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BIO 12 > unit 3 aos 1 > Flashcards

unit 3 aos 1 Flashcards

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1
Q

what are the 4 main elements and their colors

A

carbon- black
hydrogen- white
oxygen-red
nitrogen-blue
sulfer-yellow
phospherus-orange

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2
Q

what are the 4 main types of organic MOLECULES

A

-carbohydrates
-lipids
-proteins
-nucleic acid
-all biomacromoelcules apart from lipids

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3
Q

monomers vs polymers

A

(mono) -smallest molecule of a substance
(poly- multiple) units of monomers together

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4
Q

do the organic molecules

A
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5
Q

what are proteins(polypeptides)

A
  • long chain of amino acids
  • crucial to the functioning and development of all organisms
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6
Q

what are amino acids and its chemical structure

A
  • building blocks of proteins
  • central carbon atom, carboxyl group, amino group, r-group, hydrogen atom
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7
Q

protein structure

A
  • to function properly the polypeptide/s must fold into correct shape
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8
Q

types of protein folding and description

A

-polypeptide chain- primary

-secondary
-tertiary
-quaternary

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9
Q

what is the protein secretory pathway

A
  • involves various organelles that produce fold modify and package proteins before they are exported from the cell via exocytosis
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10
Q

steps of the protein secretory pathway

A

nucleus, the ribosome synthesizing it is usually
attached to the rough er
Proteins produced at ribosomes from mrna are folded in the er exit the er and are transported via vesicles to golgi apparatus, were they are modified and packaed into secretory vesicles that fuse with the cell membrane to be secreted from the cell (bulk transport)

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11
Q

what is exocytosis (bulk transport)

A
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12
Q

protein classification

A

Fiberous proteins- typically elongated and insoluable. used for STRUCTURAL PROTEINS and have little to no folding

Globular- folded and coiled into spherical tertiary and quaternary structures , generally soluable inside hydrophobic properties

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13
Q

what are factors that affect protein functioning (loss of shape)

A
  • temperature
    -ph range
  • concentration of ions and molecules that are cofactors
    -often leads to protein denaturing
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14
Q

what are amino acids

A

the building blocks of proteins

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15
Q

what are features of dna

A

weak hydrogen bonds so it can split into rna

each strand runs anti parallel

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16
Q

what is the structure of a nucleotide

A

phosphate base (attaches to 5 carbon)
pentose or five carbon sugar

nitrogenous base (attaches to carbon 1)

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17
Q

what are the two types of nucleotide structures

A

Purines- (pure angels and goodness) (a,g)

Pyrimidines ( tools and cement) (T,C)

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18
Q

what end can nucleotides be added to

A

3 prime end

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19
Q

central dogma of molecular biology

A

describes the flow of genetic info in a cell
dna-rna-protein

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20
Q

what is a gene

A

the coded instructions for making a protein

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21
Q

do prokaryotic genes or eukaryotes contain introns

A

only eukaryotic

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22
Q

what are the three stages of gene expression in eukaryotes and hwta happens

A
  • transcription- dna to mrna
    rna processing- pre mrna to mrna
    translation- decoding of mrna into amino acids forming a polypeptidechain
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23
Q

what happens during transcription

A
  • initiation- rna polymerase binds to promotor region, helicase breaks weak hydrogen bonds between nitrogenous bases

elongation- rna moves along template strand building pre mrna (has introns)

termination-reaches term region and stops transcribing

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24
Q

Rna processing

A
  • introns are removed via spicosome in splicing (makes pre mrna mrna)
  • methyl g cap added to 5 prime end, poly a tail added to 3 prime end (stable)
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25
Q

translation

A

-mrna levaes nucleaus and goes to a riosome
- riosome binds to and reads mrna molecule

-specific trna molecules with anticodon sequence pairs with complementary codon on mrna
- trna bring corresponding amino acids that form a peptide bond as one hydroxly group and hydrogen group break off to form peptide bond

anticodon and amino- unambiguous c-u-g always codes for leucine

26
Q

gene regulation prokryote in the trp operon

A
  • tryptophan is energy expensive so when there is high free floating trp it will bind to a repressor protein, changing its shape so it can bind to the operator region and stop/repress the creation of tryptophan
27
Q

what is gel electrophoresis

A

a lab technique used to measure the size of DNA fragments by SEPERATING THEM

28
Q

what are the steps of gel electrophoresis

A
  • dna samples are added into the wells at one end of agarose gel using micropipette and ladders are added usually in the first well
    -electrical current is passed through the gel ,positive on opposite end and negative near wells
    -smaller moves faster than bigger dna fragments
    -after a couple hours its turned off and dna will settle into bands
  • gel is stained with flurocent dye so its visible under UV
29
Q

what is an enzyme

A

composed of proteins
- organic catalysts- speed up chemical reactions
-enzymes bind to substrate
help!!!

30
Q

attenuation high trp

A

The attenuator sequence is found at
the end of the leader region and comes after two trp codons in a row.
When tryptophan levels are high in a cell , the process of attenuation works as follows
1 The processes of transcription and translation of the trp operon begin and occur
simultaneously.
2 The ribosome involved in translation arrives at the two tryptophan codons in a row.
The tRNA-bound tryptophan that is present in the cell travels to the ribosome and is
added to the protein that is being made by the ribosome.
3 This causes the mRNA molecule being read by the ribosome to fold in a specific way via
hydrogen bonds and form a terminator hairpin loop.
4 The folding of the terminator hairpin loop causes the mRNA molecule to separate from
the template DNA at the attenuator sequence.
5 RNA polymerase detaches from the DNA, causing transcription to stop before any
structural genes are transcribed. Without these structural genes, new tryptophan
cannot be synthesised.

31
Q

what does the trp operon consist of

A

promotor region, operator region, leader region (trpl)
and 5 structural proteins

32
Q

vectors

A

way to introduce something in this case dna

33
Q

what does universal mean

A

all amino acids are the same for all organisms

34
Q

unambiguous

A

each codon is only capable for coding one specific amino acid

35
Q

regenerate/redundant

A

multiple codons may code for the same amino acid

36
Q

non-overlapping

A

always read 3 bases at a time

37
Q

dna amplification- PCR ( polymerase chain reaction)

A
  • amplifies dna by making multiple identical copies
    -used when there is a small amount of dna needed for testing
    thermal cycler (changes temp), tube put in has buffer to stop ph change
    heats up to 95 degrees- DENATURED- heat breaks down hydrogen bonds between complementary bases
    -cooled down to 55- primers(made in dna synthesizer creates small strand of DNA with particular base sequence) anneal to DNA
    -heated to 72 degrees- taq polymerase extends the primers as 72 is enzymes optimal temp (elongation)- free nucleotide bases used to amplify dna
38
Q

what is a restriction endonuclease

A
  • palindrome (dad)
    -an enzyme that will cut a recognition site usually where a restriction site, usually a 6 base palindrome ( not always)
  • if cut in center its a blunt end cut- good for gel electrophoresis u dont want dna fragments to connect
    -if z shape sticky end- attracted to each other
39
Q

what is ligase

A
  • glue of nucleotides
  • okazaki fragments are fragments that need to be connected by this
40
Q

what is the purpose of the ligation of sticky and blunt ends

A
  • used in making recombinant DNA in gene cloning
41
Q

where does rna polymerase bind to

A

promotor region

42
Q

gene cloning

A
43
Q

what is a plasmid

A

a smal extra chromosomal loop of dna found naturally in bacteria

44
Q

attenuation low trp

A

The ribosome involved in translation arrives at the two tryptophan codons in a row.
Due to there being no tRNA-bound tryptophan in the cell, when the ribosome involved
in translation arrives at the attenuator sequence that codes for two tryptophan amino
acids it pauses. Meanwhile, the RNA polymerase involved in transcription continues
along the DNA.
3 This causes the mRNA molecule to fold in a specific way via hydrogen bonds and form
an antiterminator hairpin loop.
4 The antiterminator hairpin loop does not cause the mRNA to separate from the
template strand at the attenuator sequence.
5 RNA polymerase continues to read the DNA template strand, transcribing the
structural genes for proteins involved in the synthesis of tryptophan and translation
can continue.

45
Q

whats in a plasmid vector

A

-restriction endonuclease site- sticky end cut
- antibiotic resistant gene-ampicillin resistance
-origin of replication
- reporter gene- easily identifiable phenotype, can be used to identify if plasmid has taken up gene of interest

46
Q

basic process of recombination

A
  • restriction endonucleases splices out gene of interest
    so it can fit into spliced plasmid - sticky ends
  • dna ligase will reconnect phosphodiester bonds
47
Q

what is cdna

A

complementory dna is dna copied from mature mrna (no introns)
reverse transcriptase (dna polymerase transcribes rna to dna) is used to create single stranded cdna
- dna polymerase makes it double stranded

48
Q

what is the process of transforming bacterial cells

A
49
Q

what is the process of making human insulin through recombinant plasmids

A
  • plasmid vectors with ampicillin and lac z gene is prepared
  • the restriction endonuclease cuts target gene with sticky end cut
    -Dna ligase ‘glues’ the gene into place and target gene is inserted into restriction site cut
    -a soultion of multiple plasmids and ecoli bacteria causes plasmids to be uptaken by heatshock or electroporation
    -bacteria is added to agar plate with ampicillin antibiotic and x-gal. Colonies will turn blue if transformed or white if recombinant
  • insulin a or b
50
Q

Crisper cas 9

A

-crisper in an adaptive immune response in prokaryotes , when virus enters it takes part of its dna and stores it with its own geneome
- cas 1 and 2 find pam sequence (ngg) on bacteriophage and go upstream of it to cut out a protospacer( part of viral dna) and store it with its own dna on crisper array
- rna polymerase transcribes it into pre crRNA
- has spacers and repeats with trRNA on repeats
- RNAase cuts spacer and little bit of repeat with trRNA, becoming gRNA picked up by cas 9
- cleaves dna complementary to guide rna

51
Q

what is homologous directed repair

A

same sequence of bases
- if a homologous copy of broken dna exists the cell will try use that to repair the dna
- less error prone than non- homologous

52
Q

what is non homologous directed repair

A
  • doesn’t matter what bases the cell will just join the DNA back together
53
Q

what is cas 9

A

rna guided endonuclease that uses grna to find target dna and cut it
- pam sequence ensures it doent cut its own spacer dna

54
Q

what is a gmo

A

genetically modified organisim
- any organism whos dna has been altered by gene tech

55
Q

what is a transgenic organism

A
  • contains gene from another org
56
Q

high bound trp attenuation

A

prevents transcription from continuing
- although there may be low free trp there is still bound trp so dont want to make
-occurs in mrna leader region
- attenuator region at end is full of a,t and in rna, u
- stop codon between region 1 and 2
- rna polymerase transcribes mrna while ribosome is translating mrna being created
-ribsome goes past ugg as there is bound trp but
stops at stop codon overlapping part of region 1 and 2
- as rna polymerase goes past attenuator region 3 and 4 join (comp bases)yanking on region 4 pulls attenuator on mrna from dna
- rna polymerase flies off stopping structural genes from being transcribed

57
Q

low bound trp

A
  • if no trp available
    ribosome stops at trp codon ugg
    -region 2 and 3 form attenuator loop and doesnt pull rna away from dna and rna polymerase can transcribe structural genes
58
Q

what are bio implications

A

ethical- is it right
bio- affect org
social- affcet people ad community

59
Q

ethical approaches

A
  • consequence based
  • duty/rule- obligations
  • virtue- morals considered
60
Q

ethical concepts

A

integrity- report findings with honesty
justice- access for all
non malificence- minimise harm while producing gmo
- respect- treat with consideration- informed consent
beneficence- max bens of gmo

BIO 12 (4 decks)

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