Mastering Biology Chapter 17

Small-scale mutations within a gene can be divided into two general categories:

(1) single nucleotide-pair substitutions and (2) nucleotide-pair insertions or deletions. Insertions and deletions can involve one or more nucleotide pairs.

post-translational modifications

-Certain amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additions. -Enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chain. -In some cases, a polypeptide chain may be enzymatically cleaved into two or more pieces. -In other cases, two or more polypeptides that are synthesized separately may come together, if the protein has quaternary structure; an example is he​moglobin

Steps of Transcription

1. Initiation Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends. 2. Elongation 3. Termination

Given a DNA molecule with the sequence of bases 5′-ATTGCA-3′, what would be the sequence of the complementary strand? (It will be helpful to draw the DNA molecule when answering the question.)

3′-TAACGT-5′ Complementary strands of DNA run in opposite 5′ → 3′ directions from each other, an arrangement that is referred to as antiparallel. Wherever one strand of a DNA molecule has an A, the partner strand has a T, and a G in one strand is always paired with a C in the complementary strand. Adenine (A) pairs with uracil (U) instead of thymine (T) in RNA, as thymine (T) is not present in RNA.

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

point mutations

A change in a single nucleotide pair of a gene If a point mutation occurs in a gamete or in a cell that gives rise to gametes, it may be transmitted to offspring and to future generations. If the mutation has an adverse effect on the phenotype of a person, the mutant condition is referred to as a genetic disorder or hereditary disease.

Mutations

A change in the nucleotide sequence of an organism's DNA or in the DNA or RNA of a virus.

Mutagens

A chemical or physical agent that interacts with DNA and causes a mutation.

Final Gene Definition

A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule.

triplet code

A genetic information system in which a series of three-nucleotide-long words specifies a sequence of amino acids for a polypeptide chain. The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words. The series of words in a gene is transcribed into a complementary series of nonoverlapping, three-nucleotide words in mRNA, which is then translated into a chain of amino acids

polyribosome

A group of several ribosomes attached to, and translating, the same messenger RNA molecule.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

5' cap

A modified form of guanine nucleotide added onto the nucleotide at the 5' end of a pre-mRNA molecule. the book said 3' end here but im convinced that it meant the 5' end???? here: The 3' end, which is synthesized first, receives a 5′ cap, a modified form of a guanine (G) nucleotide added onto the 5'5′ end after transcription of the first 20-40 nucleotides have been transcribed.

insertions

A mutation involving the addition of one or more nucleotide pairs to a gene. These mutations (insertions AND deletions) have a disastrous effect on the resulting protein more often than substitutions do. Insertion or deletion of nucleotides may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation.

frameshift mutation

A mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons. All nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive missense mutations, usually ending sooner or later in a nonsense mutation that leads to premature termination. Unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional. Insertions and deletions also occur outside of coding regions; these are not called frameshift mutations, but can have effects on the phenotype—for instance, they can affect how a gene is expressed.

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. and it causes translation to be terminated prematurely; the resulting polypeptide will be shorter than the polypeptide encoded by the normal gene. Most nonsense mutations lead to nonfunctional proteins.

Introns

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Anticodon (anticodon loop)

A nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule. The protruding 3′ end acts as the attachment site for an amino acid. The loop extending from the other end of the L includes the anticodon, the particular nucleotide triplet that base-pairs to a specific mRNA codon. Thus, the structure of a tRNA molecule fits its function.

silent mutation

A nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid. -Some substitutions have no effect on the encoded protein, owing to the redundancy of the genetic code. For example, if 3'-CCG-5' on the template strand mutated to 3'-CCA-5', the mRNA codon that used to be GGC would become GGU, but a glycine would still be inserted at the proper location in the protein. wild type = mutant

signal-recognition particle (SRP)

A protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER. This particle escorts the ribosome to a receptor protein built into the ER membrane. The receptor is part of a multiprotein translocation complex. Polypeptide synthesis continues there, and the growing polypeptide snakes across the membrane into the ER lumen via a protein pore.

transcription unit

A region of DNA that is transcribed into an RNA molecule.

transcription factors

A regulatory protein that binds to DNA and affects transcription of specific genes. helps guide the binding of the RNA polymerase and the initiation of transcription

Ribsome structure

A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs, ​or rRNAs​ ​ In eu​karyotes, the subunits are made in the nucleolus. Ribosomal RNA genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm. Completed ribosomal subunits are then exported via nuclear pores to the cytoplasm. In both bacteria and eukaryotes, a large and a small subunit join to form a functional ribosome only when attached to an mRNA molecule. About one-third of the mass of a ribosome is made up of proteins; the rest consists of three rRNA molecules (in bacteria) or four (in eukaryotes). Because most cells contain thousands of ribosomes, rRNA is the most abundant type of cellular RNA.

poly-A tail

A sequence of 50-250 adenine nucleotides added onto the 3′ end of a pre-mRNA molecule. Recall that the pre-mRNA is cut and released soon after the polyadenylation signal, AAUAAA, is transcribed. At the 3′ end, an enzyme then adds 50-250 more adenine (A) nucleotides, forming a poly-A tail.

signal peptide

A sequence of about 20 amino acids at or near the leading (amino) end (N end) of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell.

exons

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed. (Exceptions include the UTRs of the exons at the ends of the RNA, which make up part of the mRNA but are not translated into protein. Because of these exceptions, you may prefer to think of exons as sequences of RNA that exit the nucleus.

Promoter

A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.

tRNA structure

A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long (compared to hundreds of nucleotides for most mRNA molecules). The tRNA ​​actually twists and folds into a compact 3-D struct​ure that is roughly L-shaped, with the 5′ and 3′ ends ​of the linear tRNA both located near one end of the structure. The protruding 3′ end acts as the attachment site for an amino acid. The loop extending from the other end of the L includes the anticodon, the particular nucleotide triplet that base-pairs to a specific mRNA codon. Thus, the structure of a tRNA molecule fits its function.

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. The mRNA nucleotide triplets are called codons, and they are customarily written in the 5'→3' direction The term codon is also used for the DNA nucleotide triplets along the NONTEMPLATE strand.

charged tRNA

A transfer RNA molecule with an amino acid attached to its 3' end. The resulting aminoacyl tRNA, also called a charged tRNA, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome.

Messenger RNA (mRNA)

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. (In eukaryotes, the primary RNA transcript must undergo RNA processing to become mRNA.)

alternative RNA splicing

A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

nucleotide-pair substitutions

A type of point mutation in which one nucleotide in a DNA strand and its partner in the complementary strand are replaced by another pair of nucleotides.

RNA splicing

After synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript (introns) that will not be included in the mRNA and the joining together of the remaining portions (exons). in which large portions of the RNA primary transcript molecules are removed and the remaining portions are reconnected. This cut-and-paste job is similar to editing a movie.

Transfer RNA (tRNA)

An RNA molecule that functions as a translator between nucleic acid and protein languages by carrying specific amino acids to the ribosome, where they recognize the appropriate codons in the mRNA. In the process of translation, a cell "reads" a genetic message and builds a polypeptide accordingly. The message is a series of codons along an mRNA molecule, and the translator is called a transfer RNA (tRNA). The function of a tRNA is to transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome. A cell keeps its cytoplasm stocked with all 20 amino acids, either by synthesizing them from other compounds or by taking them up from the surrounding solution.

ribozyme

An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing. The idea of a catalytic role for the RNAs in the spliceosome arose from the discovery of ribozymes, RNA molecules that function as enzymes.

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA. carries out the correct matching of tRNA and amino acids The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA. (Regions of both the amino acid attachment end and the anticodon end of the tRNA ensure the specific fit.)

RNA polymerase

An enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand. Like the DNA polymerases that function in DNA replication, RNA polymerases can assemble a polynucleotide only in its 5'→3'5′→3′ direction, adding onto its 3'3′ end. Unlike DNA polymerases, however, RNA polymerases are able to start a chain from scratch; they don't need to add the first nucleotide onto a pre-existing primer.

primary transcript

An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene.

what direction are anticodons written in?

Anticodons are conventionally written 3'→5' to align properly with codons written 5'→3'

Elongation

As RNA polymerase moves along the DNA, it untwists the double helix, ​exposing about 10-20 DNA nucleotides at a time for pairing with RNA nucleotides (Figure 17.10). The enzyme adds nucleo​tides to the 3'3′ end of the growing RNA molecule as it moves along the double helix. As transcription proceeds forward, the newly synthesized RNA molecule behind the RNA polymerase peels away from its DNA template, and the DNA double helix re-forms. Transcription progresses at a rate of about 40 nucleotides per second in eukaryotes.

one gene-one protein

As researchers learned more about proteins, they made revisions to the one gene-one enzyme hypothesis. First of all, not all proteins are enzymes. Keratin, the structural protein of animal hair, and the hormone insulin are two examples of nonenzyme proteins. Because proteins that are not enzymes are nevertheless gene products, molecular biologists began to think in terms of one gene-one protein.

different types of RNA polymerase

Bacteria have a single type of RNA polymerase that synthesizes not only mRNA but also other types of RNA that function in gene expression, such as ribosomal RNA. In contrast, eukaryotes have at least three types of RNA polymerase in their nuclei; the one used for pre-mRNA synthesis is called RNA polymerase II. The other RNA polymerases transcribe RNA molecules that are not translated into protein

what is important about certain sections of promotors?

Based on interactions with p​roteins (transcription factors), RNA polymerase binds in a precise location and orientation on the promoter. This binding determines where transcription starts and the direction it will travel, thus which strand of DNA is used as the template.

What does it mean to be haploid/diploid?

Because a haploid genome contains only one copy of each gene, that single copy determines the individual's expressed phenotype there can be haploid and diploid species, the difference is just that diploid species have multiple variations of a specific gene because there are they're di/two/multiple

alternative RNA splicing is one reason humans can get along with about the same number of genes as a nematode (roundworm)... why is this?

Because of alternative splicing, the number of different protein products an organism produces can be much greater than its number of genes.

Cas9

Cas9 is a nuclease that cuts double-stranded DNA molecules. The power of Cas9 for gene editing is that the Cas9 protein will cut any sequence to which it is directed. Cas9 is directed to its target by a guide RNA molecule that it binds and uses as a homing device, cutting both strands of any DNA sequence that is complementary to the guide RNA. Scientists have been able to exploit the function of Cas9 by introducing a Cas9-guide RNA complex into a cell they wish to alter. The guide RNA in the complex is engineered to be complementary to the "target" gene. Cas9 cuts both strands of the target DNA, and the resulting broken ends of DNA trigger a DNA repair system. When there is no undamaged DNA for the enzymes of the repair system to use as a template, as shown at the bottom left of Figure 17.28, the repair enzymes introduce or remove random nucleotides while rejoining the ends. Generally, this process alters the DNA sequence so that the gene no longer works properly. This technique is a highly successful way for researchers to "knock out" (disable) a given gene to study what that gene does in an organism.

nucleotide analogs and Chemical mutagens fall into several categories...

Chemical mutagens that are similar to normal DNA nucleotides but that pair incorrectly during DNA replication. Other chemical mutagens interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix. Still other mutagens cause chemical changes in bases that change their pairing properties.

what are transfer RNA molecules transcribed from?

DNA templates In a eukaryotic cell, tRNA, like mRNA, is made in the nucleus and then travels to the cytoplasm, where it will participate in the process of translation. In both bacterial and eukaryotic cells, each tRNA molecule is used repeatedly, picking up its designated amino acid in the cytosol, depositing this cargo onto a polypeptide chain at the ribosome, and then leaving the ribosome, ready to pick up another of the same amino acid.

Which of the following shows the flow of genetic information?

DNA to RNA to protein DNA directs RNA synthesis and, through RNA, controls protein synthesis; this entire process is called gene expression. The sites of protein synthesis are cellular structures called ribosomes.

Domains

Discrete structural and functional regions of proteins. Proteins often have a modular architecture consisting of discrete structural and functional regions called domains. One domain of an enzyme, for example, might include the active site, while another might allow the enzyme to bind to a cellular membrane. In quite a few cases, different exons code for the different domains of a protein

how does a gene determine primary structure and shape?

During its synthesis, a polypeptide chain begins to coil and fold spontaneously as a consequence of its amino acid sequence (primary structure), forming a protein with a specific shape: a three-dimensional molecule with secondary and tertiary structu​re. Thus, a gene determines prim​ary structure, which in turn determines shape.

What happens during transcription?

During transcription, the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized. For each gene, only one of the two DNA strands is transcribed. This strand is called the template strand because it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript

What happens during translation?

During translation, the sequence of codons along an mRNA molecule is decoded, or translated, into a sequence of amino acids making up a polypeptide chain. The codons are read by the translation machinery in the 5'→3' direction along the mRNA. Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide. Because codons are nucleotide triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product. For example, 300 nucleotides along an mRNA strand code for 100 amino acids in the polypeptide it encodes.

Mutations can arise in a number of ways...

Errors during DNA replication or recombination can lead to nucleotide-pair substitutions, insertions, or deletions, as well as to mutations affecting longer stretches of DNA.

spontaneous mutations

Errors during DNA replication or recombination can lead to nucleotide-pair substitutions, insertions, or deletions, as well as to mutations affecting longer stretches of DNA. If an incorrect nucleotide is added to a growing chain during replication, for example, the base on that nucleotide will then be mismatched with the nucleotide base on the other strand. In many cases, the error will be corrected by DNA proofreading and repair systems. Otherwise, the incorrect base will be used as a template in the next round of replication, resulting in a mutation. Such mutations are called spontaneous mutations. occur without a mutagen?

what are the two instances of molecular recognition that accurate translation of a genetic message requires?

First, a tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid, and no other, to the ribosome. The second instance of molecular recognition is the pairing of the tRNA anticodon with the appropriate mRNA codon.

what three properties of RNA enable some RNA molecules to function as enzymes?

First, because RNA is single-stranded, a region of an RNA molecule may base-pair, in an antiparallel arrangement, with a complementary region elsewhere in the same molecule; this gives the molecule a particular three-dimensional structure. -A specific structure is essential to the catalytic function of ribozymes, just as it is for enzymatic proteins. Second, like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that can participate in catalysis. Third, the ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity.

5' cap and poly-A tail share several important functions

First, they seem to facilitate the export of the mature mRNA from the nucleus. Second, they help protect the mRNA from degradation by hydrolytic enzymes. And third, they help ribosomes attach to the 5′ end of the mRNA once it reaches the cytoplasm.

wobble

Flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon. Wobble explains why the synonymous codons for a given amino acid most often differ in their third nucleotide base. Accordingly, a tRNA with the anticodon 3'-UCU-5′ can base-pair with either the mRNA codon 5′-AGA-3′ or 5'-AGG-3', both of which code for arginine

"inborn errors of metabolism" and alkaptonuria

For example, people with a disease called alkaptonuria have black urine because it contains a chemical called alkapton, which darkens upon exposure to air. Garrod reasoned that these people cannot make an enzyme that breaks down alkapton, so alkapton is expelled in their urine.

sickle cell, familial cardiomyopathy

For example, we can trace the genetic basis of sickle-cell disease to the mutation of a single nucleotide pair in the gene that encodes the ββ-globin polypeptide of hemoglobin. The change of a single nucleotide in the DNA's template strand leads to an altere​​d mRNA and the production of an abnormal protein (Figure 17.26; also see Figure ​5.1​9). In individuals who are homozygous for the mutant allele, the sickling of red blood cells caused by the altered hemoglobin produces the multiple symptoms associated with sickle-cell disease Another disorder caused by a point mutation is a heart condition called familial cardiomyopathy, which is responsible for some of the tragic incidents of sudden death in young athletes. Point mutations in several genes encoding muscle proteins have been identified, any of which can lead to this disorder.

one gene-one enzyme hypothesis

Garrod's hypothesis that a gene dictates the production of a specific enzyme

gene programming summary

Genes program protein synthesis via genetic messages in the form of messenger RNA. Put another way, cells are governed by a molecular chain of command with a directional flow of genetic information:

one gene-one polypeptide hypothesis.

However, many proteins are constructed from two or more different polypeptide chains, and each polypeptide is specified by its own gene. For example, hemoglobin—the oxygen-transporting protein of vertebrate red blood cells—contains two kinds of polypeptides, and thus two genes code for this protein, one for each type of polype​ptide (see Figure 5.18). Beadle and​ Tatum's idea was therefore restated as the one gene-one polypeptide hypothesis. Even this description is not entirely accurate, though. First, in many cases, a eukaryotic gene can code for a set of closely related polypeptides via a process called alternative splicing, which you will learn about later in this chapter. Second, quite a few genes code for RNA molecules that have important functions in cells even though they are never translated into protein. For now, we will focus on genes that do code for polypeptides.

terminator

In bacteria, a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA.

termination of transcription in bacteria

In bacteria, transcription proceeds through a terminator sequence in the DNA. The transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation

termination of transcription in eukaryotes

In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA. This is called a "signal" because once this stretch of six RNA nucleotides appears, it is immediately bound by certain proteins in the nucleus. Then, at a point about 10-35 nucleotides downstream from the AAUAAA, these proteins cut the RNA transcript free from the polymerase, releasing the pre-mRNA. The pre-mRNA then undergoes processing, the topic of the next section. Although that cleavage marks the end of the mRNA, the RNA polymerase II continues to transcribe. Enzymes begin to degrade the RNA made after cleavage, starting at its newly exposed 5'5′ end. The polymerase continues transcribing, pursued by the enzymes, until they catch up to the polymerase and it dissociates from the DNA.

RNA processing/splicing overview

In making a primary transcript from a gene, RNA polymerase II transcribes both introns and exons from the DNA, but the mRNA molecule that enters the cytoplasm is an abridged version. In the process of RNA splicing, the introns are cut out from the molecule and the exons joined together, forming an mRNA molecule with a continuous coding sequence.

self-splicing

In some organisms, RNA splicing can occur without proteins or even additional RNA molecules: The intron RNA functions as a ribozyme and catalyzes its own removal. For example, in the ciliate protist Tetrahymena, self-splicing occurs in the production of ribosomal RNA (rRNA), a component of the organism's ribosomes. The pre-rRNA actually removes its own introns! The discovery of ribozymes invalidated the idea that all biological catalysts are proteins.

summary of what the elongation stage of translation does

In the elongation stage of translation, amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain.

Molecular Components of Translation

In the process of translation, a cell "reads" a genetic message and builds a polypeptide accordingly. The message is a series of codons along an mRNA molecule, and the translator is called a transfer RNA (tRNA). The function of a tRNA is to transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome. A cell keeps its cytoplasm stocked with all 20 amino acids, either by synthesizing them from other compounds or by taking them up from the surrounding solution. The ribosome, a structure made of proteins and RNAs, adds each amino acid brought to it by a tRNA to the growing end of a polypeptide chain

RNA processing

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends.

downstream vs upstream

Molecular biologists refer to the direction of transcription as "downstream" and the other direction as "upstream." These terms are also used to describe the positions of nucleotide sequences within the DNA or RNA. Thus, the promoter sequence in DNA is said to be upstream from the terminator. The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule is called a transcription unit.

coding strand

Nontemplate strand of DNA, which has the same sequence as the mRNA except it has thymine (T) instead of uracil (U).

reading frame

On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis. Our ability to extract the intended message from a written language depends on reading the symbols in the correct groupings—that is, in the correct reading frame. The reading frame is also important in the molecular language of cells. The short stretch of polypeptide shown in Figure 17.5, for instance, will be made correctly only if the mRNA nucleotides are read from left to right (5'→3') in the groups of three shown in the figure: UGG UUU GGC UCA Although a genetic message is written with no spaces between the codons, the cell's protein-synthesizing machinery reads the message as a series of nonoverlapping three-letter words. The message is not read as a series of overlapping words—UGGUUU, and so on—which would convey a very different message.​​​​​​​​​​​​​​​​​​​

A site

One of a ribosome's three binding sites for tRNA during translation. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. (A stands for aminoacyl tRNA.) holds the tRNA carrying the next amino acid to be added to the chain. aminoacyl-tRNA binding site

E site

One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.) Discharged tRNAs leave the ribosome from the E site exit site

What determines whether a ribosome is free in the cytosol or bound to rough ER?

Polypeptide synthesis always begins in the cytosol as a free ribosome starts to translate an mRNA molecule. There, the process continues to completion—unless the growing polypeptide itself cues the ribosome to attach to the ER.

What is the link between genotype and phenotype?

Proteins are the link between genotype and phenotype.

elongation factors

Proteins involved in the elongation phase of translation, assisting ribosomes in the synthesis of the growing peptide chain. Each addition involves several proteins called elongation factors and occurs in a three-step cycle... Energy expenditure occurs in the first and third steps. Codon recognition requires hydrolysis of one molecule of GTP, which increases the accuracy and efficiency of this step. One more GTP is hydrolyzed (broken up) to provide energy for the translocation step.

Ribosomal RNA (rRNA)

RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA

what do ribosomes do during protein synthesis?

Ribosomes facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis.

template strand

The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript.

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase bound to a promoter. The whole complex of transcription factors and RNA polymerase II bound to the promoter

Archibald Garrod was first to

The first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell., Reported Alkaptonuria as the first human example of what is now known as Mendelian inheritance.

summary of what the initiation stage of translation does

The initiation stage of translation brings together an mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome.

protein-protein interactions in controlling eukaryotic transcription

The interaction between eukaryotic RNA polymerase II and transcription factors is an example of the importance of protein-protein interactions in controlling eukaryotic transcription. Once the appropriate transcription factors are firmly attached to the promoter DNA and the polymerase is bound to them in the correct orientation on the DNA, the enzyme unwinds the two DNA strands and begins transcribing the template strand at the start point.

what is the key to translating a genetic message into a specific amino acid sequence?

The key to translating a genetic message into a specific amino acid sequence is the fact that each tRNA molecule enables translation of a given mRNA codon into a certain amino acid. This is possible because a tRNA bears a specific amino acid at one end of its three-dimensional structure, while at the other end is a nucleotide triplet that can base-pair with the complementary codon on mRNA.

exon shuffling

The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a process known as exon shuffling Introns increase the probability of crossing over between the exons of alleles of a gene—simply by providing more terrain for crossovers without interrupting coding sequences. This might result in new combinations of exons and proteins with altered structure and function. We can also imagine the occasional mixing and matching of exons between completely different (nonallelic) genes. Exon shuffling of either sort could lead to new proteins with novel combinations of functions. While most of the shuffling would result in nonbeneficial changes, occasionally a beneficial variant might arise.

Your body contains tens of thousands of different proteins, each with a specific structure and function. The unique three-dimensional shape of each of these diverse proteins is based on several superimposed levels of structure. Which of the following is an accurate statement about proteins?

The primary structure of a protein is the order of amino acids in a polypeptide, as coded for by the DNA of a gene. The primary structure of a protein is its sequence of amino acids, which dictates secondary and tertiary structure. Secondary structure, such as α helices or β pleated sheets, is the result of hydrogen bonds between the repeating constituents of the polypeptide backbone. Tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids, and quaternary structure is the overall protein structure that results from the aggregation of two or more polypeptide chains into one functional macromolecule.

How is pre-mRNA splicing carried out?

The removal of introns is accomplished by a large complex made of proteins and small RNAs called a spliceosome. This complex binds to several short nucleotide sequences along an intron, including key sequences at each end. The intron is then released (and rapidly degraded), and the spliceosome joins together the two exons that flanked the intron.

what is the site of translation?

The sites of translation are ribosomes, molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains.

Transcription

The synthesis of RNA using a DNA template

Translation

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids.

how does the synthetase catalyze the attachment?

The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP. The resulting aminoacyl tRNA, also called a charged tRNA, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome.

what model is accepted as being primarily responsible for both the structure and the function of the ribosome?

The widely accepted model is that rRNAs, rather than ribosomal proteins, are primarily responsible for both the structure and the function of the ribosome. The proteins, which are largely on the exterior, support the shape changes of the rRNA molecules as they carry out catalysis during translation. Ribosomal RNA is the main constituent of the A and P sites and of the interface between the two subunits; it also acts as the catalyst of peptide bond formation. Thus, a ribosome could actually be considered one colossal ribozyme!

how many different synthetases are there?

There are 20 different synthetases, one for each amino acid. one synthetase is able to bind to all the different tRNAs for its particular amino acid.

But what about using the Cas9 system to help treat genetic diseases?

They introduce a segment from the normal (functional) gene along with the CRISPR-Cas9 system. After Cas9 cuts the target DNA, repair enzymes can use the normal DNA as a template to repair the target DNA at the break point. In this way, the CRISPR-Cas9 system edits the defective gene so that it is corrected (se​e the bottom right of Figure 17.28).​

The Functional and Evolutionary Importance of Introns

Whether or not RNA splicing and the presence of introns have provided selective advantages during evolutionary history is a matter of some debate. In any case, it is informative to consider their possible adaptive benefits. Specific functions have not been identified for most introns, but at least some contain sequences that regulate gene expression, and many affect gene products.

missense mutation

a nucleotide-pair substitution that results in a codon that codes for a different amino acid wild type does not equal mutant because the amino acid is changed little effect on the protein EXAMPLES: -sickle cell disease -albino phenotype in the Asinara donkey

release factor

a protein shaped like an aminoacyl tRNA, binds directly to the stop codon in the A site. The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain. (Water molecules are abundant in the cytosol.)

CRISPR-Cas9 system

a technique for editing genes in living cells, involving a bacterial protein called Cas9 associated with a guide RNA complementary to a gene sequence of interest Cas9 is a bacterial protein that helps defend bacteria against the viruses that infect them (bacteriophages). In bacterial cells, Cas9 acts together with "guide RNA" made from the CRISPR region of the bacterial genome.

The average length of a transcription unit along a human DNA molecule

about 27,000 nucleotide pairs, so the primary RNA transcript is also that long

gene editing

altering genes in a specific, predictable way

The average length of a transcription unit along a human DNA molecule is about 27,000 nucleotide pairs, so the primary RNA transcript is also that long. However, the average-sized protein of 400 amino acids requires only 1,200 nucleotides in RNA to code for it. Explain why this is

because most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides, regions that are not translated.

Marshall Nirenberg

identified the codons that specify each amino acid

start point

in transcription, the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA Based on interactions with p​roteins (transcription factors), RNA polymerase binds in a precise location and orientation on the promoter. This binding determines where transcription starts and the direction it will travel, thus which strand of DNA is used as the template.

The t​hree stages of transcription

initiation, elongation, and termination of the RNA chain

Where does transcription occur?

inside the nucleus

Gene expression

is the process by which DNA directs the synthesis of proteins (or, in some cases, just RNAs). The expression of genes that code for proteins includes two stages: transcription and translation.

what allows for RNA to be a catalyst and not just an informational molecule?

it can interact with itself and take on various shapes

are coding regions continuous?

no Even more surprising is that most of these noncoding sequences are interspersed between coding segments of the gene and thus between coding segments of the pre-mRNA. In other words, the sequence of DNA nucleotides that codes for a eukaryotic polypeptide is usually not continuous; it is split into segments.

P site

one of a ribosome's three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain. holds the tRNA carrying the growing polypeptide chain peptidyl-tRNA binding site

genetic engineering

the direct manipulation of genes for​ practical purposes.

Central Dogma of Molecular Biology

the flow of information only goes in one way: DNA -> RNA -> Protein This idea, that the flow of information went only one way, was named the central dogma by Francis Crick in 1956. In the 1970s, however, scientists were surprised to discover some enzymes that use RNA molecules as templates for DNA synthesis, an example of information flow from RNA to D​NA (see Concept 19.2). Still, th​ese exceptions do not discredit the idea that, in general, genetic information flows from DNA to RNA to protein. In the next section, we discuss how the instructions for assembling amino acids into a specific order are encoded in nucleic acids.

gene epression

the process by which DNA directs the synthesis of proteins

translation initiation complex

the union of mRNA, initiator tRNA, a small ribosomal subunit, and a large ribosomal subunit Proteins called initiation factors are required to bring all these components together. The cell also expends energy obtained by hydrolysis of a GTP molecule to form the initiation complex.

UTR

the untranslated regions (UTRs) at the 5'5′ and 3'3′ ends of the mRNA (referred to as the 5'5′ UTR and 3'3′ UTR); The UTRs are parts of the mRNA that will not be translated into protein, but they have other functions, such as ribosome binding. Untranslated regions - important for gene expression DO NOT CODE FOR A POLYPEPTIDE- coding starts w the start codon through the coding segment and ends at the stop codon

Is there redundancy in the genetic code?

there is redundancy in the genetic code, but no ambiguity. For example, although codons GAA and GAG both specify glutamic acid (redundancy), neither of them ever specifies any other amino acid (no ambiguity). The redundancy in the code is not altogether random. In many cases, codons that are synonyms for a particular amino acid differ only in the third nucleotide base of the triplet.

Archibald Garrod

was the first to suggest that genes dictate phenotypes through enzymes, proteins that catalyze specific chemical reactions in the cell. He postulated that the symptoms of an inherited disease reflect an inability to make a particular enzyme. He later referred to such diseases as "inborn errors of metabolism."

Which of the following clues would tell you if a cell is prokaryotic or eukaryotic?

whether or not the cell is compartmentalized by internal membranes All cells contain chromosomes, which carry genes in the form of DNA, and all cells have ribosomes, tiny complexes that make protein according to instructions from the genes. A rigid cell wall can be found surrounding the plasma membrane of prokaryotes as well as some eukaryotic cells. Within the cytoplasm of a eukaryotic cell, however, are a variety of membrane-bound organelles of specialized form and function, structures that are absent in almost all prokaryotic cells.

Does transcription and translation occur in all organisms?

yup Our understanding of transcription and translation in archaea lags behind, but we do know that archaeal cells share some features of gene expression with bacteria and others with eukaryotes.