Microbial Metabolism and Genetics

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Exam 2 Ch 6- Microbial Metabolism Ch 8- Microbial Genetics Ch 9- Gene Transfer and Genetic Engineering
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1

Chap 6: Microbial Metabolism (slides 2-92)
Chap 8: Microbial Genetics (slides 93-155)
Chap 9:Gene Transfer & Genetic Engineering(156-163)

...

2

Metabolism

All the biochemical reactions taking place in an organism.

3

Name 6 major characteristics of enzymes.

1. Catalyze all chemical reactions in cells.
2. Enzymes are resizable.
3. Enzyme activity is highly specific.
4. Enzymes have an active site.
5. Enzymes are used in very small amounts.
6. Mostly made of protein.

4

Enzymes act through enzyme-substrate complexes. What does this mean?

Enzymes increase the probability of a chemical reaction. They also bind to the substrate at the active site, which is specific to the substrate.

5

E.coli has no ____ gene but it does have a ____ gene. All living things have ____ gene.

sucrose; lactose; glucose

6

Enzymes lower the ____ ____ so a reaction is more likely to occur. How?

Activation energy; by weakening chemical bonds in the substrate.

7

Define Induced-Fit.

Enzymes pull on substrate and weaken the bonds.

8

What are enzymes made of?

Enzymes can be made entirely of protein or contain a metal ion (cofactor; inorganic; minerals) or an organic molecule (coenzyme; vitamins).

9

What are the 2 most important coenzymes?

Niasin (NAD) and Riboflavin (FAD) are both critical in cellular respiration.

10

Define substrate.

Substrate is the substance that the enzyme reacts with.

11

What is a metabolic pathway?

-Enzymes often team up in metabolic pathways.
-It is a sequence of chemical reactions.
-Each reaction is catalyzed by a different enzyme.
-The product of one reaction serves as the substrate for the next.

12

What does feedback inhibition do?

It hinders/stops metabolic pathways.
It inhibits an enzyme in the pathway so no product is available to feed the next reaction.
-Most common way to control enzymes in action.
-Example of noncompetitive inhibition.

13

What is noncompetitive inhibition do?

Does not bind to an active site but it changes the shape of an active site.

14

What is competitive inhibition?

It binds and blocks an active site.

15

Energy in the form of ___ is required for metabolism.

ATP

16

What is ATP?

Adenosine triphosphate, is the cellular "energy currency", providing energy for: movement, cell division, protein synthesis, endergonic reactions, binary fission.
-It cannot be stored and must be made.
-It's instability forces things to happen.

17

How is energy released from ATP?

When the bond holding the last phosphate group on the molecule is broken producing:
-ADP
-Free phosphate group

18

What does phosphorylation mean?

When a phosphate group is added to a molecule.

19

ATP can/cannot be stored because it is relatively unstable.

Cannot; Energy must be stored in more stable forms like glycogen or lipids in microbes.
Bacteria can store carbohydrates and lipids.

20

What does glucose contain?

Glucose contains stored energy that can be extracted.
Energy in glucose is released slowly by converting to ATP through metabolic pathways.

21

Define cellular respiration.

A series of catabolic pathwats for the production of ATP.

22

If oxygen is consumed while making ATP, it is _____ ________.

Aerobic Respiration

23

If oxygen is not used, it is ____ _________.

Anaerobic Respiration

24

What is the first stage of energy extraction?

Glycolysis

25

What happens in glycolysis?

Remember as series of 2's!**
-Glycolysis is the splitting of one 6 carbon glucose molecule into two 3 carbon pyruvate molecules.
-It requires 2 ATP to start
-It releases 4 ATP with a net gain of 2 ATP and 2 NADH molecules.

26

Before entering the Kreb's cycle, enzymes must do what?

-Remove a carbon from each pyruvate molecule. (2 pyruvate decarboxylated)
-Combine the carbon with coenzyme A (CoA) to form acetyl-CoA.
-This releases 2 NADH and 2 CO2's.

27

How is the Kreb's cycle like a constantly turning wheel?

It picks up pyruvate molecules from glycolysis and it spits out CO2, ATP, NADH, and FADH2.

28

For each two pyruvate molecules that enter the cycle, what molecules are formed?

Remember: 3-2-1-1**
6-NADH
4-CO2
2-ATP
2-FADHs

29

Where does glycolysis occur in every living thing?

The cytoplasm.

30

Where does the Kreb's cycle occur in eukaryotes? Bacteria?

In eukaryotes it occurs in the matrix of mitochondria which requires 2 ATP for active transport. In bacteria it occurs in the cytoplasm.

31

Where does the Electron Transport System (ETS) occur in the eurkaryote? Bacteria?

Eukaryote: Across membrane called cirstea
Bacteria: Across cell membrane

32

What makes the most ATP molecules? How many?

Oxidative phosphorylation; 32 ATP molecules

33

What provides electrons for oxidative phosphorylation?

Coenzyme carriers NADH and FADH2

34

The ETS chain is composed of electron carriers called ______.

Cytochromes (located in cell membrane); they are proteins that transfer electrons.

35

What is Chemiosmosis?

-The process when electrons move down the ETS chain and pump protons out of the cell.
-The protons outside the membrane build up a concentration gradient.
-Oxygen accepts the electro pair at the end of the chain, aquires 2 protons, and becomes water.

36

A channel opens and the protons flow in through a channel called ____ _______.

ATP synthase

37

What does the ATP synthase channel do?

It harnesses the energy from the flowing protons to phosphorylate ADP into ATP.

38

What is the final phase that extracts the energy and puts it into a form for living things?

Oxygen accepts the electro pair at the end of the chain, aquires 2 protons, and becomes water.

39

Proteins are broken down by ______ into ____ ____.

Proteases; amino acids
Amino Acids-->go into glycolysis and continue the normal steps of cellular respiration
Cells use proteins for energy when fats and carbohydrates are lacking.

40

Lipids (fats) are broken down by ________ into ____ and _____.

Lipase; glycerol and fatty acids
Glycerol--> goes into glycolysis and continues the normal steps
Fatty acids--> goes into the transition phase (acetyl-CoA)and then continues with Kreb's Cycle.
-Chemical bonds in fats store large amounts of energy, making fats good energy sources.

41

Carbohydrates are broken down by ______ into ____/ ______.

Amylase; into monosaccharides/glucose

42

Name other nutrients that represent potential energy sources.

Many mono-, di-, and polysaccharides can be energy sources for prokaryotes.
They must all be prepared before being processed by glycolysis, the krebs cycle, and oxidative phosphorylation.

43

Define deamination.

The replacement of the amino group in a protein with a carboxyl group in protein breakdown.

44

What are fatty acids broken down through?

Beta oxidation

45

Anaerobic Respiration

Produces ATP using other final electron acceptors in the ETS chain.
-Produces less ATP than aerobic respiration and less ATP is used, and no O2.

46

______ produces ATP using an organic final electron receptor.

Fermentation; is used when oxygen and other alternative electron acceptors are unavailable.

47

In fermentation, what can pyruvate be converted into?

Lactic acid to form NAD+ coenzymes so glycolysis can produce ATP from glucose.
End product: Saccaromyces which is used for baking and making alcohol (causes CO2 to rise)

48

Can eukaryotes also perform fermentation?

Yes they can, such as yeast used in alcoholic fermentation to create alcoholic beverages.

49

What can lactobacillus streptococcus be used for?

Identifying gram - bacteria.

50

Most enzymes are named based on their molecular composition. True or False

FALSE (most enzymes are named based on the substarte/action they act upon).

51

In ________ reactions, water is used to break bonds in molecules.

hydrolysis

52

Which components contribute to the structure of ATP?

RIBOSE, PHOSPHATE, ADENINE

53

Which features of an enzyme is the "most" unique?

Active Site

54

The combination of all reactions (catabolic and anabolic) within a cell is termed ______.

METABOLISM

55

Which atom is most often involved in electron transfer reactions in biological systems?

HYDROGEN (unlike oxygen, hydrogen has only one electron which is more readily transferred).

56

The specific region on an enzyme that binds substrate is called a(n) _______ site.

Active

57

Pyruvic acid can directly enter the Krebs cycle. TRUE or FALSE

False

58

Identify two different fermentation pathways.

ACID formation and ALCOHOLS formation

59

The molecule _ _ _ is termed cellular "money/currency" because it can be stored, spent or transferred.

ATP

60

Most enzymes are named to reflect ____ ___ __ ___?

Action of the enzyme

61

_____is the multi-step energy-yielding conversion of glucose to pyruvic acid.

Glycolysis

62

Where are the carbons found from glucose at the end of glycolysis?

2 pyruvic acids

63

Prokaryotic cells will divide by a process called

Binary Fission

64

What macromolecules can commonly act as catalysts?

Protein

65

A(n) _______ is a biological catalyst.

enzyme

66

The Krebs cycle occurs in the __________ of the eukaryotic cells and the __________ of bacteria.

mitochondrion, cytoplasm

67

Identify the locations where proteins can enter catabolic cellular respiration.

GLYCOLYSIS, KREBS CYCLE

68

The minimum amount of energy required for a reaction to proceed is termed the energy of _________.

Activation

69

Which component of sugar (C, H, O) is often involved in electron transport biological systems?

Hydrogen

70

The ________ is the term for specific molecule on which an enzyme acts.

Substrate

71

The incomplete breakdown of glucose in the absence of oxygen that yields only a small amount of ATP and produces a variety of byproducts is a process called ___________.

Fermentation

72

The electron transport chain is located in the __________ __________ membrane of eukaryotic cells and the ________ membrane of bacteria.

INNER MITROCONDRIAL, PLASMA

73

Identify two different fermentation pathways: _______ _______, ______ ______.

ACIDS formation, ALCOHOLS formation

74

The following are methods of lowering activation energy in biological systems from most to least effective:

1st INCREASING ENZYME CONCENTRATION, 2nd INCREASING SUBSTRATE CONCENTRACTION, 3rd INCREASING THERMAL ENERGY VIA HEAT.

75

A reaction that consumes energy is termed _____.

Endergonic (needs ATP)
Exergonic (ATP is released)

76

________ are subatomic particles which carry a negative charge.

Electrons

77

Which of the following compounds is typically used as an electron "carrier" bringing electrons to the electron transport system?

NAD, FAD

78

In _________ respiration, oxygen is the terminal electron acceptor.

aerobic

79

Identify any conditions which could affect enzyme function/denaturation:

Ph, Temperature, Water concentration, Salinity

80

During aerobic respiration of one molecule of glucose, 32 ATP are generated by ________ phosphorylation in the Electron Transport System.

oxidative

81

An electron transport system and chemiosmosis are used to produce ATP in nonphotosynthetic microorganisms via _______ phosphorylation.

oxidative

82

How many ATP molecules are produced by oxidative phosphorylation for each glucose that enters glycolysis?

32

83

In ________ respiration, oxygen is not the terminal electron acceptor.

anaerobic

84

Enzyme-substrate interactions are sometimes referred to as "___ and ____" interaction.

"lock and key"

85

The specific process of _________ incorporates nutrients through biosynthesis in cells.

anabolism

86

Define Anabolism (as per Dr. Williams)

Involves reactions in which molecules/compounds are used to synthesize larger compounds--"building up", and require ATP energy.
Best example: Photosynthesis

87

Define Catabolism

Involves reactions in which larger molecules/compounds are broken down primarily by the release of ATP energy--"breaking down" produces ATP.
Best example: Cellular Respiration (break down of glucose)

88

Enzyme itself does not require energy but the ____ needs ATP to react.

Substrate

89

Enzymes can contain a metal ion called ____. What are some examples?

Cofactors; minerals; Mg, Fe, Ca, Zn, inorganic (does not contain Carbon and Hydrogen)

90

Enzymes can contain organic molecules called _____.

Coenzymes; organic (contain both Carbon and Hydrogen); are vitamin derivatives

91

What are the two best examples of coenzymes that are used for cellular respiration?

Nicotinamide Adenine Dinucleotide (NAD)- derived from Niacin (B vitamin used for cellular resp.)

Flavin Adenine Dinucleotide (FAD)-derived from riboflavin (B vitamin)

92

Not all enzymes have cofactors or coenzymes, but if they do, they cannot function without them. True or False.

True.

93

***CHAPTER 8 STARTS HERE*****

***CHAPTER 8 STARTS HERE*****

94

Time line: First sign of life.

4 billion years ago; archaea

95

The hereditary molecule in all organisms is ___.

DNA

96

____ ____ came up with the Alpha Helix.

Rosalind Franklin

97

_____ _____ and ____ ____ figured out that DNA is a double helix structure.

James Watson and Francis Crick

98

What is the bacterial genome? Does it vary between organisms?

Complete set of genes; yes it does, some organisms (ex: Chlamydia trachomatis- 936) have less and others (ex: Mycobacterium tuberculosis- 3,900 or E.coli 4,000) have more.

99

Bacterial and archaeal DNA is organized within the ____.

Nucleoid
In Eukaryotes there are 46 linear chromosomes.

100

The DNA usually exists as a ____,___ chromosome in bacteria.

single, circular and it is highly compacted (coiled)

101

Histome

In eukaryotes, they are the proteins that coil DNA

102

Human genome is a set of ______ functional genes.

20,000

103

Many microbial cells also contain ____.

Plasmids

104

What do plasmids carry? Name two types.

They carry nonessential but often useful information. R plasmids are used for antibiotic resistance and F plasmids are used for fertility.

105

To copy DNA to DNA what enzyme must be used?

Polymerase

106

Where does DNA replication begin?

oriC

107

What is the 4 step process of DNA division?

Initiation, Elongation, Termination, Leading strand and lagging Strand

(I eat the lamb*)

108

What does it mean when DNA is semiconservative?

Half of the DNA strand is old and the other half is new, when copies.

109

What happens during the initiation process?

-It starts at oriC
-DNA unwinds and strands separate with DNA helicase
-Takes place at replication fork

110

What happens during the elongation process?

-DNA polymerase synthesizes new nucleotide strands of DNA on old template.
-DNA polymerase only reads in the 3' to 5' direction for leading strand.
-Lagging strand adds nucleotids with DNA ligase.

111

What happens during the termination phase?

Termination codes for stop.

112

What are nucleotides composed of?

Phosphate, Sugar (deoxyribose), and Nitrogen bases (all held together by covalent bonds)
They then bind through hydrogen bonds to the copies ex: A-T,G-C

113

What does gene expression produce?

RNA and protein for cell function.

114

___ _____ identifies the flow of genetic material (DNA->RNA->protein)

Central Dogma

115

Replication
Transcription
Translation

Replication- DNA to DNA
Transcription- DNA copied to RNA; copies one gene at a time
Translation- nucleic acid to amino acid (mRNA -> protein)

116

What codes for protein?

Genes

117

Metabolic testing is used for?

Figuring out what kind of genes each cell has.

118

Comparing Eukaryotes/Bacteria: DNA location/RNA location

Bacteria: DNA found in nucleoid and plasmids Eukarya: DNA found in nucleus, mitochondria, chloroplast
In all organisms, RNA is found in the cytoplasm and in ribosomes; in Eukarya it is also found in the nucleolus.

Both: always associated with chromosome (genes); each chromosome has a fixed amount of DNA

119

DNA contains a __-carbon sugar called _____. RNA contains a __-carbon sugar called _____.

5, deoxyribose; 5, ribose

120

DNA contains bases: ___,___,___,___
RNA contains bases: ___,___,___,___

DNA: Adenine Guanine Cytosine and Thymine
RNA: Adenine Guanine Cytosine and Uracil

121

DNA functions as the ____ _ _______ while RNA functions in ____ ___ and ____ ____.

Molecule of inheritance; protein synthesis and gene regulation

122

Size of DNA and RNA.

DNA: large double-stranded molecule.
RNA: small single-stranded molecule.

123

What are the 3 types of RNA involved in protein synthesis? What does each one do?

mRNA-carries codon to ribosome, messengers form dna to the rest of the cell.
tRNA-carries anticodon and amino acid to ribosome, carries a.a and translates codon
rRNA-together with proteins make up ribosomes

124

In ______, the gene on DNA serves as a template for new mRNA molecules. What happens?

Transcription
-RNA polymerase reads the DNA template
-Promoter starts the transcription
-Terminator ends it

125

Genetic Code

Consists of 3 letter words. Code is redundant, more than one codon specifies a specific amino acid. 64 codons in total- 1 code for start 3 codes for stop

126

_____ is the process of making the polypeptide at the ribosome. What happens?

Translation-
Chain intiation
Chain elongation
Chain termination/release

127

What is a codon?

Coding region of mRNA

128

The coding region of DNA is called ______.

Operon

129

What does an operon consist of?

It consists of a regulatory gene, promoter, structural genes and a repressor.

130

What are the three parts of an operon?

Promoter, Operator, Structural parts

131

What happens in negative feedback?

Too much product serves as a repressor and turns off the gene.

132

Transcription and translation happen at the same time once a gene is turned on. True or False.

True

133

What are mutations?

Permanent changes in a cell's DNA and are a result of heritable changes in a genome.

134

How can mutations happen?

Spontaneously (uv light, gamma radiation, chemicals) or they can be induced (by researches)

135

What is the effect of chemical mutagens? Give an example.

They permanently generate mutations. Nitrous Acid, a chemical mutagen that change the adenine permenantly.

136

What are point mutations?

Simplest; one single nucleotide changed; they can affect protein structure and function.

137

Base-pair substitutions: name/define 3 kinds.

Silent mutation: no change due to redundancy, doesn't effect protein.
Missence mutation: wrong amino acid, changes the protein, mistake.
Nonsense mutation: stop codon, very harmful, no protein is made.

138

Base-pair deletion or insertion.

Deletion or insertion result in frame shift mutation; it is harmful because the entire reading frame is changed.
(ex from class: THE CAT ATE THE RAT)

139

What is a technique used to identify potential mutagens?

Ames test; it is a quick and simple way to determine if a chemical causes mutagens. No growth- no mutagen, Growth-mutagen.

140

What are the building blocks of DNA called? What are they made of?

Nucleotides; nitrogenous base (A,T,C,G), sugar (deoxyribose), and phosphate.

141

What is the DNA backbone?

A strand of alternating sugars and phosphates. The nitrogenous bases attach at the sugar site.

142

When does DNA replication occur? Step 1?

It occurs during interphase. DNA unwinds and half strand creates a new DNA molecule from loose nucelotides in the nucleus.
Step 1: Double strand unwinds, and is unzipped by an ezyme (DNA polymerase)

143

What is step 2 of replication?

Loose nucleotides join up with their matching base pairs on both separated strands. Enzymes called DNA polymerases attach the loose nucleotides.

144

What is the result of replication?

Two chains are formed, each with one old strand and one new strand (semiconservative).

145

What do ribosomes do?

Assemble small proteins parts from the protein you eat according to your DNA. They are located on the surface of the rough ER or free floating.
Used for protein synthesis.

146

Two steps of protein synthesis?

Transcription: to read and write a copy (called RNA) of a section of DNA code for building a protein. Occurs in the nucleus.
Translation: to translate the RNA code into building proteins from amino acids. Occurs at ribosomes.

147

What are the 3 main differences between RNA and DNA?

1. The sugar in RNA is ribose and DNA is deoxyribose.
2. RNA is single stranded, DNA is double.
3. RNA contains Uracil instead of Thymine.

148

What are genes?

Sections of DNA that contain instructions for assembling amino acids.

149

What are the instructions carried in?

mRNA; messengers from DNA to the rest of the cell. mRNA created have complimentary bases to DNA. (TRANSCRIPTION)
c-g,g-c,t-a,a-u

150

mRNA leaves the nucleus to find a ribosome to give its code to and ____ begins.

Translation-translating the RNA code into building proteins from amino acids. Occurs at ribosomes.

151

Define Amino Acids.

The building blocks of protein molecules. We get them from digesting the protein (meat,etc) we eat.

152

Define Codon.

A set of 3 nitrogen bases on the mRNA that codes for creation of one amino acid. Ex. GCA codes for the amino acid alanine.

153

There will be one more complementary switch back to the original letters on the _____ codon.

tRNA; which is sometimes referred to as the anticodon

154

What does transfer RNA (tRNA) do?

During the construction of a protein, tRNA transfers each amino acid to the ribosomes as it is specifid by coded messages in mRNA.

155

What happens at the end of translation?

The amino acid is connected to the growing polypeptide (protein) chain.

156

************Chapter 9 Starts Here************

************Chapter 9 Starts Here************

157

What happens during conjugation?

Conjugation involves cell-to-cell contact for horizontal gene transfer.
-A donor cell (F+) transfers DNA directly to the recipient (F-)
-The donor cell forms a conjugation pulus to make contact with the recipient.

158

What does genetic engineering involve?

It involves deliberate transfer of genes between organisms. It also involves changing the genetic material in an organism to alter its traits or products.

159

_____ is the commercial and industrial prodcuts derived from genetic engineering.

Biotechnology

160

What is a recombinant DNA molecule?

It contains DNA fragments spliced together from 2 or more organisms.
-Specified fragments can be obtained by cutting short stretches of nucleotides with a restriction endonuclease.
-The fragments are joined by DNA ligase.

161

Genetic engineering has many commercial and practical applications.

-The genes for producing human insulin can be cloned into bacteria. (fast growth rate)

162

Bacteria could be genetically engineered to:

Break down toxic wates, produce antibiotics

163

Agricultural Applications: Transgenic Plants

Have been engineered using microbial genes for herbicidal activity, and viral resistance. (GMO)