removed
pre-mRNA
Process that removes introns from RNA transcript
Splicing
Segment that must be removed from pre-mRNA to create a functional mRNA molecule
Intron
Portion of Eukaryotic genes that will be transcribed and translated into proteins.
Exons
In Eukaryotic cells where is mRNA made
Nucleus
These ribosomes are s70, made up of 30S and 50S subunits
Prokaryotic
These ribosomes are 80s made up of subunits 40s and 60s
Eukaryotic
Process that transmits information from outside the cell inside, allowing that cell to respond to a change in environment
Signal transduction
Communication between cells allowing them to sense density of nearby cells
Quorum sensing
Mechanism of gene regulation that uses a sensor and response regulator
2-componment regulatory system
Two-component regulatory system consists of what?
What is its purpose?
Membrane-spanning sensor
Response regulator
When the sensor detects a change it starts the regulatory process of modifying the gene expression
There are two forms of natural selection in prokaryotic cells
One where they change their antigen so they are not recognized by the immune system
The other consist of random alteration of expression of bacterial structures such as fimbriae
Name these two mechanics
- Antigenic variation
- Phase variation
Group of linked genes whose expression is controlled as a single unit
Operon
Set of related genes transcribed as a seperate unit but controlled by the same regulatory protein
Regulon
Separate operons controlled by a single regulatory mechanism constitute a ______
Regulon
Simultaneous regulation of numerous unrelated genes
Global control
Enzymes that are synthesized constantly; always active
Constitutive
Type of enzyme that the synthesis can be turned on when needed.
Lac operon is an example
They are often involved in the transport and breakdown of specific energy sources
Inducible
Enzyme synthesized only under certain environmental conditions
Inducible
This enzyme type are produced routinely, but their synthesis can be turned off when they are not required
These are mostly used an anabolic pathways
Repressible
Enzyme whose synthesis can be turned off by certain conditions
Repressible enzyme
The methods a cell uses to prevent or facilitate transcription must be readily reversible
The two most common regulatory mechanism are ….
Alternative sigma factor and DNA-binding proteins
______ is a loose component of RNA polymerase that functions in recognizing specific promoters
Sigma factors
A sigma factor that recognizes promoters controlling genes needed only in non-routine situations
Alternative sigma factors
2 type of DNA-Binding proteins and their function
Repressor: Blocks transcription
Activator: Facilities transcription
A repressor a regulatory protein blocks transcription by…
Binding to the operator
Where is the operator located
Immediately downstream of the promoter.
A repressor regulatory protein may have a _____ bind to it, changing its shape and not allowing it to bind to the operator, Allowing RNA polymerase to transcribe gene.
Inducer
A repressor can play a role in 2 types of transcriptional regulatory system
Induction: Allowing transcription
Repression: Blocking transcription
A molecule that binds to an inactive repressor, thereby allowing it to function as a repressor.
Corepressor
Nucleotide sequence that precedes an ineffective promoter and to which an activator binds to facilitate transcription
Activator-binding site
In gene regulation, a protein that enhances the ability of RNA polymerase to initiate transcription
Activator
A regulatory mechanism that allows cells to prioritize use of carbon/energy sources
Carbon catabolite repression
Two-phase growth pattern is called
Diauxic growth
When lactose is present:
High levels of glucose cause Low Levels of cAMP
This represses or activates the Lac Operon?
Repression
When Lactose is present
Low levels of glucose and high levels of cAMP
Is there Repression or Activation of the Lac Operon
Activation
Type of carbon carabolite repression that prevents a carbon/ energy source from being transported into the cell
Inducer exclusion
In the lac operon
If glucose is present, the activator _____ is not active , so the lac operon is not transcribed
Glucose is available, _________ prevents lactose from entering the cell
If lactose is absent, the _____ is active, blocking transcription of the lac operon
CAP
Inducer exclusion
Repressor
In the lac operon model
If glucose is not available, the activator ______ is _______, so it facilitates transcription of the lac operon
CAP / active
An activator enhances transcription when it binds to ______
Activator-binding site
Inducers bring about gene expression by binding either to repressors doing this _______
Or to activators doing this ______
Disabling them
Enabling them
Cellular mechanism that targets specific mRNA molecules for destruction by using small RNA fragments to id it
RNA interference
RNA interference join with _______ a multi-protein unit to destroy mRNA
RNA-induced silencing complex
RISC
2 types of RNA molecules uses in RNAi
miRNA (MicroRNA)
short interfering RNA (siRNA)
Stretch of DNA, generally longer than 300 base pairs that begin with a start codon and end with a stop codon.
Computers search for these to read the DNA
Open reading frame
Cultivation-independent study of microbial communities or their members by analyzing the total microbial genomes in a sample take from the environment
Metagenomics
This begins at the origin of replication and is semiconservative
DNA replication
The bidirectional progress of replication around a circular DNA molecule creates two_____
Replication forks
In DNA REPLICATION; ______ synthesizes DNA in the 5’ to 3’ direction, using one strand as a template to generate the _______ strand
DNA polymerase/ complementary
During TRANSCRIPTION: _______ synthesizes RNA in the 5’ to 3’ direction, producing a single-stranded RNA molecule complementary and antiparallel to the _______
RNA polymerase/ DNA template
During translation, info encoded by mRNA is decoded using
The genetic code
______ locate key punctuation sequences on the mRNA molecule including a _________
Ribosomes/ Start codon
______ carry specific amino acids and act as keys that intemperate the genetic code.
tRNA
Ribosomes move along ______ in the 5’ to 3’ direction, translation terminates when it reaches a ______
mRNA / Stop Codon
In _____, transcription and translation occur at the same time
Prokaryotic cells
In Eukaryotic cells mRNA must be transported out of the _____ to the ____
Nucleus/ cytoplasm
Bacteria use ____ to activate genes that are only useful when expressed in critical mass
Quorum sensing
_____ is a random alteration in characteristics of surface proteins
Antigenic variation
_______ is the random switching on and off of certain genes
Phase variation
_______ enzymes are constantly made.
_____ enzymes can be turned on by certain conditions.
_____ enzymes can be turned off by certain conditions
Constitutive
Inducible
Repressible
The lac operon uses a repressor that (prevents / initiates) transcription of genes when lactose is not available.
Prevents transcription
_____ prevents transcription of the lac operon when glucose is available
Carbon catabolic repression
A molecule that regulates gene expression in 2 ways
Binding to Repressors Disabling them
Binding to Activators
Inducer
Rna polymerase is used in …
RNA polymerase is used in TRANSCRIPTION. This is the first step in gene expression in which a single strand of double-stranded DNA is used as a template to synthesize a complementary single-stranded RNA.
DNA polymerase is used in
DNA replication as in mitosis and meiosis
Catabolite activator protein(CAP)
acts as a glucose sensor. It activates transcription of the operon, but only when glucose levels are low. CAP senses glucose indirectly, through the “hunger signal” moleculecAMP.
What is the “hunger signal” molecule
cAMP
When lactose is not available the “lac repressor” is located where?
Doing what?
Bound to the operator, overlapping the promoter.
Stopping RNA polymerase from transcription of lactase
The _______ is a negative regulatory site bound by the lac repressor protein which over laps the promoter.
Operator
The ___________ is a positive regulatory site that is bound by catabolite activator protein (CAP). When CAP is bound to this site, it promotes transcription by helping RNA polymerase bind to the promoter.
CAP binding site
The lac operon is considered ________ (this type of operon) because it is usually turned off (repressed), but can be turned on in the presence of the inducer allolactose.
Inducible operon
CAP is only active when glucose levels are low (cAMP levels are _____)
What is cAMP
High
A hunger molecule
Glucose present, lactose absent:
No transcription of the lac operon occurs. That’s because the ___________ remains bound to the operator and prevents transcription by RNA polymerase. Also, cAMP levels are ____ because glucose levels are high, so ____ is inactive and cannot bind DNA.
Lac repressor
Low
CAP
Glucose absent, lactose present:
Strong transcription of the lac operon occurs. The lac repressor is released from the ______ because the inducer (allolactose) is present. cAMP levels are high because glucose is absent, so ____is active and bound to the DNA. CAP helps RNA polymerase bind to the promoter, permitting high levels of transcription.
Operator
CAP
What determines the structure and function of a protein
Amino acid sequence
Many enzymes in replication form an “assembly line” called ….
Replisome
Where does the energy for DNA replication come from ?
Hydrolysis of the phosphate bonds within the DNA
Can DNA polymerase initiate replication?
No it needs DNA primase
Which end can DNA polymerase add nucleotides to?
3’ end
** Correct **
In transcription RNA polymerase binds to sequence called
Promoter
Is a primer needed in transcription?
No
Transcription starts at…
Ends at…
Promoter
Terminator
RNA will have the same sequence as the (+ or -) strand?
+
Start and stop codons are used in…
Translation
Initiation of translation
Part of the ribosome binds to mRNA sequence called __________
Ribosome binding site
3 steps of translation
Initiation
Elongation
Termination
Elongation continues until the ______ reaches the stop codon
Does tRNA recognize a stop codon?
Ribosome
No
Multiple ribosomes can be on the same mRNA
T or F
True
Polypeptides destined for outside the cell are modified with….
Signal sequences (shipping tags)
Translation during transcription is only possible in this type of cell
Prokaryotic
A set of regulated genes transcribed as single mRNA along with its control sequence is ….
Operon
Seperate operons controlled by single regulatory mechanism constitute …
Regulon
Simultaneous regulation of numerous genes all together
Global control
2 most common regulatory mechanism to control transcription are …
Alternative sigma factors
DNA binding proteins
DNA binding proteins can act as repressors by binding to _____ stopping RNA polymerase.
The operator
2 mechanisms of repressors
- Induction.
“Inducer molecule “ binds to the Repressor, Repressor unable to bind transcription is (On / Off)
2 Inactive Repressor. Repressor cannot bind to operator
A Co-Repressor attaches to “Inactive-Repressor “ complex now binds to operator transcription is (On / Off)
On
Off
____ binds to the Repressor and alters its shape so it can no longer bind to the operator
Inducer
DNA-binding proteins can act as _____
Activators
What prevents the expression of genes that metabolize lactose in presence of glucose
Carbon catabolite repression
If glucose is available the activator CAP is ( active / not active)
Not active
If glucose is present lactose is not permitted to enter the cell from
Inducer exclusion
If lactose is present the repressor is (active/ inactive)
Lactose not present
Inactive
Active
RNA interference involves 2 things
RNA-induced silencing complex RISC
RNA strand that serves as Probe for binding to mRNA to be destroyed
What was the first genome published in 1995
Haemophilus influenzae
Prokaryotic DNA sequence
+ Strand used to represent sequence of RNA transcript
______ in (+) DNA indicates a possible start codon
ATG
Presence of lactose acts as _______
It attaches to the lac operor repressor and turns it into a ________
Inducer
Inactive repressor
Sigma factors are multi-domain subunits of bacterial RNA polymerase that play critical roles in ________ initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis
Transcription
________ is a DNA sequence where the RNA polymerase binds to initiate transcription. _______ is the DNA segment where the repressor molecule binds to the operon model.
Promoter / Operator
________ is a DNA sequence where the RNA polymerase binds to initiate transcription.
Promoter
______ is the DNA segment where the repressor molecule binds to the operon model.
Operator
What helps RNA polymerase find the promoter
Sigma factors
_________ is a DNA sequence where the RNA polymerase binds to initiate transcription. _______ is the DNA segment where the repressor molecule binds to the operon model.
Promoter / operator
