Bio 106: Transcription & Translocation

chromosome

structure that consists of DNA and associated proteins, carries part (eukaryotes) or all (bacteria) of a cell's genetic info for making new organism

DNA in eukaryotic cell __ is organized as one or more chromosomes that differ in length and shape

nucleus (humans have 22 pairs of autosomes, 1 pair of sex chromosomes)

gene

A segment of DNA on a chromosome that codes for a specific trait; encodes a protein (functional production)

transcription and translocation

expression of info in a gene occurs in these 2 stages

Central Dogma of Molecular Biology (Watson and Crick)

DNA contains original codes for making proteins that living things need; DNA --(transcription)--> RNA --(translation)--> protein

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome; ribosome then reads its coding sequences and puts the appropriate amino acids together

transcription

process of converting a nucleotide sequence of a gene (genetic info in DNA) into a complementary strand of RNA; produces an RNA copy (TRANSCRIPT!) of a gene

complementary strand of RNA in transcription is made by

RNA polymerase: messenger RNA (mRNA), a single stranded RNA (ssRNA) molecule

RNA polymerase vs DNA polymerase

RNA polymerase uses DNA as a template to make RNA; DNA polymerases uses DNA as a template to make DNA

both are DNA-dependent

RNA contains __ in place of thymine

uracil (A-U and G-C base pairings between DNA and RNA)

RNA uses __ in place of deoxyribose nucelotides

ribose nucleotides

oxygen (hydroxyll group) in RNA explains why

RNA lasts very SHORT time, is catalytic, but UNSTABLE in comparison to DNA that is missing oxygen and lasts very long time

3 stages of transcription

initiation, elongation, termination

initiation (transcription)

recognition step; RNA polymerase and regulatory proteins bind to promoter (most time-consuming, complicated step in transcription)

elongation (transcription)

RNA polymerase synthesizes RNA, linking nucleotides together (5' to 3')

termination (transcription)

termination sequence causes polymerase and RNA transcript to dissociate from DNA

role of promoter in transcribing a gene into RNA

signaling the beginning of transcription; sequence of DNA where polymerase binds

role of regulatory sequence in transcribing a gene into RNA

site for binding of regulatory proteins; influences the rate of transcription -- determines what and when genes are expressed

transcribed region

contains the information that specifies an amino acid sequence for mRNA

terminator region on DNA

signals the end of transcription

transcription initiation factors

specialized proteins that assist in formation of pre-intiation complex; RNA polymerase requires these factors to LOCATE and BIND TO promoter regions of genes (different factors dependent on gene type)

enhancer in DNA

Regions of DNA where factors that regulate transcription can also bind

activator and mediator proteins

link bridge between enhancer and transcription factors

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

sigma factors

proteins in prokaryotic (BACTERIA) cells that bind to RNA polymerase and direct it to specific classes of promoters; assists RNA pol. to find and bind promoter

polymerase holoenzyme

polymerase with other factors bound

in DNA replication, helicase is needed to unzip DNA; in RNA replication during initiation step, __ acts as its own helicase (doesn't matter if DNA closes back up)

RNA polymerase

during elongation, copy of RNA is made from __ strand

template (antisense)

RNA synthesis occurs in __ direction

5' to 3'

RNA sequence made during elongation is equivalent to __ (or coding strand)

non-template (sense)

__ strand of DNA can be used as template in elongation

either

termination stage of transcription =

not well understood; different for different systems; often involves looping that prevents DNA polymerase from getting through

one gene can be transcribed by

multiple RNA polymerases all at once

RNA transcription occurs in nucleus (in eukaryotes) but info is converted into protein in __

cytoplasm

post-transcriptional modifications in eukaryotes

changes in RNA before leaving the nucleus in eukaryotes

pre mRNA consists of

introns and extrons

introns

nucleotide sequences that are removed from a new RNA; snipped OUT

Extrons

Sequences of RNA that are translated into proteins; stay IN the RNA

mature mRNA contains only

exons

alternative splicing

allows a single gene to encode multiple proteins; can piece together different exons that result in different proteins being made; allows cells to increase coding capacity without increasing amount of DNA (viruses do this best!)

mRNA 5' caps play a role in

RNA stability, nuclear export, translation; cap = 5' carbon on guanine

Poly(A) tails

added after transcription

- enhance mRNA stability, nuclear export, translation efficiency

- play a role in transporting the mature mRNA from the nucleus to the cytoplasm

similar to caps

sequence that tells enzymes to cleave

translation

information carried by mRNA is decoded into linear sequence of amino acids, resulting in polypeptie (protein) chain that folds into protein

protein translation occurs on

ribosomes

Central Dogma (flow of genetic information)

DNA -> RNA -> Protein

4 basic units in DNA/RNA (adenine, cytosine, guanine, thymine/uracil) are converted into __ basic units (amino acids) found in proteins

20

features of genetic code

64 different 3 nucleotide "codons"; nonoverlapping; 3 different "reading frames" on each strand; 6 possible reading frames; redundancy of genetic code; only 20 amino acids to be encoded by 64 possible codons in the triplet code; most amino acids specified by two or more codons; synonymous codons specify same amino acid

linear order of codons in mRNA determines

linear order of amino acids in a polypeptide chain

codon

sequence of THREE mRNA nucleotides that codes (specifies) for a specific amino acid; reading in 3 basic chunks creates reading frames

length of a codon is 3 because

length needed to give at least 20 unique codons (corresponding to 20 unique proteins)

which codon specifies for methionine (met)?

AUG

starting codon

AUG (methionine)

some amino acids can be coded by

more than 1 codon (most have 2-3 variations)

mRNA is read from

5' to 3' by ribosome

stop codons (no amino acid specified to them)

UAA, UAG, UGA

not typical for a protein/ribosome to start reading at exact start of a sequence because

this can cut the sequence short

to determine which strand in double helix DNA is the template for mRNA

look for AUG start codon

Mis-sense substitution mutation

amino acids have been changed

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created

nonsense mutation (truncation)

insertion of stop codons "knock out" a gene to stop proteins from being made --> results in protein being too short

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide --> can result in protein being too short/long

translation machinery consists of

mRNA (messanger RNA)

ribosomes, which link amino acids into polypeptide chains

- each ribosome consists of 2 subunits - 1 large and 1 small

- both subunits contain rRNA (ribosomal RNA) and proteins

ribosome structure (general structure same for prokaryotic and eukaryotic ribosomes)

large subunit,small subunit

translation involves 3 types of RNA

messenger RNA, ribosomal RNA, transfer RNA

transfer RNA

type of RNA molecule that delivers amino acids to ribsomes; has an ANTICODON that is complementary to an mRNA codon

tRNA structure

anticodon at one end; codon-anticodon connection is complementary and antiparallel

amino acid attachment site at other end

3 stages of translation

initiation, elongation, termination

initiation (translation)

1- initiation complex is formed when small ribosomal subunit binds to mRNA

2- anticodon of intiator tRNA base-pairs with the start codon (AUG / Met) of mRNA

3- large ribosomal subunit joins small ribosomal subunit

intitation complex (small + large ribosomal subunit) consists of

3 sites: E,P,A

elongation (translation)

ribsome assembles polypeptide chain as it moves along mRNA; initator tRNA carries methionine (first amino acid in chain) into P site

(lagre subunit) ribosome joins each amino acid to polypeptide chain with a peptide bond

order of tRNA movement during elongation (translation)

A site --> P site --> E site ("ejector site")

termination (translation)

when ribosome encounters a stop codon, polypeptide synthesis ends

- release factors bind to ribsome

- enzymes detach the mRNA and polypeptide chain from ribosome

stop codons cause everything to fall apart (still sequence that won't be translated)