MCAT kaplan biochemistry Ch 7

missense mutation

(Point mutation) a mutation where one amino acid substitutes for another

The first base transcripbed from DNA to RNA is defined as the ______ base of that gene region left? right?

+1 -bases to the left of this start point (upstream or toward the 5' end) are given in negative numbers: -1, -2, -3, ... -bases to the right of this start point (downstream or toward 3' end) are given in positive numbers: +2, +3, +4 ... -no nucleotide is numbered 0

response elements

- sequences of DNA that binds only to specific transcription factors

Inducible systems

- the repressor is bound tightly to the operator system and thereby acts as a roadblock -RNA polymerase is unable ti get from the promotor to the structural gene bc repressor is in the way -inducer must bind to the repressor protein so that the RNA polymerase can move down the gene - normally "off" but can be turned "on" w signal

Promotor site

provides a place for RNA polymerase to bind (similar to pro motors in eukaryotes) -upstream from operator site

As the concentration of inducers increases, it will

pull more copies of the repressor off of the region, freeing up those genes for transcription

snRNP/snRNA complex

recognizes both the 5' and 3' splice sites of the introns -the introns are excised int he form of a lariat (lasso-shaped structure) and then degraded

Splicing

removal of noncoding sequences (introns) and keep coding sequences (Exons) -accomplished by splicesome -

wobble position

-3rd position of the codon -two bases are usually the same - the third base in the codon is usually variable -an evolutionary development -used to protect against mutations in the coding regions of DNA -mutations in this position tend to be *silent or degenerate* - there is no effect on the expression of the amino acid and therefore no adverse effects on the polypeptide sequence

repressible system

-allow constant production of a protein product. -the repressor made by the regulator gene is inactive until it binds to a corepressor. -tend to serve as negative feedback -often final product can serve as a corepressor. -as product levels increase, it can bind the repressor and the complex will attach to the operator region to prevent further transcription of the same gene. ex: trp operon normally "on" but can be turned "off" by signal

Activation of Amino Acid for Protein Synthesis

-each type of amino acid is activated by different aminoacyl-tRNA synthetase that requires 2 high-energy bonds from ATP -attachment of amino acid is an energy rich bond -this high energy bond Will be used to supply the energy needed to create a peptide bond during translation

Ribozymes

-enzymes made of RNA molecules instead of peptides -catalyze the formation of peptide bonds and is imp in splicing out its own introns within the nucleus

Trp operon

-negative repressible system -when tryptophan is high in the local enviroment, it acts as the corepressor -binding of the repressor with tryptophan will cause the repressor to bind to the operator site -they cell will stop making its own tryptophan -will stop wasting energy making their own tryptophan because it is easily available in the enviroment

posttranlational processing

-proper folding -cleavage events possible events: -phosphorylation -carboxylation -glycosylation -prenylation

Jacob-Monod Model

-used to describe the structure and function of operons -operons contain structural genes, an operator site, a promoter site, and a regulator gene

elongation (translation)

A three step sycle that is repeated for each amino acid added tp the protein after the initiator methionine A, P, E

Two types of operons

1. *Inducible* - operon is turned ON by substrate: 2. *Repressible* - genes in a series are turned OFF by the product synthesized

3 steps of translation

1. Initiation 2. Elongation 3. Termination specialized factors (IF, EF, and RF) as well as GTP is required for each step

Eukaryotic ribosomes contain 4 strands of rRNA designated the :

28S, 18S, 5.8S, and the 5S rRNAs S values indicates the size of the strand

RNA polymerase I transcribes the

28S, 18S, and 5.8S rRNAs as a single unit within the nucleolus -results in a 45S ribosomal precursor RNA -this 45S pre-rRNA is processed to become —— the 18S rRNA of the 40S (small) ribsosomal unit , ——-and the 28S and 5.8S rRNAs of the 60S (large) subunit

RNA polymerase travels along the template strand in the ___ to ___ direction which allows for construction of mRNA in the ___ to ___ direction

3' to 5' 5' to 3'

Messenger RNA is synthesized in the__ to ___ direction

5' To 3'

In eukaryotes, the small ribosomal subunit binds to the ??

5' cap structure

The ribosome translates the mRNA in the __ to ___ direction. It synthesizes the protein from the ____ terminus to the _____ terminus

5' to 3' amino (N-terminus) to the carboxy (C-terminus)

All codons are written in the ___ to ___ direction and the code is ______

5' to 3' unambiguius : each codon is specific for one and only one amino acid BUT most amino acids are represented by multiple codons

RNA polymerase III transcribes their __S rRNA

5S rRNA outside of the nucleolus -this is found in the 60S (large) subunit of the ribosome

Prokaryotic ribosomes

70S (30S and 50S subunits)

Gene

A unit of DNA that encodes a specific protein or RNA molecule , and through transcription and translation , that gene can be expressed

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex. -named for its high concentration of thymine and adenine bases

nonsense mutation

A mutation where the codon now encodes for a premature stop codon. (also known as truncation mutation)

Transcription results in

A single strand of mRNA synthesized from one of the 2 nucleotide strands of DNA called the template strand

3 binding sites in ribosome for tRNA

A site (aminoacyl) P site (peptidyl) E site (exit)

Start codon

AUG (methionine)

aminoacyl-tRNA synthetase

An enzyme that joins each amino acid to the appropriate tRNA. -transfers the activated amino acid to the 3' end of the correct tRNA -each tRNA has a CCA nucleotide sequence where the amino acid binds

Where does the TATA box usually lie?

Around -25

3' poly-A tail

At 3' end of mRNA transcript - polyadenosyl (poly A) tail is added -composed of adenine bases functions: -protects mRNA against rapid degregation -assists exportation of mRNA from nucleus

5' cap

At 5' end of the hnRNA molecule -7-methylguanylate triphosphate cap is added -added during process of transcription Functions: -recognized by the ribosome as a binding site - protects mRNA from degregation in cytoplasm

In prokaryotes, the ribosome starts translation when?

Before the mRNA is even complete -both transcription and translation occur in cytoplasm

Messenger RNA (mRNA)

Carries information specifying amino acid sequences of proteins from DNA to ribosomes -transcribed from the template DNA strands by RNA polymerase enzymes in the nucleus of cell -may undergo a host of posttranscriptional modifications prior to release

tRNA molecule is said to be _____ when an amino acid connects to it

Charged or activated

Structural gene

Codes for the protein of interest

Ribosome

Composed of proteins and rRNA -has large and small subunit (these only bind together during translation) -

Splicesome

Contains small nuclear RNA (snRNA) molecules coupled with proteins known as small nuclear ribonucleoproteins (snRNPs) - this snRNP/snRNA complex recognizes both the 5' and 3' splice sites of the introns

RNA is synthesized by a

DNA-dependent RNA polymerase

Synthesis of secretory, membrane, and lysosomal proteins

During translation, signal sequences designate protein for certain area

How does the peptide bond form in translation?

Forms as polypeptide is passed from the tRNA in the P site to the tRNA in the A site -requires peptidyl transferase (enzyme that is part of the large subunit) -GTP is used for energy during the formation of this bond

During initiation of transcription, several enzymes including _____ and ____ are involved in unwinding the double-stranded DNA and preventing formation of the supercoils

Helicase and topoisomerase

What do transcription factors do?

Help the RNA polymerase locate and bind to this promotor region of the DNA (TATA box) , helping to establish where transcription will start -does not require a primer to start generating a transcript

A site

Holds the incoming aminoacyl-tRNA complex

mRNA is the only type of RNA that carries DNA's protein building instructions, to do so, it is read

In 3 nucleotide segments called codons

mRNA is ______ in eukaryotes

Monocistronic : each mRNA molecule translates only one protein product -always in eukaryotes and in some prokaryotes

Operator site

Nontranscribable region of DNA capable of binding a repressor protein (upstream of structural gene)

coding strand (sense strand)

Not used during transcription because it is also complimentary to the template strand, making it exactly the same as the mRNA strand -except all the T has been replaced with U

Ribosomal RNA (rRNA)

Synthesized in the nucleolus -functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm -many function as ribozymes -helps catalyze the formation of peptide bonds and is imp in splicing out its own introns within the nucleus

mRNA may be _____ in prokaryotes

Polycistronic : starting process of translation act diff locations in the mRNA can result in diff proteins

heterogenous nuclear RNA (hnRNA)

Preprocessed mRNA -converted to mRNA by posttranscriptional modifications -which are : adding a poly-A tail and 5' cap and splicing out introns

RNA polymerase locates genes by searching for specialized DNA regions known as

Promotor regions

Chaperones

Proteins that assist in protein folding during posttranslational processing

In eukaryotes, ____ is the main player in transcribing mRNA and its Binding site in the promotor region is known as the _______

RNA Polymerase II TATA Box

Three types of RNA polymerases and thier function

RNA polymerase I: located in nucleolus, synthesized rRNA RNA Polymerase II: located in nucleus, synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA) RNA polymerase III: located in nucleus, synthesizes mRNA, tRNA, and some rRNA

Transfer RNA (tRNA)

Responsible for converting the Language of nucleic acids to the language of amino acids and peptides -each one contains a folded strand of RNA that includes a 3 nucleotide anticodon

In prokaryotes, the small ribosomal subunit binds to the ??

Shine-Dalgarno sequence in the 5' untranslated region of the mRNA

Cleavage events in posttranslational processing

Single sequences must be cleaved if the protein Is to enter the organeelle and accomplish its function another ex is insulin: must be cleaved from a larger, inactive peptide to achieve its active form

initiator tRNA

Special tRNA that initiates the translation of an mRNA in a ribosome -binds to AUG start codon -It always carries the amino acid methionine. -initiates binding of large subunit to small subunit

Poly-A tail and time bond analogy

The longer the polyA tail, the more time the mRNA will be able to survive before being digested in the cytoplasm

gene amplification

The selective synthesis of DNA, which results in multiple copies of a single gene, thereby enhancing expression. eukaroytes form of operons

What occurs during elongation stage of translation if the protein being made contains a signal sequence?

This designates a particular destination for the protein -ex: hormones and digestive enzymes occur: -signal sequence directs the ribosome to move to the Endoplasmic reticulum (ER) so that the protein can be translated directly into the lumen of the rough ER -from there the protein can be sent to the Golgi apparatus and be secreted from a vesicle via exocytosis other signal sequences can direct proteins to the nucleus, lysosomes, or cell membrane

Stop codons

UAA, UAG, UGA Mneumonic: UAA: U Are Annoying UGA: U Go Away UAG: U Are Gone

termination of translation

When anyof the 3 stop codons move into the A site, a protein called Release factor (RF) binds to the termination codon -this cause a water molecule to be added to the polypeptide chain -this allows the peptidyl transferase and transcription factors to hydrolyze the completed polypeptide chain from the final tRNA -peptide chain is released from the P site and the 2 ribosomal subunits dissociate

frameshift mutation

When some number of nucleotides are added to or deleted from the mRNA sequence -usually results in changes in amino acid sequence of premature truncation of the protein

E site

Where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome -as tRNA enters the E site, it quickly unbind from the mRNA and is ready to be recharged once it exits ribosome

Operon

a cluster of genes transcribed as a single mRNA -uses a single promoter -occurs in prokaroytes -ex: E coli

Corepressor

a small molecule that cooperates with a repressor protein to switch an operon off

Carboxylation

addition of carboxylic acid groups, usually to serve as calcium-binding sites

Prenylation

addition of lipid groups to certain membrane-bound enzymes

Glycosylation

addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination

elongation factors (EF)

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

initiation factors (IF)

bind to small subunit of the ribosome and aid in binding the small subunit of the ribosome to the mRNA -also aids in binding the large subunit to the small subunit

DNA binding domain

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

Regulator gene

codes for repressor protein -upstream from promotor site

Translation occurs in the _____.

cytoplasm

The genetic code is

degenerate: More than one codon Can specify a single amino acid

Unlike DNA polymerase, RNA polymerase

does not require a primer does not proofread its work

Point mutation

gene mutation in which a single base pair in DNA has been changed silent and expressed

Anticodon

group of three bases on a tRNA molecule that are complementary (and antiparallel) to an mRNA codon

P site

holds the tRNA carrying the growing polypeptide chain -where 1st amino acid (methionine) binds -peptide bond is formed

The lac operon

is assisted by binding of the Catabolite activator protein (CAP) -CAP is a transcriptional activator used in E Coli when glucose levels are low to signal alternative carbon sources should be used -falling glucose levels cause an increase in the signaling molecule cyclic AMP (cAMP) which binds to CAP. -this induces a confirmational change in CAP allows it to bind the promoter region of the operon -this further increases transcription of the lactase gene -this is example of positive control mechanims

example of inducible system

lac operon which contains the gene lactase -bacteria can digest lactose but it is more energically expensive tha digesting glucose -bacteria only want to use this option if lactose is high and glucose is low -lac operon is induced by presence of lactose

2 types of expressed point mutations

missense nonsense

posttranscriptional processing

modifications of pre-mRNA that make it into mature mRNA, - 5' cap - 3' poly A tail - intron/exon splicing

mRNA exits the nucleus through

nuclear pores -goes to cytoplasm to find a ribosome to begin translation

Phosphorylation

the addition of a phosphate group (PO4 2-) by protein kinases to activate or deactivate proteins most commonly seen in: serine, tyrosine, and threonine

Positive control

the binding of a protein to DNA increases transcription

Negative control

the binding of a protein to DNA stops transcription of a gene

template strand

the strand of DNA that specifies the complementary mRNA molecule also called antisense strand

Transcription factors

transcription-activating proteins that search the DNA looking for specific DNA-binding motifs -in eukaryotes -tend to have 2 domains: DNA-binding domain and activation domain