MCAT Biochemistry Chapter 7- RNA and the Genetic Code

Central Dogma

transfer of genetic information

DNA-->RNA-->proteins

Gene

unit of DNA on a chromosome that is encoded with the instructions for a single protein or RNA, and expressed in transcription and translation

Degenerate code

- genetic code

- more than 1 codon can specify a single AA (except Met and Try)

- allows for mutation in DNA that doesn't always result in altered protein structure or fucntion

codon

read in three nucleotide segments to translate into aa

- 64 codons possible (61 codon for 20 aa; 3 codons for termination of translation - UAA, UAG, UGA)

- 5' to 3'

- 1 codon = 1 aa

Anticodon

codon on tRNA, recognized by complementary mRNA

codon of mRNA is recognized by a complementary anticodon on a tRNA

Start codon

AUG (methionine)

Stop codons

UGA, UAA, UAG

mnemonic

UAA = U are annoying

UGA = U go away

UAG = U Are Gone

Wobble position

- third base in the codon is variable (1st and 2nd = same)

-an evolutionary development designed to protect against mutations in the coding region of our DNA

- mutation in wobble position = silent or degenerate = no effect on express of AA or polypeptide sequence

Point mutation

nucleotide changed in a codon = missense or nonsense mutation

- expressed mutations

Silent mutation

no effect on protein synthesis

1 nt change --> same codon

Nonsense mutation (truncation mutation)

produce a premature stop codon

1 nt change --> stop codon

Frameshift mutation

result from nucleotide addition or deletion, and change the reading frame of subsequent codons

- insertion or deletion = shift RF --> changes in aa sequence or premature truncation of protein

- more serious than point mutation

- heavily dependent on where within DNA sequence mutation occured

Missense mutation

produce a codon that codes for a different amino acid

1 nt change --> differ AA --> differ codon

Differences between RNA and DNA

-substitution of a ribose sugar for deoxyribose

-substitution of uracil for thymine

-single-stranded instead of double-stranded

Three types of RNA

mRNA, rRNA, tRNA

mRNA

-messenger RNA

-carries the message from DNA in the nucleus via transcription of the gene; travels into the cytoplasm to be translated

- syn mRNA strand is anitparallel and complementary to DNA template strand

- transcribed from DNA template by RNAP in cycles --> posttranscriptional modifications --> leave nucleus

- euk = monocistronic = each mRNA molecule translate into only one protein product

- prok = polycistronic = thousand of differ proteins made

tRNA

-transfer RNA

-brings in amino acids, recognizes the codon on the mRNA using its anticodon and antiparallel

- converts nucleic acids to aa and peptides

- charged/activated by aa attaching to 3' OH + aminoacyl-tRNA synthase + ATP

- anticodon recognizes and pairs with appreciate codon on mRNA molecule while in the ribosome

- mature tRNA are in cytoplasm

- aa activated by differ aminoacyl-tRNA synthase

- each tRNA has a CCA nuclotide sequence where the aa binds

- aa-tRNA bond will be used to supply the energy needed to create a peptide bond during translation

rRNA

-ribosomal RNA

- ribozymes = made of RNA molecules

-enzymatically active

-synthesized in nucleous

- help catalyze the formation of peptide bonds and splicing introns in nucleus

Monocistronic

each mRNA molecule translates into only one protein product

Polycistronic

starting the process of translation at different locations in the mRNA can result in different proteins

Transcription

the creation of mRNA from a DNA template

we transcribe information, we

use the same language to write it

down

Template strand

-aka antisense strand

-used to synthesize the single strand of mRNA

Promoters

-portion of DNA upstream from a gene

-contains the TATA box, which is the site where RNA polymerase II binds to start transcription

Transcription factors

help the RNA polymerase locate and bind to the promoter region of the DNA, helping to establish where transcription will start

RNAP

travel along template strand in 3' to 5'

transcribed 5' to '

doesn't proofread

RNA polymerase I

located in the nucleolus and synthesizes rRNA

RNA polymerase II

transcription in eukaryotes and binds to TATA box (promoter) (associated w/ TF to help bind to promoter)

located in the nucleus and synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA)

RNA polymerase III

located in the nucleus and synthesizes tRNA and some rRNA

- dont require primer

TATA box

-25 upstream (toward 5' end)

where RNA polymerase II binds

coding strand

the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine

complementary to template strand

hnRNA (like preMrna)

- preprocessed mRNA

Heterogeneous nuclear RNA; the primary transcript made in eukaryotes before splicing.

- primary transcript formed

- mRNA derived from hnRNA via post transcriptional modification

Types of post transcriptional processing (mRNA )

-splicing

-5' cap

-3' poly-a tail

*Note: only occurs with eukaryotic mRNA

Splicing: Introns and Exons

-remove noncoding sequences (introns) and ligate coding sequences (exons) together\

-accomplished by the spliceosome

- introns stay in nucleus; exons exit nuclease as part of the mRNA

- maturation of hnRNA includes splicing of the transcript to remove non coding sequences and ligate coding sequence

- accompanied by spliceosme - small nuclear RNA (snRNA) with proteins - small nuclear ribonuceloproteins (snRNP)

- recognizes both 5' and 3' split sites of the introns

- noncodifn sequenze are excised in form of variant and degraded

Spliceosome

-small nuclear RNA (snRNA) molecules couple with proteins known as small nuclear ribonucleoproteins (snRNPs)

-recognizes both the 5' and 3' splice sites of the introns

-noncoding sequences are excised in the form of a lariat and then degraded

introns evolution

regulation of cellular gene expression levels and in maintaining the size of our genome

- rapid protein evolution

- mutation = won't change the protein sequence because introns are cleaved out of the mNA transcript prior to translation

lariat

non-coding sequences are excised in the form of lasso shaped structure and degraded

5' cap

- 5' end of hnRNA

-7-methylguanylate triphosphate cap (inverted Guanine residue that is methylated on position 7; 2 OH --> 2 CH3)

- added by capping enzyme complex (CEC) coupled with RNAP during the process of transcription when 5' end emerged from RNAP

- recognized by the ribosome as the binding site

- regulation of nuclear export

- protects mRNA from degradation in the cytoplasm

- promote splicing of exon closest to the 5' end of mRNA

3' poly-a tail

- polyadenosyl (poly) tail = composed of adenine bases

- added to the 3' end of the mRNA transcript after splicing

- protects the message against rapid degradation

- also assists with export of the mature mRNA from the nucleus

- untranslated region still exist at 5' and 3' edges bc ribosome initates translation at the start codon and end at stop codon

mature mRNA

- only exon remain

- cap and tail added

- transport to cytoplasm for protein translation

- untranslated regions = still exists 5' to 3' edges bc the ribosome initiates translation at start codon (AUG) and and at stop codon (UAA, UGA, UAG)

Alternative splicing

combing different exons in a modular fashion to acquire different gene products - lead to different encoded proteins

- function in regulation of gene expression + generates protein diversity

-produce multiple variants of proteins encoded by same original gene

nuclear pores (in translation)

transcript mRNA pass through to go to cytoplasm and find a ribosome to begin translation

Translation

-converting mRNA transcript into a functional protein

-requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP

- occurs in cytoplasm

Terminology and 5'-->3'

DNA _RNA _PROTEIN

DNA=replication; new DNA synthesized in 5'--3' direction

-DNA-> RNA=transcription; new RNA synthesized in 5'-->3' direction (template is read 3'-->5')

-RNA-->protein

=translation; mRNA read in 5'-->3' direction

Ribosomen(in translation)

-factories where translation occurs

-composed of proteins and rRNA

-made of large and small subunits

- different in pork than eek (allowing antibiotics to target the ribs of prokaryotes and prevent translation of proteins)

Three binding sites in ribosome

-A site= aminoacyl (lands)

-P site= peptide (builds)

-E site= exit

(APE order)

Initiation in prokaryotes of translation

-occurs when 30S ribosome attaches to the Shine-Dalgarno sequence and scans for a start codon(AUG) to bp with anticodon (UAC) within P site

-lays down N-formlymethionine in the P site of the ribosome

- Large subunit (50S) binds to small subunit assisted by initiation factors

Initiation in eukaryotes of translation

- charged inactive tRNA binds to AUG (met) through bp with its anticodon within P site

-occurs when the 40S ribosome attaches to the 5' cap and scans for a start codon (AUG) to bp with anticodon (UAC) within P site

-lays down methionine in the P site of the ribosome

- Large subunit (60S) binds to small subunit assisted by initiation factors

Elongation in translation

- ribosome moves 5' to 3' discretion along mRNA, synthesizing the protein from N to C terminus adds to the methionine.

-the addition of a new aminoacyl-tRNA into the A site of the ribosome and transfer of the growing polypeptide chain from the tRNA in the P site to the tRNA in the A site

-now inactivated (uncharged) tRNA pauses in the E site before exiting the ribosome

A site in translation

aminoacyl-tRNA binds to w/ GTP + EFs

P site in translation

holds the tRNA that carries the growing polypeptide

peptide bond forms using peptidyltransferase in large subunit

GTP = energy

E site in translation

inactivated tRNA pauses transiently before existing ribosome

translation of ribosome 3 nucleotides alone the mRNA + GTP + EFs

Elongation factors (EF)

assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used

signal sequence

some eukaryotic proteins contain to direct ribosome to move the ER so that protein can be translated directly into the lumen of RER --> Golgi --> vesicle via exocytosis

OR direct proteins to nucleus, lyosomes or CM

Postranslation modifications

-folding by chaperones

-formation of quartenary structure

-cleavage of proteins or signal sequences

-covalent addition of other biomolecules

proper protein

functioning. For example, several

clotting factors, including prothrombin,

require posttranslational carboxylation

of some of their glutamic acid residues

in order to function properly. Vitamin K

is required as a cofactor for these reactions;

thus, vitamin K deficiency may

result in a bleeding disorder.

covalent addition of other biomolecules

Phosphorylation—addition of phosphates by protein kinases to activate or

deactivate proteins

• Carboxylation—addition of carboxylic acid groups, usually to serve as

calcium-binding sites

• Glycosylation—addition of oligosaccharides as proteins pass through the ER

and Golgi apparatus to determine cellular destination

• Prenylation—addition of lipid groups to certain membrane-bound enzymes

Termination

-occurs when the codon in the A site is a stop codon

-release factor places a water molecule on the polypeptide chain and thus releases the protein

- peptidyly transferase and termination factors to hydrolyze complete polypeptide chain from final tRNA

Operon

-a cluster of genes transcribed as a single mRNA

-both inducible and

repressible systems, and offer a

simple on-off switch for gene control in

prokaryotes.

- Jacob- Monod model describes the structure

What do operons contain

-structural genes

-operator site

-promoter site

-regulator gene

Structural gene in lac operon complex

codes for protein of interest

Operator site in lac operon complex

-nontranscribable region of DNA that is capable of binding a repressor protein

-upstream of structural gene

Promoter site in lac operon complex

-further upstream of operator

-similar in function to promoters in eukaryotes

-provides a place for RNA polymerase to bind

Regulator gene in lac operon complex

-furthest upstream

-codes for protein known as the repressor

Inducible system in lac operon complex

- repressor binds blocking RNAP bind to promoter = reduces transcription avidity = negative control

- competitive inhibition = remove repressor by adding more inducers

- example: Lac operon system

-goes by positive control mechanism

-bound by a repressor under normal conditions

-can be turned on by an inducer pulling the repressor from the operator site

Repressible system in Trp operon complex

example: Tryptophan operon

-goes by negative control mechanisms

-transcribed under normal conditions

-can be turned off by a corepressor coupling with the repressor and the binding of this complex to the operator site

operon systems

positive and negative (how do they work?)

negative control = binding of protein to DNA stops transcription

postive control = binding of protein to DNA increases transcription

inducible sytem = normally off but made to turn on on a given signal

repressible sytem = normally on but made to turn off on a given signal

any combination of console and system: lac operon = negative inducible system and tap operon = positive repressible system

Transcription factor

-transcription-activating proteins that search the DNA looking for specific DNA-binding motifs

-have two domains, DNA-binding domain and an activation domain

- produced and translocated back to nucleus = trans regulators bc they travel through the cell to their point of action

DNA-binding domain on transcription factors

binds to specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery

Activation domain on transcription factors

allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in the remodeling of the chromatin structure

amplified - means what in terms of gene control and how does it do it

expression increased in response to hormones, GF, or intracellular conditions

DNA regulatory base sequences

- promoters, eahnccers, response elements = cis regulators bc they are in the same vin city as the gene they control

Enhancer in gene amplification

a collection of several response elements that allow for the control of one gene's expression by multiple signal

gene duplication

duplicated in series on the same chromosome

duplicated in parallel by opening the gene with helices and permitting DNA replication only of that gene

heterochromatin vs. euchromatin in terms of gene expression and structure

HeteroChromatin = Highly Condensed (transcriptionally inactive)

euchromatin = less condensed, transcriptionally active ("truly transcribed")

Histone acetylases

Coactivator acetylate lysine residues found in the amino terminal tail regions of histone proteins

Acetylation (CH3CH) of histone proteins

decreases the positive charge on lysine residues and weakens the interaction of

the histone with DNA, resulting in an open chromatin conformation that allows

for easier access of the transcriptional machinery to the DNA.

acetylation of histones

-occurs on histone proteins

-decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA

-results in open chromatin conformation

- overall increase in gene expression levels in the cell

Histone deacetylases

remove acetyl groups from histones, resulting in closed chromatin conformation and overall decrease in gene expression levels in the cell

DNA methylation

-DNA methylases add methyl groups to cytosine and adenine nucleotides

-linked with silencing of gene expression

During development, methylation plays an important

role in silencing genes that no longer need to be activated. Heterochromatin

regions of the DNA are much more heavily methylated, hindering access of the

transcriptional machinery to the DNA