Transcription and Translation

transcription and translation

two stages of gene expression are called

recap of mutations

-silent mutations: lead to translation of same amino acid, no nothing changes the final protein -missense mutations: lead to different amino acid being used, with effects depending on which amino acid was substituted or where it was substituted -nonsense mutations: lead to shorted protein because of premature stop codon -frameshift mutations: complete chaos

differences between DNA replication and RNA transcription

1.) DNA polymerase is extremely accurate and requires helicase and a primer to get started. RNA polymerase is less accurate (because its work isn't a permanent copy), but requires no primers to get started and unzips DNA itself - the ultimate self-starter. 2.) During DNA replication, both strands are complemented. During transcription, only the template strand is complemented. RNA polymerase ignoring the coding strand. 3.) During DNA replication, the DNA strand stays attached to the old strand and is complemented. In transcription, the new RNA strand is immediately removed and the two DNA strands come back together. 4.) DNA replicated using DNA nucleotides (including T), while RNA transcription uses RNA nucleotides (including U).

start codon

AUG not only coding for the amino acid Met anywhere in the protein, but also signaling the start codon for translation; so all proteins start with amino acid Met, regardless of what comes after

3 keys sites ribosomes performing translation

P site - holds the tRNA carrying the growing protein chain A site - holds the tRNA carrying the next amino acid to be added to the chain E site - where used tRNAs that have donated their Aino acid exit the ribosome

TATA Box and TATA-binding protein

a DNA sequence in eukaryotic promoters critical in forming the transcription initiation complex

stop signals for translation

UAA, UAG, UGA

GTP

acts just like ATP but instead of using an adenine nucleotide, it uses a guanine

synthesizing of complimentary mRNA

after the making complimentary mRNA molecule, it is then synthesized in an antiparallel direction to the template strand of DNA using the 5'-3' direction

replication proceeds in a 5'-3' direction, while transcription proceeds in a 3'-5' direction

all of the following are differences between RNA replication and transcription EXCEPT

-rRNA -mRNA -small subunit -E-site -P-site

all of the following are parts of the ribosome except:

functions of introns

allow for single gene to encode more than one version for a protein, depending one which segments are treated as exons during RNA processing, can get multiple protein products - alternative RNA splicing; so common that the average of three differently spliced mRNA's coming from each gene in human genome

27,000 nucleotides, but only takes 1,200 nucleotides to code for the aver-sized person

average length of a transcription unit along a human DNA molecule

each tRNA molecule

bears a specific amino acid at one end; other end is a nucleotide triplet - anticodon, which base-pairs code with a complementary codon in the mRNA

initiation in bacteria

binding of ribosomal subunit with mRNA and initiator tRNA occurs at a unique RNA sequences, just upstream of AUG; this unique RNA sequence establishes the codon reading frame in bacteria

multiple different tRNAs

brings amino acids to a ribosome and mRNA to see which of the 20 different amino acids comes next int he protein; ribosome will manage the process and link together the amino acids but will not be reading the mRNA to see which nucleotide comes next like tRNA

initiation

brings together an mRNA, a tRNA with the first amino acid, and two ribosomal subunits

messenger RNA

carrier of information form DNA to the cell's protein-synthesizing machinery that is transcribed from the template strand of a gene

sickle cell disease

caused by a mutation of a single nucleotide pair in the gene that encodes part of the protein hemoglobin; hemoglobin is critical to red blood cells; change in a single nucleotide in DNA's template strand leads to abnormal protein, causing the disease

mutations

changes in the DNA of a cell (or virus)

top strand is the coding strand

consider the following double-stranded DNA sequence that codes for a short polypeptide; which strand is the coding strand?

ribosome

consists of a large and small subunit, each made of proteins and ribosomal RNA (rRNA; in both bacteria and eukaryotic cells large and small subunits join together to form a functional ribosome

structure of tRNA molecule

consists of a single strand of about 80 nucleotides folded back on itself to form a three-dimensional structure; includes a loop containing the anticodon and an attachment site at the 3' end for an amino acid (anticodon nucleotides bind to the codon nucleotides during translation)

downstream or upstream

direction of transcription used by molecular biologists

DNA (genotype)

donates the synthesis of functional RNAs and proteins which are the link between genotype and phenotype

template strand

during transcription, the DNA strand that provides a template for ordering the sequences of nucleotide bases in an mRNA transcript

transcription

during which a DNA strand provides a template for the synthesis of each new complementary RNA strand; a protein-coding gene produces a messenger RNA (mRNA) molecule

codon

each set of three-letters

redundancy but no ambiguity

exists in genetic code but no ambiguity; several codons may specify same amino acids (redundancy) but no condone specifies more than one amino acid (no ambiguity)

process of initiation

first, small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine

genetic instructions in DNA

for a polypeptide chain where letters are written as a series of three-nucleotide "words"; every combination of three letters (AAA, ATA, CAC, etc) matches an amino acid

A, T, G, C

forms the information in genes, AKA: genotype

poly-A tails and 5' cap functions

functions of modifications: they signal that the mRNA is ready to leave the nucleus, they help the ribosomes attach to the mRNA, they crate "off switches" in the mRNA that can be removed later to stop translation

reason for a stop codon

in order for ribosome to so hold onto an mRNA, it needs to be longer than just the codons that is wanted (on both sides!); not only does it need to be told to stop before it gets to the end, but it also needs to be told where to start so AUG serves a dual role

transcription factors

in order to start transcription, what binds to the promotor segment on DNA?

phenotype

information inherited by an organism as traits

stages of translation

initiation, elongation, and termination - all three require protein "factors" that aid in the translation process; both initiation and elongation require energy provided by a relative ATP called GTP

insertion and deletion mutations

instead of swapping nucleotides, these add or subtract; likely to result in a shift in three-letter pattern of codons; unless insertion/deletion is a multiple of three letters, it causes a frameshift mutation; all nucleotides downstream of deletion/insertion will be improperly grouped into codons; results in extensive missence, ending sooner or later in sequence - premature termination

transfer RNA (tRNA)

interpreter between two languages of nucleotides to amino acids during translation

bacteria

lacks a nuclei so their DNA is not segregated from ribosomes and other protein-synthesizing equipment, allowing the coupling of transcription and translation; ribosomes attach to the leading end of an mRNA molecule while transcription is still in place

ribosomes

large enzymes that organize the assembly of amino acids into polypeptide chains and are sites of translation

pre-mRNA

made by eukaryotes after transcription is over; cannot be translated or exported until enzymes in the eukaryotic nucleus make three modifications: the 5' cap, the 3' poly-A tail and iron splicing; these modifications help form final mRNA molecule that is ready for export from the nucleus and translation

complimentary mRNA molecule

made using the regular-base pairing rules, just like when making new DNA (except that uracil is the complimentary base to adenine)

RNA polymerase II

makes mRNA for protein synthesis

triplet code

match between DNA letters and amino acids

determines the protein code

match between tRNAs and the amino acids they carry

mutations in gametes

may be transmitted to future generations; adverse effect on phenotype of organism causes mutation conditions know as genetic disorder or hereditary disease (ie. sickle cell disease)

single mRNA

may be used to make copies of a polypeptide simultaneously as multiple ribosomes, polyribosomes, or polysomes trail along same mRNA; polyribosomes can be found in both bacteria and eukaryotes

central dogma of molecular biology

molecular chain of command in a cell that has a directional flow of genetic information: DNA > RNA > Protein

reason for so many nucleotides in a transcription unit

most eukaryotic genes and their RNA transcripts have long non-coding stretches of nucleotides, called intervening regions or introns; remaining regions are called exons and are eventually expressed by being translated into amino acid sequences (introns are in the way, exons are expressed)

inhibition in detail

most tightly controlled part of RNA transcription; a lot of DNA in a cell and most isn't where RNA polymerase is starting the transcription so promotors and transcription factors are there to tell RNA polymerase where to start; transcription factors bind to DNA in promoter then after attachment, RNA polymerase II binds to it, making TATA box; RNA moves along DNA, unzips double helix, 10-20 nucleotides at a time; enzyme adds nucleotides to 3'-5' end of RNA growing strand; behind point of RNA synthesis, double helix re-forms and RNA molecule peels away

silent mutation

mutation that causes a change in a nucleotide pair may transform one codon into another that is translated into the same amino acid

gametes (sperm and egg cells)

mutations can be passed on to the next generation (offspring), if they occur in

missense mutations

mutations that alter the codon enough to change the amino acid; some cases are minimal; if amino acids switched properties or if mutation occurs in a region where the exact sequence is not essential for function, the change might not even cause a phenotype; BUT if occurs at critical sites, esp. active sites on an enzyme, can have major effects

nonsense mutations

mutations that change an amino acid codon into a stop codon, causing premature termination of translation and nearly always leading to nonfunctional protein; many recessive genes are actually nonsense mutations that produce no functional protein (ie white phenotype of purple/white pea flowers)

RNA polymerase; promoter

name of the enzyme that transcribes DNA into RNA is called _____ and it starts the site of DNA called the _____

redundancy

never random; codons that are synonyms for a particular amino acid differ only in the third nucleotide of the triplet; ie all four option for CU_ code for Leu; third letter doesn't even really matter in this case

4^3 = 64

number of every possible combination of the four letters to make a three-letter words gets a maximin combination

primary transcript

occurs in eukaryotic cells as the initial RNA transcript of any gene

one amino acids

one codon matches

alternative mRNA splicing

one explanation for how a single gene can code for more than one version of a protein is

in eukaryotes, ribosomes only attach to mRNA AFTER the mRNA is completely made, while in prokaryotes, ribosomes attach to the mRNA BEFORE the mRNA is completely made

one important difference between green expression in eukaryotes and bacteria is

substitution mutation

one of multiple point mutations where the replacement of one nucleotide and its partner with another pair of nucleotides; some nucleotide-pair substitutions have no effect on protein function - due to redundancy of third letter in many codons

UTRs

parts of the mRNA that will not be translated into protein (untranslated regions)

gene expression

process by which DNA directs protein synthesis, including two stages of transcription and translation

translation

process where a cell converts a genetic message (nucleotides) into a protein (amino acids)

genes

program protein synthesis via genetic messages in the form of messenger RNA

transcription factors

proteins that bind to DNA sequences in the promoter

transcription process

provides a template for assembling a sequences of RNA molecules, just like a DNA strand providing a template for the synthesis of each new complementary strand during DNA replication

ribosomes

responsibilities include aligning the tRNAs with the mRNA message and acts as an enzyme that binds the new amino acid to the growing protein chain (forms the peptide bond between amino acids)

elongation stage

second step in translation where amino acids are added one by one to the previous amino acid at the end of the growing chain; after each amino acid is added, the mRNA is moved through the ribosome in a 5'-3' direction by 3 letters, or one codon, creating new space for tRNAs to try to complement the codon; the empty tRNAs that are released from E site return to cytoplasm where they're reloaded with appropriate amino acid

RNA polymerase

separates the DNA strand at the appropriate point and joins RNA nucleotides complementary to the DNA template strand; can assemble a strand only in 5'-3' direction like DNA but unlike DNA polymerase, can start a chain from scratch - do NOT need helicase or a primer

tempalate sequence of DNA

sequence of nucleotides in mRNA is complimentary to

RNA

similar to DNA, except the tis contains ribose instead of deoxyribose as its sugar and substitutes the nitrogenous base uracil for thymine (DNA) - consists of a single strand

introns are removed

splicing is when

inhibition

stage where RNA polymerase binds to precise location facing downstream on the promoter, which determines where transcription starts and which of the two strand of the DNA helix is the template

termination

stage where RNA polymerase continue until it reaches sequences that mark the end of a message; in prokaryotes, this is a completed RNA transcript since there is no nucleus, so ribosomes are already working on translation before termination of transcription even happens; in eukaryotes, RMA undergoes some processing steps before it's exported form nucleus to cytoplasm to be translated into proteins on ribosomes

elongation

stage where the RNA polymerase unzips the DNA, reading the DNA in the 3'-5' direction and synthesizing RNA in the 5'-3' direction; RNA polymerase knows which nucleotides to place in new RNA strand, like DNA polymerase, tries them at random until finds a complimentary pair

initiation, elongation, and termination

stages of transcription of the RNA chain

5' cap

the 5' end of the pre-mRNA where a modified form of the guanine nucleotide (G) is added; not to be translated

poly-A tail

the end of 3' end where an enzyme adds 50 to 250 adenine nucleotides (A); not to be translated

missene

the original mRNA sequence is AUG, CCA, GGG, UGU, UGA but after mutation the sequence of the mRNA is AUG, CGA, UGU, UGA; what type of mutation?

RNA splicing

the removal of a large portion of the RNA molecule in a cut-and-paste job

initiation in eukaryotes

the small subunit with the initiator already bound, binds to the 5' cap of the mRNA and then moves, or scans, downstream until it reaches the first AUG start codon AUG; this first AUG establishes the codon reading frame in eukaryotes; the union of mRNA, initiator tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit

translation

the synthesis of a protein, using information in mRNA; during which, there is a change of coding language from nucleotides (DNA and RNA) to amino acids (protein)

other strand of DNA

these codons on the mRNA are identical to the letters in the non-template strand of DNA (except have U instead of T), so called coding strand; even though not being used at all during transcription, it predicts exactly how the mRNA will read

termination

third stage that occurs when one of the three stop codons reaches the A site of the ribosome; a release factor binds to the stop codon and causes hydrolysis of the bond between polypeptide and its tRNA in the P site; this frees the polypeptide, which is released through the exit tunnel of the ribosome's large subunit; translation complex then disassembles

initiation, elongation, termination

three major steps of translation are:

stop codons

three of the total number of possible codons in the mRNA specify for

eukaryotic cell

transcription occurs in the nucleus and the transcription of a protein-coding eukaryotic gene results in pre-mRNA; the primary-transcript is then further processed resulting in finished mRNA, which is then exported to the cytoplasm, binding to a ribosome and translated into protein

tRNA

translator because it reads a nucleic acid work (the mRNA codon). and interprets it as a protein word (the amino acid); works as codon by codon the genetic message os translated as it deposits amino acids in the order prescribed and the ribosome connects to amino acids into chain

mutations

ultimate source of new genes; include large-scale mutations, in which long segments of DNA are affected (ie. translocations, duplications, and inversions), as well as point mutation, changes in just one nucleotide pair of a gene

codon triplet of genetic code

use the codon triplet to figure out amino acid; first nucleotide is chosen from the right side, second nucleotide is chosen from the top panel and third nucleotide is chosen from right side

mRNA codons

what molecular "language molecular" does tRNA interpret into amino acids?

silent mutation

when a mutation does not cause a change in the amino acid coded for it, it is called a

process of translation

when the sequence of codons along an mRNA molecule that is translated into a sequence of amino acids that make up the polypeptide chain, reading in a 5'-3' direction; codon then specifies which of 30 amino acids will be incorporated at the corresponding position along a polypeptide chain

promoter

where RNA polymerase attaches and initiates transcription along specific sequences of nucleotides of the DNA strand where gene expression begins and ends

exons

which of the following in mRNA is coded into protein (amino acids)?

-the genetic code can code more than one amino acid -the genetic code is unambiguous -the genetic code is triplet-based -each codon represents a different amino acid

which of the following is not a true statement regarding genetic code?

RNA uses ribose as a sugar, while DNA uses deoxyribose

which of the following is the major difference between DNA and mRNA