AP Bio Chapter 17

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gene expression

conversion of the information encoded in a gene first into messenger RNA and then to a protein
includes two stages: transcription and translation

Archibald Garrod

- The first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell.
- said that symptoms of an inherited disease reflect a person's inability to make an enzyme
- example: alkaptonuria

Beadle and Tatum

These people identified mutants that couldn't survive on minimal medium b/c they couldn't synthesize certain essential molecules from minimal ingrediants, showed that each gene encodes a particular substance ("one gene, one enzyme" concept).

one gene-one enzyme hypothesis

The function of a gene is to dictate the production of a specific enzyme

one gene-one polypeptide hypothesis

Many proteins are constructed from two or more different polypeptide chains, and each polypeptied is specified by its own gene

transcription

- synthesis of RNA under the direction of DNA
- DNA provides a template to assemble a sequence of RNA nucleotides

messenger RNA (mRNA)

carries a genetic message from the DNA to the protein-synthesis to the protein-synthesizing machinery of the cell

translation

actual synthesis of a polypeptide, which occurs in the direction of mRNA
- in this stage, the cell must translate the base sequence of an mRNA molecule into the amino acid sequence of a polypeptide

ribosomes

- sites of translation
- complex particles that facilitate the orderly linking of amino acids into polypeptide chains

Why aren't proteins simply translated from DNA

1. It provides protection to the DNA and its genetic material
2. It allows more copies of a protein to made simultaneously, since many RNA transcripts can be made from one gene

Prokaryotes

In a cell lacking a nucleus, mRNA produced by trancription is immediately translated without addition processing

Eukaryotes

The nucleus provides a separate compartment for transcription. The original RNA transcript, called pre-mRNA, is processed before leaving the nucleus

The molecular chain of demand

DNA -> RNA -> protein

Triplet Code

the genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words

template strand

the DNA strand that provides the pattern, or template, for ordering the sequence of nucleotides in an RNA transcript

codons

the mRNA base triplets are called ______, and they are most commonly written in the 5' --> 3' direction

reading frame

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

RNA polymerase

an enzyme that pries the 2 strands of DNA apart and hooks together the RNA nucleotides as they base pair along the DNA template

promoter

a nucleotide sequence on a DNA molecule to which an RNA polymerase molecule binds, which initiates the transcription of a specific gene

terminator

In prokaryotes, a special sequence of nucleotides in DNA that marks the end of transcription

transcription unit

stretch of DNA that is transcribed into an RNA molecule

Three stages of Transcription

iniation, elongation, termination

Role of Promoter during Initiation

- promoter of a gene includes the transcription start point
- serve as binding site for RNA polymerase
- determines which of the two strands of the DNA helix is used as the template

Prokaryotes vs. Eukaryotes

- In prokaryotes the RNA polymerase itself specifically recognizes and binds to the promoter
- In eukaryotes, transcription factors must be used

transcription factors

collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription

TATA Box

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

The interaction between eukaryotic RNA polymerase II and transcription factors

example of the importance of protein-protein interactions that control transcription
- one polymerase attaches to promoter DNA, the strands unwind and enzymes transcribe the template strand

Elongation of the RNA Strand

- As RNA polymerase moves along the DNA, it continues to untwist the double helix , exposing 10 to 20 DNA bases at a time
- rate: 60 nucleotides per second
- congregation of many polymerase molecules simultaneously transcribing a single gene increases amount of mRNA made

Termination of Transcription

- In prokaryotes , a transcribed terminator of RNA sequence causes the polymerase to detatch from the DNA and release the transcript and is available for immediate use as mRNA
- In eukaryotes, polymerase continues to transcribe a sequence on the DNA called polyadenylation signal and 10 -15 nucleotides down, it cuts off
also, transcription is terminated whn the polymerase falls off the DNA

5' Cap

The 5' end of a pre-mRNA molecule modified by the addition of a cap of guanine nucleotide.

poly-A tail

The modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides.

Importance of 5' Cap and poly-A tail

- they facilitate the export of the mature mRNA from the nucleus
- they protect the mRNA from degradation by hydrolytic enzymes
- once mRNA reaches the cytoplasm, both structures help ribosomes attach to the 5' end

RNA splicing

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

introns

a non-coding, intervening sequence within a eukaryotic gene

exons

A coding region of a eukaryotic gene. Exons, which are expressed, are separated from each other by introns.

spliceosomes

A spliceosome is a complex of specialized RNA (snRNPs) and protein subunits that removes introns from a transcribed pre-mRNA (segment. This process is generally referred to as splicing.

ribozymes

An enzymatic RNA molecule that catalyzes reactions during RNA splicing

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

domain

an independently folding part of a protein

translation

the portion of protein synthesis that takes place at ribosomes and that uses the codons in mRNA molecules to specify the sequence of amino acids in polypeptide chains

Transfer RNA (tRNA)

The type of RNA that binds to specific amino acids and transports them to the ribosome during protein synthesis

anticodon

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

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the correct tRNA.

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 (3' end) of a codon

ribosomal RNA

type of RNA that makes up the major part of ribosomes, The most abundant type of RNA, which together with proteins, forms the structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons.

P site (peptidyl-tRNA site)

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

A site (aminoacyl-tRNA site)

One of a ribosome's three binding sites for tRNA during translation. This site in the ribosome holds the tRNA carrying the next amino acid to be added to the polypeptide chain.

E site (exit site)

Discharged tRNAs leave the ribosome at the ____ ______.

Energy in Translation

provided by hydrolysis of GTP

Initiation Stage of Translation

- small ribosomal subunit attaches to a region near the 5' end of the mRNA
- a tRNA (with UAC) carries the methionine amino acid and attaches to mRNA at the start codon AUG
- large ribosomal subunit attaches to the mRNA, forming a complete ribosome with the tRNA at the P site

Elongation of Translation

- begins when the next tRNA (bearing an amino acid) binds to the A site of the ribosome
- the methionine is removed from the first tRNA and attached to the amino acid on the newly arrived tRNA
- first tRNA is released

Termination of Translation

The final stage of protein synthesis, which occurs when a termination (stop) codon is reached, causing the completed polypeptide chain to be released from the ribosome

polyribosomes

Found in eukaryotic and prokaryotic cells, enable a cell to make many copies of a polypeptide very quickly during translation; multiple ribosomes attached to an MRNA strand

Protein Folding and Post-Translational Modifications

- may be chemically modified by the attachment of sugars, lipids, phosphate groups
- enzymes can remove some amino acids
- some polypeptide chains can be cut or synthesized

Two Populations of Ribosomes

- free
- bound
- ribosomes themselves are identical

Free ribosomes

suspended in cytosol which will function in cytosol

Bounded Ribosomes

attached outside ER and nuclear envelope
- make proteins of the endomembrane system (the nuclear envelope, ER, Golgi Apparatus, Lysosomes, Vacuoles, Plasma Membranes)

Signal Peptide

A stretch of amino acids on a polypeptide that targets the protein to a specific destination in a eukaryotic cell.

Signal-Recognition Particle

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

Ability of RNA to perform different functions

- RNA can hydrogen-bond to other nuclei acid molecules (DNA or RNA)
- it can assume a specific 3-D shape by forming hydrogen bonds between bases in different parts of its chain
- can act as a catalyst

same gene; diffuses

One major difference is that prokaryotes can transcribe and translate the _______ ____-simultaneously. The new protein quickly ________ to its operating site.

mutation

changes in the genetic material of a cell (or virus).

point mutation

A chemical change in just one base pair of a gene

base- pair substition

A point mutation that results in the replacement of a pair of complementary nucleotides with another nucleotide pair

silent mutations

altered nucleotides still code for the same amino acids because of redundancy in the genetic code.

missese mutation

those that still code for an amino acid but a different one

nonsense mutations

change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

insertions; deletions

_________ and ________ are additions or losses of nucleotide pairs in a gene

frameshift mutations

Unless insertions or deletions mutations occur in multiples of three, they cause a _______ ________.

spontaneous mutations

Mutations can occur in a number of ways. Errors can occur during DNA replication, DNA repair, or DNA recombination. These can lead to base-pair substitutions, insertions, or deletions, as well as mutations affecting longer stretches of DNA. These are called ______ __________.

Mutagens

chemical or physical agents that interact with DNA to cause mutations

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