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Lecture 2 Flashcards

1
Q

Atoms

A
  • both living and nonliving things are made up of atoms
  • water, bacteria, humans
  • atoms react with each other and make molecules -> organelles -> cell -> tissue -> organ -> organ systems -> organism
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2
Q

structure of atoms

A
  • proton +
  • neutron
  • electron -
  • proton + neutron = nucleus
  • nucleus is positive
  • electrons orbit nucleus
  • # protons = # electrons
  • atoms are neutral (charges cancel)
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3
Q

electrons

A
  • orbit around nucleus
  • arranged in shells
  • electron shell- space were electrons are located around the nucleus
  • shell 1- max of 2e-
  • shell 2- max of 8 e-
  • shell 3- max of 8 e-
  • most atoms do not have a max # of electron in their outermost shell -> unstable
  • unstable atoms will interact to form stable shells
  • form chemical bonds to form molecules
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4
Q

ionic bond

A
  • atoms gain or lose electron
  • NaCl
  • ion atom- gained or lost e-
  • sodium has a single e on outermost shell -> loses electron
  • chloride is missing one e on outermost shell -> gains electron
  • they complete each others shells
  • Na becomes +
  • Cl becomes -
  • attraction is the ionic bond
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5
Q

covalent bond

A
  • atoms get together and share electrons
  • electrons orbit around the nucleus of both atoms
  • common
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6
Q

hydrogen bonds

A
  • water molecules are held together with hydrogen bonds
  • H2O has covalent bonds holding the molecule together between atoms
  • electrons are not shared equally
  • electrons stay closer to O bc its larger and has more protons
  • O is slightly neg
  • H is slightly positive
  • polar molecule
  • heat breaks down H bonds -> water evaporates
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7
Q

water: solvent

A
  • a good solvent
  • NaCl goes into solution readily (dissociates, ionizes)
  • play an important role in chemical rxn that take place in cell
  • dehydration synthesis
  • hydrolysis
  • water surrounds NaCl and pulls the charges apart -> forms ions
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8
Q

acids, bases, and salts

A
  • acids ionize- H+ and a negative ion
  • HCL -> H+ + Cl-
  • bases ionize -OH- (hydroxide ion) and a positive ion
  • NaOH -> Na+ + OH-
  • salt- positive ion and a negative ion (not H+ or OH-)
  • NaCl -> Na+ + Cl-
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9
Q

pH

A
  • hydrogen ion concentration
  • 0-14
  • 7- neutral -> H+=OH-
  • acid- <7
  • base >7
  • household bleach- basic
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10
Q

carbohydrates

A
  • C, H, O
  • 2 to 1 ratio of hydrogen to oxygen
  • monosaccharides- simple sugars
  • glucose C6H12O6
  • glucose is main source of energy in cells
  • ribose- one of the molecules found in RNA
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11
Q

disaccharide: dehydration synthesis

A

-sucrose- made up of fructose and glucose -> sugarcane
-glucose and fructose combine through dehydration synthesis
-produces a H2O as a result
-

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12
Q

hydrolysis

A
  • breaking down molecules
  • sucrose -> fructose and glucose
  • water is used in the rxn
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13
Q

lactose

A
  • disaccharide
  • milk sugar
  • made up of glucose and galactose
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14
Q

maltose

A
  • disaccharide
  • made up of two glucoses
  • breakdown product of starch
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15
Q

polysacchrides

A 
-made up of many units of simple sugars
polymers of glucose:
-cellulose- plant cell wall
-glycogen- glucose is stored in animals
-starch- glucose is stored in plants
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16
Q

lipids

A
  • C, H, O
  • there is no 2 to 1 ratio
  • simple lipids- triglyceride
  • triglyceride- made up of glycerol and 3 fatty acids
  • ^ energy storage molecules
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17
Q

triglyceride

A
  • glycerol is the vertical portion

- 3 fatty acids attach to the glycerol through ester linkages

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18
Q

phospholipids

A
  • plasma membranes
  • organelles
  • made up of glycerol and two fatty acids and phosphate
  • glycerol and phosphate make up the hydrophilic head
  • fatty acids -> hydrophobic tail
  • form a bilayer -> fatty acids in the interior
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19
Q

proteins

A
  • C, H, O, N, S
  • building blocks- amino acids
  • 20 different amino acids
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20
Q

amino acid

A
  • amino group- NH2
  • carboxyl group- COOH
  • side group- R group
  • alpha carbon
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21
Q

peptide bond

A
  • amino acids form polypeptides through peptide bonds
  • C of carboxyl group and N of amino group
  • C-N bond
  • water product
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22
Q

protein structure

A
  • primary- amino acid sequence of polypeptide chain
  • secondary- twisting & folding of the polypeptide chain -> due to hydrogen bonds
  • tertiary- disulfide bonds is formed between diff parts of the polypeptide -> 3D shape
  • quaternary- two or more polypeptide chains interact to make a functional protein/enzyme
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23
Q

hemoglobin

A
  • polypeptide chains
  • polypeptides have a specific amino acid sequence
  • valine-histidine-leucine-glutamic acid
  • sickle cell anemia -> diff sequence -> valine takes on glutamic acid spot
  • shape of the protein changes
  • RBCs sickle shaped
  • not flexible- trouble getting through the capillaries
  • health problems
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24
Q

Adenosine triphosphate

A
  • ATP
  • three phosphates
  • adenine and ribose = adenosine
  • when terminal phosphate is removed -> energy is released and used
  • quick source of energy in cells
  • energy carrier molecules
  • synthesis, movement, transport
  • ATP -> ADP + phosphate + energy
  • ADP + phosphate + energy (comes from catabolic processes) -> ATP
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25
metabolism
-all the chemical rxn that take place in a cell
26
catabolism
- metabolic process - larger molecules are broken down into smaller molecules - break down process - cellular respiration- glucose is broken down in to CO2 and H2O - release energy - energy released is stored in ATP -> used to make ATP
27
anabolism
- metabolic process - synthetic process - larger molecules are synthesized from smaller molecules - photosynthesis - CO2 and H2O are used to make glucose - energy is used
28
enzymes
- constantly taking place - depends on enzymes - biological catalysts - speed up chemical rxn - come out of rxn unchanged - not used up - in absence of enzymes- cells cannot survive bc rxn are so slow - specific for substrate - substrate- substance with which the enzyme react - speed up chemical rxns by bringing molecules together so they can react with each other so a larger molecule is synthesized - some weaken chemical bonds in molecules -> molecule is broken down
29
denaturation
- temperature- at high and low temperature enzymes are slow - pH - substrate concentration- as substrate increases enzyme activity increases until it can not longer increase -> levels off - proteins lose 3D shape -> no longer functions
30
enzyme inhibitors: competitive
- competitive - competitve- compete with the substrate for the active site on the enzyme - ex. sulfanilamide- synthetic drug- UTI - converts para aminobenzoic acid (PABA) to -> folic acid - drug takes the place of PABA on the enzyme - inactivates the enzyme - bacteria needs folic acid to reproduce so the inhibitor will kill the bacteria
31
enzyme inhibitors: noncompetitive
- binds to the allosteric site on enzyme - allosteric site- site other than the active site - shape of the active site is changed - enzyme is inactivated - cyanide
32
cellular respiration
- glucose is catabolized - oxidation reduction rxn - loss of electron or hydrogen atom- oxidation - gain of electron of hydrogen atom- reduction - leo says ger - these rxns are coupled - organic molecules are oxidized - NAD+- coenzyme/electron carrier picks up the H+ (reduced) -> NADH
33
catabolism of glucose
- energy is released - energy is used to make ATP from ADP and phosphate - cellular respiration- glucose metabolism
34
aerobic respiration
- O2 is used - most common - C6H12O6 + 6O2 > 6CO2 +6H2O + energy - glucose is oxidized to CO2 -> glucose loses all 12 H atoms - O2 reduced to water -> picks up the H glucose lost - glucose is not directly converted to CO2 and water (too much energy would be released) - extracts energy from glucose a little at a time - involves glycolysis, transition rxn - krebs cycle, oxidative phosphorylation (electron transport chain)
35
glycolysis
- sugar splitting - takes place in cytosol (liquid part of cytoplasm) - conversion of glucose to glucose phosphate -> uses an ATP - carries out 7 different rxn before it gets ATP out of glucose - products: 2 pyruvic acid + 2 NADH + 4ATP - net gain of 2 ATP (2 ATP were used during glycolysis) - substrate level phosphorylation- phosphate is added from a substrate to ADP
36
glycolysis
- sugar splitting - takes place in cytosol (liquid part of cytoplasm) - carries out 7 different rxn before it gets ATP out of glucose - products: 2 pyruvic acid + 2 NADH + 4ATP - net gain of 2 ATP (2 ATP were used during glycolysis) - substrate level phosphorylation- phosphate is added from a substrate to ADP -> makes ATP - phosphate and energy are directly transferred from a substrate ADP to make ATP - 10 different rxns 10 different enzymes in glycolysis
37
transition reaction
- pyruvic acid goes into transition reaction - takes place in matrix of mitochondria - pyruvic acid is oxidized and decarboxylated -> acetyl CoA - NAD+ is reduced to NADH - CO2 is released from pyruvic acid as a waste product of aerobic respiration (exhale) - each molecules of glucose -> 2 acetyl CoA + 2NADH + 2 CO2 - Acetyl CoA goes into krebs cycle
38
Krebs cycle
- takes place in matrix of mitochondria - reactant- 2 acetyl CoA + 2NADH + 2 CO2 - product- 6NADH + FADH2 +4CO2 + 2ATP - Acetyl CoA comes out of transition rxn and reacts with oxaloacetic acid -> makes citric acid - NAD+ is reduced to NADH - 2 ATP is made by substrate level phosphorylation - 4 oxidation reduction rxns take place - CO2 is released as a waste product (exhale) - NADH and FADH has some of the energy from glucose -> has to extract energy from here to make more ATP
39
electron transport chain
- NADH and FADH interact with the electron transport chain to use the energy they carry from glucose and make it into ATP - takes place in inner membrane of mitochondria - in the membrane: flavin mononucleotide (FMN), uniquinone (Q), cytochromes (cyt) - NADH interacts with the 1st molecules of ETC -> FMN -> NADH is oxidized into NAD+ (first time NADH is being oxidized) - FMN grabs the H+ and gets released into intermembrane space -> the e- it holds onto has energy - when e- is moved from one molecule to another energy released and is used to pick up H+ from the matrix and release the H into the intermembrane space - eventually the e- get picked up by O2 (reduced) -> O2 then reacts with H and makes water -> reduced water -> final electron acceptor - chemiosmosis- build up of H in the intermembrane space -> diffuse into the matrix through a tiny transport channel hole made by ATP synthase -> rush in with force - energy from the H+ helps the cell make ATP from ADP and phosphate -> oxidative phosphorylation - makes 3 ATP molecules per NADH -> there are 10 NADH -> 30 ATP molecules - makes 2 ATP per FADH -> there are 2 FADH -> 4 ATP - net 2 ATP made in glycolysis - 38 ATP per glucose
40
mitochondria
- outer membrane- smooth, unfolded - inner membrane- folded (ETC is here) - innermost part- matrix (transition rxn and krebs cycle) - narrow space between the outer and inner membrane -> intermembrane space- plays a role in extracting energy from NADH and FADH - phospholipid bilayer
41
anaerobic respiration
- similar to aerobic respiration (all the same stages) - final e- acceptor is an inorganic substance other than O2 - pseudomonas aeruginosa uses nitrate ion as the final e- acceptor - doesnt produce as much ATP - more than 2 and less than 38 - depends on species
42
fermentation
- O2 is not used - only glycolysis takes place - 2 ATP are made - organic molecule is the final e- acceptor - not anaerobic respiration but it is anaerobic process
43
lactic acid fermentation
- only glycolysis takes place - glucose is broken down to 2 pyruvic acid - 2 NADH - 2 ATP - once pyruvic acid is made it is converted to lactic acid - NADH is oxidized to NAD+ - pyruvic acid gets reduced to lactic acid - regenerates NAD+ - NAD+ participates in glycolysis again to get 2 more ATP - pyruvic acid is the organic molecule final e- acceptor - lactobacillus does this (aerotolerant anaerobe- even in presence of O2 it doesnt use it)
44
alcohol fermentation
- glylocysis - 2 ATP - 2 pyruvic acid - 2 NADH - pyruvic acid is converted to acetaldehyde - CO2 comes out - NADH is oxidized to NAD+ - acetaldehyde is reduced to ethanol - final e- acceptor is acetaldehyde - ex. saccharomyces- yeast (Facultative anaerobe- grows in presence or absence of O2 but grows better with O2) -> that means we must make sure there is no O2 to make alcohol - if there is O2 it will carryout aerobic respiration and make water
45
lipids
- used for energy - when glucose isnt around - triglyceride -> glycerol + 3 fatty acids - exoenzyme- lipase -> breaks down triglyceride - glycerol is then converted to dihydroxyacetone phosphate (intermediate molecules in glycolysis) - goes into glycolysis and so on - fatty acids that came out of triglyceride can be used too - fatty acid is broken down into many units of acetyl CoA -> goes into krebs cycle
46
proteins
- used for energy - when glucose isnt around - breaks protein down into amino acids - protein broken down by proteases - amino acids are converted into intermediates of glycolysis or krebs cycle
47
photosynthesis
- plants and algae - chloroplasts - chloroplasts specialize in photosynthesis - 6CO2 + 6H2O -> C6H12O6 + 6O2 - light dependent reactions - light independent reactions (calvin-benson reaction)
48
light dependent reaction
- chlorophyll - cell light hits cholophyll molecules - e- absorb light -> energized - e- jump out of chlorophyll molecule - e- go through electron transport chain in chloroplast - similar to aerobic respiration ETC - chemiosmosis -> makes ATP by photophosphorylation - energized e- ends up with NADP+ -> NADPH - e- that come out of chlorophyll molecule are replaced by e- from water -> breaks down water into O2 and H -> releases O2
49
DNA
- deoxyribonucleic acid - genes - genes are made of DNA - DNA and genes have genetic information for structure and function of cells - DNA is made up of many nucleotides - nucleotides made up of: deoxyribose, phosphate, nitrogen base (differ in nitrogen base) - nitrogen base: adenine, guanine, cytosine, thymine - genetic information is in the nitrogen base sequence
50
structure of DNA
- double helix - 2 chains of nucleotides - alternating units of sugar and phosphate backbone - nitrogen base is attached to the sugar molecule - complementary base pairing - adenine is not attached to phosphate its attached to sugar - hydrogen base forms between nitrogen bases -> responsible for keeping strands together
51
complementary base pair
- cytosine pairs with guanine - adenine pairs with thymine - plays a major role in DNA replication and protein synthesis
52
gene
segment of DNA that codes for a functional product - functional product- protein - most genes code for proteins - .1% of genes have instructions to make tRNA and rRNA - genes are passed on from one cell to another- one generation to another - DNA has to be replicated
53
DNA is long
- -DNA is a long molecule - E.coli chromosomes has 4 million base pairs (nucleotides) - DNA is replicated segment by segment bc it is so long
54
DNA replication
- replicated segment by segment - segment unwinds and separates - hydrogen bonds are broken - each strand functions as a template for the synthesis of a new strand - free DNA nucleotides are in the area of replication - complementary base pairing takes place between the nitrogen base on free nucleotides and the nitrogen base on the template strand - DNA polymerase links them together - new strand spirals around the old stand - prokaryotes- in cytoplasm - eukaryotes- nucleus
55
replication fork
region of DNA where the replication is taking place
56
semiconservative
- an old strand and new strand - DNA replication - each copy of the DNA has one old and one new strand - parent strand - daughter strand - survival value - helps organism to survive under certain conditions
57
origin of replication
- where replication start - in circular e.coli chromosome... - made up of DNA and unique nitrogen base sequence - 2 replication fork forms here - one moves counterclockwise - the other moves clockwise - two replication forks meet -> replication is complete - 2 copies are made - when cell divides copies are passed onto 2 daughter cell -> identical - genetic information has been passed form parent to daughter
58
genetic information: protein synthesis
- flows within the cell -> instruction from genes are used by the cell to make proteins - gene is transcribed to make the mRNA - mRNA is translated to make a protein - transcription genetic information from the gene is coped onto mRNA
59
transcription
-make mRNA
60
translation
- genetic information from the gene is copied onto mRNA | - make protein
61
gene
- segment of DNA - codes for a functional product -> protein - e. coli chromosome has 1,000s of genes - each gene has a unique nitrogen base sequence* - nitrogen base sequence is responsible for differentiating genes
62
promoter
where gene begins - control regions - unique nitrogen base sequence - made up of DNA
63
terminator
where gene ends - control regions - made up of DNA - unique nitrogen base sequence
64
coding sequence
- transcribe onto mRNA - copied onto mRNA - between the promoter and terminator
65
RNA polymerase
- transcription- DNA is copied onto mRNA - makes mRNA - enzyme - major role in transcription - attaches itself to the gene near the promoter - segment of gene separates - one strand is template strand (instructions) - attaches RNA nucleotides together -> chain - free RNA nucleotides are floating around where ever transcription is taking place - once nitrogen base are exposed on template strand complementary base pairing takes place between nitrogen base on the free RNA nucleotide and the nitrogen bases on the template strand - uracil on the free RNA pairs with the adenine on the template strand - RNA polymerase attaches the pairs - moves segment by segment - polymerase is released from the gene at the terminator - mRNA has a specific nitrogen base sequence
66
DNA polymerase
-major role in DNA replication
67
RNA
- has uracil nitrogen base instead of thymine - single strand molecule - made up of one chain of RNA nucleotides - ribose sugar
68
DNA
- doesnt have uracil -> thymine instead - deoxyribose sugar - double strand of DNA nucleotides
69
codon
- 3 nitrogen base sequences next to each other on the mRNA - codes for an amino acid - different codons can code for the same amino acid -> degeneracy of the genetic code - associated with mRNA - ex. UAG
70
mRNA
- nitrogen base sequence of mRNA is complementary to the template strand of the gene - form of codons - has the genetic information in the language of RNA - brings the message to ribosome
71
translation
-interaction between mRNA, tRNA and ribosomes
72
stop codon
- signal the end of translation - nonsense codon - doesnt code for an amino acid
73
degeneracy of the genetic code
- helps cell survive under certain conditions | - different codons can code for the same amino acid
74
start codon
- translation starts - protein synthesis starts here - AUG - codes for MET
75
transfer RNA (tRNA)
- one end has anticodon - other end picks up amino acid from the cytosol - transfers amino acids from the cytosol to the ribosome - specific group of tRNA for each amino acid - specificity is based on the anticodon it has - reads the message - ex. tRNA is specific for alanine -> cant pick up any other amino acid -> specific anticodon for alanine
76
anticodon
- triplet of nitrogen bases | - associated with tRNA
77
ribosome
- holds mRNA so tRNA can read the message and bring the appropriate amino acid to the ribosome - has the enzyme that attaches amino acids together (peptide bonds)
78
enzyme
- catalyzes peptide bond formation during translation | - ribosome has the enzyme
79
translation steps
- attachment of ribosome (large and small subunit) to the mRNA near the start codon - tRNA recognizes the codon - tRNA brings MET to the ribosome - complementary base pairing occurs on the codon on the mRNA and the anticodon on the tRNA - tRNA molecules are held in place and the amino acids are next to each other - enzyme attaches the amino acids together -> dipeptide - dipeptide gets transferred on to tRNA and it moves on to next segment - forms a polypeptide - ribosome reaches stop codon -> end of translation
80
post translation
- polypeptide is released - tRNA subunits come apart - mRNA and tRNA is released from ribosome - mRNA is translated again to make another copy of the polypeptide chain
81
amino acid sequence
- important for shape of protein - important for function of protein - based on the sequence of mRNA - sequence of codons is based on the nitrogen base sequence of the gene from which it was transcribed - change in nitrogen base of the gene -> change the codon of mRNA -> can change amino acid sequence - if it is changed the protein becomes less active or inactive
82
genetic information
-flows from the gene to mRNA to protein
83
mutation
-change in the nitrogen base sequence
84
missense mutation
- single nitrogen base on a specific site on the gene is replaced by another nitrogen base - sequence of codon is changed - when mRNA is translated the polypeptide sequence is changed - protein doesnt function correctly - sometimes the mutation doesnt show up on the polypeptide chain -> codon is changed but it still codes for the same amino acid -> degeneracy of the genetic code
85
silent mutation
- sometimes the mutation doesnt show up on the polypeptide chain -> codon is changed but it still codes for the same amino acid -> degeneracy of the genetic code - possible bc of the degeneracy of the genetic code - survival value for the cell bc most mutations are lethal to the cell
86
cause of mutation
- can take place spontaneously - DNA polymerase makes a mistake and inserts a wrong nitrogen base during DNA replication - mutation frequency is increased by certain agents -> mutagens - mutagen chemicals- nitrous acid changes shape of adenine so that it pairs with cytosine - x-ray mutagen- pull e- out of molecules -> break in the chromosome - UV light- mutagen
87
UV light
- mutagen - induces the formation of thymine dimers in DNA - adjacent thymine molecules in DNA come together - when DNA is replicated DNA polymerase is confused - inserts the wrong nitrogen base in the new DNA being synthesized - cells have evolved so that enzymes can separate thymine dimers - if there are too many thymine dimers not all the thymine dimers will be separated -> accumulate -> mutation - sunlight - accumulation of thymine dimers causes mutations in skin cells -> skin cancer - caused by excessive sun tanning
88
genetic transfer and recombination
- contributes to genetic diversity in a bacterial population - new strains pop up -> genetic recombination is partly responsible - 2 DNA are in the same cell and come in contact -> pieces of DNA are exchanged - each DNA molecule becomes a recombinant DNA
89
crossing over
- chromosome A and chromosome B in the same cell come in contact - random process - twist around each other - pieces of DNA are exchanged - makes recombinant chromosome
90
genetic transfer
- 2 DNA in the same cell - piece of DNA is transferred from a donor to a recipient - bacteria has one DNA molecule - if genetic transfer takes place the bacteria can have 2 DNA molecules - 3 methods of transfer: - transformation - conjugation - transduction
91
genetic transfer: transformation
- DNA from a donor cell is transferred to recipient - donor cell is dead - when bacterial cell dies the DNA is released into the environment - DNA gets fragmented into pieces - recipient cell comes in contact - DNA penetrates cell wall of recipient -> 2 DNA molecules - own chromosome and donor DNA present - when the own chromosome and donor DNA come in contact -> crossing over - donor DNA aligns with complementary bases - *can make the recipient cell more pathogenic -> picks up genes that can code for capsules - becomes a capsulated bacteria- more pathogenic bc capsule protects bacteria from phagocytosis
92
genetic transfer: conjugation
- subspecies of the same cell - F+- has the pilus (filamentous structure found on the surface) and small circular DNA (F plasmid/factor) - F+ cell has plasmid and chromosome (they are separate) - F-- does not have pilus - F+ uses it pilus and attached to F- and conjugates - F plasmid- has genes for the pilus - plasmid gets replicated and copy gets transferred to the F- cell through the pilus - F- becomes F+ -> makes two F+ cells - F+ has 2 DNA molecules (chromosome and plasmid) - f plasmid gets inserted into chromosome -> becomes an Hfr cell (high frequency of recombination cell) - Hfr cell- very good at conjugation - Hfr cell- makes the pilus - Hfr and F- cell conjugation: - during conjugation the DNA gets replicated and starts in the middle of the f plasmid - piece of f plasmid and piece of chromosome get replicated and transferred into the F- cell - F- cell never gets the entire chromosome or plasmid bc it is much larger than the cell and they dont stay conjugated for long enough - F- gets only a piece of donor DNA and plasmid -> inserts into chromosome and becomes recombinant -> doesnt become F+ cell and does not make pilus - can make an F- cell resistant after it picks up DNA from another Hfr cell -> shares resistance
93
genetic transfer: transduction
- DNA of donor cell is transferred with recipient cell - bacteriophage is a virus (acellular) that infects bacteria - bacteriophage picks up donor DNA and releases it into recipient cell - bacteriophage gets into host cell to reproduce itself - bacteriophage attached to donor cell - phage DNA gets released into host - phage DNA gets replicated - donor chromosome gets fragmented - assembly of phage takes place -> - by mistake sometimes fragments of bacterial DNA gets enclosed into the protein code of the phage - transducing phages- have bacterial DNA in them instead of phage DNA - donor cell breaks down and dies - phages are released including transducing phages - transducing phage comes in contact with bacteria and releases donor DNA into bacteria (receiving cell) - donor DNA gets inserted into the chromosome of the recipient cell -> recombinant - sometimes transducing phages pick up toxic genes and spreads it
94
regulation of gene expression
- most genes are expressed constantly - constitutive genes- constantly transcribed and translated and expressed - genes that code for enzymes of glycolysis are constitutive genes - hexokinase gene is a constitutive gene - some genes are expressed only when their products are needed -> inducible genes - beta galactosidase gene is an inducible genes
95
beta galactosidase gene
- inducible gene - codes for the enzyme beta galactosidase - enzyme breaks down lactose to glucose and galactose - needed only when lactose is in the medium - expressed in the presence of lactose - gene is part of the lactose operon - lactose operon is located on e. coli chromosome
96
operon
- many genes are controlled by the same control region (promoter) - has many genes - controlled by the same control region (promoter) - regulation - genes of the same operon share a promoter
97
lactose operon
- 3 structural genes - Z- beta galactosidase - Y- permease- transports lactose into cytoplasm - A- transacetylase - controlled by the same promoter and operator - each gene has its own nitrogen base sequence - next to lactose operon -> I gene- regulatory gene - regulates the expression of lactose operon -> codes for repressor protein - in the absence of lactose the lactose operon is inactive
98
regulation of lactose operon: inactive lactose operon
- repressor protein hop onto the operator protein and block RNA polymerase - when RNA polymerase attached to promoter it cannot get to structural genes bc of the repressor blockage - only when the RNA polymerase is able to pass over the structural genes will the mRNA of the structural genes will be made - no mRNA -> no translation -> no proteins - inactivates lactose operon
99
regulation of lactose operon: active lactose operon
- if lactose is in environment it will bind to repressor protein -> inactive repressor protein - pulls the repressor protein from the lactose operator -> no more blockage - RNA polymerase is able to make mRNA for the structural genes - lactose activates the lactose operator by inactivating the suppressor
100
repressor protein
- on the operator - if something is bound it is pulled form the operator -> inactive - if nothing is bound it block RNA polymerase from making mRNA of the structural genes
101
regulation of lactose operon: in presence of glucose and lactose
- carabolite repression - if glucose and lactose are present - cell will use glucose over lactose - doesnt need beta galactose - RNA polymerase has a hard time attaching the promoter - glucose prevents the RNA polymerase from attaching - prevents mRNA coding - once glucose is used up the RNA polymerase can easily attach to promoter and make mRNA - lactose binds to suppressor and actives lactose operon - as long as glucose is present lactose operon is inactive
102
catabolite repression
-in the presence of glucose catabolism of other sugars is repressed
103
lactose operon
- active in absence of glucose and presence of lactose | - both conditions have to be satisfied for the activation of the lactose operon
104
growth of cells that have glucose only vs lactose only
- cells grow fast with glucose only - cells grow slower with lactose only - lactose is a disaccharide -> needs to break down lactose first -> time consuming
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growth of cell that have glucose and lactose
- uses all the glucose up first (fast rate) - lag time- cell stops growing for a while after glucose runs out - cell starts growing again by using lactose (slower) - cells stop growing for a bit bc it takes a while for the cells to activate the lactose operon
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inducible gene
- beta galactosidase gene - helps the cell to save its energy and chemical resources such as amino acids - cell is not making something that it does not need
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plasmids (R plasmid)
- small circular DNA - R plasmids- resistance plasmids - R plasmid genes code for antibiotic resistance - they code for enzymes that break down antibiotics - bacteria is not killed by antibiotics - unique to prokaryotic cells
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R- bacterial cell
- does not have r-plasmid - sensitive to antibiotics - damage to cell wall
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R+ bacterial cell
- has r-plasmid - resistant to antibiotics - r-plasmid has a gene that codes for penicillinase - enzyme breaks down antibiotic
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R100 plasmid
- resistance for many different antibiotics - also has genes for making pilus - if bacteria picks up this plasmid it will be very resistant - pilus allows conjugation and transfer of plasmid to other bacteria - can be transferred between E. coli, klebsiella, and salmonella - resistance spreads
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dissimilation plasmids
- have genes that code for enzymes that break down petroleum - found in pseudomonas - used in bioremediation- use of microbes to clean up chemical pollutants
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bacteriocin plasmids
- code for toxins - toxic to certain species of bacteria - ex. lactococcus lactis has a bacteriocin plasmid - codes for toxin -> nisin - nisin prevents the germination of clostridium endospore - helps lactococcus lactis -> prevents growth of other bacteria so it has more nutrients for itself - preserve cheese
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transposons
- small segment of DNA - transposed (move) one region of DNA to another - jumping genes - can cause problems by messing up sequences - doesnt move often tho - found in all organisms - simple transposons (insertion sequences)- has a gene that codes for an enzyme -> transposase - transposase- helps simple transposon to move from one part of the DNA to another - unique nitrogen base sequence on each side
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transposition
-cutting and resealing of DNA
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complex transposons
- unique nitrogen base sequence on each side - made up of 2 insertion sequences - in between there is a gene that codes for antibiotic resistance - found in bacteria - often found in r-plasmid - can move from the plasmid to the chromosome - can be transferred through conjugation
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genetic engineering
- deliberate manipulation of genes in an organism - done in a lab by scientists - makes therapeutic substances such as human insulin
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insulin
- came from pancreas obtained from slaughtered animals before genetic engineering -> did work well - genetically engineered E. coli cells to make human insulin
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genetic engineering mechanisms
- use plasmid (small circular DNA found in some bacterial cells) as a vector and insert a gene of interest (human insulin) into the plasmid - plasmid becomes a recombinant plasmid - recombinant plasmid is introduced into a bacterial cell (E. coli) -> becomes the recombinant cell/transformed bacteria - E. coli transcribes and translates the gene and makes the human insulin - once recombinant cell is made it can be grown in a nutrient broth like any other e. coli cell -> descendants of the recombinant will also be recombinant - easy to make a lot human insulin
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tools used in genetic engineering: restriction enzymes
- restriction enzymes come from bacteria - used to breakdown phage DNA in the bacteria - extract the restriction enzyme from bacteria and use it for genetic engineering - EcoR1, BamHI -> recognize specific sequences - restriction enzymes make staggered cuts in the DNA - they fragment DNA - ends of the fragment are single stranded
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Restriction enzyme: EcoR1 example
- restriction enzyme cuts double stranded DNA at he specific nitrogen base sequence it recognizes (can have more than one site of recognition) - staggered cuts DNA and produces a fragment with 2 sticky ends - bc the cuts are staggered a piece of DNA comes out and has single stranded ends -> sticky/cohesive ends - restriction enzyme cuts a piece of bacteria DNA and human DNA -> bc they are cut at the same recognition sites they have the same nitrogen base sequence on the sticky ends - this allows the piece of DNA to join by complementary base pairing -> recombinant DNA - enzyme DNA ligase is used to unite the two DNA fragments
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vectors
- carry the gene of interest into a bacterial cell - plasmids - small enough -> they can enter into the cell easily - they have selection markers which are antibiotic resistance genes - antibiotic resistant genes are on the plasmid and help in selecting the cells that have the gene of interest - acts like a tag - plasmid has recognition sites that restriction enzymes can recognize - has selection markers (antibiotic resistance genes)-> amp
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introducing the recombinant plasmid into the cell
- take a bunch of recombinants and put them into a tube with host cell (e. coli) - some of the e. coli will come in contact with the recombinant plasmid and pick it up and some will not - incubation - there will be two populations of e.coli (one with recombinant and one without) - they select the recombinant cell by plating the mixture on the medium with the ampicillin antibiotic -> incubate - the colonies that show up on the plate are the ones with the recombinant plasmids bc they have the selection markers (antibiotic resistant genes) in their plasmid
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cDNA
- complementary DNA - cDNA does not exist in nature - cDNA- synthetic gene that only has exons - mRNA is used to make cDNA (by scientists- not in nature) - DNA nucleotides and reverse transcriptase enzymes are added to the tube with mRNA - reverse transcriptase uses mRNA as a template to make a complementary strand of DNA - DNA polymerase is then added to the tube and uses the DNA strand as a sample to make the second strand -> makes cDNA - cDNA only has exons
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eukaryotic genes: introns and exons
- introns- noncoding regions - exons- coding regions - prokaryotic genes only gave exons - when the eukaryotic gene is transcribed the RNA also has exons and introns - eukaryotic cells have certain enzymes that remove introns and stitch the exons to make the mRNA
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why do we make cDNA
- if we want to introduce eukaryotic gene into a prokaryotic cell we use cDNA - if we place natural eukaryotic gene into bacterial cell it wont be able to remove the introns - functional protein will not be produced by the prokaryotic cell
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applications of genetic engineering
- used to make therapeutic substances (insulin make by e. coli) - hormones- insulin - used to make growth hormone -> somatotropin (treats stunted growth) - produced by genetically engineered E. Coli cells - before genetic engineering they got growth hormone from pituitary gland removed during autopsy -> transferred diseases
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vaccine: hepatitis B vaccine
- genetic engineering is used to make vaccines - hepatitis B vaccine: - genetically engineered saccharomyces cells (eukaryotic) - vaccine has only the protein part of the virus - does not have the genetic material of the virus - no chance of getting the disease due to vaccination
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E. coli
-prokaryote
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genetic screening
- DNA technology is used - used to see if someone is a genetic carrier for a genetic disorder - xeroderma pigmentosum (XP)- genetic disorder - there is a mutation in a gene-> the gene codes for an enzyme that repairs DNA damage caused by UV rays - enzyme is not functional - sensitive to sunlight -> get sunburn within a few minutes - various health problems are also associated with this condition - if a person has the diesase -> there are symptoms - some people can be carriers -> one XP gene (father) one normal gene (mother) -> heterozygous for XP (no symptoms) - if 2 carriers have a baby the baby can have the disease - uses the southern blotting procedure
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southern blotting
- used in genetic screening - take blood and DNA - fragment DNA using restriction enzyme (made from bacteria) - DNA fragments are separated by gel electrophoresis by size - the DNA bands show up - smaller pieces move faster in the gel (more further down the smaller) - DNA bands are transferred onto nitrocellulose filter/membrane - nitrocellulose filter holds onto molecules like DNA - place the nitrocellulose filter and attached DNA into a zip lock bag - a solution containing many copies of the radioactively labeled probe (complementary to gene of interest) is added - incubate - probe will hybridize/comes together with gene of interest through complementary base pairing - remove and rinse nitrocellulose filter - expose to x-ray film - where ever there there is radioactive activity it will blacken -> tells us where the probe and therefore the gene of interest is - a black band shows up for carrier - a black band show up larger and wider for someone with the disease (bc twice as many copies of the gene of interest)
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probe
-single strand of DNA that is complementary to the DNA of interest
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genetic engineering: agriculture
- makes plants that are resistant to insects - take BT toxin gene from bacillus thuringiensis - put the BT toxin gene into a vector (plasmid) -> recombinant plasmid - recombinant plasmid is introduced into pseudomonas fluorescens bacteria - transformation process is used to transfer DNA -> bacteria picks up DNA from its environment - recombinant pseudomonas fluorescens cell makes BT toxin - pseudomonas fluorescens is released onto the leaves of the plant -> reproduce other recombinant cells -> covers the leaves with BT toxins - when insect nibbles on leaves it ingest toxins and dies - the plant itself is not genetically engineered -> it has genetically engineered bacteria on it - we cant just use bacillus thuringiensis bc it cannot colonize the leaf -> they only live in soil - as long as the plant is alive it will be resistant
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PCR
- polymerase chain reaction - used to amplify DNA - makes more DNA to get more sample for testing - target DNA is placed in a tube with a solution, DNA nucleotides, and DNA polymerase - tube is heated and cooled several times -> causes the DNA to become replicated - billions of copies of target DNA are made at the end of PCR

Microbiology (8 decks)

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