Micro 2 Lecture 08

Front 1

Sum total of genetic material of an organism.

Back 1

genome

Front 2

Define the genome for:

-Eukaryotes?
-Prokaryotes?
-Viruses?

Back 2

-for Eukaryotes, it includes the DNA in the nucleus, mitochondria and
in photosynthetic cells, chloroplast
-for Prokaryotes, it includes the circular DNA & plasmids (if it has them)

-for Viruses, it includes whatever DNA or RNA is inside of the capsid

Front 3

A length of DNA containing genes.

Back 3

chromosome

Front 4

A fundamental unit of heredity responsible for a given trait.

Back 4

Gene

Front 5

One chromosome has multiple __________ on it.

Back 5

genes on it.

Front 6

What do genes encode?

Back 6

genes encode one specific protein or RNA molecule

Front 7

The _________ of one cell is made up of multiple _________, Chromosomes are made up of Multiple _________; all is composed of:

List the hierarchy from smallest - largest:

Back 7

The Genome of one cell is made up of multiple chromosomes, Chromosomes are made up of Multiple Genes; all is composed of: DNA

hierarchy: DNA → Genes → Chromosomes → Genome

Front 8

The genetic information of an organism is carried on its _______.

Back 8

DNA

Front 9

How many chromosomes do we have?

Back 9

46; two sets of 23, one set from each parent.

Front 10

Describe the hierarchy of genetic info. in the cell by greatest - smallest.

Back 10

Genome of cell → Chromosomes → Genes → DNA

Front 11

Humans cells have about _________ genes.

Back 11

31,000 genes.

Front 12

E. Coli has about _________ genes.

Back 12

4,000 genes

Front 13

Viruses carry about ___ to___ genes in their genome.

Back 13

1-10

Front 14

What are the names of the nitrogenous bases?
A
T
C
G
U

Back 14

A- Adenine
T- Thymine
C- Cytosine
G- Guanine
U- Uracil

Front 15

5' (five prime) refers to the covalent bond of:

Back 15

the five prime Carbon on deoxyribose to the Phosphate.

Front 16

Each individual strand of DNA is composed of building blocks called:

Back 16

nucleotides.

Front 17

Each nucleotide is composed of:

Back 17

the sugar/phosphate backbone (a deoxyribose or ribose group + a phosphate group) & a nitrogenous base

Front 18

The sugar group can either be:

Back 18

ribose or dioxyribose

Front 19

If the sugar group is ribose, then it would be called:

If the sugar group is deoxyribose, then it would be called:

Back 19

ribonucleic acid; deoxyribonucleic acid

Front 20

how are nucleotides connected to make a strand?

Back 20

the phosphate group of one is connected to the sugar group of another.

Front 21

every strand of DNA is sided; what are the sides?

Back 21

one end is a free phosphate group, called the 5 prime end;
the other end is a free sugar group, called the 3 prime end.

Front 22

What are the nitrogenous bases attached to?

Back 22

the sugar group

Front 23

how many possible nitrogenous bases are there for DNA? What are they?

Back 23

there are 4 possible nitrogenous bases for DNA. They are:

-Thymine (T)
-Adenine (A)
-Cytosine (C)
-Guanine (G)

Front 24

When the two strands of DNA come together, one strands 5 prime ends meets the other strands 3 prime end. This is called:

Back 24

antiparallel.

Front 25

In the double helix, the two strands are bound together by:

Back 25

by the nitrogenous bases

Front 26

The nitrogenous bases bind together in a predictable pattern called:

Back 26

complementary base pairing

Front 27

in complementary base pairing:
-A always binds to:
-C always binds to:

Back 27

A always binds to T
C always binds to G

Front 28

What controls the genetic information of DNA?

Back 28

the order and length of the nitrogenous bases.

Front 29

Define semiconservative as used in DNA replication:

Back 29

During DNA replication, each new chromosome will end up with 1 NEW strand of DNA and 1 OLD strand of DNA.

Front 30

Replication always begins at a specific site in the DNA called the:

Back 30

ORI (Origin of Replication)

Front 31

A particular site and a particular _____________ of nitrogenous bases make up the ORI.

Back 31

particular sequence

Front 32

Replication is ___________, occurring in two directions at the same time.

Back 32

bi-directional

Front 33

The bubble that is formed between the strands of DNA as replication is occurring:

Back 33

replication bubble.

Front 34

Does replication take place on both strands at once?

Back 34

yes

Front 35

What is the name of the enzyme that does DNA copying?

Back 35

DNA polymerase III

Front 36

What exactly does DNA polymerase lll Do?

Back 36

DNA polymerase lll reads one strand of DNA and synthesizes a complementary antiparallel strand.

Front 37

DNA polymerase lll can only add nucleotides to which end?

Back 37

to the 3 prime end.

Front 38

All new DNA is made from the ___ prime and to the ____ prime end.

Back 38

5 prime end → 3 prime end last.

Front 39

What are the limitations of DNA polymerase lll?

Back 39

1) It can only add new nucleotides in the 5 prime → 3 prime direction.
2) it cannot initiate DNA synthesis on his own, he needs a primer

Front 40

What develops because of this limitation of DNA polymerase lll.

Back 40

a leading strand & lagging strand.

Front 41

In the leading strand, DNA polymerase lll starts adding complimentary base pairs on the ___________ end of the template strand.

Back 41

3 prime end of the template strand.

Front 42

What prime end of the template strand does the lagging strand start at?

Back 42

at the 5 prime end of the template strand

Front 43

Describe what the lagging strand has to do?

Back 43

Front 44

the short segments that DNA polymerase lll has to add by moving ahead and going backwards, adding pairs from 5prime → 3prime are called:

Back 44

Okazaki fragments

Front 45

What are the enzymes involved in the DNA replication process?

Back 45

-Helicase
-Primase
-DNA Polymerase lll
-DNA Polymerase l
-DNA Ligase

Front 46

The OLD strands of DNA that gets copied by DNA Polymerase lll are called:

Back 46

Template Strands

Front 47

What initiates DNA synthesis?

Back 47

primase

Front 48

What does primase do?

Back 48

primase makes an RNA primer for DNA polymerase lll to attach to.

Front 49

DNA replication begins when:

Back 49

when an RNA primer is synthesized at the ORI

Front 50

What digests out the primer and fills in the spots with DNA?

Back 50

DNA polymerase l

Front 51

What seals the gaps in DNA?

Back 51

Ligase

Front 52

So what are the steps in DNA synthesis?

Back 52

1) Helicase grabs on to the ORI and unwinds the Double Helix, pulling the two strands apart
2) Primase makes the RNA primer for DNA Polymerase lll
3) DNA Polymerase lll attaches to the primer and synthesizes DNA in a 5prime → 3 prime direction
4) DNA Polymerase l digests out the primer and fills in the spots with DNA
5) Ligase seals up any gaps left over.

Front 53

How many primers are needed on the leading strand?

On the lagging strand?

Back 53

1 on the leading strand

many on the lagging strand.

Front 54

What does Helicase do? Where does that occur?

Back 54

Helicase unwinds the DNA double helix.

Occurs at the ORI

Front 55

Why does replication occur in such a small section of the DNA at a time?

Back 55

Because there is six feet of DNA in every cell, it is not possible to unwind the whole DNA.

Front 56

How many ORIs does a Prokaryote have?

Back 56

1

Front 57

How many ORIs does a Eukaryote have to have?

Back 57

at least 1 per chromosome; many times Eukaryotes have many ORIs on each chromosome, allowing increase speed of replication

Front 58

Remember, DNA is bi-directional:

Back 58

Front 59

What two ways can bacteria pass DNA to one another?

Back 59

1) From one generation to the next
2) Through adult cells of the same generation

Front 60

How do bacteria pass DNA to one another from one generation to the next?

Back 60

through a form of asexual reproduction called: binary fission (mother cell divides to give rise to daughter cells that have exact same genome)

Front 61

What are the 3 ways that bacteria pass DNA to one another from adult cell to adult cell?

Back 61

-Conjugation
-Transformation
-Transduction

Front 62

Describe Conjugation:

Back 62

requires the attachment of two related species & formation of a pilus that can transport DNA

Front 63

Describe Transformation:

Back 63

the uptake of naked DNA (relatively rare), as cell wall precludes this ability

Front 64

What can we do to increase the likely hood of transformation?

Back 64

a series of chemical treatments and heat that creates pores in the cell.

-electricity also creates holes in cell

Front 65

Describe Transduction:

Back 65

DNA transfer mediated by a bacteriaphage (when a capsid gets loaded with bacterial DNA accidentally)

Front 66

Does Transduction kill the bacteria?

Back 66

No

Front 67

Do bacteria want to get DNA from their environment and from other cells? Can it be useful?

Back 67

absolutely; it is always worth getting DNA from other sources.

-Sometimes genes that are picked up can be useful:
-like picking up a gene that allows you to digest more sugar.
-or an anti-bacterial resistance gene

Front 68

How many chromosomes do bacteria have?

Back 68

1

Front 69

How does the definition of "growth" in microbiology differ from the usual definition?

Back 69

Unlike multicellular organisms, for most microbes growth entails an increase in the number of cells not the size of individual cells. (population size,not individual size)

Front 70

The growth of bacteria is via:

Back 70

binary fission (asexual reproduction)

Front 71

What is step 1 of binary fission?

Back 71

The mother cell prepares for division by copying her chromosome and developing notches that will eventually form the transverse septum. She also enlarges her cell wall, cell membrane, and overall volume.

Front 72

What is step 2 of binary fission?

Back 72

Both copies of chromosome are attached to cell membrane and they are pulled away from each other to separate ends of the cell. Transverse septum grows inwards.

Front 73

What is step 3 of binary fission?

Back 73

The septum grows completely through the cell center and the cell membrane patches itself so that there are 2 separate cell chambers.

Front 74

What is step 4 of binary fission?

Back 74

At this point the daughter cells are divided. (In some species, they will remain attached)

Front 75

The length of time it takes for 1 cell to become 2 cells in binary fission is called:

Back 75

the doubling time

Front 76

The Doubling Time can vary:

Back 76

-from one species to the next
-depending on environmental factors

Front 77

What is the doubling time for:
-E. coli?
-Mycobacterium leprae?

Back 77

-E. coli = 20 min.
-Mycobacterium leprae = weeks

Front 78

If E. coli can reproduce so quickly, why aren't we swimming in it?

Back 78

because E. coli, like most organisms, doesn't live in an open system; most organisms live in a closed system with finite nutrients.

Front 79

the closed system has a very ______________ pattern of growth.

Back 79

predictable

Front 80

A closed environment could be:

Back 80

1 test tube
1 petri dish
1 human body (during infection)
1 soil sample

Front 81

What are the phases of the bacterial growth curve in a closed environment?

Back 81

1) Lag phase
2) Exponential growth phase
3) Stationary phase
4) Death phase

Front 82

Describe the Lag phase:

Back 82

In the Lag phase, cells are adjusting to their environment: sensing what nutrients are available & starting to produce the right enzymes to digest those nutrients.

Front 83

Describe the Exponential growth phase:

Back 83

In the exponential growth phase, the bacteria have adjusted to their new environment and the cell number is doubling with each Doubling Time.

Front 84

Describe the Stationary phase:

Back 84

The bacteria run out of nutrients & the growth rate = the death rate; the overall cell number stays CONSTANT.

Front 85

Describe the Death phase:

Back 85

The death rate is greater than the growth rate; so the overall cell number decreases.

Front 86

What causes the transition from the Stationary phase to the Death phase?

Back 86

Generally, it is because of the build up of toxins (waste products), the overall culture is dying.

Front 87

What are the ways of measuring bacterial growth?

Back 87

-spectrophotometer (which measures turbidity.)
-direct count

Front 88

How does the spectrophotometer measure turbidity?

Back 88

By detecting how much light passes through a sample.

Front 89

Turbidity is a good predictor of ________. The higher the turbidity the higher the ______________.

Back 89

cell number; cell number

Front 90

Describe the Direct Count method of measuring bacterial growth:

Back 90

In the Direct Count method, you put a sample of bacteria on a slide that has a container with a grid pattern, and count them. You then multiply out how many bacteria are in the greater culture.

Front 91

What are the 4 big environmental influences on microbial growth?

Back 91

1) Temperature
2) Osmotic pressure
3) Oxygen requirements
4) pH

Front 92

Every organism has these three temperatures related to growth:

Back 92

-Minimum temp.
-Optimum temp.
-Maximum temp.

Front 93

Describe a Psychrophile

Back 93

An organism with an optimal growth temperature of about -5 to 20 deg. C

Front 94

Describe a Mesophile:

Back 94

An organism with an optimal growth temperature of about 20 to 50 deg. C

Front 95

Describe a Thermophile:

Back 95

An organism with an optimal growth temperature of about 50 to 80 deg. C

Front 96

According to optimal growth temperature, most Human pathogens are:

Back 96

Mesophiles

Front 97

Describe a Hyperthermophile

Back 97

An organism with an optimal growth temperature of greater than 80 deg. C

Front 98

An organism that is actually a Mesophile, his optimal growth temp. is in a moderate range. However, he has a very wide curve and he can grow at lower temperatures.

Back 98

Psychrotroph (Facultative Psychrophile)

Front 99

The growth rate of organisms is affected by pH and they grow between these three pH ranges:

Back 99

-Minimum pH for growth
-Maximum pH for growth
-Optimum pH for growth

Front 100

The vast majority of organisms on the planet enjoy a ___ pH environment.

Back 100

neutral pH environment;

Front 101

Describe a Neutrophile:

Back 101

Organisms that have an optimum pH between 6 and 8

Front 102

Describe an Acidophile:

Back 102

Organisms that have an optimum pH below 6

Front 103

What are some general examples acidophiles?

Back 103

Archeae & fungi

Front 104

Are some fungus Acidophiles?

Back 104

yes

Front 105

In general, what can survive better in acid conditions: fungi or bacteria?

Back 105

fungi

Front 106

Describe Alkalinophiles:

Back 106

Organisms that have an optimum pH above 8

Front 107

Are Alkalinophiles rare?

Back 107

yes

Front 108

What is an example of an Alkalinophile?

Back 108

the bacteria that breakdown Urea.

Front 109

Define Isotonic solution:

Back 109

The concentration of solute outside the cell is the same as inside the cell; water would freely flow in and out of the cell.

Front 110

Define Hypotonic solution:

Back 110

The concentration of solute outside the cell is less than inside the cell; water will flood into the cell.

Front 111

Define Hypertonic solution:

Back 111

The concentration of solute outside the cell is greater than inside the cell; water will flood out of the cell.

Front 112

The vast majority of microbes prefer to live in which osmotic environments?

Back 112

either an isotonic or slightly hypotonic solution.

Front 113

Which osmotic environment is deadly to almost all microbes?

Back 113

hypertonic solution

Front 114

The process of a microbe cell dying by crenation because of a high salt environment; (like salted beef) is called:

Back 114

plasmolysis

Front 115

Organisms that live in high osmotic pressure environments are called:

Back 115

Osmophiles

Front 116

Osmophiles can survive in which osmotic environment?

Back 116

hypertonic environment

Front 117

An example of an Osmophile would be a:

Back 117

Halophile, which like to live in high salt environments.

Front 118

What other environments would create a high osmotic pressure environment besides salt?

Back 118

High sugar, honey

Front 119

Oxygen is dangerous to ALL organisms because, anytime oxygen is present it will release:

Back 119

free radicals

Front 120

Any cell that lives in an oxygen environment has to have:

Back 120

enzymes to get rid of free radicals, otherwise their DNA will be damaged.

Front 121

Why is oxygen toxic to some organisms?

Back 121

because they don't have the enzymes to deal with free radicals.

Front 122

Medium that contains a substance that absorbs oxygen or slows penetration of oxygen into medium; used for growing _______________.

Back 122

Reducing medium; used for growing anaerobic bacteria

Front 123

Describe what it would look like if you have Aerobes growing in Reducing Medium:

Back 123

Aerobes would be growing at the very top of the tube.

Front 124

Describe what it would look like if you have anaerobes growing in Reducing Medium:

Back 124

Anaerobes would be growing at the very bottom of the tube.

Front 125

Describe a Facultative anaerobe:

Do they have enzymes to get rid of free radicals?

Back 125

Facultative Anaerobes don't require oxygen, but they can use oxygen

Yes, they have to have enzymes to get rid of free radicals.

Front 126

Describe what it would look like if you have Facultative Anaerobes growing in Reducing Medium:

Back 126

there would be growth throughout the test tube.

Front 127

Describe the process of making an anaerobic environment in the CO2 incubator container:

Back 127

In the container is a packet that will absorb O2 & produce CO2 when water is added to it. An "anaerobic indicator strip" of methylene blue is added which will turn clear in the absence of O2

Front 128

What do most anaerobes smell like?

Back 128

awful