Lecture 6 Flashcards by John Villaluz

pointed out the connection between gees and enzymes

Archibald Garrod

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a human disease in which urine turns black upon exposure to air

alkaptonuria

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studied alkaptonuria

Archibald Garrod

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is alkaptanoria genetically contorolled?

yes

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what is non functional in the pathway in Alkaptonuria

HA oxidase ( this causes the accumulation of HA (alcapton) and leading to genetic block

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what is not functional in the Phenylketonuria (PKU)

phenylalanine hydroxylase

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in Phenylketonuria, Phenylalanine is converted into _______ which inhibits the production of ______ since phenylpyruvic acid inhibits the function of Trp hydroxylase

phenylpyruvic acid - serotonin

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In albinism, the enzyme that is non-functional is

tyrosinase

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what does one-gene one enzyme hypothesis state?

a gene is responsible for an enzyme
an enzyme catalyzes a step in a metabolic reaction (if you have a mutant gene, therefore you will have a nonfunctional enzyme thus causing a genetic block in the metabolic pathway)

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what does one-gene one protein state?

-Protein are gene products
-not all proteins are enzymes (enzymes only make a subset of proteins)
eg. keratin - structural protein of the hair
insulin - protein hormone

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what does gene one polypetide state?

each polypeptide chain in a functional protein is encoded by a gene

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polypeptides in hemoglobin

2 alpha and 2 beta chains

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antibody of hemoglobin (how many heave chain and light chain)

2 heavy chain and 2 light chain

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is replication a pre-requisite in gene expression

no (you have a separate pathway for it)

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Contains information for making 1 RNA and most cases, 1 polypeptide

Gene

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a DNA sequence to which transcription enzymes binds

promoter

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the transcription enzyme

RNA polymerase

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T OR F: conserved sequences - the sequence in different species is the same or conserved

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Two bacterial sequences in the promoter

10 seq. TATAAT (pribnow box)
35 seq. TTGACA

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upstream of the initation site means

bases prior to the initiation site

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succeeding bases following the initiation site

(+) downstream

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elements that are bound by the sigma factor and RNA polymerase to start transcription

-35 element TTGACA
-10 TATAAT or Pribnow box

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direction of transcription

5 prime to 3 prime

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In the Initiation, If template strand (anticoding) is in 3’-5’ direction, the synthesize will be at__________

antiparallel, 5’-3’

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In the transcription, the RNA polymerase will use the template _______ which complements the coding strand

Anti-coding strand

the RNA polymerase at the promote site together with the sigma factor, they will bind the promoter site and start the complementation of the DNA with RNA bases starting at the +1 site

key enzyme in elongation

RNA polymerase

process where it will complement the DNA template strand in the 5' to 3' direction with respect to the elongating DNA

Elongation

during this process, the RNA polymerase will reach the terminator site

Termination

the Rho Factor aid in the termination of transcription

Rho dependent

some bacteria do not require the rho factor in the termination of transcrition

Rho independent termination

In transcription what will be produced is the exact copy of the coding strand but only in

RNA Form

In order to produce a copy of the coding strand of the DNA, the anticoding strand will be complemented to produce the mRNA which is the exact copy of the coding strand except instead of thymine, you have URACIL

MAIN TAKEAWAY IN TRANSCRIPTION

carries the message

mRNA

triplet of bases

codon

brings amino acids to the site of synthesis

transfer RNA

the amino acids is attached in the __ of the tRNA

3 prime end (at the top)

the tRNA has three arms, one important arm is called the __________

anticodon arm

type of RNA which is a major component of the ribosomes

Ribosomal RNA (rRNA)

In sverdberg value, the higher the ______ the more dense the component is

coefficient

In prokaryotic ribosome, the small subunit _ S which is composed of the _ S rRNA and _ ribosomal proteins (all are numbers)

30 S (Svedberg Value) 16 S rRNA 21 ribosomal proteins

In prokaryotic ribosome, the large subunit _ S which is composed of the _ S rRNA and _ S rRNA and _ ribosomal proteins (all are numbers)

50 S 23 and 5 S rRNA 31 ribosomal proteins

the three sites of ribosomes

E, P, and A site

Exit site in Ribosome

E site

Peptidyl-tRNA binding site (growing polypeptide: amino end) in Ribosome

P site

Aminoacyl-tRNA binding site (next amino acid to be added to polypeptide chain) in ribosome

A site

the site in the ribosomes where the tRNA binds with the growing polypeptide (amino end)

P site

the site in the ribosomes where the tRNA binds with the next amino acid to be added to polypeptide chain

A site

Prokaryotic Ribosome _ S Eukaryotic Ribosome _ S

80S (40 S AND 60 S) 70S (30 S AND 50 S)

mammalian subunits are not ___ , when you combine 40 S and 60 S, they form the 80 S

additive

boxes in Eukaryotic Transcription where the binding of the RNA polymerase and several transcription factors to initiate transcription

-25 to -30 TATA box (Goldberg-Hogness Box) -75 to -80 CAAT box

Prokaryotic Transcription - 1 kind of RNA polymerase Eukaryotic Transcription - _ kinds of RNA polymerase

Eukaryotic Transcription: RNA Pol I - ________ RNA Pol II - _______ RNA Pol III - _______

large r RNAs mRNAs tRNAs small rRNAs other small nuclear RNAs

3 base sequences in mRNA that species an amino acid

Codon

3 base sequences in tRNA that base pairs with specific codon

Anticodon

set of 64 codons and corresponding amino acids they stand for

Genetic Code

single protein chain

polypeptide

TRANSCRIPTION: message of the DNA is expressed into _____ TRANSLATION: eventually this would be translated into a

mRNA polypeptide

the anticoding strand will be used as template, it will be trasncribed to produce mRNA, that will be read codon by codon to specifiy the sequence of amino acids that will make up the polypeptide chain.

TRANSCRIPTION - TRASNLATION

carries the specific amino acid

tRNA

three stop codons

UAA, UAG, UGA

this will bond to the stop codon in the A site that will trigger the hydrolysis or release of the three polypeptide chain in the tRNA and disasembly of the large, small subunit, tRNA, and the rRNA

RF (Releasing Factor)

find the mRNA sequence and amino acid sequence DNA sequence: TAC TTA GTA GCA TAA

AUG AAU CAU CGU AUU (Thymine-Adenine; Adenine - Uracil; Cytosine - Guanine) Met Asn His Arg lle

products of translation

polypeptide chain primary protein structure - specified by the amino acid sequence functional protein

the modification, folding, and association with other polypeptides of the amino acid sequence leads to the formation of

functional protein

in the _______ cell, translation and transcription can occur at the same time since they dont have compartments and they only have nuclear zone

prokaryotic

in the _______ cell, translation and transcription can occur at the same time since they dont have compartments and they only have nuclear zone

prokaryotic

in the _______ cell, translation and transcription can occur at the same time since they dont have compartments and they only have nuclear zone

prokaryotic

In the _____ cell, transciption happens in the nucleus, and the messenger RNA travels outside the nucleus for the translation in the cytoplasm

eukaryotic cell

where do the following processes occur in a eukaryotic cell? Transcription: Translation:

Nucleus Cytoplasm

where do the following processes occur in a prokaryotic cell?

Transcription: Cytoplasm Translation: Cytoplasm

set of 61 codons that specify the amino acids

Genetic Code

proposed the need for a genetic coding system

George Gamow (1950s)

made synthetic RNAs using polynucleotide phosphorylase

Marianne Grunberg-Manago Severo Ochoa

Addition of CTP would yield _

poly C

Addition of GTP would yield _

poly G

addition of ATP would yield

poly A

addition of UTP would yield _

poly U

produced artificial mRNA and introduced into a cell free system

Marshall Nirenberg and Johann Heinrich Matthaei (1961)

Nirenberg and Matthaei -combination of _______ (______) gave polyphenylalanine

poly U (UUU)

Nirenberg and Matthaei -combination of _______ (______) gave proline

poly C (CCC)

1. established the code for several amino acids and 2. proposed that the genetic code is triplet 1 nucleotide = 1 amino acid 94 types of amino acids) 4^2 = 16 (short of 4 a.a.) 4 = number of paces 2 = number of bases 4^3 = 64 (more than 20 amino acids) 3. proposed that the code is degenerate -one a.a. may be coded for more than one codon 4. the code is not overlapping 5. the base sequence is read from a fixed start point 6. Proposed the Wobble hypothesis -precise pairing occurs in the 1st and 2nd bases of the codon and anticodon

Francis Crick and his students

-Constructed synthetic mRNA with different repeating nucleotide combinations -deduced UCU - serine CUC - leucine -Used repeating dinucleotide, trinucleotide, tetranucleotide synthetic mRNA -Contributed to the final identification of codons for the 20 amino acids

Har Gobind Khorana

Who won the Nobel Prize in 1968 for cracking or elucidating genetic code

Khorana, Nirenberg, and Holley

Lecture 6 Flashcards

(84 cards)