chapter 7 Flashcards
The segments of DNA that are transcribed into RNA are called
genes
RNA is made of nucleotides that are linked by
phosphodiester
bonds
Same phosphodiester bond that links nucleotides in RNA…
is same as DNA
the structure of
RNA differs from that of DNA
in __ ways
3
RNA and DNA differences
1.RNA contains ribose not deoxyribose, has an additional -OH group.
2. RNA contains uracil instead of thymine in DNA
3. RNA is single stranded, no double helix
The nucleotides in RNA are
ribonucleotides
Uracil differs from thymine by the
absence of methyl group
Uracil, like thymine, can form
base-pairs with adenine (A)
How does RNA fold into a variety of shapes…
forming base-pairs between
nucleotides within the same strand
Base pairing always occurs between
anti-parallel strands
The ability to fold into shapes allows RNA to perform…
structural, regulatory, or catalytic roles in cells
__ produces an RNA molecule that is
complementary to one strand of DNA
Transcription
One of the two strands of DNA serves as a __ for RNA synthesis
template
Ribonucleotides are added
1 by 1 to rna molecule
The nucleotide sequence of the RNA chain is determined by
complementary base pairing with the DNA template strand
RNA is transcribed in what direction….
Nucleotides are added to what end…
5’-to-3’ direction (nucleotides are added to the 3’ end)
The DNA template strand is read in the
3’-to’5’ direction
same base sequence as RNA transcript
Non-template strand = coding strand
complementary to RNA transcript
Template strand
Write the sequence of the RNA transcript that is generated using the bottom strand of the following DNA sequence as the template:
5’-TTTTT-3’
3’-AAAAA-5’
3’-AAAAA-5” (template)
5’- UUUUU-3’ (rna transcript sequence)
Write the sequence of the RNA transcript that is generated using the top strand of the following DNA sequence as the template:
5’-CGGAATC-3’
3’-GCCTTAG-5’
5’-CGGAATC-3’ (template)
3’- GCCUUAG-5’ rna transcript sequence)
read 5’-GAUUCCG-3’
Using the DNA sequence below, identify the coding strand for the following RNA
transcript: 5’-AUCGA-3’
DNA sequence:5’-ATCGA-3’
3’-TAGCT-5’
5’-ATCGA-3’
is an enzyme that catalyzes the formation of phosphodiester
bonds that link ribonucleotides together
RNA polymerase
RNA polymerase unwinds the DNA helix to expose a region of the..
template strand for complementary base pairing
The RNA strand elongates one nucleotide at a time in the
5’-to-3’ direction
used to direct the synthesis of proteins In eukaryotes
mRNA
each mRNA carries information transcribed from a
single gene
What kind of rna play regulatory,
structural and catalytic roles in cells
Noncoding RNAs (e.g. rRNA, tRNA, miRNA)
The promoter is located
upstream (a.k.a. before) of the starting point for RNA synthesis
binds the promoter and begins transcription
RNA polymerase
Transcription proceeds until RNA polymerase encounters a
terminator
Every promoter has a
polarity
Bacterial promoters contain __ different nucleotide sequences that are laid out in a specific __ order
2, 5’-to’3’
RNA polymerase always moves in the __ direction on the template DNA strand
3’-to-5’
what determines which strand will serve as the
template?
The polarity (orientation) of the promoter sequence at the
beginning of each gene
Terminators have specific…
nucleotide sequences
Terminator sequences are
palindromic
cause a stem-loop structure to form in the RNA
transcript
terminator sequences
What causes the transcipt to dissociate from the DNA template
stem loop stricture in the RNA transcript
Transcription in bacteria: Bacterial RNA polymerase contains a subunit called a
sigma factor
recognizes and binds the promoter of a gene
sigma factor
in bacterial transcription, once transcription begins what is released
sigma factor
In bacterial transcription, RNA polymerase opens the double
helix immediately in
front of the promotoer
synthesizes a chain of RNA by base pairing with the template strand
RNA polymerase
When RNA polymerase reaches the terminator…
It stops and releases the DNA template and the
RNA transcript
Bacteria use a __ RNA polymerase for transcription, while eukaryotic cells use __
single, 3 (RNA poly 1, 11, 111)
Which polymerase transcribe genes encoding tRNA, rRNA and other small RNAs (regulatory RNA)
RNA polymerase I and III
which polymerase transcribes mRNA and other RNAs
RNA polymerase II
Bacterial RNA polymerase (with its sigma factor) initiates transcription on its own, while eukaryotic RNA polymerases require a…
large set of
accessory proteins
Accessory proteins can include
general transcription factors
assemble at
each promoter along with the polymerase before transcription can
begin
general transcription factors
Transcription in eukaryotes requires the
General Transcription Factors
Step 1 in transcription factors of eukaryotes
TFIID binds a short sequence
of DNA that is rich in T and A nucleotides à called the “TATA box
TFIID binding to the TATA box…
distorts DNA double helix
Step 2 in transcription factors of eukaryotes
TFIID recruits RNA
polymerase II and others to form a transcription initiation complex
Step 3 in transcription factors of eukaryotes
TFIIH pulls apart the double
helix at the transcription start point and phosphorylates RNA
polymerase II
Step 4 in transcription factors of eukaryotes
Transcription begins
Eukaryotic transcription occurs in the
nucleus
Translation occurs on ribosomes in the
cytosol
Before a eukaryotic mRNA can be translated into protein, it must be transported
out of the nucleus
Before RNA is exported, it must go through
RNA processing
What is involved in RNA processing
capping, splicing and polyadenylation
Processing occurs ___ transcription
during and after
RNA-processing proteins bind
to the phosphorylated tail of __, it gives them access to the
RNA polymerase II, RNA transcript as it emerges from the polymerase
modifies the 5’ end of the transcript by adding an
atypical guanine nucleotide with a methyl group
RNA capping
addition of a series of repeated adenine (A) nucleotides to the 3’ end
Polyadenylation
Capping and polyadenylation promote the
stability, export and
translation of mRNAs
RNA capping and polyadenylation occur on all
RNA transcripts that become
mRNA molecules
contain single stretches of nucleotides that encode
the amino acid sequence of proteins
Bacterial genes
The coding sequences of most eukaryotic genes are interrupted by noncoding “intervening sequences” called
introns
The protein-coding sequences are called “expressed sequences” or
exons
Most of the nucleotide sequences
of introns are
unimportant
involves the precise removal of introns
splicing
The intron is removed as a __
structure, which is degraded in the __
lariat, nucleus
Once an intro is removed, the two exons are joined together…
covalently
allows increased genetic diversity and complexity
Alternative splicing
Fully processed mRNAs are recognized as
mature transcripts
that are allowed to leave the nucleus
Proteins bind to __ cap, splice junctions and poly-A tail and promote:
5’, transport out of the nucleus, mRNA stability, translation
Prokaryotes don’t have a nucleus, so transcription and translation happen in the
cytosol
Prokaryotes don’t need
RNA processing
In eukaryotes, transcription happens in the
nucleus
In eukaryotes, mRNA must be processed via
5’ capping, 3’ polyadenylation, and splicing before it is exported into the
cytosol and translated
mitochondria and chloroplasts
have their own
RNA polymerases
The process of transcription begins with RNA polymerase binding to a region of the gene called a
promotor
TFIID contains a subunit called __ that binds to a sequence in the promotor known as __
TATA binding protein, TATA box
TFIIH has two important functions:
- it partially unwinds the DNA to expose the
template strand at the promoter - it phosphorylates RNA polymerase II to release it from the general transcription factors
cap is added to the 5’ end of the mRNA
Capping
poly-A-tail pf 100 or more repeated adenine nucleotides is added to the 3’ end of the mRNA
Polyadenylation
Splicing is performed by a molecular machine known as the
splicesome
deflects in splicing are the cause of
some human disease
Nucleotides are read in groups of three called
codons
__ possible codons used to specify 20 amino acids
64
Most amino acids are specified by
2 or more codons
__ codons are used as a translation stop signal
3
Genetic code can be described as
redundant
Each mRNA has 3 possible __, only __ encodes the correct protein sequence
reading frames, 1
Small adaptor molecules known as __ are responsible for matching the
proper amino acid to the correct mRNA codon.
tRNAa
site of protein synthesis
ribosomes
There are __ different nucleotides in mRNA but __ different amino
acids in proteins
4, 20
The nucleotide sequence of an mRNA is translated into amino acids
using
codons
Each codon consists of nucleotides
3
Codons are translated sequentially in the _ direction, without overlaps or spacers
5’ to 3’
The genetic code is
redundant
In the genetic code, __ codons are used to specific 20 amino acids
64
what RNA translate the code
tRNAs
Transfer RNAs (tRNAs) fold into a
cloverleaf structure
The cloverleaf structure from tRNA folds further into a
L shaped structure
set of three nucleotides that bind the complementary
codon in an mRNA molecule
anticodon
in the tRNA, the amino acid that matches the codon is __ attached to the single stranded region at the __ end of the tRNA
covalently, 3’
Two regions of the tRNA are crucial for translation
amino acid and anticodon
In the genetic code, multiple codons…
encode the same amino acid
Codons are most variable at the __ position
3rd
Some tRNAs require accurate base-pairing only at the
first 2 positions
tRNA base pairing can tolerate a mismatch at the __ position
(wobble), 3rd
__ tRNAs for __ total codons in humans
48, 61
establish the tRNA code
tRNA synthetases
covalently attach each amino acid to the appropriate tRNAs
tRNA synthetases
There are __ tRNA synthetases
20
a key link between the nucleotide and amino acid
languages
tRNA synthetases
The same mRNA sequence can specify __ different amino acid sequences, depending on the nucleotide at which translation begins
3
Translation begins at the initiation codon __
AUG
AUG encodes a
methionine
The position of the initiation codon sets the translation __
reading frame
catalyzes protein synthesis
ribosome
Ribosomes are composed of
one large subunit and one small subunit
Eukaryotic ribosomes are made from __ ribosomal RNAs (rRNAs) and more than 80 proteins
4
Each ribosome has how many binding sites for mRNA and rRNAs
mRNA- 1
tRNA- 3
The ribosome’s 3 tRNA binding sites are called
the A site, the P site and the E site
Four step cycle of translation…
step 1: growing polypeptide chain is linked to the tRNA in the P site
step 2: new peptide bond is catalyzed by RNA in large ribosomal subunit
step 3: large ribosomal subunit shifts forward to move 2 tRNAs into E and P sites
step 4: small subunit moves forward 2 nucleotides along the mRNA to rejoin large subunit; movement ejects the spent tRNA from E site and resets the ribosome with an empty A site so next tRNA can bind
In the first step of translation, to add an amino acid to a growing peptide chain, a
tRNA enters A site, w base pairing on complimentary mRNA
In eukaryotes, translation of mRNA begins with __ and requires __
AUG codon, initiator tRNA
In eukaryotes. the initiator codon always carries the amino acid
methionine
In translation in eukaryotes, Newly made proteins all have methionine as the first amino acid at their
N-terminal end
In translation in eukaryotes, __ is loaded into the __ site of the __ ribosomal subunit along with __
initiator tRNA, P, small, translation initiation factors
In translation in eukaryotes, the small ribosomal subunit then binds to the __ end of the mRNA
5’
After the small ribosomal subunit binds to the mRNA in translation, the small ribosomal subunit then scans the mRNA in the
5’-to-3’ direction until it encounters the first AUG codon
In translation in eukaryotes, when the AUG is recognized by the initiator tRNA, several initiation factors dissociate, allowing….
the large ribosomal
subunit to bind
in translation in eukaryotes, Because the initiator tRNA is
bound to the P site, protein
synthesis is ready to begin
with the addition of the next
tRNA to the A site
to initiate translation in prokaryotes, there’s no __ for the small ribosomal subunit to bind on bacterial mRNAs/ Instead ribosomes…
5’ cap, bind directly to specific sequences adjacent to coding
regions
Most bacteria mRNAs are
polycistronic
a single mRNA encodes several different proteins, usually with related functions
polycistronic
in translation in prokaryotes each ribosome has…
its own ribosome-binding site instead of scanning for aug
How to terminate translation
Stop codons; release factors bind to stop codon in the A-site; peptide chain is transferred to a water molecule, ending synthesis
what are the stop codons
UAA, UAG, UGA
can be translated by multiple
ribosomes at the same time
A single mRNA
simultaneously translate the same mRNA
Polyribosomes
A single gene can be transcribed by multiple RNA polymerases at the same time T or F
True
Misfolded or damaged proteins and proteins that are meant to be short-lived are degraded by the
proteasome
large protein complex that contains enzymes
called proteases
proteasome
cut proteins into short peptides
proteases
Proteins are marked for degradation by the covalent attachment of
a small protein called
ubiquitin
