Chapter 13: The Genetic Code and Transcription

Addition of 5′ cap (7-mG cap)

"methyl cap" via methylation -It provides a site for ribosome binding in the cytoplasm -To protect the transcript from degradation The 5' cap is essential for recognition of the mRNA by ribosomes in the cytoplasm.

/in vivo/

(Latin for "within the living") refers to experimentation using a whole, living organism as opposed to a partial or dead organism. Animal studies and clinical trials are two forms of in vivo research. In vivo testing is often employed over in vitro because it is better suited for observing the overall effects of an experiment on a living subject.

/in vitro/

(Latin for within the glass) refers to the technique of performing a given procedure in a controlled environment outside of a living organism. Many experiments in cellular biology are conducted outside of organisms or cells.

initiation of transcription

(a) RNA polymerase searches for a promoter site. (b) It recognizes a promoter site and binds tightly, forming a closed complex. (c) The holoenzyme unwinds a short stretch of DNA, forming an open complex. Transcription begins, and the σ factor is released. The RNA transcript is shown, beginning with adenosine triphosphate (pppA), carrying on through an indeterminate number of nucleotides [(Np) n ], and ending with NOH.

Transcription

(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA composed by codons (bases) which compliments to an anti codon of tRNA

Prokaryotes have what kind of ribosomes?

*70S Ribosomes composed of 30S (SMALL SUBUNIT) and 50S (LARGE SUBUNIT)* Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit. Their small subunit has a 16S RNA subunit (consisting of 1540 nucleotides) bound to 21 proteins. The large subunit is composed of a 5S RNA subunit (120 nucleotides), a 23S RNA subunit (2900 nucleotides) and 31 proteins.

_NO COMMAS_

*DUH*

_no overlaps_

*DUH*

Which of the following is characteristic of transcription in eukaryotes but not in prokaryotes?

*Exon splicing catalyzed by the spliceosome* A single transcript may be transcribed and translated simultaneously. A 5' untranslated leader sequence A 3' untranslated trailer sequence

Which of the following best describe(s) the function of the 5' mRNA cap? Select all that apply.

*It provides a site for ribosome binding in the cytoplasm.* *To protect the transcript from degradation* To provide a binding site for poly(A) polymerase Termination of transcription

[THE CODE IS UNIVERSAL]

*NOSSSSHIT*

Eukaryotic mRNAs require processing to produce mature mRNAs; what is this processing?

*Posttranscriptional modifications * Addition of 5′ cap (7-mG cap) Addition of 3′ tail (poly-A tail) Excision of introns

Which statements are true? Select all that apply.

*Since prokaryotes lack a nucleus, translation can begin before the transcript is fully transcribed.* *Eukaryotic RNA polymerase II requires general transcription factors for initiation of transcription.* Intrinsic termination in prokaryotes occurs when the rho termination factor interacts with the growing RNA transcript. *Three different RNA polymerases in eukaryotes transcribe different classes of genes.*

When considering the initiation of transcription, one often finds consensus sequences located in the region of the DNA where RNA polymerase(s) binds. Which of the following is a common consensus sequence?

*TATA* satellite DNAs any trinucleotide repeat TTTTAAAA GGTTC

Considering the activities of RNAs, what might be the general functions of 3-polyadenylation? Check all that apply.

*regulation of mRNA transport to the cytoplasm* regulation of mRNA splicing regulation of mRNA proofreading regulation of introns' length *regulation of mRNA longevity* *regulation of mRNA association with cellular components, like proteins, lipids, or nucleic acids*

general functions of 3-polyadenylation

*regulation of mRNA transport to the cytoplasm* *regulation of mRNA longevity* *regulation of mRNA association with cellular components, like proteins, lipids, or nucleic acids*

Which subunit of RNA polymerase establishes template binding to a promoter in prokaryotes?

*sigma* beta prime alpha beta

When scientists were attempting to determine the structure of the genetic code, Crick and coworkers found that when three base additions or three base deletions occurred in a single gene, the wild-type phenotype was sometimes restored. These data supported the hypothesis that ________.

*the code is triplet* there are three amino acids per base AUG is the initiating triplet the code contains internal punctuation the code is overlapping

Repeating copolymers

-Synthesized long polymers from known di-, tri- and tetranucleotides Used for in vitro translation to determine more codon assignments

Triplet Binding Assay

-developed by Nirenberg and Leder to determine other specific codon assignments -ribosomes bind to single codon of three nucleotides -complementary amino acid-charged tRNA can bind utilized synthetic mRNA for this discovery led to the conclusions that genetic code is degenerate and unambiguous /led to discovery of anticodons (which contains 3 nucleotides)/

overlapping genes

-single mRNA has multiple initiation points -creates different reading frames -specifies more than one polypeptide *creates overlapping open reading frames* /ORFs overlap to allow the virus to produce more than 1 polypeptide from a single gene/

RNA polymerase

/directs synth of RNA using DNA template/ *nucleotides contain ribose* reads the sequence of DNA bases from only one of the two strands of DNA: the template strand. The RNA polymerase reads the code from the template strand in the 3' to 5' direction and thus produces the mRNA strand in the 5' to 3' direction. enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides. RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand)

How can trans-acting factors control gene expression?

/factor may be expressed in a specific tissue manner (spatial regulation) factor may be expressed in at specific time in development (temporal regulation) factor may require modification (phosphorylation) factor may be activated by ligand binding factor may be sequestered until an appropriate environmental signal allows it to interact with the nuclear DNA/

1 codon for ____ amino acid.

1

three ribonucleotides specifies how many amino acids?

1

Proteins that facilitate RNAP II binding and initiation of transcription

1. General transcription factors: Required for all RNAP II-mediated transcription 2. Transcription activators and repressors: Influence efficiency or rate of RNAP II transcription initiation

30S subunit

16S rRNA + 21 proteins

Where do various forms of posttranscriptional processing in eukaryotes take place on the mRNA?

5' end 3' end internal

There are __ codons to code for __ amino acids?

64 20

Eukaryotes have what kind of ribosome?

80S composed of 60S (LARGE SUBUNIT) and 40S (SMALL SUBUNIT)

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

16S rRNA

A large polynucleotide (~1500 bases) that functions as part of the small subunit of the ribosome of Bacteria and Archaea and from whose gene sequence evolutionary information can be obtained; its eukaryotic counterpart is 18S rRNA

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain.

chromatin remodeling

A mechanism for epigenetic gene regulation by the alteration of chromatin structure. is the rearrangement of chromatin from a condensed state to a transcriptionally accessible state, allowing transcription factors or other DNA binding proteins to access DNA and control gene expression.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds.

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex. Core-promoter element Binds TATA-binding protein (TBP) Determines start transcription start site /trans acting factor/

Reading Frame

A reading frame refers to one of three possible ways of reading a nucleotide sequence. Let's say we have a stretch of 15 DNA base pairs: acttagccgggacta We can start translating, or reading, the DNA from the first letter, 'a,' which would be referred to as the first reading frame. Or we can start reading from the second letter, 'c,' which is the second reading frame. Or we can start reading from the third letter, 't,' which is the third reading frame. The reading frame affects which protein is made. In the example below, the upper case letters represent amino acids that are coded by the three letters above and to the left of them. reading frame: 123 ||| acttacccgggacta first reading frame T Y P G L second reading frame L T R D third reading frame L P G T The illustration above shows three reading frames. However, there are actually six reading frames: three on the positive strand, and three (which are read in the reverse direction) on the negative strand.

triplet code

A set of three-nucleotide- letters that specify the amino acids for polypeptide chains.

buffer

A solution that minimizes changes in pH when extraneous acids or bases are added to the solution.

Codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

σ subunit

A subunit of RNA polymerase which facilitates its initial binding to the promoter. /The dissociative subunit of RNA polymerase allows RNA polymerase to recognize and bind specifically to promoter regions. First, the holoenzyme searches for a promoter (Figure 10-9a) and initially binds loosely to it, recognizing the −35 and −10 regions. The resulting structure is termed a closed promoter complex (Figure 10-9b). Then, the enzyme binds more tightly, unwinding bases near the −10 region. When the bound polymerase causes this local denaturation of the DNA duplex, it is said to form an open promoter complex (Figure 10-9c). This initiation step, the formation of an open complex, requires the sigma factor./

Reading frame shift

A type of gene mutation wherein the addition of deletation of (a number of) nucleotide(s) causes a shift in the reading frame of the codons in the mRNa, thus, may eventually lead to the alteration in the amino acid sequence at protein translation

reading frame shift

A type of gene mutation wherein the addition or deletation of (a number of) nucleotide(s) causes a shift in the reading frame of the codons in the mRNa, thus, may eventually lead to the alteration in the amino acid sequence at protein translation

In vertebrate mitochondria "___" and "___" are also stop codons,

AGA AGG

Dinucleotide fold

ATP/NAD binding - *highly conserved* - Found in enzymes that bind to ATP

start codon

AUG (methionine) initiates translation

ribonucleosides

Adenosine Cytidine Guanosine Uridine

addition of poly A tail (3' polyadenylation)

After polyadenylation sequence, 50-250 As are added on 3' end; ensures that mRNA is transported safely to ribosome in cytoplasm

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template. is an enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis. Since primase produces RNA molecules, the enzyme is a type of RNA polymerase. An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

Helicase

An enzyme that untwists the double helix at the replication forks, separating the two parental strands and making them available as template strands.

Location and Functions of Different Classes of RNA Molecules

Class of RNA Cell Type Location of function in eukaryotic cells Function Ribosomal RNA (rRNA) "Prokaryotic Eukaryotic" Cytoplasm Structural and functional components of the ribosome Messenger RNA (mRNA) "Prokaryotic Eukaryotic" Nucleus and cytoplasm Carries genetic code for proteins Transfer RNA (tRNA) "Prokaryotic Eukaryotic" Cytoplasm Helps incorporate amino acids into polypeptide chain Small nuclear RNA (snRNA) Eukaryotic Nucleus Processing of pre-mRNA Small nucleolar RNA (snoRNA) Eukaryotic Nucleus Processing and assembly of rRNA MicroRNA (miRNA) Eukaryotic Nucleus and cytoplasm Inhibits translation of mRNA Small interfering RNA (siRNA) Eukaryotic Nucleus and cytoplasm Triggers degradation of other RNA molecule Piwi-interacting RNA (siRNA) Eukaryotic Nucleus and cytoplasm Suppresses the transcription of transposable elements in reproductive cells CRISPR RNA (crRNA) Prokaryotic -- Assists destruction of foreign DNA Long noncoding RNA (incRNA) Eukaryotic Nucleus and cytoplasm Variety of functions

Polyadenylation further explained

Cleavage and polyadenylation (C/P) of nascent transcripts is essential for maturation of the 3′ ends of most eukaryotic mRNAs. Over the past three decades, biochemical studies have elucidated the machinery responsible for the seemingly simple C/P reaction. Recent genomic analyses have indicated that most eukaryotic genes have multiple cleavage and polyadenylation sites (pAs), leading to transcript isoforms with different coding potentials and/or variable 3′ untranslated regions (UTRs). As such, alternative cleavage and polyadenylation (APA) is an important layer of gene regulation impacting mRNA metabolism. Here, we review our current understanding of APA and recent progress in this field. (to continue reading https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800139)

Ribonucleotide reductase

Contains two types of allosteric regulatory sites for activity and specificity. Converts ribonucleotides to deoxyribonucleotides.

cis-acting elements

DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression /Core promoter Proximal-promoter elements Enhancers Silencers/

promoters

DNA sequences region of a gene where RNA polymerase can bind and begin transcription Specific DNA sequences in 5′ region upstream of initial transcription point

splicosome

Different particles that recognize splice sites are compiled in a large assembly. A complex of RNA and protein subunits. Removes introns from a transcribed pre-RNA segments. * Reaction involves snRNAs and formation of lariat structure* snRNA

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

polynucleotide phosphorylase

Enzyme that catalyzes production of synthetic mRNAs bacterial enzyme that metabolically degrades RNA *however* /in vitro/ and _high concentration of ribonucleoside diphoshpates, the reaction is reversed to form RNA instead of degrade it_

Polynucleotide phosphorylase

Enzyme that catalyzes production of synthetic mRNAs mRNAs serve as template for in vitro (cell-free in test tube) system Probability of adding a specific ribonucleotide is dependent on its relative availability

Topoisomerase

Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

general transcription factors (GTFs)

Five different proteins that play a role in initiating transcription at the core promoter of structural gens in eukaryotes.

snRNA

Found only in the nucleus of eukaryotes and functions to remove introns from mRNA *SPLICING* includes lariat structure

Enhancers and silencers

Found upstream, within, or downstream of gene Modulate transcription from a distance Enhancers increase transcription levels Silencers decrease them Act to increase or decrease transcription in response to cell's requirement for gene product /feedback loop... *regulates proteins*/

substitution editing

Identities of individual nucleotide bases are altered; prevalent in mitochondria and chloroplast RNA derived in plants

1. DNA 2.RNA 3.Protein 4.Transcription 5.Translation

Label the central Dogma (#6 = central dogma)

core promoter

Located immediately upstream of the eukaryotic promoter, DNA sequences to which the basal transcription apparatus binds.

Which type of mutation helped lead to the understanding that the genetic code is based on triplets?

Missense mutation within the promoter Base substitution (substitution of one base for another) *Frameshift* Nonsense

degeneracy of the genetic code

More than one codon codes for an amino acid, making third codon position "wobble" allows more "wobble" room for errors

sense mutation

Mutations that change a termination codon into one that codes for an amino acid. Such mutations produce elongated proteins.

Does the genetic code overlap?

NO

RNA is made where?

Nucleus

hairpin secondary structure

Often created by the newly formed RNA during bacteria transcription. ~40 nt, is a part of the forming RNA that folds up on itself and is crucial for transcription termination

Splicing

One type of eukaryotic mRNA processing in which introns are removed from the primary transcript and exons are ligated together. Splicing of transcripts can be different in different tissues.

Translation

Process by which mRNA is decoded and a protein is produced

RNA splicing

Process by which the introns are removed from RNA transcripts and the remaining exons are joined together.

Transcription factors (TFs)

Proteins that bind promoters and are functional in transcription. *RNAP is dependent on this* /*Function:* recognize target sequences in DNA, interact with other transcription factors/ *Each TF has a characteristic motif.*

Triplet code

Provides 64 codons to specify 20 amino acids

___ __________ creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides. ___ __________ adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand)

RNA Polymerase

mixed copolymers

RNA heteropolymers which helped solidify that all 20 amino acids are coded via triplet code rule (*via proportions*)

RNA homopolymers

RNA nucleotides with only one type of ribonucleotide used for synthesizing polypeptides in vitro UUUUUU AAAAAA CCCCCC GGGGGG is the mRNA used in cell free protein synthesizing system

In prokaryotes, which component must disassociate to allow for elongation of the transcriptional complex?

RNA polymerase rho none of these are correct *sigma subunit*

Termination in prokaryotes

RNA polymerase stops at termination sequence

rho (p)

RNA synthesis termination protein large and hexameric facilitates termination via biochemical reaction with growing RNA strand *only found in prokaryotes*

Self-Splicing RNAs

Self-excision group I introns occurs in bacteria, lower eukaryotes, and higher plants

Consensus sequences

Short stretches of DNA that appear, with little variation, in many different genes. DNA sequences homologous in different genes of same organism E. coli promoters have two consensus sequences TTGACA and TATAAT

polyribosomes

Strings of ribosomes that work together to translate a RNA message. in prokaryotes and eukaryotes

lariat structure

Structure that spliced RNA forms

*UGAGCC* There are three principles to keep in mind when predicting the sequence of the mRNA produced by transcription of a particular DNA sequence. 1. *The RNA polymerase reads the sequence of DNA bases from only one of the two strands of DNA: the template strand.* 2. The RNA polymerase reads the code from the template strand in the 3' to 5' direction and thus produces the mRNA strand in the 5' to 3' direction. 3. In RNA, the base uracil (U) replaces the DNA base thymine (T). Thus the base-pairing rules in transcription are A→U, T→A, C→G, and G→C, where the first base is the coding base in the template strand of the DNA and the second base is the base that is added to the growing mRNA strand.

Suppose that a portion of double-stranded DNA in the middle of a large gene is being transcribed by an RNA polymerase. As the polymerase moves through the sequence of six bases shown in the diagram below, what is the corresponding sequence of bases in the RNA that is produced? Enter the sequence of bases as capital letters with no spaces and no punctuation. Begin with the first base added to the growing RNA strand, and end with the last base added.

TBP (TATA binding protein)

TBP of TFIID binds to TATA to initiate transcription; introduces kinks in DNA - Phe side chains wedge between T and A in TATA box

H bond between 3rd codon base and the 1st anticodon base & wobble hypothesis explained

The 16S RNA in the 30S ribosomal subunit possesses a means of examining whether the standard Watson-Crick base pairs have formed between the 1st codon base and the 3rd anticodon base, as well as between the 2nd codon base and the 2nd anticodon base. However, there is no system to check whether the 3rd codon base and the 1st anticodon base are complimentary to one another and this amounts to the more lenient base-pairing that is witnessed exclusively at the 3rd position [7].

Elongation

The RNA is always synthesized in the 5′ → 3′ direction, with nucleoside triphosphates (NTPs) acting as substrates for the enzyme. /bases are added toward 3′ side/ ribosomes are added to RNA chain The chain grows by the formation of a bond between the 3′ hydroxyl end of the growing strand and a nucleoside triphosphate, releasing one pyrophosphate ion (PPi). This results in the net addition of one phosphate, which is incorporated into the backbone of the new strand. DNA grows by reaction with deoxyribonucleoside triphosphates, and RNA grows by reaction with ribonucleoside triphosphates

Initiation codon (start codon)

The codon in mRNA that specifies the first amino acid (fMet in bacterial cells; Met in eukaryotic cells) of a protein; most commonly AUG. Methionine AUG

mature mRNA

The final product that results when the pre-mRNA in eukaryotes undergoes processing events before it exits the nucleus *Splicing and /smaller than initial rna/

colinearity of gene mutations.

The genetic map of point mutations (determined by recombinational analysis) corresponds linearly to the changed amino acids in the different mutants (determined by fingerprint analysis).

reading frame

The way a cell's mRNA-translating machinery groups the mRNA nucleotides into codons

Transcription Factor (TF) motif

These motifs are short structures which comprise only a small portion of the protein. These motifs are used to define a specific class of trans-acting factors. /The following are specific examples of trans-acting factors, each with a defined and specific motif. steroid receptors zinc finger proteins - Zn++ binds at a specific site leucine zipper proteins - leucine appears every seven amino acids in a region of the protein/

initial step in genetic flow of information?

Transcription

RNA heteropolymers

Two or more different ribonucleosides were used to decipher relative proportion of each type of ribonucleotide diphosphate in synthetic mRNA /mixed copolymers/ _Nirenberg & Matthaei_

C changed to A in the third position of the codon. G changed to C in the second position of the codon. *G changed to A in the first position of the codon. *

Which of the following single base changes would result in alanine being substituted for threonine?

how to synthesize polypeptides?

_1._ In Vitro mixture containing all essential cell parts necessary for protein synthesis. _2._ one or more amino acid must be radioactive _3._an mRNA is added to serve as template for translation

heteroduplex

a DNA double helix composed of single strands from two different DNA molecules introns present in dna but not RNA

trinucleotide repeats

a form of mutation associated with the expansion in copy number of a nucleotide triplet in or near a gene (Huntington's disease, myotonic dysphoria)

intron

a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes. (regulation factor) not in prokaryotes

open reading frame (ORF)

a sequence of DNA or RNA that could be translated to give a polypeptide is the part of a reading frame that has the ability to be translated. An ORF is a continuous stretch of codons that contain a start codon (usually AUG) and a stop codon (usually UAA, UAG or UGA). /this results in a series of amino acids making up a polypeptide./

mRNA (messenger RNA)

a single-stranded RNA molecule that encodes the information to make a protein

termination sequence (transcription)

about 40 base pairs in length transcribed from DNA into RNA hairpin structure conformation takes place *dependent on termination factor rho (p)*

How to re-establish the reading frame?

add / remove 3 ribonucleotides

ssRNA

antisense strand; viral RNA is transcribed to a + strand to serve as mRNA for protein synthesis

σ subunit disassociation

begins the process of elongation after initiating transcription

Ribozymes

catalytic RNA molecules that function as enzymes and can splice RNA /ex: rRNAs mitochondria/chloroplasts/

base substitution

changes the base of a single DNA nucleotide

Ordered nature of the genetic code

chemically similar amino acids share 1-2 middle bases *THUS, buffers the potential effects of mutation (which would translate to a mutated protein function)*

DNA is found

chromosomes in the nucleus of eukaryotes

stop codon

codon that signals to ribosomes to stop translation (UAA, UAG, UGA)

response elements / cis acting element properties

contain short consensus sequences modules are related but not identical not fixed in location but usually within 200 bp upstream of the transcription start site a single element is usually sufficient to confer a regulatory response can be located in a promoter or an enhancer assumed that a specific protein binds to the element and the presence of that protein is developmentally regulated

Termination codon (stop codon)

does not code for any amino acid, therefore, it is not recognized by tRNA stops translation regulation and control mech

unambiguous genetic code

each codon encodes precisely one amino acid

Exon

expressed sequence of DNA; codes for a protein

trans-acting factors

factors, usually considered to be proteins, that bind to the cis-acting sequences to control gene expression

What revealed the triplet nature of codon code?

frame shift mutation

Mitochondrial DNA (mtDNA)

genetic material in the mitochondria of the cytoplasm of a cell; only inherited from the mother *revelation to exception to universality of gene code* /UGA is normally termination codon, but in mtDNA, UGA codes tryptophan in yeast and humans/

Anti-codon

group of three bases on a tRNA molecule that are complementary to an mRNA codon

the efficiency of promoter site bonding is dependent upon what factor?

how well RNA polymerase binds to the promoter and initation site is bonded

rna polymerase breaks what kind of bonds?

hydrogen

Transcription activators and repressors

influence the efficiency or the rate of RNP II transcription initiation bind to enhancer/silencer elements

RNA is the ____________ molecule in the information flow between DNA and protein synthesis.

intermediate

degenerate

lacking some property, order, or distinctness of structure previously or usually present, in particular.

Rho

large

proximal promoter elements

located close to the promoter and bind regulatory proteins.

fMet

mRNA start codon (AUG) codes for N-formylmethionine in proks that stimulates neutrophil chemotaxis

Use the codon chart to predict the amino acid sequence produced during translation by the following short hypothetical mRNA sequences. Sequence 2: 5'-AUGCCGGAUUAAGUUGA-3'

met-pro-asp-(stop)

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

ribonucleotides

monomers of RNA

redundant genetic code

most amino acids are coded for by more than one codon /64 possible codons for 20 possible AAs/

frameshift mutation

mutation that involves the insertion or deletion of a nucleotide in the DNA sequence Insertions or deletions shift reading frame and change codons downstream Triplet nature code was revealed by frameshift mutations with profavlin

do prokaryotes have introns?

no

Both the codons UUU and UUC specify the amino acid phenylalanine. This is possible because the genetic code is __________.

nonoverlapping unambiguous *degenerate* universal

Insertion/deletion editing

nucleotides are added to or subtracted from the total number of bases

Transcription in Eukaryotes

occurs in the nucleus mRNA must leave nucleus for translation Chromatin remodeling: Chromatin must uncoil to make DNA accessible to RNA Pol RNA polymerases rely on transcription factors (TFs) to scan/bind DNA Enhancers and silencers control transcription regulation Eukaryotes possess three forms of RNA polymerase

multiple/different initiation points create ___________ _____

overlapping genes (ONLY RNA)

where does genetic _"wobble"_ take place?

position 1 of anticodon (tRNA) position 3 of codon (mRNA)

amount of RNA is generally ____________ to the amount of protein in a cell

proportional

universality of genetic code

refers to the fact the the correspondence between amino acids and codons is the same in nearly all organisms. Genes can therefore be transferred from one organism to another and still produce the correctly functioning protein.

ribonucleoside diphosphates

reverse degradation of RNA, to restore it (in high concentrations)

where does protein synthesis take place?

ribosomes

Colinearity

sequence of codons in a gene is colinear with the sequence of amino acids, making the encoded protein

Ribosome

site of protein synthesis

The Splicosome

snRNA + protein= small nuclear Ribonuclear Proteins (snRNPs) 5 snRNPs (U1,U2, U4, U5, and U6) Non-snRNP proteins

transcription can also results in

ssRNA

non-sense codons

stop codon UAA, UAG, UGA

properties of trans-acting factors

subunits of RNA polymerase bind to RNA Polymerase to stabilize the initiation complex bind to all promoters at specific sequences but not to RNA Polymerase (TFIID factor which binds to the TATA box) bind to a few promoters and are required for transcription initiation; these are positive regulators of gene expression

mRNA is made from

template DNA strand (exons)

sense codons

the 61 codons that specify amino acids

coding strand of DNA

the DNA that is being mimicked by the RNA

polyadenylation

the addition of multiple adenine nucleotides to the 3' end of a newly synthesized mRNA molecule

codon recognition

the anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome

RNA polymerase holoenzyme

the bacterial multisubunit complex composed of the four subunits of the core enzyme plus the sigma factor

wobble hypothesis

the hypothesis that some tRNA molecules can pair with more than one mRNA codon, tolerating some variations in the third base, as long as the first and second bases are correctly matched /H bond between 3rd codon base and the 1st anticodon base is less spatially constrained, allowing genetic flexibility. / *i.e. allows anticodon (tRNA) to pair with more than one triplet of codon (mRNA)*

colinearity rule

the order of homeotic genes along the chromosome correlates with their expression along the anteroposterior axis of the body * The correspondence between the location of a mutant site within a gene and the location of an amino acid substitution within the polypeptide translated from that gene. *

The Genetic Code

the ordering of nucleotides in DNA molecules that carries the genetic information in living cells

sense strand

the strand of DNA that runs 5' to 3' and contains the genetic code for a protein.

degenerate code

there are more codons (64) than there are amino acids to be coded, so most amino acids are coded by more than one code.

trinucleotide

three joined nucleotides

RNA polymerase II (RNAPII)

transcribes mRNA in eukaryotes - *composes many genes* *Dependent on cis-acting elements and trans-acting factors. * is the most complex, with a total of nearly 60 polypeptides (Table 1), only a few of which are required for transcription by the other nuclear Pols. / typically begins with the binding of gene-specific regulatory factors near the site of transcription initiation. These factors can act indirectly on the transcription machinery by recruiting factors that modify chromatin structure, or directly by interacting with components of the transcription machinery. In the simplest form of gene activation, both the direct and indirect mechanisms result in recruitment of the transcription machinery to a core promoter (the minimal DNA sequence needed to specify non-regulated or basal transcription;/

intrinsic termination

transcriptional termination that does not require the function of the rho protein

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

dinucleotide

two nucleotides covalently bonded together by a phosphodiester bond

gyrase

unwinds DNA in front of fork

Gyrase

unwinds supercoiling of DNA

Components of transcription

σ subunit RNA Polymerase holoenzyme