Chapter 17: Transcription, Rna Processing, And Translation

Front 1

Proteins

Back 1

They are what gives shape to our cells, controls the chemical reactions that go on inside them, and regulate how material move into, out of, and through them

Front 2

Transcription: how it works

Back 2

Synthesize an RNA version of the instructions from DNA. RNA polymerases are responsible for synthesizing mRNA

ribonucleoside triphosphate (NTP) which contain an extra -OH group ( making it a ribose sugar) it matches to a base on the DNA template. THE RNA polymerase cleaves off two phosphates and catalyzes it by forming a phosphodiester linakge. This forms a growing mRNA chain

Only 1 of the two DNA strands is used as a template and transcribed by the RNA plolymerase.

Front 3

RNA polymerases: how it works

Back 3

ribonucleoside triphosphate (NTP) which contain an extra -OH group ( making it a ribose sugar) it matches to a base on the DNA template. THE RNA polymerase cleaves off two phosphates and catalyzes it by forming a phosphodiester linakge. This forms a growing mRNA chain

Only 1 of the two DNA strands is used as a template and transcribed by the RNA plolymerase.

Front 4

Template strand

Back 4

The stand of DNA that is read by the enzyme (making the mRNA)

Front 5

Non-Template Strand/ Coding Strand

Back 5

DNA strand not read by the enzyme (making the mRNA)

it is called a coding strand as the sequence matches the sequence of the RNA that is transcibed from the template strand and codes for a polypeptide except that it has Uracid (U) rather than Thymine (T)

Front 6

Transcription in Bacteria

Back 6

They have a single RNA polymerase

Front 7

initiation phase of transcription (bacteria)

Back 7

Bacterial RNA polymerases cannot initiate transcription on its own. Instead a detachable protein subunit called sigma must bind to the polymerase before transcription can begin.

Front 8

Sigma (bacterial)

Back 8

A detachable protein subunit called sigma must bind to the polymerase before transcription can begin.

it allows the holoenzyme to bind to only specific sections of the DNA

Front 9

Holoenzyme (bacterial)

Back 9

when bacterial RNA polymerase and sigma form

it consists of a core enzyme ( RNA polymerase) which contains the active site for catalysts and other required proteins (such as sigma)

Front 10

Core Enzyme (bacterial)

Back 10

part of the holoenzyme it consists of a core enzyme ( RNA polymerase) which contains the active site for catalysts and other required proteins (such as sigma)

Front 11

Bacterial Promoters

Back 11

These are bonding sites on the holoenzyme and they are called this because they are section of DNA that promote the start of transcription

Front 12

David Pribnow

Back 12

he analyzed the base sequence of promoters from various bacteria and ciruse that infeced bacteria

He found that promoters where 40-50 base pairs long nd had a particular section in comon - a series of bases identical or similar to TATAAT

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-10 box (bacterial)

Back 13

The six-base-pair sequence it is called this as it is cntered about 10 bases from the point where bactrial RNA plymerase starts transcription

Front 14

Downstream DNA

Back 14

Dna that is located in the direction RNA polymerase moves during trancription

Front 15

Upstream DNA

Back 15

DNA located in the opposite direction as RNA polymerase when it moves during transcription

Front 16

+1 Site (bacterial)

Back 16

The place where transcription begins is called the +1 site.

Front 17

-35 box (bacterial)

Back 17

The sequence TTGACA also occured in promoters and was about 35 bases upstream from the +1 site.

Front 18

Events inside the Holoenzyme (bacterial)

Back 18

in bacteria, transcription begins when sigma, as part of the holoenzyme binds to the -35 and -10 boxes. Sigma not RNA polymerases makes the initial contact with DNA of the promoter. sigmas binding to a promoter determines where and in which direction RNA polymerase will start synthesizing RNA

Once the holoenzyme is bound to a promoter for a bacterial gene the DNA helix is opened by RNA polymerase, creating separate strands of DNA. Incoming NTP comes and pairs with complementary bases, then the RNA polymerization begins.

Front 19

Elongation phase of transcription (bacterial)

Back 19

Once RNA polymerase begins moving along the DNA template synthesizing RNA, the elongation phase of transcription is underway.

RNA polymerase is a macromolecular machine with many different parts.

1. Interior of enzyme

2. Group of amino acids forms a rudder to help steer the template and non-template strand through channels indied enzyme

3. Zipper which helps separate the newly synthesized RNA from the DNA template.

during elongatin all channels and groves in the enzyme are filled.

Front 20

Termination phase of transcription (bacterial)

Back 20

this ends transcription. In bacteria, transcription stops when RNA polymerase transcribes a DNA sequence that functins as a transcription-termination signal

Then Rna folds back on itself forming a hairpin (loop) this structure disrupts the interaction between RNA polymerase and the RNA transcript resulting in the physical seperation of the enzyme and its product.

When transcription terminates, the reuslt is a mature mRNA that is ready to be translated int a protein

Front 21

Transcription in Eukaryotes

Back 21

1. Eukaryotes have 3 polymerases - pol I, II, and III. Each transcibes only certain types of RNA in eukaryotes.

2. Promoters in Eurkarytic Dna are more divers that bacterial promoters. They inlude a sequence called the TATA box

3. Instead of using a sigma protein, Eukaryotic RNA polmerases recognize promoters using a group of proteins called basal transcription factors.

4. Termination involves a short sequence called the polyadenylation singal or poly (A) signal

Front 22

Primary transcript

Back 22

When eukaryotic genes of any type are transcribed the initial product is termed a priamary transcript. This RNA must undergo multistep processing before it is functional.

pre-mRNA is the primary transcript for protein-coding genes

Front 23

Split Eukaryotic Genes

Back 23

Eukaryotic genes do not consist of one continuous DNA sequence that codes for a product, as do bacterial genes. Regions in a eukarytic gene that code for proteins are intermittently interrupted by streches of hundreds or even thousands of intervening bases. To make functional RNA eukaryotic cells must dispose of certain sequences and then combine the separate sections into an integrated whole.

Front 24

Phillip Sharp

Back 24

They wanted to determine the location of genes within the DNA of a virus that infects mammalians. They discovered that theire is not a one-to-one correspondence between the nucleotide sequence of a eukaryotic gene and its mRNA.

Front 25

Exons

Back 25

regions of eukaryotic genes that are a part of the final mNA because they are expressed

Front 26

Introns

Back 26

Regions of eukaryotic cells that not part of the final mRNa because they are intervening. Because of introns eukaryotic genes are much large thena their corresponding mture RNAs.

Front 27

RNA splicing (eukaryotic)

Back 27

The transcriptio of eukaryotic genes by RNA polymerase generates a primary transcript that contains both exons and intons. as transcription proceeds, the intons are removed from the growing RNA strand by a process known as splicing.

Splicing occurs within the nucleus while transcription is still underwa and reuslts in an RNA that contains an uniterupted genetic message.

Front 28

Small nuclear ribonucleoproteins snRNPs

Back 28

splicing of primary transcripts is catalyzed by RNs called small nuclear RNAs working with a comple of protiens. These protien plus-RNA marcormolecules are known as snRNPs

Front 29

Process of Splicing (eukaryotic)

Back 29

1. The process begins when snRNPs bind to the 5' exon- intron boundery, which is maked b the baes GU, and to a ke adenine ribonucleotide ( A) near the end intron

2. Once the intial snRNPs are in place, other snRNPs arrive to form a multipart complex called spliceosome.

3. The intron forms a loop plus a single-stranded stem (a lariat) with the adenine at its connecting point

4. The lariat is cut out, and a phosphodiester linkag links the exons on either side producing a continuous coding sequence - mRNA

Front 30

Adding caps and Tails to Transcripts (UTRs)

Back 30

for pre-mRNAs, intron splicing is accompanied by other important processing which makes the pre-mRNA mature. THey protect the mRNAs from degrading

1. as soon as the 5' end of a eukaryotic pre-mRNA emerges from RNA polymerase, enzymes add a structure called the 5' cap. The cap consists of a modified guanine nucleotide with three phosphate groups

2. An enzyme cleaves the 3' end of the pre-mRNA downstream of the poly (A) signa. Another enzyme adds a long row of 100-250 adenine nucleotides that are not encoded on the DNA template strand. This is called the poly (A) tail

Front 31

5' Cap (Eurkroytic)

Back 31

As soon as the 5' end of a eukaryotic pre-mRNA emerges from RNA polymerase, enzymes add a structure called the 5' cap. The cap consists of a modified guanine nucleotide with three phosphate groups

Front 32

Poly (A) tail

Back 32

An enzyme cleaves the 3' end of the pre-mRNA downstream of the poly (A) signa. Another enzyme adds a long row of 100-250 adenine nucleotides that are not encoded on the DNA template strand. This is called the poly (A) tail

Front 33

Reasons for Having a tail/cap on mRNA (Eurkaryotic)

Back 33

1. experimental mRNAs that have a cap and a tail last longer when they are introduced into cells than do experimental mRNAs that lack a cap or tail

2. Experimental mRNAs with caps and tails produce more proteins than do experimental mRNAs without caps and tails

Front 34

RNA processing

Back 34

this is generally the term for any of the modifications, such as splicing or poly (A) tail addition, needed to convert a primary transcript into a mature RNA.

Front 35

Ribosomes

Back 35

This is where translation occurs. This is the site where protein synthesis occurs.

They attach to mRNAs and begin synthesizing proteins even before transcription is complete.

Front 36

Polyribosome (bacterial)

Back 36

multiple ribosomes attach to each mRNA forming polyribosomes so that many copies of a protein can be produced from a single mRNA.

This can occur because there is no nuclear envelope to separate transcription from translation

Front 37

Crick hypothesis for mRNA forming an Amino Acid

Back 37

he though that there had to be some sort of adapter molecuel that holds the amino acid in place while interacting directly and specifically with a codon in mRNA by hdrogen bonding. He predicted a physical connection between the two types of molecules.

Front 38

transfer RNA (tRNA)

Back 38

amino acids are transferred from the RNA to a growing polypeptide. And it also acts as and interpreter during translation: tRNAs are Cricks adapter molecules

They serve as chemical go-betweens that allow amino acids to interact with an mRNA template.

Front 39

tRNA stucture

Back 39

They are relatively short. They can form secondary structure and some sequences of bases in the tRNA moleuce can form hydrogen bonds with complementary base sequences elsewhere in the same molecule (Stem-and-Loop structures). It also has a tertiary stucture and folds into an L-shaped molecule.

A CCA sequence at the 3' end of each tRNA molecule offered a site for amino acid attachment, while a triplet on the loop at the other end of the sturcture could serve as and aniticodon.

Front 40

anticodon

Back 40

a set of three ribonucleotides that form base paris with the mRNA codon.

Front 41

How are amino acids attached to tRNAs

Back 41

1. ATP is required to attach an amino acid to a tRNA

2. Enzymes called aminoacyl-tRNA synthetases catalyze teh addition of amino acids to t-RNA

3. For each of the major 20 amino acids there is a different aminoacyl-tRNA synthetase and one or more tRNAs

Front 42

aminoacyl-tRNA synthetases

Back 42

Enzymes called aminoacyl-tRNA synthetases catalyze the addition of amino acids to t-RNA

For each of the major 20 amino acids there is a different aminoacyl-tRNA synthetase and one or more tRNAs

Each aminoacyl-tRNA synthetase has a binding site for a particular amino acid and a particular tRNA.

Front 43

Aminoacyl tRNA

Back 43

the combination of a tRNA molecule covalently linked to an amino acid

Front 44

wobble hypothesis

Back 44

1. many amino acids are specified by more than one codon

2. codons for the same amino acid tend to have the same nucleotides at the first and second position

crick proposed that certain bases in the third position of tRnA anticodons can bind to bases in the third position a condom that does not match the base pairs. This would allow flexibilty.

Front 45

ribosomal RNAs (rRNAs)

Back 45

1. Large subunit

Where the peptide-bond formation takes place

2. Small subunit

holds the mRNA in place during translation

Front 46

Protein synthesis set up

Back 46

1. the tRNA carries an amino acid. The tRNA's position in the Ribosome is called the A site- "A" for acceptor or aminoacyl

2. The tRNA that hilds the growiing polypeptide chain that occupies the P site for peptidyl

3. tRNA no longer ahs an amno acid attached and is about to leave the ribose it occupies the ribosomes E site

Front 47

Protein synthesis process

Back 47

1. an aminoacyl tRNA diffuses into the A site, if its anitcodon matches a codon in mRNA it stays in the ribosome

2. A peptide bond forms between the amino acid held by te aminoacyl tRNA in the A site and the growing polypeptide, which was held by a tRNA in the P site

3. The ribosome moves down the mRNA by one codon, and all three tRNAs move one position within the ribosome. The tRNA in the E site exits, the tRNA in the P site moves to the E site, and the tRNA in the A site switches to the P site

Front 48

Initiating Translation

Back 48

to translate an mRNA properly, a ribosome must begin at a specific point in the message, translate the mRNA up to the message's termination codon, then stop. the start codon (usually AUG) is found near the 5' end of all mRNAs and it codes for the amino acid methoionine.

Front 49

Ribosome binding site or Shine-Dalgarno Sequence

Back 49

a section of rRNA in a small ribosomal subunit binds to a complementary sequence on the MRNA called the ribosome binding site. Its about 6 nucleotides upstream from the start codon

Front 50

Initiation Factors

Back 50

the interactions between the small subunit, the message, and the tRNA are mediated by proteins called initiation fators.

They help prepare the ribosome for translation including binding the first aminoacyl tRNA o the ribosome.

bacteria= modified form of methinine N-formylmethionin e

Eukaryotes= normal methionine

Front 51

Translation Initiation Process

Back 51

1. The mRNA binds to a small ribsomal subunit

2. The initator aminoacyl tRNA bearing f-met binds to the start condon

3. The large ribosomal subunit binds, completing the complex

Front 52

Elongation: extending the polypeptide

Back 52

When both the P site and A site are occupied by tRNAs the amino acid on the tRnas are in the ribosome's active site. This is where peptide-bond formation - the essence of protein synthesis- occurs.

Front 53

How is protein synthesis catalyzed

Back 53

by ribozymes this supports the RNA-world hypothesis

Front 54

Translocation

Back 54

this occurs when proteins called elongation factors help move the ribosome relative to the mRNA so that translation occurs in the in the 5'--> 3' direction.

It moves the uncharge RNA into the E site; it moves the tRNA containing the growing polypeptide into the P site; and it opens the A site exposed a new mRNA codon. The empty tRNA that finds itself int eh E site is ejected into the cytosol.

Front 55

Terminating Translation

Back 55

There are 3 stop codons: UAA, UAG, UGA

when the translocating ribosome reaches one of the stop codons, a protein called a release factor recognizes the stop codon and fills the A site.

Front 56

Release factors

Back 56

a proton called a release factor recognizes the stop codon and fills the A site. It does not carry an amino acid but fits tightly into the A site because they have the size and shape of a tRNA coming into the ribosome.

the protein's active site catalyzes the hydrolysis of the bond that links the tRNA in the P site to the polypeptide chain.

Front 57

Post-Translation Modification

Back 57

proteins are not fully formed and functional when termination occurs. They fold undergo chemical modification by adding or removing a phosphate group.

Front 58

molecular chaperones

Back 58

proteins that speed up a protein folding. They bind to the ribosome near the tunnel where the growing polypeptide emerges from the ribosome.