genetics 2 Flashcards by angela moraine

transcription occurs in nucleus, mRNA from DNA, antisense strand is used to transcribe RNA from 3’ to 5’
translation occurs in ribosome, protein is made, codons read from 5’ to 3’

central dogma (francis crick)

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codons read in unbroken chain, groups of codons called reading frames, clear start and stop location

continuity

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each amino acids is associated with tree possible codons, first two bases are what matter, third is wobble position

redundancy

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third letter of codon, may code for same amino acid regardless, protects against mutation e.g. point mutation, still codes for same amino acid, contributes to efficiency

wobble position

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genetic code is the same in all living organisms bacteria to animals, evolutionary significance, indicates common ancestor

universality

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not evenly spaced, inherited, length and number of chromosomes not related

genes

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increase or decrease gene expression, e.g. promoter sequences which help to determine which genetic processes will be activated

regulatory regions

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binding site for the apparatus that copies a gene and it can either block or enhance binding, determining when a specific gene will be expressed

promoter sequence

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exons, code for a particular polypeptide product

coding regions

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introns, interspersed with exons

non coding regions

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developmental and regulatory functions, regulate gene expression, can silence or initiate gene activity and is correlated with developmental complexity

introns

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a gene can code for more than one polypeptide product by copying different combinations of exons

alternative splicing

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frequency (more) and length (longer) of introns is positively correlated with the developmental complexity of an organism

developmental complexity

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repetitive sequences of DNA that contain base pairs that repeat over and over - minisatellites and microsatellites

variable number tandem repeats (VNTRs)

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high mutation rate, leading to diversity in population, e.g. telomeres and centromeres

minisatellites

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shorter than minisatellites, show variation in length (# of repeats) among individuals, can be used in DNA fingerprinting, paternity testing, forensics etc.

microsatellites

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clusters of genes that are the same/very similar and are located in a specific region, usually code for products in high demand e.g. genes that code for histone proteins

multigene families

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jumping genes, sequences of DNA randomly inserted throughout genome, contribute to existence of multigene families: are either LINES (long interspersed nuclear elements) or SINES (short interspersed nuclear elements)

transposons

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copies of the genes of multigene families that have mutated to the point where they no longer function

pseudogenes

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mRNA, snRNA, tRNA, rRNA

types of RNA involved in protein synthesis

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messenger RNA, carries a blueprint of DNA

mRNA

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small nuclear RNA, joins with proteins to create spliceosomes which cut out introns and join exons together in mRNA

snRNA

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transfer RNA, clover leaf shaped molecule that carries amino acids to the mRNA for polypeptide formation

tRNA

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ribosomal RNA, forms the active rivosome and assists in reading the mRNA

rRNA

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initiation, elongation, termination

transcription steps

antisense strand selected to synthesize, transcriptions begins at the promoter sequence when transcription factors bind to the TATA box, RNA polymerase begins working, 5' to 3'

initiation

promoter sequence, rich in T and A, binding site of transcription facors

TATA box

completed assembly of transition factors and RNA polymerase on the promoter

transcription initiation complex

rna polymerase moves along DNA, unwinding a section and synthesizing mRNA from 5' to 3', adding nucleotides, double helix reforms after RNA polymerase passes through and the mRNA strand separates from the DNA, more than 1 mRNA can be created at a time due to many RNA polymerases

elongation

RNA polymerase does not need rna primers, does not proofread (transcription less accurate), rna polymerase subs T for U

differences between transcription and DNA replication

termination sequence (rich in G & C followed by string of A on antisense strand) signals for stop, G&C form base pairs with itself and fold into hairpin loop structure, RNA polymerase separates from DNA antisense terminating transcription and RNA polymerase can now bind to another promoter sequence

termination

needs to undergo processing, 5' end is capped with a 5' cap of 7 guanine nucleotides and a long series of adenine nucleotides are added to the 3' end of mRNA (poly A tail) and mRNA splicing occurs to remove introns

precursor mRNA

7 guanine nucleotides, protects it from degenerative enzymes and serves as the initial attachment site of mRNA for translation to occur

5' cap

protects mRNA from degradative enzymes in cytoplasm, added by poly A polymerase

poly A tail

spliceosome (premRNA, proteins and snRNA) cleave premRNA at ends of each intron, splicing together exons by causing introns to loop out

mRNA splicing

base pairing btwn complementary nucleotides make clover leaf shape, has 2 binding sites one for mRNA and one for amino acid

transfer RNA (tRNA)

anticodon has a nucleotide triplet that is complementary to mRNA codon, anticodon can pair with more than one codon due to third nucleotide in wobble position

mRNA binding site

accepting end, 3' end, binds to specific amino acid determined by anticodon mRNA pairing

amino acid attachment site

tRNA attached to amino acid

amino-acytl tRNA (aa-tRNA)

site of translation, made up of two subunits large and small

ribosomes

contains 2 linear strands of rRNA and abt 30 proteins

large subunit

1 linear strand of rRNA and abt 20 proteins

small subunit

A site, P site, E site

sites on active ribosome

exit site

E site

polypeptide (peptidyl-tRNA) binding site

P site

amino acid (amino acyl tRNA) binding site

A site

with help from initiation factors (IF), small subunit of ribosome binds to a leader sequence just ahead of the AUG, next initiator RNA with anticodon UAC and methionine base pairs with AUG with help from initiation factors, initiator aa-tRNA, mRNA and small subunit of the ribosome form the initiation complex, large subunit of the ribosome

initiation

located in the p site of the ribosome

initiator aa-tRNA

another aa-tRNA then base pairs with the next codon on the mRNA at the A-site, methionine from the initiator aa-tRNA is covalently linked to the incoming amino acid forming a peptide bond between the amino acids btwn aino acids, ribosomes moves along mRNA from 5' to 3' to the next codon translocation, initator tRNA moves into the E site (released) incoming aa-tRNA moves to P site, A site now open for the arrival of the next aa-tRNA

elongation

when ribosome reaches mRNA stop codon in A site, release factor binds in A site, polypeptide is released from tRNA, tRNAs are released from ribosome and will be used again, ribosome separates into its large and small subunits which will be used again

termination

many ribosomes bound to one mRNA

polyribosome (polysome)

always needed and always being transcribed/translated

housekeeping genes

turning specific genes on or off

gene regulation

transcriptional, post transcriptional, translational, post translational

gene control types

regulates which genes are transcribed, controls rate of transcription (introns)

transcriptional

introns are removed and exons are spliced together to create mRNA

post transcriptional

controls rate of translation and lifespan of mRNA strand (poly A tail)

translational

controls the lifespan of the active functional protein

post translational

recognized by regulatory proteins that bind to DNA sequence to control transcription

regulatory sites

e. coli has lac z, which codes for b-galactosidase (splits lactose into glucose and galactose) on the lac operon, which is made of 3 genes (lac z, lac y, lac a) that code for proteins, promoter and regulatory sequence - operator. operator functions as a control, either allowing RNA polymerase to begin transcription or preventing transcription from occurring, inducible operon

operon model (bacteria)

in absence of lactose, repressor protein (lac I) binds to operator region, making it impossible for RNA polymerase to bind to the promoter, no transcription of lac operon gene. if lactose is present, it binds to lac I repressor, causing the repressor to change shape and detach from the operator site. Lactose acts as an inducer (signal molecule) and RNA polymerase then binds to promoter sequence and transcription can occur

negative gene regulation in lac operon

repressible operon, contains 5 genes, a promoter and an operator sequence. Outside operon, separate gene codes for a repressor protein. Normally e. coli makes enzymes that synthesize tryptophan but if tryp is present, it will bind to repressor (tryp now a corepressor molecule) changing shape and allowing repressor to bind to operator, blocking transcription

co repression in tryp operon

altering a DNA sequence and multiplying a particular gene or gene products

genetic engineering

enzymes found in bacteria that act as molecular scissors and can cut double stranded DNA at its recognition site by disrupting hydrogen bonds between bases and phosphodiester bonds in backbone

restriction endonucleases

PALINDROMIC !! usually 4-8 base pairs long and have 2 fold symmetry (same when read 3'-5' and 5'-3')

recognition sites

short single stranded overhangs lacking complementary bases, can be joined tgt with another fragment cut by the same restriction endonucleases through complementary base pairing

sticky ends

restriction endonuclease cleaves btwn nucleotides opposite each other, no overhang

blunt ends

dna made up of different organisms spliced together

recombinant dna

naturally attracted by complementary base pairing and hydrogen bonding, then DNA ligase reforms the phosphodiester bonds through condensation reactions

sticky ends rejoining

dont have natural attractions, must use t4 DNA ligase

blunt ends rejoining

to protect bacteria from viruses by cutting up foreign DNA, needs to recognize own DNA (through methylation)

role of restriction endonucleases

methylases are enzymes that add a methyl group to DNA at recognition site, no longer recognized by restriction endonuclease

methylation

independent of bacterial chromosome, lack a protein coat, small, exist naturally in cytoplasm of bacteria, can be shared btwn bacteria through bacterial conjugation

plasmids

insert foreign gene in plasmid, so that it produces that gene, then restriction endonuclease is used to create sticky ends, inserted into plasmid, recombinant DNA is formed (how insulin is made)

transformation

plasmid that contains foreign DNA

vector

change in DNA of an organism can be harmful - genetic disorder, neutral/silent or benefit

mutations

occur in gonads and may be inherited, most mutations occur in somatic cells and aren't inherited

genetic mutations

due to errors in DNA replication

spontaneous mutations

from exposure to mutagens directly altering DNA in cells

induced mutations

substance that can cause mutations and directly alters the DNA in cells

mutagen

radiation, uv light, x rays

physical mutagens

tobacco smoke, pollutants e.g. carbon monoxide, base analogs (mimic DNA nucleotides) , intercalating agents

chemical mutagens

one base or small grp of bases, substitution, insertion, deletion, inversion of two adjoining base pairs

point mutations

insertion or deletion of a base

frameshift mutations

translocations - movements of entire genes from one chromosome to another

chromosomal mutations

triplet of codons

reading frame

nucleic acid fragments are separated by their differing lengths

size separation

DNA is negatively charged bc of phosphates and will move toward positive electrode

charge separation

gel box containing agarose gel covered in buffer solution, prevents a medium for flow of electric current and prevents overheating and drying out, placed between two electrodes and the wells of the gel are at the negative electrode

gel electrophoresis

dna fragments of known size placed at loading wells of negative electrode, that can be used for comparison aka DNA ladder, loading dyes are used as well

molecular markers

ethidium bromide, chemical that inserts itself and binds to DNA carcinogenic and fluorescent under UV light

DNA staining

created dna sequencing used to determine sequence of bases in a dna strand and won nobel prize

sanger

chains of DNA sequences are terminated when dideoxynucleotides ddNTP are added, which prevent the binding of the next nucleotide, don't have a hydroxyl group on 3' end of sugar and therefore nucleotide cant attach and dye will make fluorescent identifying which base terminated sequence

sanger sequencing

so that entire sequence can be analysed and multiple lengths of the chain will be created

4 diff ddNTPS

restriction enzyme digestion

cutting dna

in vitro polymerase chain reaction

amplifying dna

gel electrophoresis and dye staining

visualizing dna

sanger sequence

sequencing dna

create millions of copies, Dr. kary mullis, uses taq polymerase as it can withstand high temps and not denature unlike dna polymerase iii

polymerase chain reaction

denaturation to break hydrogen bonds + separate strands, primer annealing (2) are added to each strand and anneal to complementary sequences at target, elongation polymerase attaches to primers to create complementary copies of target sequence on both strands

pcr cycle

paternity testing, forensics testing

applications of pcr and dna sequencing

genetics 2 Flashcards

(101 cards)