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SDSU / Biomed Engr/Joint / Bio 100 / Why is genetic engineering important?

Why is genetic engineering important?

Why is genetic engineering important?

Description

School: San Diego State University
Department: Biomed Engr/Joint
Course: General Biology
Professor: Greg vallarino
Term: Fall 2018
Tags: evolution, DNA, RNA, transcription, translation, darwin, Polymerase, ligase, and promoter
Cost: 50
Name: Biology Unit 2 Study Guide
Description: This goes over everything covered in class from lectures 12 through 20; mostly chapters 6 and 7 in the textbook. It is organized by topic and color coded with highlighted vocabulary and important concepts.
Uploaded: 10/30/2018
6 Pages 20 Views 8 Unlocks
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Biology Study Guide Unit 2 Test 


Why is genetic engineering important?



6.1-6.2 

● Each nucleotide has a sugar, a phosphate, and a base

● A & T and G&C

● 5’ prime end has a phosphate group attached to it

● 3’ prime end has an OH- group attached to it

● DNA replication 

○ DNA unzips and each single strand serves as template

○ DNA replicates before cell chromosomes duplicates

○ DNA polymerase: an enzyme that connects to original DNA strand to build new, complementary strand

● New DNA always made 5’ to 3’ direction

○ So the lagging strand builds daughter strand discontinuously, in pieces ○ Leading strand builds daughter strand continuously

6.3-6.7 


What are the types of gene regulation?



● DNA directs production of proteins through RNA

● RNA is different from DNA- it is single stranded, the sugar in it is ribose, and it has U (Uracil) instead of T

Transcription:

1. RNA polymerase unwinds DNA to single strands

a. Promoter: DNA sequence near the beginning of a gene, signals RNA polymerase to begin transcription

2. Single strand builds 1 RNA strand only with U--makes mRNA If you want to learn more check out Which part of the newborn's body is the least controlled?

a. Inside RNA polymerase, 1 strand of RNA made from 1 strand of DNA, the other DNA strand doesn’t do anything

b. Introns are removed from mRNA transcripts

i. RNA splicing: introns spliced out and exons join together


What are the steps of replication?



ii. RNA splicing done by an enzyme separately from RNA polymerase 3. mRNA gets cap and tail added to ends before leaving nucleus

Translation:

1. mRNA has codons, each with 3 nucleotides

a. AUG is start codon, UGA UAA AUG are end codons

2. RNA: instructions for making a protein

3. Ribosome: where each mRNA codon translates into an amino acid

a. Each ribosome has a binding site for tRNA and mRNA

4. rRNA: works as an enzyme to work with proteins that make ribosomes 5. tRNA: has anticodon on one end to connect with mRNA codon to make its amino acid 6. First, subunits of ribosome assemble on an mRNA

7. Then, tRNA brings amino acids that match the codon in mRNA If you want to learn more check out What are the properties of consumer preferences?

6.8 

● Gene regulation: process of turning genes on/off

○ Not all genes are expressed everywhere - diff genes need diff cells expressed ○ Happens at diff levels:

● DNA level:

○ Chromosomes compact DNA so tightly around histone proteins, it prevents transcribing

■ Wrapped DNA around histone proteins forms chromatin We also discuss several other topics like What are party eras?

○ When it wraps around not so tightly, it makes “open chromatin” and that part of the gene is expressed

■ Open chromatin is the place where RNA polymerase has access to If you want to learn more check out What does bench trial denote?

○ One of the 2 chromosomes becomes completely useless/inactivated early in embryonic stage

■ This X chromosome inactivation controls the amount of proteins made by X chromosome

● Calico Cats:

○ Almost all calico cats are female heterozygous cats

■ So they have one allele for black fur and one allele for orange fur (Cc) ■ Both chromosomes are heterozygous, so when one chromosome is

inactivated, the other chrom will still have orange and black on it

○ They have 2 X chromosomes, which is why they are almost all female ■ Except when the genes are XXY, then it’s male

● Transcription level:

○ RNA can be spliced in diff ways, so diff introns will be included/excluded ■ Alternative splicing: diff mRNA’s form, leads to diff polypeptides (proteins) for the same gene--exons may be rearranged

○ Transcription factors bind @ diff places on DNA to turn on transcription ○ TATA box: sequence of DNA in the promoter, right before the place where transcription starts

■ Transcription factors needed at TATA box location in order to start

transcr.

■ Promoter: DNA sequence near beginning of a gene; signals RNA

polymerase to begin transcription

● Translation Level: If you want to learn more check out What does hominin mean?

○ mRNA is translated into an amino acid sequence of a protein by genetic code her ○ ORF: open reading frame, AKA the sequence of RNA coded for a protein ○ Proteins can be modified here and can be broken down at diff places/times

6.9, 6.13-6.15: 

● Gene expression-used to make sure all genes don’t produce the same proteins ○ It’s controlled by cell-to-cell communication

● Signal Transduction Pathway (STR) 

○ A molecule exits cell #1, and binds to receptor protein outside cell #2, signaling genes to turn off/on in cell #2

● Induction: when 1 group of cells influences development of another group ○ Can cause cells to change shape, migrate or even destroy other cells ● Homeotic genes: master control of genes, directs location of head and body parts Genetic Engineering 

● DNA can be mixed and matched for

● Biotechnology: manipulation of organisms to make useful stuff Don't forget about the age old question of What does it mean when a firm has comparative advantage?

● Cloning done by inserting DNA into bacteria

○ Restriction enzyme: proteins that cut DNA @ specific nucleotide sequences, “cut and paste DNA”

○ Results in restriction fragments 

○ Fragments with complementary sticky ends connect w/each other

○ DNA ligase: joins DNA fragments together

○ Plasmid: circle of DNA in bacteria that self replicates

● Recombinant DNA: DNA string from diff sources

● Genomic library: collection of cloned DNA fragments, includes the entire genome of that organism

● Genetically modified animals not yet part of the food supply, but they do help produce genetically modified drugs for medicine

Lecture 6.16-6.17: 

● Polymerase chain reaction (PCR): method of analyzing a specific segment of a dna molecule--quick and precise

○ Product is double stranded, short DNA fragments

○ Ingredients: DNA template, dNTP monomers (nucleotides), DNA polymerase, thermocycler

● Step #1: denature DNA with heat=hydrogen bonds between nucleotides break apart= becomes single stranded DNA

● Step #2: primers: short DNA segments, single stranded, bind to start and end points of DNA being amplified

● Step #3: DNA polymerase adds nucleotides

● Step#4: thermocycler: cycles temperature

○ First, it heats DNA to denature it

○ 2nd, it cools so that primers can attach

○ 3rd, it heats again while DNA polymerase adds nucleotides (DNA polymerase is heat-stable)

● Step #5: it cools so the double helix with hydrogen bonds reform

● After PCR, gel electrophoresis sorts DNA molecule by size

○ PCR is placed at 1 end of a porous gel

○ Current is applied and neg charged DNA moves from pos to neg side ○ The further it travels, the shorter the fragment

● Gel electrophoresis used to match DNA with a suspect

● 13 STR: 13 locations on the chromosome that are known to vary a lot from person to person--NO person can have the same number of repeats for all 13 locations ● DNA profiling: analysis of DNA fragments to determine probability that they came from a particular individual

DNA Sequencing: 

● DNA sequencing: Figuring out the correct order of bases

● Every protein always starts with an ATG amino acid

● Sanger sequencing: dna sequencing by chain terminating inhibitors (ddNTPs) ○ Ingredients: dna template, primers(bind to template to start), dna polymerase, and chain terminating versions of the nucleotides

○ Chain terminating inhibitors: each labeled with a diff color dye, main difference: they don’t have an oxygen in the 3’ end

○ 1-DNA amplified with modified nucleotides, 2-computer laser reads colored dyes, 3-chromatograph shows computer’s read, 4-final DNA sequence derived ● Sanger-suitable for small projects, but expensive

Next generation sequencing:

● Bioinformatics: uses biology and computer science to manage biological data ● Whole genome originally costed 2.7 billion to produce, now is under 1,000 ● Making cDNA (complementary DNA for DNA sequencing)

1. mRNA template made through transcription

2. Reverse transcriptase produces cDNA from mRNA

3. DNA polymerase makes other DNA strand

● There’s tissue specific gene expression

● Ancestry sites associate alleles with geographic location

Darwinian Evolution: 

● Darwin: made theory of biological evolution, wrote Origin of Species 

○ Provided great amount of evidence and proposed mechanism for how it all works- natural selection 

■ Like how similar species have similar DNA and protein sequences

● Explains that all species come from a common ancestor

○ We and chimps come from a common ancestor--we do not come directly from chimps

● Voyage of the Beagle: he collected an enormous amount of new specimens ○ Included Galapagos islands visit, where he noted the difference in finches beaks depending on the island they were on and their diet there

● Natural selection is NOT random-they are selected if desirable

● Overproduction + limited resouces = competition/survival of the fittest ● Bacteria went through natural selection and as a result, became resistant to certain antibiotics

Evidence for Evolution:

● Fossils -show transitional forms-of one species evolving into another

● Anatomy -shows similar features of the body of ancestors

● Molecular biology -similar genetic code shows similarity

● Biogeography -geographic distribution of species-shows how pangea affected it and how geographic isolation changed evolution of some species

● Direct observation of species

Darwinian Evolution (cont’d): 

● Population: smallest unit that can evolve, a group of individuals of same species in same place that interbreed

● Gene pool: all versions of all genes carried by individuals in a population ○ Mutation and sexual reproduction lead to genetic variation

● Microevolution: generation to generation change in gene pool

○ How beneficial genes become more common, it increases the allele frequency ● Darwinian fitness: contribution that an individual makes to a gene pool og the next generation

○ Doesn’t mean the strongest necessarily

○ Many adaptations can improve “fitness”

● Mechanisms of Evolution

○ Genetic drift: change in the gene pool due to chance

■ Ex.one indiv has a certain allele and it dies= that allele is lost from pool ○ Bottleneck: pop drastically reduced ex.Meteorite

○ Gene flow: alleles flow/transfer genetic variation to diff populations--causes diff populations to become more similar

○ Sexual selection: individual’s ability to attract mates

● Macroevolution: genetic change on a large scale

○ Novel features can cause large scale evolution

■ Ex. feathers turned later into the ability to fly--so structures can have their role changed

○ Mass extinction causes macroevolution by causing rapid species diversification ■ Mass dino extinction caused mammalian diversification

● Speciation: evolutionary formation of a new species

○ Nonbranching evolution: ancestral change into a new pop gradually

○ Branching evolution: ancestral pop splits into two or more species

7.10-7.13 

● Species: a group of interbreeding individual’s capable of healthy offspring ○ Doesn’t depend on appearance similarity

○ Doesn’t apply to organisms that produce asexually (bacteria)

● Reproductive barriers: species can’t interbreed bc of these

○ Behavioral isolation: members of species identify other members with specific rituals/behaviors they do

○ Mating time differences: species mate at diff times of year

○ Habitat isolation: species live in diff places, never meet

○ Mechanical incompatibility: diff anatomy/body parts can be incompatible ○ Gametic incompatibility: gametes of diff species often don’t fertilize each other ○ Hybrid weakness: hybrids of 2 species cannot reproduce (ex. ligers)

● Speciation occurs when an ancestral species evolves into one or more new species ○ Some event can separate it into 2 diff species ex.ancestral species pop becomes geographically isolated = evolution into 2 diff new species

● Allopatric speciation: physical barriers isolates pop’s

● Sympatric speciation: occurs without geographic isolation, happens from large scale genetic changes

○ So you don’t need barriers to produce a new species

○ Done with hybriding plants into new plants

● Graduated model: how a new species can evolve over a long time by acquiring many small adaptations over millions of years

● Phylogenetic tree: one way to reflect the evolutionary history of related species and organisms in general

● Tips of trees represents most recently evolved species

● To determine how related 2 species are, find how long ago they had a common ancestor

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