BIOL 1115: CHAPTER 17

List at least three types of proteins that we have talked about so far in this course and their functions?

1. fibrous: providing external protection, support, shape, and form

2. globular: act as: Enzymes, by catalyzing organic reactions taking place in the organism in mild conditions and with a great specificity

3. membrane: ferrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating chemical signals into intracellular action, and sometimes anchoring the cell in a particular location

What correctly indicates the complementary base pairing of adenine in DNA and RNA?

Adenine and thymine in DNA and with uracil in RNA

The information carried by a DNA molecules is in:

The order of bases in the molecule

What is RNA polymerases?

Synthesizes an mRNA version of the instructions stored in DNA

What is a template strand?

The strand of DNA that is used to make the copy of mRNA in transcription.

What is non-template, or coding strand?

the DNA strand that is not read by the enzyme

Briefly describe transcription

As a region of DNA unwinds, one strand is used as a template for the RNA transcript to be made

What are nucleoside triphosphates (NTPs) used for?

They are used to produce an RNA transcript that is complementary to the template strand

Which four NTPs are used for RNA synthesis?

ATP, GTP, CTP, UTP

Which way does the new strand grows?

5'-3'

In which direction is the DNA template strand read?

3'-5'

What are the three steps to transcription?

1. Initiation

2. Elongation

3. Termination

What is initiation?

RNA polymerase and associated proteins binds to the DNA duplex at promoter sequences

What does the promoter sequences contain?

Sequences that indicate where a gene starts and which DNA strand is the template strand

Where are promoter sequences located?

Upstream of the transcription start site

Steps of Termination

1. Transcription ends with termination

2. RNA polymerase transcribes a transcription

3. termination signal- In prokaryotes, this codes for RNA that forms a hairpin structure

4. causes the RNA polymerase to separate from the RNA transcript

5. in eukaryotes a poly(A) signal is transcribed rather than a hairpin, and the RNA downstream is cut

True or false: RNA nucleotides are always added to the 3'end of a growing RNA polynucleotide

True

What is primary transcript and what does it contain?

The RNA transcript that comes off the template DNA strand and contains the information of the gene that was transcribed

What is mRNA?

the RNA molecule hat combines with the ribosome to direct protein synthesis

what is the primary transcript in prokaryotes?

mRNA

where does RNA processing occur in both prokaryotes and eukaryotes?

it occurs in the cytoplasm and there is no nuclear envelope to spatially separate transcription from translation

what is there in eukaryotes between transcription and translation (the nuclear membrane)?

a barrier

What is RNA processing?

The primary transcript undergoes a complex process of chemmical modifications

What are the three types of chemical modification that occur before the mRNA is translated by the ribosome?

1. RNA splicing

2. Addition of a 5' cap

3. Polyadenylation

What is RNA splicing process?

the modification of the primary transcript by the excision of certain sequences known as introns leaving intact the exons

what percentage of human genes contain at least one intron?

90%

what does splicing allow?

different mRNAs and proteins to be produced from a single gene

what is alternative RNA splicing?

one primary transcript can code for multiple proteins; which protein is formed depends on how the transcript is spliced

primary RNA transcripts are also processed by the addition of what?

A 5' cap: a modified guanine nucleotide that enables ribosomes to bind and protects from degradation 3' poly(A) tail: 100-250 adenine nucleotides; is needed for translation and protects from degradation

what needs to happen for the product of a mature mRNA to form?

splicing and addition of the cap and tail

what do mature mRNAs contain at both ends?

untranslated regions (UTRs)

during transcription, one of the two DNA strands called the template strand provides what?

a template for ordering the sequence of nucleotides in an RNA transcript

how are the mRNA base triplets, called codons, read during translation?

read in the 5' to 3' direction

what does each codon do?

it specifies which of the amino acid to be place at the corresponding position along a polypeptide

Which amino acid does the codon AAC code for?

Asparagine Asn

Where do transcription and and translation occur in the prokaryotes?

in the cytoplasm

Where do transcription and translation occur in eukaryotic cells?

1. Transcription occurs in the nucleus

2. Translation occurs in the cytoplasm

why is the sequence of bases in an mRNA decoded in translation?

to synthesize the amino acids sequence in a protein

what do ribosomes do?

catalyze translation of the mRNA sequence into protein

where do polyribosomes form?

where multiple ribosomes are attached to a single mRNA at a single time

what is produced from one mRNA?

many copies of a protein

what do tRNAs do?

they bind to amino acids and then transfer them to the growing polypeptide

what do ribosomes do in bacteria?

they often begin translating an mRNA before transcription is complete

what happens to transcription and translation in eukaryotes?

they are separated

1. mRNAs are synthesized and processed in the nucleus

2. Mature mRNAs are transported to the cytoplasm for translation by ribosomes

tRNA structure

relatively short: 75-85 nucleotides long.- flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf

why do tRNAs twist and fold into a three-dimensional molecule

because of hydrogen bonds

what shape is tRNA?

roughly L-shaped

what is the binding site for amino acids?

A CCA sequence at the 3' end

what is an aminoacyl tRNA?

a tRNA linked to its amino acid

what forms the anticodon?

the loop at the opposite end- has a sequence of three nucleotides- Can base-pair with the mRNA codon

what do enzymes called aminoacyl-tRNA synthetases do?

it "charges" the tRNA by catalyzing the addition of amino acids to tRNAs

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

An intron is _____

RNA that is removed during the processing of an RNA molecule and remains inside the nucleus

characteristics of each of the 20 amino acids

1. there is a different aminoacyl tRNA synthetase

2. there are one or more tRNAs

how many different codons are there?

61 different codons

how many tRNAs are there in most cells?

40

who proposed the wobble hypothesis?

Crick

What is the wobble hypothesis?

the anticodon of tRNA can still bind successfully to a codon in mRNA whose third position requires a nonstandard base pairing

relationship between a tRNA and a type of codon

one tRNA is able to base-pair with more than one type of codon

How is it possible that an mRNA could have the correct sequence yet still not be translated appropriatly?

The 5' cap was not added and the polyA tail was not formed

what can ribosomes be separated into?

the small subunit and the large subunit

where do the tRNAs fit in the ribosome?

the A site, the P site and the E site

what does the A site do?

It is the acceptor site

what does the P site do?

it is the peptidyl site where a peptide bond forms

What does the E side do?

it is where tRNAs without amino acids exit the ribosome

what does the ribosome do?

it's a molecular machine that synthesizes proteins in a three-step sequence

the three-step sequence that synthesizes proteins

1. An aminoacyl tRNA carrying the correct anticodon for the mRNA codon enters the A site

2. A peptide bond forms between the amino acid on the A-site tRNA and the polypeptide on the P-site tRNA

3. The ribosome moves down the mRNA by on codon and all three tRNAs move down one position

- the tRNA in the E site exits

- the A site is available for another tRNA to bind

what happens to the protein each time there is a repeat of the three-step sequence that synthesizes proteins?

the protein grows by one amino acid

what is always added to the carboxyl end (C-terminus) of the polypeptide?

amino acids

where does the initiation phase of translation begin?

near the AUG start codon

what happens at the ribosome binding site?

the small ribosomal subunit binds to the mRNA

where is the ribosome binding site located with respect to the start codon?

it's about 6 bases upstream from the start codon

what is the initiation process mediated by?

intitiation factors

what is the initiator tRNA?

the first tRNA- it carries a modified methionine

three-step process of translation initiation in bacteria

1. the mRNA binds to a small ribosomal subunit

2. The initiator tRNA bearing f-Met binds to the start codon

3. The large ribosomal subunit binds so that the initiator tRNA is in the P site

what happens at the start of elongation?

- The initiator tRNA is in the P site

- The E and A sites are empty

- an aminoacyl tRNA binds to the codon in the A site

what forms a peptide bond?

the amino acid on the P-site tRNA connecting to the amino acid on the A-site tRNA

when does translocation occur?

when the ribosome slides one codon toward the 3' end of the mRNA

what do elongation factors do?

they help move the ribosome

what are three things that translocation accomplishes?

1. the uncharged tRNA from the P site moves into the E site and is ejected form the ribosome

2. The tRNA attached to the growing protein moves into the P site

3. Opens the A site to expose a new codon, which is available to accept a new aminoacyl tRNA

When does termination occur?

when the A site encounters a stop codon

characteristics of a proton called a release factor that enters the A site

- resembles tRNAs in size and shape

- But does not carry an amino acid

- Hydrolyzes the bond linking the P-site tRNA to the polypeptide chain

what separates from the mRNA?

the newly snthesized polypeptide, tRNAs, and ribosomal subunits

What is post-translational modification?

an extensive series of processing steps that most proteins go through before they are completely functional

what determines a protein's shape and function?

folding

what do molecular chaperones do?

they speed protein folding