Cell Bio Chapter 7
the ribosome is composed of ...
(4 in eukaryotes) (3 in prokaryotes) ribosomal RNAs and over 80 ribosomal proteins
ribosomal bonding site for incoming RNA
A site (aminoacyl RNA)
link amino acids to corresponding tRNA
Aminoacyl-tRNA synthetases
At the 3' end of each tRNA is a single stranded region that contains the nucleotide sequence _______. What happens at this location?
CCA; amino acid is attached (aka amino accepting arm
flow of genetic information
DNA -> RNA -> Protein transcription and translation
The RNA polymerase like DNA polymerase resembles a crab cla, where the claw holds the____ and in between the claws is the ______________________
DNA; active site for linking the rNTPs together
ribosomal bonding site for the tRNA that is going to be released after aa has been attached to the growing polypeptide chain
E site
After release of the polypeptide chain and release factors, the ribosome will still be attached to the mRNA with tRNA in what sites?
P and E
ribosomal bonding site for attached tRNA
P site (peptidyl tRNA)
_________ is the addition of a methylated guanine to the 5' end of the RNA transcript. when does this occur?
RNA capping; as soon as it exits the RNA polymerase II complex
Differences between DNA and RNA
RNA is one strand of nucleotide as opposed to two strands. RNA contains ribose and DNA contains deoxyribose. RNA has uracil instead of thymine. RNA has a hydroxyl OH group at 2' carbon end, DNA has two hydrogens.
RNA polymerase that transcribes most rRNA genes
RNA polymerase I
_________________ and _____________ are involved in transcribing specialized RNA-encoding genes, such as rRNA and t RNA
RNA polymerase I and III
There are 3 main RNA polymerases and each are comprised of different subunits. What are they
RNA polymerase I, II, III
RNA polymerase that transcribes all protein coding genes, plus genes for other noncoding RNAs
RNA polymerase II
Upon binding, the structure of the TATA box is altered causing the recruitment of additional TF's, followed by ________
RNA polymerase II
___________________ is the main RNA polymerase and is involved in transcribing most protein coding genes and miRNAs
RNA polymerase II
Various GTFs will bind to their appropriate sequences in the promoter region and recruit ________. They will also aid in unwinding the DNA and pushing RNA polymerase II into the ___________
RNA polymerase II; elongation phase
RNA polymerase that transcribes tRNA, 5S rRNA, genes for small RNA
RNA polymerase III
a ribonuclease molecule involved in generating tRNA molecules from a larger precursor RNA molecules
RNase P
The _________ subunit is involved in the binding with the TATA box. Other subunits recognize and bind to other promoter regions
TBP
__________ binds to the TATA box to begin the formation of the transcription of the initiation complex.
TFIID
_________ binding causes unwinding of the promoter of DNA
TFIIH
What is transcription?
The sequence of DNA nucleotides in a gene is copied to a sequence of RNA nucleotide.
Each ORF specifies __________ and starts and ends _______
a single protein; internal sites within mRNA
bases in RNA
adenine, guanine, cytosine, uracil (similar to T but lacks a methyl group)
If two stretches are near each other, RNA may....
adoptone of various stem-loop structures
Some pre-mRNAs can be spliced in more than one way, generating alternative mRNAs. As a result _________
alternative splicing; one gene can produce more than one mRNA/protein
A tRNA that has its ________ attached is said to be charged
amino acid
__________ covalently attaches the amino acid to its appropriate tRNA in 2 steps. there are 20 of these, each specific to each amino acid
amino acyl- tRNA synthetases
First stage of transcription is called_______. RNA polymerase and associated (transcription) factors first bind to a specific sequence of DNA located in front of a gene, called the ________. Only one strand of DNA is used as the template. This step of transcription process is the most important for ________.
initiation; promoter; gene expression regulation
How does the terminator trigger termination?
directly or indirectly by changing the structure of the RNA transcript or causing specific proteins to bind to the end of RNA transcript
________ starts translation and carried first amino acid which is a _______
initiator tRNA; methionine (met tRNA)
During elongation, the RNA molecule being made ___________ from the DNA template as it moves along.
dissociates
four short segments of folded tRNA are ___________. Once segment forms the __________, a set of 3 nucleotides that bind, through base pairing to the complementary codon in mRNA molecule
double helical; anticodon
The RNA polymerase will add on rNTPs to the growing chain of RNA based on base-pairing/complementation to the template strand of DNA. As it moves forward, it unwinds the DNA in front of it, while reannealing the DNA behind it
elongation
Prokaryotic vs eukaryotic transcription
eukaryotic: three types of RNA polymerases, RNA is first transcribed in nucleus, transported through nucleaur membrane, then translated in cytoplasm, and more stable with lifespan of hours to days. prokaryotic: one type of RNA polymerase, occurs simultaneously with translation, and less stable with lifespan of seconds to minutes.
Coding sequences of a gene are called ________ (generally _____ nucleotides in length). Non coding sequences are called _____ (how long?)
exons (150); introns (vary in length, up to several hundred thousand bases)
Transport of mRNA is regulated. Proteins called ________ identify the molecule as mRNA destined for export out of nucleus
exportins
Unit of heredity containing the instructions that dictate the characteristics or phenotype of an organism
gene
a segment of DNA that directs the production of a particular protein or functional RNA molecule
gene
the process by which information from a gene is used in the synthesis of a functional gene product
gene expression
in order for the initiation of transcription to occur, specific types of proteins are required, called ________ to locate __________ and bring in ___________
general transcription factors (GTF);promoter;RNA polymerase
RNA is not considered ________ and has many functions
genetic material
3 steps of translation. What are they? All of this takes less than a minute
initiation- brings mRNA, tRNA with first aa, and ribosome at start codon. elongation- series of cycles as each aa is added to preceding one. termination- when one of the 3 stop codons is reached resulting in release of polypeptide
When a protein is made, the enzymes involved in translation are unable to distinguish between introns and exons, thus all would be translated into amino acids. Therefore, the _______ must be removed before translation
introns
one of the subunits of TFIIH has _______, an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule
kinase activity
Binding of new initiation factors stimulates the binding of _________, which causes the release of remaining initiation factors
large subunit
Transcription is more/less accurate than replication.Explain.
less because for transcription 1 mistake for every 10,000 nucleotides added, for replication 1 mistake for every 10million nucleotides added
The genetic info contained within the order of nucleotides in mRNA is interpreted to generate the _________
linear sequence of amino acids
code for proteins
mRNA
provides the genetic information (template) to be translated into amino acids. Products of transcription
mRNA
in order for RNA polymerase II to begin transcription, it needs to be activated by _______. Also _______ are removed from the initiation complex, as it begins transcription
phosphorylation; TFs
____________________ is the addition of several hundred Adenines to the _____ end of the RNA transcript. Special polymerase used in this?
polyadenylation; 3'. poly-A-polymerase
In initiation the small ribosomal subunit is mediated by transition initiation factors which do what?
position the initiator tRNA into the P site of the small subunit
RNA polymerase is similar in function to DNA polymerase, but does not need a _________ and has __________
primer; helicase ability
As RNA is transcribed, it will undergo several RNA processing steps before leaving the nucleus. There are three main ______ that occur as the RNA is being synthesized and after it has occured
processing steps
The ___________ is a set of DNA sequences required for transcription initiation by RNA polymerase. how long is it?
promoter; 40-60 nucleotides long in front of gene (5' directionften have v similar sequences for all genes **often have v similar sequences for all genes
Release factors mimic tRNA. They recognize stop codons via ________. There is a 3 aa sequence in the release factors that is critical for the interaction called the __________
protein RNA interaction; peptide anticodon
Majority of genes are used to make __________
proteins
RNA also had minor/major grooves like DNA, but the major groove is very narrow and deep that is not accessible to most _________.
proteins
form the core of the ribosome's structure and catalyze protein synthesis
rRNA
in front of the promoter, other sequences are present, called _______, that are also required for transcription to occur. It will bind regulatory proteins that are involved in activating or re+pressing transcription
regulatory sequences
In termination, stop codons are recognized by _________, which will activate ______ of the polypeptide from tRNA.
release factors; hydrolysis
in many cells, there are specific nucleotide sequences that are part of the gene that act as a signal for termination called the ________. What does this trigger?
terminator or stop site; rna polymerase to dissociate from the DNA and release the RNA product
The DNA nucletide sequence of a gene is used to determine what?
the RNA nucleotide sequence of an RNA molecule (transcription)
The RNA nucletide sequence is used to determine what?
the amino acid sequence of a protein (translation)
it is important that the synthetases are able to bind with their appropriate aa bc ___________. what is error rate of synthetases?
the ribosome is unable to distinguish between what is right and what is wrong (will accept any tRNA with proper codon-anticodon interaction).1 in 1 million
What is the function of RNA capping?
to stabilize end of 5' end of RNA by preventing exonuclease degradation, stimulates translation (by marking it as mRNA)and additional transcript processing, and facilitates nuclear export
_________ is the first step in the process of gene expression
transcription
in initiation, dsDNA is unwound and forms a ________. Transcription occurs in which direction?
transcription bubble 5'--->3'
The GTFs are involved in the transcription of most genes, but specificity comes from other transcription factors that are specific for different genes. the TFs with RNA polymerase II forms the ____________. Where?
transcription initiation complex formed at the TATA box region of the promoter
acts as an adaptor between the codons of mRNAs and amino acids
transfer RNAs (tRNAs)
eukaryotic ribosomes are larger, but have similar overall makeup. Eukaryotes have more ______ but less _______. eukaryotes also have a slwoer process (1 aa/sec compared to 20 aa /sec)
translation initiation factors; release factors
serve as adaptors between mRNA and amino acids during protein synthesis
tRNA
provides the interface between the mRNA and their corresponding amino acids. Transports amino acids to site of translation
tRNA (80 nucleotides in length)
There is no direct interaction between the nucleotides of mRNA and associated amino acids, but by the adapter RNA molecules, ________ . They are attached to specific amino acids that are then transferred to the growing polypeptide chain during translation
tRNAs
Upon completion of transcribing the gene, RNA polymerase stops and releases the RNA product
termination
Once RNA polymerase II mades a transcript longer than _____, it is said to have escaped the promoter and transitions into the __________
10 nucleotides; elongation phase
How fast can the ribosome translate mRNA
2 amino acid / second
how many bonding sites does ribosome have to form a peptide bond? what are they?
3 A P E
tRNAs have a characteristic and highly conserved structure of single stranded and double stranded RNA regions that look like a _______.
3 leaf clover
Which end of the ORF is determined by the stop codons....
3'; UAA, UAG, UGA
What end of the ORF is determined by the start codon (______)? it defines the reading frame for all subsequent codons (first codon determines second etc)
5';AUG
The small subunit and associated factors will then scan the mRNA in what direction for the start codon? The start codon is recognized by base pairing with the ______. This base pairing results in a ________
5-3; anticodon of initiator tRNA structural conformation change , which in turn causes some of bound initiation factors to be release and new ones to bind
tRNAS are small RNA molecules comprised of about _____ nucleotides in length. They are then attached to specific amino acids that are transferred to polypeptide chain during translation
80
how many genes undergo alternative splicing?
95%
Since met-tRNA is in the P site, the __________ site is available to accept a charged tRNA
A
Specific Codons in mRNA Signal the Ribosome WHere to Start and to Stop Protein Synthesis: First, _________ binds to the a site. The a peptide bond is formed between _(__2__). As new charged tRNA enters A site, the growing polypeptide chain exits through the _______ site. mRNA or ribosome complex translocates to the next codon, making the A site available for a new aminoacyl-tRNA. This translocation will continue until ________
aminoacyl-tRNA; aminoacyl-tRNA in A site with peptidyl tRNA in P site;E; a stop codon enters the A site
ribozymes contain ....
an active site (binding site for substrate) and possibly binding site for allosteric molecules
each synthetase has the ability to recognize specific nucleotides in both _________ and ____________ of the correct tRNA. Can distinguish different amino acids based on size, shape, and chemical compostion
anticodon and amino-acid accepting arm
RNA can fold back on itself to form _______ between _________
base-paired segments(H- bonds), short stretches of complementary sequences
RNA's from eukaryotes undergo post-transcriptional modifications including __________, _________, and _________. These are not as complex in prokaryotes.
capping, polyadenylation, and splicing
Unlike in prokaryotes where transcription and translation occur almost at the same time, in eukaryotes, translation is completely separate from transcription. It is separated by __________
cell compartmentalization
V arious proteins allow for transcription to occur in the presence of histones by removing the histones from the nucleosome as the RNA polymerase II complex approaches and then puts them back as the complex passes by. These are called _________
chromatin remodeling complexes
polyadenylation has similar functions to capping. It is also associated with the ....
cleavage of RNA transcript, degradation of the remaining RNA associated with RNA polymerase II, and termination of transcription
in translation, only a portion of mRNA is decoded. The protein coding region of the mRNA consists of an ordered series of three consecutive nucleotide units, called _______, that specify the order of amino acids that form the protein
codon
______ determine which amino acid it is, creating how many possible combinations of codons for 20 amino acids
codon; 64
after transcription, RNA is transported into the _______ where _______ occurs to make a ________
cytoplasm; translation ; polypeptide
macromolecules can pass through nuclear pores via ______, but RNA molecules need help by utilizing energy, thus considered _____
diffusion (passive transport); active transport (via exportins
the machinery involved in translating the language of mRNAs into proteins involves what 4 components
mRNA tRNA Aminoacyl-tRNA synthetases ribsomes
What form is the functional gene product
mainly proteins, also rRNA and tRNA
a ribosome can synthesize one protein at a time but multiple ribosome can be attached to mRNA simultaneously, resulting in _________. AN mRNa with multiple ribosomes attached is known as a ______, Ribosomes can be spaced as closes as _________ nucleotides apart along a single mRNA
many proteins being made at the same time; polyribosome (polysome); 80
intermediate molecule between the gene and the protein synthesizing machinery
messenger RNA
initiator tRNA is charged with the aa ________. All newly made polypeptides will have this as their first aa, but it will eventually get removed
methionine
regulate gene expression
miRNA
Eukaryotic mRNAs contain information from a single gene. This is called __________ . Where as prokaryotic mRNAs contain information from multiple different genes on a single mRNA.This is called __________
monocistronic; polyciistronic
In eukaryotic cells, the nucleotides that make up a gene are not all used to code for a protein. The coding sequence is periodically interrupted by _____________.
non coding sequences
For some genes, the final product is a functional RNA molecule, aka _________
noncoding RNAs
export of mRNA takes place through ________ embedded in nuclear membrane
nuclear pore complexes
where are the ribosomal subunits organized?
nucleolus
as elongation is occuring, the RNA polymerase II complex must have access to DNA but __________ are in its path.
nucleosomes/histones
Where is information in cells encoded?
nucleotide sequence of DNA
where does transcription take place? what is it?
nucleus; DNA genes transcribed into RNA
The protein coding region in mRNA is composed of a contiguous, nonoverlapping string of codons called an _________
open reading frame (ORF)
used in RNA splicing, gene regulation, telomere maintenance, and many other processes
other noncoding RNA
Once the mRNA has been fully process, it is transported _________ for ________
out of nucleus into cytoplasm; translation
where does translation occur
outside of nucleus at ribosomes
Another region of the release factors interact with the ________ of the ribosome which activates __________
peptidyl transferase center; hydrolysis
unlike DNA, RNA is not _________
permanent
a structural molecule involved in making up a ribosome
ribosomal RNA (rRNA)
____________ refers to the release of the ribosome from the mRNA and tRNAs, and dissociation of ribosome into its subunits
ribosome recycling
_________ interacts with elongation and initiation factors to recycle the ribosome _______ interact with the ribosome to release tRNA __________ are involved in the release of the ribosome from the mRNA
ribosome recycling factor; elongation factor; release factors
in elongation, tRNA are delivered to the _____ with help from elongation factor proteins. The proteins will bind to the factor binding center of the ______ after _________. A _______ is then formed between tRNA and A site, and the chain is attached to the tRNA in the _______ site
ribosome; large subunit ; tRNA enters the A site and a correct codon-anticodon match is made; peptide bond; p
a large complex of RNA and proteins involved in the translation of mRNA into protein
ribosomes
3 examples of ribozymes
ribosomes, snRNA, RNase P
coordinates recognition between the mRNA and corresponding tRNA and catalyzes peptide bond formation between tRNA associated amino acids
ribosomes; 2 subunits of tRNA proteins make one ribosome
recent research has identified that some forms of RNA can act as enzymes called ________
ribozymes
the polymerase also performs proofreading. In comparison to DNA replication where different enzymes are performing similar functions, the ______ has all these abilities in one molecule
rna polymerase
The introns are removed from the pre-mRNA transcript by a process known as ________. It converts pre-mRNA into mature functional mRNA that is ready to be translated
rna splicing
each protein has a unique______________, which dictates how the chain will fold to form a molecule with a distinctive shape and function.
sequence of amino acids
The ribosome is compoased of 2 subunits of rRNA and associated ribosomal proteins. The small ribosomal subunit does what? the large subunit?
small (40s)- matches tRNA to codons in mRNA large(60s)- catalyzes the formation of peptide bonds that covalently link the aa together into polypeptide chain
specific sequences within pre-mRNA determine the location of the exons and introns and where splicing should occur. Splicing occurs by _________ and other proteins, called ___________ that form a larger complex called ________
small nuclear RNAs; small nuclear ribonucleoproteins; spliceosome
During initiation, the _____ ribosomal subunit associates with an initiator tRNA. Where does this occur? it is then recruited to the 5' end of the RNA
small; P site
involved in the splicing process of removing introns from pre-mRNAs
snRNAs (small nuclear RNA)
what direction does translation happen in
starts at the 5' end of ORF and proceeds one codon at a time to the 3' end of ORF
3 of the 64 codons are used as a ______ for the process of translation and are not translated into amino acids. 1/64 codons has a dual function of ________
stop signal (UAA, UAG, UGA). start signal of translation and will be translated into an amino acid (AUG)