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Lecture 2 Flashcards

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Biology 101 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
Q

metabolism

A

-all the chemical rxn that take place in a cell

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26
Q

catabolism

A
  • 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
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27
Q

anabolism

A
  • metabolic process
  • synthetic process
  • larger molecules are synthesized from smaller molecules
  • photosynthesis
  • CO2 and H2O are used to make glucose
  • energy is used
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28
Q

enzymes

A
  • 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
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29
Q

denaturation

A
  • 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
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30
Q

enzyme inhibitors: competitive

A
  • 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
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31
Q

enzyme inhibitors: noncompetitive

A
  • 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
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32
Q

cellular respiration

A
  • 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
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33
Q

catabolism of glucose

A
  • energy is released
  • energy is used to make ATP from ADP and phosphate
  • cellular respiration- glucose metabolism
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34
Q

aerobic respiration

A
  • 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)
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35
Q

glycolysis

A
  • 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
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36
Q

glycolysis

A
  • 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
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37
Q

transition reaction

A
  • 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
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38
Q

Krebs cycle

A
  • 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
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39
Q

electron transport chain

A
  • 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
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40
Q

mitochondria

A
  • 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
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41
Q

anaerobic respiration

A
  • 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
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42
Q

fermentation

A
  • 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
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43
Q

lactic acid fermentation

A
  • 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)
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44
Q

alcohol fermentation

A
  • 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
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45
Q

lipids

A
  • 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
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46
Q

proteins

A
  • 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
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47
Q

photosynthesis

A
  • plants and algae - chloroplasts
  • chloroplasts specialize in photosynthesis
  • 6CO2 + 6H2O -> C6H12O6 + 6O2
  • light dependent reactions
  • light independent reactions (calvin-benson reaction)
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48
Q

light dependent reaction

A
  • 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
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49
Q

DNA

A
  • 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
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50
Q

structure of DNA

A
  • 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
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51
Q

complementary base pair

A
  • cytosine pairs with guanine
  • adenine pairs with thymine
  • plays a major role in DNA replication and protein synthesis
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52
Q

gene

A

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
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53
Q

DNA is long

A
  • -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
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54
Q

DNA replication

A
  • 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
Q

replication fork

A

region of DNA where the replication is taking place

56
Q

semiconservative

A
  • 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
Q

origin of replication

A
  • 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
Q

genetic information: protein synthesis

A
  • 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
Q

transcription

A

-make mRNA

60
Q

translation

A
  • genetic information from the gene is copied onto mRNA

- make protein

61
Q

gene

A
  • 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
Q

promoter

A

where gene begins

  • control regions
  • unique nitrogen base sequence
  • made up of DNA
63
Q

terminator

A

where gene ends

  • control regions
  • made up of DNA
  • unique nitrogen base sequence
64
Q

coding sequence

A
  • transcribe onto mRNA
  • copied onto mRNA
  • between the promoter and terminator
65
Q

RNA polymerase

A
  • 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
Q

DNA polymerase

A

-major role in DNA replication

67
Q

RNA

A
  • has uracil nitrogen base instead of thymine
  • single strand molecule
  • made up of one chain of RNA nucleotides
  • ribose sugar
68
Q

DNA

A
  • doesnt have uracil -> thymine instead
  • deoxyribose sugar
  • double strand of DNA nucleotides
69
Q

codon

A
  • 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
Q

mRNA

A
  • 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
Q

translation

A

-interaction between mRNA, tRNA and ribosomes

72
Q

stop codon

A
  • signal the end of translation
  • nonsense codon
  • doesnt code for an amino acid
73
Q

degeneracy of the genetic code

A
  • helps cell survive under certain conditions

- different codons can code for the same amino acid

74
Q

start codon

A
  • translation starts
  • protein synthesis starts here
  • AUG
  • codes for MET
75
Q

transfer RNA (tRNA)

A
  • 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
Q

anticodon

A
  • triplet of nitrogen bases

- associated with tRNA

77
Q

ribosome

A
  • 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
Q

enzyme

A
  • catalyzes peptide bond formation during translation

- ribosome has the enzyme

79
Q

translation steps

A
  • 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
Q

post translation

A
  • 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
Q

amino acid sequence

A
  • 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
Q

genetic information

A

-flows from the gene to mRNA to protein

83
Q

mutation

A

-change in the nitrogen base sequence

84
Q

missense mutation

A
  • 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
Q

silent mutation

A
  • 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
Q

cause of mutation

A
  • 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
Q

UV light

A
  • 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
Q

genetic transfer and recombination

A
  • 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
Q

crossing over

A
  • 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
Q

genetic transfer

A
  • 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
Q

genetic transfer: transformation

A
  • 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
Q

genetic transfer: conjugation

A
  • 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
Q

genetic transfer: transduction

A
  • 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
Q

regulation of gene expression

A
  • 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
Q

beta galactosidase gene

A
  • 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
Q

operon

A
  • 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
Q

lactose operon

A
  • 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
Q

regulation of lactose operon: inactive lactose operon

A
  • 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
Q

regulation of lactose operon: active lactose operon

A
  • 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
Q

repressor protein

A
  • 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
Q

regulation of lactose operon: in presence of glucose and lactose

A
  • 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
Q

catabolite repression

A

-in the presence of glucose catabolism of other sugars is repressed

103
Q

lactose operon

A
  • active in absence of glucose and presence of lactose

- both conditions have to be satisfied for the activation of the lactose operon

104
Q

growth of cells that have glucose only vs lactose only

A
  • cells grow fast with glucose only
  • cells grow slower with lactose only
  • lactose is a disaccharide -> needs to break down lactose first -> time consuming
105
Q

growth of cell that have glucose and lactose

A
  • 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
106
Q

inducible gene

A
  • 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
107
Q

plasmids (R plasmid)

A
  • 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
108
Q

R- bacterial cell

A
  • does not have r-plasmid
  • sensitive to antibiotics
  • damage to cell wall
109
Q

R+ bacterial cell

A
  • has r-plasmid
  • resistant to antibiotics
  • r-plasmid has a gene that codes for penicillinase
  • enzyme breaks down antibiotic
110
Q

R100 plasmid

A
  • 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
111
Q

dissimilation plasmids

A
  • have genes that code for enzymes that break down petroleum
  • found in pseudomonas
  • used in bioremediation- use of microbes to clean up chemical pollutants
112
Q

bacteriocin plasmids

A
  • 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
113
Q

transposons

A
  • 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
114
Q

transposition

A

-cutting and resealing of DNA

115
Q

complex transposons

A
  • 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
116
Q

genetic engineering

A
  • deliberate manipulation of genes in an organism
  • done in a lab by scientists
  • makes therapeutic substances such as human insulin
117
Q

insulin

A
  • came from pancreas obtained from slaughtered animals before genetic engineering -> did work well
  • genetically engineered E. coli cells to make human insulin
118
Q

genetic engineering mechanisms

A
  • 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
119
Q

tools used in genetic engineering: restriction enzymes

A
  • 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
120
Q

Restriction enzyme: EcoR1 example

A
  • 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
121
Q

vectors

A
  • 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
122
Q

introducing the recombinant plasmid into the cell

A
  • 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
123
Q

cDNA

A
  • 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
124
Q

eukaryotic genes: introns and exons

A
  • 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
125
Q

why do we make cDNA

A
  • 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
126
Q

applications of genetic engineering

A
  • 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
127
Q

vaccine: hepatitis B vaccine

A
  • 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
128
Q

E. coli

A

-prokaryote

129
Q

genetic screening

A
  • 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
130
Q

southern blotting

A
  • 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)
131
Q

probe

A

-single strand of DNA that is complementary to the DNA of interest

132
Q

genetic engineering: agriculture

A
  • 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
133
Q

PCR

A
  • 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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