the act or process of making a copy

Coping DNA into RNA sequence

site for RNA polymerase binding (signals the beginning of transcription)

located just upstream of the site where transcription of a gene actually begins

the bases are numbered in relation to the transcription start site

the promoter region consists of

-35 sequence   16-18 bp    -10 sequence

mRNA

translation begins near this site for mRNA

(in eukaryotes the ribosome scans the mRNA for start condons)

specifies the first amino acid in a polypeptide sequence

(mRNA)

3-nucleotide sequence within the mRNA that specify particular amino acids.

(the sequence of codons in mRNA determins the sequence of amino acids in a polypeptide)

the nontemplate strand in DNA... it is the back up strand to reference for mutations

it has the same sequence as the mRNA except for lacking U and having T

1. initiation
2. elongation
3. termination

1. the promoter functions as a recognition site for transcription factors
2. the transcription factors enable RNA polymerase to bind to the promoter.
3. following binding, the DNA is denatured into a bubble (in the RNA polymerase) called the open complex.

(synthesis)

RNA polymerase slides along the DNA in an open complex to synthesize RNA

1. 90% of all genes are structural genes that transcribe into mRNA (the final product are polypeptides)
2. other RNA molecules are never translated (the final functional products are RNA molecules that can still confer cellular funcitions)

(messanger)

encodes the sequence of amino acids within a polypeptide,

bacteria encodes for either a single polypeptide or multiple (polycistronic)

eukaryotes encodes for a single polypeptide except for earthworms that are polycistronic

(transfer)

necessary in the translation of mRNA

(ribosomal)

necessary for the translation of mRNA. composed of both rRNA and protein subunits

a noncoding DNA sequence

regulates the expression of a gene

(TATA box)

(Silencers)

(Enhancers)

exert their effect only over a particular gene

More complex

• larger, more complex cells (organelles)
• added cellular complexity, meaning more genes that encode proteins are required
• multicellularity adds another level or regulation (expressing genes at only the right place and time)

Polymerase

transcribes all rRNA genes except 5S rRNA

Transcribes all structural genes

(synthesizes all mRNAs)

Transcribes some snRNA genes

transcribes all tRNA genes

and the 5S rRNA gene

• regulatory elements
• TATA box
• Transcription start site

short DNA sequence that affects the binding of RNA polymerase tho the promoter

they are found between the -50 and -100 region of the promoter

There are two types

1. enhancers
2. silencers

• Cis-acting elements
• trans-acting elements

• regulatory proteins that bind to such DNA sequences

Describe the colinearity of gene expression (transcription)

general idea

the sequence of DNA in the coding strand corresponds to the sequence of nucleotides in mRNA in the mRNA.

The sequence of codons in the mRNA provides the instructions for the sequence of amino acids in the polypeptide

the RNA is cleaved into two parts and exons are connected back together after introns are removed from the mRNA

common in eukaryotes

occasional in bacteria

the attachment of a 7-methylguanosine cap (m^7G) to the 5' end of mRNA, plays a role in...

1. splicing of introns
2. exit of mRNA from nucleus
3. binding of mRNA to ribosome (early stages of translation)
   

occurs in Eukaryotes, as pre-mRNA is being synthesized by RNA pol II

3 step process

the attachment of a string of adenine containing nucleotides to the 3' end of mRNA at a site where the mRNA is cleaved. it is important for RNA stability and translation in eukaryotes

occurs in eukaryots and occasionally in bacteria

a large complex that splices pre-mRNA

it consists of several subunits know as snRNPs (snurps)

snRNPs the subunits of spliceosomes

small nuclear RNA and a set of proteins

1. bind to an intron sequence and precisely recognize the intron-exon boundaries
2. hold the pre-mRNA inthe correct configuration
3. catalye the chemical reactions that remove introns and covalently link exons

pre-mRNA with multiple introns can be splice in different ways (generatin mRNAs with different combinations of exons)

occurs in different cells at different stages of development

two or more polypeptides can be derived from a single gene

sllowing and organism to carry fewer genes in a genome

AUG

methionine

• UAA
• UAG
• UGA

are hydrophobic

(scared of water)

often buried within the interior of a folded protein (to avoid water)

hydrophilic

(like water)

likely to be on the surface of a protein

R groups of amino acids

each amino acid contains its own side chain or R group...each R group has its own particular chemical properties

amino acids are either hydrophilic or hydrophobic

• primary-string of amino acids
• secondary-some degree of folding
• tertiary-not linear (TNF alpha binding receptor-folding)
• quaternary-lots of folding

a compact 3D sturcture

(never in linear form)

these are different shapes of seconday structures

1. alpha helix
2. B sheet

certain amino acids are good candidates for each structure

 these secondary structures are stabalized by the fromation of hydrogen bonds

1. hydrophoic interactions
2. ionic interactions
3. hydrogen bonds
4. Van der Waals interactions

the characteristics of a cell depends on they types of proteins it makes

• cell shape and function
• transport
• movement
• cell signaling
• cell surface recognition
• enzymes

accelerate chemical reactions within a cell

divided into two main categories

• anabolic-synthesize molecules and macromolecules
• catabolic-break down large molecules into small ones (important for generating cellular energy)

exhibits a clover leaf pattern

contains

1. three stem-loop structure
2. a few variable sites
3. an acceptore stem with 3' single strand region

commonly contains modified nucleotides along with the normal A,U,G,C

the enzyme that attaches amino acids to tRNA

there are 20 types (one for each amino acid)

1. amino acid
2. tRNA
3. ATP

1. proteins
2. rRNA

bacterial lacks a nucleaus so both translation and transcription can occure at the same time...as soon as mRNA is long enough a ribosome attaches to its 5' end

termed coupling

• viral infections (stop virus from manufacturing viral proteins)
• starvation (cell conserves resources)