Genetic Code

Front 1

what is genetic code?

Back 1

-sequence of nucleotides in DNA or mRNA that determines the specific amino acid sequence in synthesis of proteins

-can be expressed as either RNA or DNA codon

-Codon: set of 3 nucleotides that specifiies a particular amino acid

-RNA codon occur in mRNA and are actually read during translation

-each mRNA acquires its sequence of nucleotides by transcription form the corresponding gene.

Front 2

adenine + guanine + adenine =

Back 2

arginine

Front 3

how did 4 nucleotides A, T, G, C could encode more than 20 amino acids?

Back 3

marshal nirenberg used a cell-free system to translate a poly-uracil RNA sequence & discovered that polypeptide consisted of only amino acid phenylalanine.

-thus deduced the codon UUU specified amino acid phenylalanine.

Front 4

there are 61 possibles codons which must code for what?

Back 4

20 different amino acids, 3 stop codons

Front 5

The cod is degenerate means what?

Back 5

-with 4 nucleotides at each position (A,T,CG), there are 4^3 = 64 codon combos w/ a triplet codon of 3 nucleotides, a value well in exceed of number amino acids

-this means that many amino acids are specified by more than 1 codon called "degeneracy or the code is degenerate"

Front 6

codons specifying the same amino acid is called what?

Back 6

"Synonyms"

ex: UUU & CCC specifiy phenyalainine. UUU & UUC are synonyms for phenyalanine.

Front 7

All but two of which amino acids can be encoded by 2-6 diff. codons?

Back 7

methionine & tryptophan

Front 8

a codon is defined by what?

Back 8

initial nucleotide from which translation starts

-every sequence can be read in 3 reading frames, each of which will produce a diff. amino acid sequence w/ double stranded DNA = 6 possible reading frames

-open reading frame: a start codon, usually the first AUG codon in the mRNA sequence and 1 of the 3 stop codons.

Front 9

AUG serves two related functuions which are?

Back 9

1.) signals the start of translation, start codon

2.) translated 1st with METHINIONNE (AUG)

Front 10

there are 3 stop codons also known as define it?

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"nonsense" or "termination" codons

-proteins end in a stop codon which codes for no amino acid

Front 11

the genetic code defines what?

Back 11

mapping btw tri-nucleotide sequences & amino acid

Front 12

in most cases, third bases of the code can be what?

Back 12

altered w/out changing the amino acid or the third codon base on mRNA is less strictly specced in the genetic code.

Front 13

the 1st two nuclides are identical and the third nucleotide can be what?

Back 13

C/U or A/G and codon will still code for the same amino acid

-EX: UUU & UUC = phen

Ex: UUA & UUG = leu

Front 14

G or C in the first 2 codon positions...?

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in the 3rd position any nucleotides = specify same amino acid

Ex: CCU, CCC, CCA, CCG = Pro

Front 15

properties of genetic code make it more what?

Back 15

fault tolerant for point mutations

Front 16

chart code features of amino acids

Back 16

Front 17

G:C base pairs are stronger than what?

Back 17

A:U.

Front 18

if the 1st two positions make strong G:C base pairs then...

Back 18

the mismatches in pairing the third codon base are more tolerated

Front 19

there are 3 stop codons whihc are?

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1.) UAA

2.) UAG

3.) UGA

-also called nonsense or termination codons which direct chain termination

Front 20

proteins end in one of the 3 codons which codes for what?

Back 20

NO amino acid

Front 21

3 stop codons are not read by what but by what?

Back 21

tRNA but by specific proteins called "release factors

Front 22

what are the names of the 3 stop codons UAA, UAG, UGA?

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UAA- ochre

UAG - amber

UGA - opa or umber

Front 23

what happens if there is a wobble in the anticodon of tRNA?

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if each tRNA anticodon specify every codon, 64 RNA's would be present. In fact most of organism have fewer than 45 tRNAs. So one tRNA may recognize several different codons = WOBBLE theory.

Front 24

name the 5 anticodon bases?

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C, A, G, U and I (derived from Adenine)

Front 25

the 5' base anticodon binds to what?

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-3" base, the other 2 bases could have non-standard base pairing - Wobble pairing

Front 26

Wobble base pairing allows what?

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-less stringent pairing btw the 3' base of the codon and the 5' base of anticodon. this allows fewer tRNAs to accommodate all codons.

Front 27

what is wobble base pairing?

Back 27

-wobble base pair is non-watson crick base pairing btw 2 nucleotides in RNA molecules

-has four main wobble base pairs (G-U, I-U, I-A, I-C)

-wobble base pairs are fundamental in RNA secondary structure and are critical for the proper translation of the genetic code.

Front 28

image of base pairing 2

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Front 29

what is alternative genetic code?

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genetic code is almost universal.

-researchers discovered human mitochondrial genes used as alternative code = diff. from standard code

Ex: AGA & AGG codes for arginine in universal code but specify stop codon in mammalian mitochondrial.

Front 30

there are four stop codons in mammalian mitochondrial?

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UAA

UAG

AGA

AGG

Front 31

the coding mechanism is the same for all organisms which are?

Back 31

-3 bases codons,

-tRNA

-ribosomes

-reading the code in the same direction

-translating the code 3 letters at a time into sequences of amino acids

Front 32

list the 3 rules that govern the genetic code?

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1.) codons are read in units of three from 5' to 3'

2.) codons are non overlapping & message contains no gaps

3.) Translated in a fixed reading frame set by the initiation codon, start codon

Front 33

image of 3 rules govern of genetic code

Back 33

Front 34

gene mutations include?

Back 34

deletions, insertions, inversions translations and other changes that can affect one base pair to hundreds or thousands of base pairs of DNA sequence

Front 35

genetic code is related to what?

Back 35

genetic mutation and is usually involved in alterations of a single or a few base pairs, or point mutations and may or may not change the encoded amino acid.

Front 36

what is silent mutation?

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point mutation in which new nucleotide alters the genetic codon, but not alters amino acid in the protein product

{alters code but no alter amino acid}

Front 37

example of what mutation

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Front 38

WHAT IS missense mutation?

Back 38

point mutation in which new nucleotide alters the codon so as to produce an altered amino acid in protein product

{alters codon = altered amino acid}

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name the mutation

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missense

Front 40

what is conserative mutation?

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original amino acid changed, but replaced amino acid has same biochemical properties as original amino acid (leucine for valine). {CHANGE WILL NOT AFFECT PROTEIN FUNCTION.}

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what is non-conserative mutation?

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original amino acid and replaced amino acid have diff. biochemical properties (proline for glutamine). CHANGE WILL AFFECT PROTEIN FUNCTION.

Front 42

WHAT IS NONSENSE MUTATION?

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-point mutation that results in premature stop codon and translates a truncated, incomplete and usually nonfunctional protein product.

11% of diesese related gene mutations are nonsense mutations.

Front 43

image of what mutation?

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Front 44

what is a frame shift mutation?

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caused by insertion or deletion of nucleotides that alters the reading frame.

-amino acids in the chain after the frameshift mutation are affected!

Front 45

image of what type of mutation?

Back 45

frame shift

Front 46

point mutation do not always have phenotypic effect look at the table

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Front 47

detection of gene mutations include...

Back 47

-gene mutations involve one or few base pairs

-not detectable by cytogenetic method

-detected at the DNA sequence level

Front 48

what are the types of mutation detection methods?

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1.) hybridization base-method:single strand conformation polymorphism (SSCP), ASO, melt curve, array technology

2.) sequence base method: SSP-PCR, allelic discrimination, direct sequencing,

3.) cleavage base method: RFLP, nuclease cleavage, invader

Front 49

what is SSCP?

Back 49

single strand conformation polymorphism

-hybyridizaiton method,

-based on intra-strand folding

-scans for the presence of several base pairs

-strict temp . requirements

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steps of SSCP?

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1. amplify region to be scanned using PCR

2.) denature and dilute the PCR products

3. separate conformers by PAGE or CGE

4.) analyze results by comparison of reference normal control

5.) detecth PAGE bands by silver staining

(PCR to PAGE)

Front 51

what is ASO?

Back 51

allele-spcific oligomer hybridization

-oligonucleotide that is used to detect specific allele

-act as a probe for prescence of the target in a souther blot assay

-relies on binding effects of mismatches

Front 52

what is melt curve analysis?

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based on sequence effect on Tm

-can be performed w/ or w/out probes

-requires doubt stranded DNA w/ dyes such as ethidium bromide, SYbr Green

-melt curve indicates which sequence is present by temperature

Front 53

what is array technology/

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reverse dot blot methods

uses to investigate must. genomic sites simutaenously

DNa is labeled, probe is catching labeld DNA

-2 major applications gene expression and genetic variation analysis

Front 54

what is RFLP?

Back 54

-CLEAVAGe base method

restriction enzyme site recognize presence of sequences. like ELISA

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what is Invader technology?

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-cleavaged based method

-cleavege = fluoresce therfore normal

-non-cleavage = not fluoresce = mutation

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SSP-PCR?

Back 56

-sequence based method

-primer designed to detect mutations in DNA.

-amplification = normal

-no amplificaiton = mutation