12| THE GENETIC CODE AND TRANSCRIPTION Flashcards by Jessica Slone

Term that explains why multiple codons can code for a single amino acid

wobble hypothesis

Crick; occurs because that base has been chemically modified; redundancy

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like DNA Poly in many ways
only difference is the strand, ribosenucleotides
and no primer required

describes what term

RNA Polymerase

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The sequence, TATAAT, which is an essential part of a promoter site on DNA for transcription to occur in bacteria is termed

pribnow box

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Molecules that bind to DNA elements

a. cis-acting
b. trans-acting

trans-acting

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Genetic Code is….

name seven

1- Unambiguous (one triplet specifies one amino acid)
2 -Degenerate (redundancy, mostly at 3rd base)
3 -Commaless
4 -Nonoverlapping
5 -Universal ( recombinant DNA technology, exceptions to universal-ness are at the wobble base)
6 -Linear (ribonucleotide bases, composing mRNA as letters)
7 - Initiates and terminates

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Some amino acids are specified by more than one codon, only tryptophan and methionine are coded by single codons.

This can be termed as… (think about the genetic code and what it is)

2 -Degenerate (redundancy, mostly at 3rd base)

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what are the three termination (stop) codons?

UAG, UAA, UGA)

-They do not code for any amino acid

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When does initiation of transcription begin…

Signals in DNA indicate to RNA polymerase where it should start and end transcription.

These signals are special sequences in DNA that are recognized by the RNA polymerase or by proteins that help RNA polymerase determine where it should bind the DNA to start transcription.

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Transcription Start Site, where transcription begins is achieved how….

Once RNA polymerase explores the length of DNA and recognizes the promoter region

Transcription begins when RNA polymerase binds to a promoter sequence. RNA polymerase uses othe template strand to make a new, complementary RNA molecule.
Transcription ends in a process called termination.
ie: 3’—Promoter located —- initiator sequence (transcription begins)——————————— termination

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Refers to sequences located toward the 5’ end of the coding strand…..

-promoter located here

Upstream

-downstream refers to the 3’ end

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Encodes more than one related proteins, can be termed as a…

-genes in bacteria are called cistrons

polycistronic message

-euk have Monocistronic mRNA

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T or F a single tRNA contains a single Anticodon?

-during translation codons pair with anticodons which allows the correct AA to be linked to a given codon

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Where might you find overlapping genes?

in viruses

ie: OX174 phage

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T or F there are different reading frames in different tissues

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During RNA synthesis, this enzyme cleaves off triphosphate from the DNA template

RNA Polymerase

the initial step in gene expression is the synthesis under the direction of RNA polymerase from a strand of RNA complementary to a DNA template strand

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Enzyme responsible for directing synthesis

RNA Polymerase

the initial step in gene expression is the synthesis under the direction of RNA polymerase from a strand of RNA complementary to a DNA template strand

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The four main enzymes involved in transcription….

RNA poly

DNA PI, PII and PIII

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The three main enzymes involved in translation….

aatRNA
GTP Realease Factor
Peptidyl transferase

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assembly of amino acids, DETERMINES SPECIFIC CHARACTERISTICS of the higher order of orginization

a. primary
b. secondary
c. tertiary
d. Quaternary

primary

“STRUCTURE”
single chain——> alpha / Beta —-> packed to a protein —-> oligometric macromolecule

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FOLDING of the alpha helix and beta sheets. H- between back bone to stabalize.

a. primary
b. secondary
c. tertiary
d. Quaternary

secondary

“FOLDING”

correct folding is dependent on chaperone proteins
single chain——> alpha / Beta —-> packed to a protein —-> oligometric macromolecule

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Packaging 3D single unit related to the specific FUNCTION of any protein

a. primary
b. secondary
c. tertiary
d. Quaternary

tertiary

“FUNCTION”
single chain——> alpha / Beta —-> packed to a protein —-> oligometric macromolecule

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Interacting macromolecule with more then 1 AA/ PP chain (combination of subunits)

a. primary
b. secondary
c. tertiary
d. Quaternary

Quaternary

single chain——> alpha / Beta —-> packed to a protein —-> oligometric macromolecule

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when beta pleated sheets of hemoglobin are altered as a result from a single AA change the result is

sickle cell

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What direction is the polypeptide chain…

“temis”

amino (N+) termis ——–> Carboxyl (C-) termis

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What does a functional ribosome contain during elongation? ..... name four

mRNA charged tRNA monosome peptidyl transferase

"Elongation factors", during translation in the ribosome

Elongation Factors = GTP (Mg 2+)

Carries the AA (Anticodon) in translation

tRNA

Roles of proteins.....

Enzymes (Biochemical reactions, metabolism), transport, structure, receptors, hormones, immunity

a polymer made by reaction of two different monomers, with units of more than one kind....

Copolymer -repeating sequences, to repeating triplets; UG ------------> UGU or GUG UUG------------> UUG, UGU or GUU UAUG ------------> UAU, CUA, UCU or AUC -use of the triplet binding assay and repeating copolymers determined specific sequence triplet codons designating specific amino acids.

What would you use if you wanted to force RNA into artificial synthesis

rNDPs, ribonucleoside diphospates

Translation or Transversion; a. pyrimidine replace and pyrimidine b. purine replaces pyrimidine

translation (pyrimidine replace and pyrimidine). transversion (purine replaces pyrimidine).

– bind DNA, interfere with replication and repair. Can lead to cancer. – component in cigarette smoke, heterocyclic amines, chard burgers. Chemically mutagenetic, mustard gas, Ethylmethyl Sulfonate (EMS) termed; a. Acridine Dyes b. Adduct forming agents

Adduct forming agents

– chemical mutagen dyes (colors) affecting positively/ negatively the bases - results in frameshift (side by side mutation) a. Acridine Dyes b. Adduct forming agents

Acridine Dyes

How does repair recognize which strand is correct template and which contains the incorrect base?

the unmethylated strand after excision, it is temporarily unmethylated post replication

Induced point mutations -Result from influence of an extraneous functions name five ways point mutations can be induced

1. ionizing radiation – xrays, gamma rays, cosmic rays - penetrate deep tissue - form free radicals; - can break phosphodiester bond - result in point mut. And break 2. 2.chromosomes - radiation therapy; affects offspring 3. UV- shorter (higer E) wavelengths more damaging - effect pyrimidine dimers, adj. thymidine residue 4. Alkylating Agents 5. Base Analogs

Spontaneous point mutations can occur naturally - From replication errors and as modifications, normal biological/ chemical processes

1. Depurination vs Demiation -base pairing keto 2. Transposons 3. Replication Error- slippage 4. Oxidative damage 5. Tautomeric Shift- spontaneous, loss of 1 nuc. Affects H- affinity. Base pairing change T=G, C+A 6.

a type of Spontaneous point mutation that Disrupts reading frame. Byproducts/ free radicals/ exposure to high-energy.

Transposons -Spontaneous point mutations can occur naturally

What type of point mutation is being described by the following - HOT SPOTS: some DNA sequences are more susceptible to mutagen - SEQUENCE DEPENDENT

Spontaneous point mutations -can occur naturally and have a variable rate genome to genome

Elements that can move with in a genomes reading frame creating mutation and altering expression of genes. They may contribute to evolution and are used in genetic research such as cloning...

Transposons -A transposable ELEMENT is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material

________ like transposons also move by a "copy and paste" mechanism but in contrast to the transposons described above, this copy is made of RNA, not DNA. The RNA copies are then transcribed back into DNA

Retrotransposons (defined as the same thing as transposons) -A transposable ELEMENT is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition often results in duplication of the same genetic material

Not all genetic traits become apparent at the same time during an organism's life span. in most cases, the age at which a mutant gene exerts a noticeable phenotype depends on events during the normal sequence of growth and development. Ie Tay Sachs and huntingtons (expressed 30-50 yo), DMD (3-5 yo) can be termed as

onset of genetic anticipation -while genetic anticipation is the phenomenon where by a genetic disorder is passed onto the next generation at an earlier age with each generation. In most cases with an increase in severity is also noted.

A final example involving genetic background is called _______, whereby the process of selective gene SILENCING occurs during early development. Impacting subsequent phenotypic expression.

Imprinting -(aka genomic Imprinting or parental Imprinting )

The proportion of mtDNA molecules that determines both the penetrance and severity of expression of some diseases....

Heteroplasmy

Term that referes to a cell that has a uniform collection of mtDNA: either completely normal mtDNA or completely mutant mtDNA

Homoplasmy

Also known as an abasic sites, this is a location in DNA that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage.

an APURINIC (AP) site

These point mutations can range from NEUTRAL or SILENT to LOSS or GAIN of FUNCTION to lethality

autosomal or X-linked -not the same as somatic/ germ line mutations which occur in the body or the x and y linked regions

Not affected by natural selection a. mutations (may or may not alter structure or fx) b. polymorphisms (discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms.)

b. polymorphisms (discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms.)

affected by natural selection a. mutations (may or may not alter structure or fx) b. polymorphisms (discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms.)

a. mutations (may or may not alter structure or fx)

Three types of polymorphisms are... -polymorphisms (discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms.)

1. SNP, single nucleotide polymorphism 2. CNV, Copy number variation 3. Epigenetics (Chemical modifications in enviroment) - polymorphisms (discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species. A discontinuous genetic variation divides the individuals of a population into two or more sharply distinct forms.)

The four subcategories of point mutations... -a single base pair change

1. somatic/ germline 2. induced - base analogs/ alkylating agents 3. spontaneous- can be naturally occuring (hot spots) 4. autosomal/ x-linked - neutral or silent, loss or gain

Loss-of-function (complete loss of function) a. null mutations b. dominant mutations c. haploinsuficancy d. frame shift mutations (side by side mutation)

null mutations - dominant mutations and haploinsuficancy are a gain-of-function dominant mutations-non functioning product inactivates wild-type haploinsuficancy - results in enhanced, reduced, or new functions

INSERTIONS OR DELETIONS, the most devastating mutation types cab happen at the stop codon, the earlier in the frame the worse a. null mutations b. dominant mutations c. haploinsuficancy d. frame shift mutations (side by side mutation)

frame shift mutations (reading frame shift; side by side mutation) - dominant mutations and haploinsuficancy are a gain-of-function. null mutations are Loss-of-function dominant mutations-non functioning product inactivates wild-type haploinsuficancy - results in enhanced, reduced, or new functions

Name the repair mechanism The enzymes, error rate is 1:100,000 bp

proofreading repair - exonuclease

Name the six type of repair mechanism and there method...

1. proofreading repair - exonuclease 2. miss-match repair - recognized, excised, DNA poly fills in the gap 3. post replicational repair - recA protein, recombinational exchange 4. post replicational repair - SOS 5. Light Damage Repair - reduced dimers 6. Excision and Repair - cut out, DNA poly replaces, ligase seals a. base repair - glycolysis b. nucleotide repair - Pi+base

Xeroderma Pigmentosum in Humans, the patients were deficient in DNA synthesis and this repair mechanism led to increased insight into this condition....

6. Excision and Repair - cut out, DNA poly replaces, ligase seals b. nucleotide repair - Pi+base, dimers and gap fill

Self splicing RNAs attract specific _______ RNA to the splicosome

snRNAs -Self splicing RNAs include; ribozymes (Catalytic not in humans?), splicosomes and consensus sequences (near intron/exon junction)

Different combinations within exons of the same gene that can be brough together to make isoforms (different related protein products) ... a. Self splicing RNAs b. alternative splicing

alternative splicing -Self splicing RNAs include; ribozymes (Catalytic not in humans?), splicosomes and consensus sequences (near intron/exon junction)

phenotypes recorded by counting whole numbers Ie hens eggs a. meristic trait b. threshold trait c. continuous trait

meristic trait

a small number of discrete (discontinuous traits) phenotypic classes; environmental factors cause like DM II a. meristic trait b. threshold trait c. continuous trait

threshold trait

If true breading P1 generation is always homozygous (red x white) and the F1 generation is pink, the F1 will have an expanded phenotype pool closer or away from the mean range?

closer or Regresed towards the middle