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)