Gene Expression
How many nucleotide bases are in DNA?
4
Transcription progresses at a rate of ___ nucleotides per seconds in eukaryotes.
40
In translation, what way to the codons, the mRNA base triplets, read?
5'---->3' direction
Of the 64 triplets, how many code for amino acids and how many code for "stop" at the end of translation?
61 code for amino acids, 3 triplets are "stop" signals
What determines a primary structure & primary, secondary, tertiary structures in turn determines shape?
A Gene
During RNA processing, both ends of the primary transcript are usually _______.
Altered
The DNA _____ by an organism leads to specific traits by dictating the synthesis of proteins.
Inherited
What does initiation bring together?
Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits
What are the three stages of transcription?
Initiation, Elongation, Termination
What are the three stages of translation? what do all of the stages require?
Initiation, elongation, termination They require protein "factors" that aid and the translation process and energy
What produces a frameshift mutation?
Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation
What are insertions and deletions? And what effect do the have on the resulting protein?
Insertions and deletions are additions or losses of nucleotide pairs in a gene. These mutations have a disastrous effect on the resulting protein more often than substitutions do.
Some ____ contain sequences that may regulate gene expression.
Introns
What are noncoding regions called?
Introns
What is RNA synthesis catalyzed by?
It is catalyzed by RNA polymerase, which pries he DNA strands apart and joins together the RNA nucleotides.
What is the purpose of the template strand during transcription?
It provides a template for ordering the sequence of complementary nucleotides in an RNA transcript.
What did the discovery of the ribozymes render?
It rendered the obsolete belief that all biological catalysts were proteins.
What does transcription to produces?
Messenger RNA (mRNA)
What does a missense mutation do?
Missense mutations still code for an amino acid, but not the correct amino acid
How is a polyribosome (polysome) formed?
Multiple ribosomes can translate a single mRNA simultaneously
What are mutagens?
Mutagens are physical or chemical agents that can cause mutations
What are mutations?
Mutations are changes in the genetic material of a cell or virus
What does a nonsense mutation do?
Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein
What two categories can point mutations within a gene be divided into?
Nucleotide-pair substitutions One or more nucleotide-pair insertions or deletions
What are Point Mutations?
Point mutations are chemical changes in just 1 base pair of a gene The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein e.g. sickle cell anemia
What does the 3' end get?
Poly-A tail
During its synthesis, a _______ ______ begins to coil & fold spontaneously to form a protein with a specific 3-D/4-D structure
Polypeptide Chain
______ _____ are modified after translation or targeted to specific sites in the cell.
Polypeptide Chains
Where does polypeptide synthesis begin?
Polypeptide synthesis always begins in the cytosol
________ enable a cell to make many copies of a polypeptide very quickly.
Polyribosomes
_______-_______ ________ may be required before the protein can begin doing its particular job in the cell
Post-translational modifications
______ consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites.
Spliceosomes
When can spontaneous mutations occur?
Spontaneous mutations can occur during DNA replication, recombination, or repair
_____ finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER.
Synthesis
What is the promoter that is crucial in forming the initiation complex in eukaryotes?
TATA box
What two populations of ribosomes are evident in cells?
Two populations of ribosomes are evident in cells: free ribosomes (in the cytosol) and bound ribosomes (attached to the ER)
RNA synthesis follows the same base-pairing rules as DNA EXCEPT that
Uracil substitutes for Thymine
What have we considered as a gene through the evolution of genetics?
We have considered a gene as A discrete unit of inheritance A region of specific nucleotide sequence in a chromosome A DNA sequence that codes for a specific polypeptide chain
What does a tRNA molecule look like?
When flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf
Can free ribosomes and bound ribosomes able to switch roles?
Yes
No ______ specifies more than one amino acid.
codon
The ____ content of genes is in the specific sequences of nucleotides
information
Usually certain _____ of the molecule are cut out, and the _____ are spliced together.
introns, eons
_____ transfer amino acids to the growing polypeptide in a ribosome.
tRNA's
The mechanism of _______ are different in bacteria and eukaryotes.
termination
A cell translates an mRNA message into protein with the help of ____.
transfer RNA (tRNA)
Often ______ is not sufficient to make a functional protein.
translation
Where are nucleotides added to the ___' end of the growing RNA molecule.
3
RNA polymerase does not need any _______.
primer
What three properties of RNA enable it to function as an enzyme?
1.) It can form a 3-dimensional structure because of its ability to base-pair with itself. 2.) Some bases in RNA contain functional groups that may participate in catalysis. 3.) RNA may hydrogen-bond with other nucleic acid molecules.
What three modifications do the caps and poly-a tails share for several functions?
1.) They seem to facilitate the export of mRNA to the cytoplasm. 2.) The protect mRNA from hydrolytic enzymes. 3.) They help ribosomes attach to the 5' end.
As RNA polymerase moves along the DNA, it untwists the double helix, __ to __ bases at a time.
10, 20
What two ribosomal subunits are made of ribosomal proteins and ribosomal RNAs?
2 ribosomal subunits--large and small Ribosomal proteins--80 ribosomal RNAs--18S, 5S, 5.8S, 28S
By coupling transcription and translation, what does a bacteria cell ensure?
A bacterial cell ensures a streamlined process by coupling transcription and translation In this case the newly made protein can quickly diffuse to its site of function
What is our modern day definition of a gene?
A gene can be defined as a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule
What end does the 5' end receive?
A modified nucleotide 5' cap (Guanine)
What does a Nucleotide-pair substitutions do?
A nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotides
What binds to the signal peptide? What does SRP bring to the ER?
A signal-recognition particle (SRP). The SRP brings the signal peptide and its ribosome to the ER.
Why is the genetic code redundant?
Because more that one codon may specify a particular amino acid
What do bound ribosomes do?
Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell
Central Dogma
DNA--->RNA--->Protein
Proteins often have a modular architecture consisting of discrete regions called ____ __ ____.
Domains e.g. Antibodies
What are the steps in elongation?
During elongation, amino acids are added one by one to the C-terminus of the growing chain Each addition involves proteins called elongation factors and occurs in 3 steps: codon recognition, peptide bond formation, and translocation Energy expenditure occurs in the first & third steps Translation proceeds along the mRNA in a 5′ → 3′ direction
Polypeptides are destined for the __ or for _____ are marked by a ___ _____.
ER, secretion, signal peptide
What does each codon specify?
Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide
What are other regions called? They are eventually expressed, usually translated into amino acid sequences.
Eons
______ ___ transcripts are modified through ____ processing to yield the finished _____.
Eukaryotic RNA, RNA, mRNA
_____ _______ may result in the evolution of new proteins.
Exon Shuffling
What are the steps in initiation?
First, a small ribosomal subunit binds with mRNA and a special initiator tRNA (met).Then the small subunit moves along the mRNA until it reaches the start codon (AUG) Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
What two steps does an accurate translation have?
First: a correct match between a tRNA & an amino acid, done by the enzyme aminoacyl-tRNA synthetase Second: a correct match between the tRNA anticodon & an mRNA codon
What is a flexible pairing at the third base of a codon called and what does it allow tRNA to do?
Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon
What do free ribosomes do?
Free ribosomes mostly synthesize proteins that function in the cytosol
_______, the process by which DNA directs protein synthesis, includes two stages: ______ and ______.
Gene Expression, transcription, translation
_____ can be transcribed and translated after being translated from one species to another.
Genes
What process of genetic information flows from mRNA to protein?
Genetic information flows from mRNA to protein through the process of translation
What happens in prokaryotic translation and transcription?
In prokaryotes, translation of mRNA can begin BEFORE transcription has finished. Thus meaning transcription and translation are coupled.
______ are the link between genotype & phenotype.
Proteins
What is the bridge between genes and the proteins for which they code?
RNA
What removes introns and joins eons?
RNA Splicing
A gene can be transcribed simultaneously by several ____ _______.
RNA polymerases
In some cases, what can be carried out by spiceosomes?
RNA splicing
What are the sites of translation?
Ribosomes
What facilitates specific coupling of tRNA anticodons with mRNA codons in protein synthesis?
Ribosomes
_______ are catalytic RNA molecules that function as enzymes and can splice RNA.
Ribozymes
What does a silent mutation do?
Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code
What is alternative RNA splicing?
Some genes that can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing... Consequently, the number of different proteins an organism can produce is much greater than its number of genes.
What happens in termination?
Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome The A site accepts a protein called a release factor The release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide, and the translation assembly comes apart
What are the three binding sites for tRNA?
The P site holds the tRNA that carries the growing polypeptide chain The A site holds the tRNA that carries the next amino acid to be added to the chain The E site is the exit site, where discharged tRNAs leave the ribosome
What is the DNA sequence that RNA polymerase attaches to?
The Promoter
In eukaryotes, what transcribes the polyadenylation signal sequence?
The RNA transcript is released 10-35 nucleotides past this polyadenylation sequence.
What can catalyze the splicing reaction?
The RNA's of the spliceosome
What is the stretch of DNA that is transcribed called?
The Transcription Unit
How are the instructions for assembling amino acids into proteins encoded into DNA?
The flow of information from gene to protein is based on a triplet code: a series of non-overlapping, three nucleotide words
What separates in a eukaryotic cell for transcription and translation to occur?
The nuclear envelop separates transcription from translation.
______ is the synthesis of a polypeptide, using information in the mRNA.
Translation
What is always the same strand for a given gene?
The template strand
How many nucleotides correspond to an amino acid?
The words of a gene are transcribed into complementary non-overlapping three-nucleotide words of mRNA. These words are then translated into a chain of amino acids, forming a polypeptide.
How many amino acids are there?
There are 20 amino acids
What do most eukaryotic genes and their RNA transcripts have between coding regions?
They have long noncoding stretches of nucleotides that lie between the coding regions.
What do the promoters signal?
They signal the transcriptional start point and usually extend several dozen nucleotides upstream of the start point
What is the first phase of gene expression?
Transcription
_______ is the synthesis of RNA using information in DNA.
Transcription
What is the completed assembly of transcription factors and RNA polymerase II bound to a promoter called?
Transcription Initiation Complex
What mediates the binding of RNA polymerase and the initiation of transcription?
Transcription factors
In many cases, different ______ code for the different domains in a protein.
exons
If a _______ has an adverse effect on the phenotype of the organism the condition is referred to as a genetic disorder or hereditary disease
mutation
The genetic code is _______ _______. And where are they found?
nearly universal, shared by the simplest bacteria to the most complex animals
Each end of a ______ ________ is modified while still in the nucleus.
pre-mRNA
Enzymes in the eukaryotic nucleus modify ________ before the genetic messages are dispatched to the cytoplasm.
pre-mRNA (RNA processing)
Non-universal codes are ______. And where are they found?
rare, found in mitochondria and protists
Codons must be read in the correct ________ _______ in order for the specified polypeptide to be produced.
reading frame
What is a difference between bacterial and eukaryotic ribosomes?
some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes
A ____ molecule consists of a single RNA strand that is only about 80 nucleotides long.
tRNA
Each ____ carries a specific amino acid on one end.
tRNA
What is complementary to the DNA strand?
the RNA strand
What does the anticodon base-pair with on the mRNA?
the anticodon base-pairs with a complementary codon on mRNA
In bacteria, the polymerase stops __________ at the end of the terminator and the mRNA can be translated without further modification.
transcription
