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1

The study of organisms too small to be seen with the human eye

Microbiology

2

Microbiology includes several sub-disciplines:
By organism type & by application

By organism type:
1) Bacteriology
2) Virology
3) Mycology
4) Parasitology
By application:
1) Food microbiology
2) Environmental microbiology
3) Forensic microbiology

3

The existence of microorganisms was hypothesized for many centuries before their actual discovery. _______ _______ asserted the existence of unseen microbiological creatures living in earth, water, air and fire.

Mahavira (6th century BC)

4

Microbiology born as a science in?

1674

5

* Dutch drapery merchant
* Ground lenses to view fabric
* Used lens to peer into a drop of lake water
– First glimpses of microbial world – Called organisms “animalcules”

Anthony van Leeuwenhoek

6

Theory of Spontaneous Generation
The theory states that?

“organisms can arise from non-living matter”

7

The theory of spontaneous generation had its supporters and detractors. Detractors included?

– Francesco Redi
– Louis Pasteur
– JohnTyndall
* Each contributed to disproving the theory

8

Spontaneous generation debate led in part to scientific method which is?

1) Observation leads to question
2) Question generates hypothesis
3) Hypothesis is tested through experiment(s)
4) Results prove or disprove hypothesis
– Accepted hypothesis leads to theory/law – Reject or modify hypothesis

9

* Italian biologist and physician
* Demonstrated maggots found on rotting meat came from eggs of flies landing on meat

Francesco Redi

10

* Considered the father of modern microbiology
* Demonstrated that air is filled with microorganisms
* Identified the cause of fermentation
* Developed the germ theory of disease

Louis Pasteur

11

To show air is filled with microbes Pasteur developed? Was able to demonstrate infusions remained sterile even if flask was left open

Swan-necked flask

12

Studied causative agents of disease
– Anthrax
– Examined colonies of microorganisms

Robert Kosh

13

Koch’s Contributions

Koch’s Contributions
1) Simple staining techniques
2) First photomicrograph of bacteria
3) First photomicrograph of bacteria in diseased tissue
4) Techniques for estimating CFU/ml
5) Use of steam to sterilize media
6) Use of Petri dishes
7) Techniques to transfer bacteria
8) Bacteria as distinct species

14

Louis Pasteur demonstrated that yeast in grape juice reproduced and produced?
Bacteria also fermented the?

Alcohol with or without exposure to air
– Facultative anaerobes
Grape juice producing acid

15

Many scientists were skeptical of Pasteur’s results. Some scientists could not reproduce same results. Who was able to explain discrepancies?

John Tyndall was able to explain discrepancies

16

Tyndall concluded different infusions required different?

Boiling times. Some infusions were sterile after boiling for five minutes, others did not achieve sterility after five hours of boiling. He attributed contamination to a heat-resistant life-form later called an endospore. German botanist Ferdinand Cohn discovered endospores in the same year

17

Who was able to establish endospore role in disease transmission

Robert Koch

18

The Theory of Spontaneous Generation was disproved and the Golden Age of Microbiology was born
– Golden Age was from?

1854–1914

19

Golden age of microbiology.
Between ___ and ___ most disease-causing bacteria
were discovered

Between 1875 and 1918

20

What did the Golden Age of Microbiology do?

1) Time of great interest in the study of microorganisms
2) Between 1875 and 1918 most disease-causing bacteria
were discovered
3) Work on viruses began
4) Lead to the initiation of prevention and treatment of disease

21

How do microbes have enormous impact on human existence?

– Microorganisms have killed more people than have ever been killed in war
– Without certain microorganisms life could not exist. Some microorganisms produce oxygen and nitrogen which are key elements for all living organisms
–Microorganisms are decomposers. Responsible for the breakdown of a wide variety of materials

22

Describe the food production of microbiology

Food production
– Beer, wine, bread, soy products, sauerkraut
– Fermentation of milk to produce numerous products like yogurt, cheese, and buttermilk

23

Describe microbiologies role in bioremediation

Use organisms to degrade environmental waste. Degrade PCB’s, DDT, clean up oil spills and treat radioactive waste

24

Bacteria can synthesize numerous products such as?

– Ethanol
– Pesticides
– Antibiotics
– Dietary amino acids

25

Define genetic engineering

Introduce genes of one organism into an unrelated organism to confer new properties on the organism

26

Benefits of genetic engineering

1) Applications include engineering organisms to produce medically important products and vaccines
2) Engineered plants resist disease
3) Potentially therapeutic
– Gene therapy

27

More people died worldwide of what in the 1918 epidemic than died in WWI, WWII, the Korean War and the Vietnam war combined

Influenza

28

Modern sanitation, vaccination and effective antimicrobial treatments have reduced?

Incidences of the worst diseases

29

Resurgence of old diseases. Diseases thought to be “defeated” increasing in frequency. Often more serious. Causative agents usually resistant to treatment. Reasons for resurgence?

1) Increase travel.Visitors to foreign regions bring organisms from home and bring other organisms home with them
2) Unvaccinated individuals susceptible to infection. Causative agents of controlled diseases are still around and infect vulnerable individuals

30

All living things can be classified in one of three groups. Also known as domains. Organisms in each domain share certain properties. These properties distinguish them from organisms in other domains. Three domains are?

– Bacteria
– Archaea
– Eukarya

31

Define strain

Variations within a species. Not all organisms from the same species/types are necessarily the same

32

Briefly describe bacteria and archaea

– Both are single-celled organisms
– Contain no membrane bound nucleus
– Termed PROKARYOTES = pre nucleus
– Pro=pre
– karyote = nucleus
– Do not contain any other organelles
– Cytoplasm is surrounded by rigid cell wall

33

Describe eukarya

– Organisms contain membrane bound nucleus
– Termed EUKARYOTE = true nucleus
– Eu = true
– karyote = nucleus
– Contains internal organelles
– Making organism more complex. Example = mitochondria
– May be single celled or multicellular

34

Most common cause of human infection. Members widely diverse

Bacteria

35

Most prominent features of bacteria include

1) Specific shapes
* Rod-shaped, spherical and spiral
2) Rigid cell walls
* Responsible for cell shape
3) Multiply by binary fission
* One cell divides into two
* Each cell is genetically identical to the first
4)Some bacteria are motile
* Move by means of flagella

36

Archaea share a number of attributes with Bacteria

– Same shapes
– Multiply through binary fission
– Move by means of flagellum

37

Archaea exhibit significant differences, which are?

– Chemical composition of cell wall differs from organisms in other domains
– Organisms of Archaea domain found in extreme environments such as extreme temperatures and environments with high concentrations of salts

38

Microbial world includes Eukarya which are

– Algae
– Fungi
– Protozoa

39

What are algae?

1) Diverse group
2) Includes single and multicellular organisms
3) All contain chlorophyll which the pigments absorb the energy of light which is used in photosynthesis. Some contain other pigments.
4) Usually found near surface waters
5) Have rigid cell wall. Distinct from bacterial cell walls

40

Fungi are diverse single celled and multicellular organisms: – Single-celled =
– Multicellular =

– Single-celled = yeast
– Multicellular = molds, mushrooms

41

Gain energy from organic materials. Found wherever organic materials are present

Fungi

42

What are protozoa?

– Microscopic, single-celled organism
– Found in water, animal hosts, and on land
– Complex
– Much larger than prokaryotes
– Do not have a rigid cell wall
– Gain energy from organic matter
– Most are motile. Means of motility is diverse and a feature of their classification

43

Viruses, Viroids, Prions are?

1) Non-living elements
2) Called agents (not organisms)
3) Usually consist of only a few molecules found in living cells

44

Viruses contain a protein?

Coat surrounding nucleic acid. Essentially protein bag of nucleic acid

45

Viruses termed obligate intracellular parasites. They must have?

Host machinery to replicate. Inactive outside of host

46

What are viroids?

1) Viroids are simpler than viruses. They still require host cell for replication
2) Consist of a single short piece of RNA –Contain no protective protein coat
3) Viroids smaller than viruses
4) Generally cause plant diseases

47

What are prions?

1) Infectious proteins. There is no nucleic acid
2) Responsible for at least seven neurodegenerative diseases:
– Animal disease like scrapie in sheep and mad cow disease in cattle
– Human disease like Kuru and Creutzfelt-Jakob

48

Atomic number is?

The number of protons in the nucleus

49

What is atomic mass (atomic weight)?

The sum of masses of protons, neutrons, and electrons

50

Consist of a single type of atom

Element

51

99% of all living matter is made up of four elements?
What makes up additional 0.5%?

1) Carbon (C)
2) Oxygen (O)
3) Hydrogen (H)
4) Nitrogen (N)
Additional 0.5% is phosphate (P) and sulfur (S)

52

Atoms combine by sharing or transferring valence electrons, this is called?

Chemical bonds

53

Two or more atoms held together by chemical bonds

Molecule

54

A molecule composed of one or more elements

Compound

55

Covalent bonds achieve stability through?

The sharing of electrons between atoms. Creates a strong bond; difficult to break. Requires significant energy, usually in the form of heat. Never breaks spontaneously at physiological temps. Needs an enzyme to break at lower temps.

56

Covalent bonds can be?

Polar or non polar

57

Universal solvent is

Water because of its polar property

58

Ionic bonds are formed by?

Gaining or losing electrons. Electrons completely leave first atom and become part of outer orbital of second atom.

59

The loss and gain of electrons leads to?

Charged atoms called ions. An atom that loses an electron becomes positively charged. An atom that gains an electron becomes negatively charged.

60

Charged atoms are attracted to each other & form a bond between ions

Ionic bond

61

Ionic bonds are weaker than?

Covalent bonds. They dissociate in water, they are easily broken at room temp., approximately 100 times weaker than covalent bonds.

62

Important among weak forces holding biological molecules together

Ionic bonds

63

Hydrogen bonds are

Weak bonds formed from the attraction of positively charged hydrogen atoms. Hydrogen atoms in polar covalent bonds are attracted to negatively charged atoms or molecules (most commonly, oxygen, or nitrogen).

64

Hydrogen bonds occur between molecules such as

Water and DNA

65

Weakest of the biological bonds

Hydrogen bonds

66

Constantly being formed and broken at room temp.

Hydrogen bonds

67

At room temp. the average lifetime of a single hydrogen bond is?

A fraction of a second

68

Large numbers of hydrogen bonds can?

Hold molecules together firmly (DNA)

69

Bonding properties of water

1) Water molecules are cohesive
2) Water is an excellent solvent
3) Remains liquid at wide range of temps
4) Absorb considerable amounts of heat energy without change temp.
5) Participate in many chemical reaction inside cells

70

Acidity is measured as?

pH

71

What is pH?

Defined as concentration of H+ ions. Potential Hydrogen

72

On a pH scale 0 is?

Highly acidic

73

On a pH scale 14 is?

Highly alkaline (basic)

74

Acidity is based on ionization of?

Water to H+ and OH- ions. When H+ and OH- ions are equal solution is neutral

75

High H+

Acid

76

High OH-

Basic

77

All cells contain small?

Organic and inorganic molecules. Approximately 1% of dry weight of bacteria composed of inorganic ions (Na+, K+, Mg2+, Ca2+, Fe2+, Cl-, PO43-, & SO42-)

78

Certain enzymes require positively charged _____ for proper functioning

Ions

79

Negatively charged phosphate ions are essential in?

Energy metabolism

80

Small organic molecules act as?

Precursor metabolites. These are converted to the building blocks of macromolecules. Monomers: Nucleotides, amino acids, monosaccharides

81

Biological macromolecules are divided into 4 classes

1) Lipids
2) Polysaccharides (carbohydrates)
3) Proteins
4) Nucleic acids

82

Critical component of cell membranes

Lipids

83

Heterogeneous group of molecules, made up of different subunits

Lipids

84

Insoluble in water

Lipids

85

Smallest of the 4 macromolecules

Lipids

86

Lipids can be divided into two general categories

Simple lipids and compound lipids

87

Most important compound lipid

Phospholipid

88

Compound lipids contain

Fatty acids, glycerol and other elements

89

Phospholipid is made up of?

A phosphate and two fatty acids attached to a glycerol molecule

90

Phosphate head is?

Polar and soluble in water (hydrophilic)

91

Fatty acids are non-polar and

Insoluble in water (hydrophobic)

92

Carbohydrates are a diverse group of molecules with various sizes. They are important in all organisms because

1) They are a common source of food and energy
2) Component of nucleic acids
3) Component of bacterial cell walls

93

Carbohydrates contain

Carbon, hydrogen, and oxygen in 1:2:1 ratio. Generally each carbon atom is bound to two hydrogen atoms and one oxygen atom (CH20)

94

Polysaccharides are?
Oligosaccharides are?
Monosaccharides are?

Poly-Large molecules made of carbohydrate molecules
Oligo- Short chains of carbohydrates
Mono- Single carbohydrate molecule

95

Monosaccharide are classified by?

The number of carbons in the molecule

96

The most common monosaccharides

Five and six carbon sugars
-Pentose (5C), ribose and deoxyribose
-Hexose (6C), glucose, fructose, and galactose

97

The carbohydrate disaccharides are produced by?

Joining two monosaccharides through dehydration synthesis

98

Most common disaccharide in nature is

Lactose and sucrose
Lactose is: glucose + galactose
Sucrose is: glucose + fructose

99

Less common disaccharide is

Maltose which is glucose + glucose

100

Proteins constitute over ___% of cell dry weight

50%

101

Proteins are made up of?

Amino acid subunits including the elements: carbon, hydrogen, oxygen, nitrogen, and sulfur

102

Proteins are the most versatile macromolecule, some responsibilities include:

1) Composition and shape of certain bacterial structures
2) Gene regulation
3) Nutrient procurement
4) Enzymatic catalysis
5) Transportation
6) Defense and offense

103

Proteins are composed of numerous combinations of ___ amino acids

20

104

A proteins function depends upon the?

Shape of the protein and the proteins shape depends on the sequence of amino acids

105

The amino acids that form proteins are held together by?

Peptide bonds which is a unique type of covalent bond between the carboxyl group of one amino acid and amine group of the following amino acid

106

Proteins have 4 potential levels of structure

1) Primary
2) Secondary
3) Tertiary
4) Quaternary

107

Describe protein denaturation

Proteins must have specific shape to have proper function. Environmental conditions can break bonds within the protein which can cause shape change. Shape change causes protein to stop functioning. This is called denaturation

108

Protein denaturation can be?

Reversible or irreversible. The environment determines reversibility

109

There are two types of nucleic acids

DNA- carry genetic code in all cells
RNA- Decodes nucleic acid sequence into amino acids to produce proteins. Acts as transcript (mRNA), as enzymes (rRNA), and binds amino acids sequence during protein assembly (tRNAs)

110

Subunits of nucleic acids are

Nucleotides

111

Master molecule, determines specific properties of the cell

DNA

112

DNA nucleotides are composed of 3 units

1) Nitrogenous base
- Purine: adenine & guanine
- Pyrimidine: Thymine and cytosine
2) Five carbon sugar molecules
- deoxyribose
3) Phosphate molecule

113

DNA in living organisms is a?

Double-stranded helical molecule. Hydrogen bonding between the nitrogenous bases

114

Three hydrogen bonds form between

C & G

115

Two hydrogen bonds form between

T & A (DNA) or between U & A (RNA)

116

DNA is double stranded in most cells and viruses.

Two strands are complementary and two strands are antiparallel

117

RNA is

Necessary for decoding DNA. The structure is similar to DNA

118

How does RNA differ from DNA?

1) Thymine is replaced by uracil (there is no thymine base in RNA)
2) The sugar is ribose in place of deoxyribose
3) RNA is generally shorter
4) Exists as a single-stranded molecule not double stranded

119

Characteristics of each cell is dictated by?

Information contained in DNA. DNA holds the master blueprint

120

All cell structures and processes directed by

DNA

121

Complete set of genetic information is referred to as?

Genome

122

Genome of all cells is composed of?

DNA. Some viruses have RNA genome

123

Functional unit of genome is?

The gene

124

Gene coes for?

Gene product which is most commonly protein

125

Study of transfer of genes is?

Genetics

126

Study of sequence of DNA is?

Genomics

127

Living cells must accomplish 2 general tasks to multiply

1) DNA replication
2) DNA expression

128

What is DNA expression?

Gene expression. Central dogma of molecular biology. Flow of information from DNA to RNA to protein. Expression involves 2 processes:
1) Transcription- copies information in DNA to RNA
2) Translation- interpret RNA to synthesize protein

129

DNA is replicated to create?

Second copy of molecule which is identical to original

130

DNA replication is bidirectional

Replication begins at specific starting point and proceeds in opposite directions building from 5' to 3'

131

DNA replication: Two strands are unwound and separated. The free, unbound nucleotides match up to the newly separated nitrogenous bases of the?

Parent strand

132

Also called template strand

Parent strand

133

In DNA replication, base pairing (bp) is?

Specific. Where adenine is present only thymine binds in the new strand and vice verse. Where guanine is present only cytosine binds in the new strand and vice versa

134

In DNA replication, what happens to bases that are improperly inserted?

They are removed and replaced with the correct base

135

Newly added bases are added by the enzyme

DNA polymerase

136

DNA replication begins

At the origin (specific DNA sequence)

137

In DNA replication the DNA strands unwind and a?

Replication fork is created. Helicase unwinds the helix and gyrase and topoisomerase relieve strain upstream of fork

138

In DNA replication as nucleotides are added, the replication fork moves?

Down the parental (leading) strand

139

DNA pol requires an?

RNA primer to begin synthesis. RNA primers are laid down by primes.

140

DNA replication: DNA polymerase adds nucleotides to?

3' hydroxyl end. DNA replicated to the 5' to 3' direction. DNA template is read in 3' to 5' direction

141

DNA is antiparallel so the two new strands with grow in

Opposite directions. One strand is the leading strand and one strand is the lagging strand.

142

What is required for each fragment of the lagging strand?
What joins the fragments of the lagging strand?

RNA primers
Joins fragments is DNA ligase.
A second DNA polymerase removes any RNA primers from newly synthesized DNA fragments

143

DNA replication is complete when?

The replication fork reaches the end of the parent strand. The original parent strand and the newly synthesized daughter strand rewind. Each new strand of DNA consists of one parent strand and one daughter strand

144

DNA replication is referred to as?

Semiconservative

145

Portion of DNA acts as template for?

RNA polymerase. Either strand of DNA can act as template.

146

RNA molecule that is produced is called?

Transcript. Numerous transcripts can be produced from one chromosome

147

Three different functional groups of RNA

1) Messenger RNA (mRNA)
2) Ribosomal RNA (rRNA)
3) Transfer RNA (tRNA)

148

Regulating gene expression

- Nucleotide sequence encodes gene regulation mechanism
- Mechanisms determine the duration of synthesis of gene products (products are only made when required)
- Key mechanisms is transcription regulation

149

Specifics of transcription (3 steps)

1) Initiation: RNA polymerase binds to a region of the DNA called the promoter (only one strand of DNA acts as a template, this is called the sense strand, the strand not transcribed is the nonsense strand)
2) Elongation: RNA polymerase adds one complementary nucleotide at a time to the nascent mRNA.
3) Termination: RNA polymerase continues down strand of DNA until it reaches a site on DNA called the terminator. There RNA polymerase and the new mRNA are released from strand of DNA

150

What is gene expression translation?

The decoding of the mRNA sequence into the amino acid sequence of proteins.

151

What 2 additional RNA molecules are involved in translation?

Ribosomal RNA (rRNA) & Transfer RNA (tRNA)

152

What does ribosomal RNA (rRNA) do?

Forms part of the ribosomal machinery used in protein synthesis. rRNA and riboproteins build the ribosomes. Ribosomes are the site of translation (they make proteins)

153

Site of translation

Ribosome

154

What does transfer RNA (tRNA) do?

tRNA each recognize a specific codon of the mRNA and brings the correct amino acid to build a new polypeptide chain (protein)

155

What is a codon?

Three nucleotide sequence of mRNA

156

The language of mRNA is in the form of?

Codons
* Codons are groups of three sequential nucleotides
* Codons are written in terms of their mRNA base sequence
* 61 are sense codons that encode an amino acid
* 3 are stop codons; they do not code for an amino acid

157

The sequence of codons determines the?

Sequence of amino acids in the protien

158

Translation has 3 steps

1) Initiation
2) Elongation
3) Termination

159

3 basic steps for translation initiation

1) Ribosomal subunits binds at the start site
2) tRNA carrying a.a. recognizes the start codon (AUG) of mRNA and attaches (fMet starts every prokaryote protein)
3) Together this forms the initiation complex

160

Start codon

AUG

161

2 basic steps for translation elongation

1) The next tRNA binds to the A site, recognizing the codon and carrying the correct amino acid
2) The prior amino acid forms a peptide bond with the amino acid of the next tRNA

162

3 basic steps for translation termination

1) A stop codon is reached
2) There is ago amino acid and so a pause occurs
3) New polypeptide chain is released from ribosome and mRNA complex

163

Many organisms adapt to changing environments by?

Altering the level of gene expression. The mechanisms include signal transduction and natural selection

164

Signal transduction is

1) The process that transmits information from external environment to inside the cell. This allows cells to respond to changes
2) Two-component regulatory systems. Relies on sensor & response regulator proteins, sensor recognizes change in environment, response regulators activate or repress gene expression
3) Quorum sensing. Organisms sense density of population, enables activation of genes beneficial to the mass

165

Natural selection is?

Mechanisms to enhance survivability
1) Antigen variation: alteration in characteristics of certain surface proteins (ex. Neisseria gonorrhoeae hides from host immunity by changing numerous surface proteins)
2) Phase variation: routine switching on and off certain genes. Altering expression allows portions of population to survive and multiply

166

Before each cell divides is must?

Copy its genetic material in a process called DNA replication

167

DNA replication

1) At the origin of replication the two strands of DNA separate serving as templates for making new strands. The result is a replication bubble
2) The bubble grows in both directions forming two replication forks
3) Many proteins work together at the replication fork
4) DNA polymerases build new strands of DNA

168

DNA polymerase always begins a new strand by ?

Adding to an existing RNA primer that has been constructed first

169

Because strands in a DNA double helix run in opposite directions and DNA polymerase can only add nucleotides in one direction the new strands must be made in different ways.

One new strand, the leading strand, is built continuously. The other new strand, the lagging strand, is built in pieces

170

Synthesis of the leading strand

1) DNA polymerase builds a new strand of DNA by adding DNA nucleotides one at a time
2) Each new nucleotide must pair up with its complementary nucleotide on the parental strand

171

Synthesis of the lagging strand

1) Each piece of the lagging strand begins with a short segment of RNA
2) A protein clamps the RNA & attaches to DNA polymerase which builds the rest of the new piece as DNA
3) When the piece is finished it is released from DNA polymerase

172

How are pieces of the lagging strand joined together?

A different DNA polymerase removes RNA & replaces it with DNA however it cannot finish connecting the pieces. An enzyme called DNA ligase joins the pieces together

173

Finishing replication: Growth of the leading and lagging strands continues on both sides of the replication bubble until?

There are two identical DNA molecules

174

Transcription

1) An enzyme zips along the DNA forming RNA
2) RNA nucleotides line up with their complementary DNA partners transcribing the information in DNA into RNA
3) As the RNA grows it is processed in several ways: 1st a modified

175

Steps of DNA replication

1) Helicase unwinds DNA at point of origin
2) Single strand binding (SSB) proteins bind to DNA strands and keep them separated
3) Primase comes in and makes RNA primers on both strands (this is important because if DNA polymerase comes in it won't know where to start)
4) DNA polymerase begins to build bases. Can only work in the 5' to 3' direction

176

What does the enzyme primase do?

Synthesizes a short RNA molecule that is complementary to the template DNA strand. This RNA primer provides the 3' hydroxyl group that is required by DNA polymerase III

177

What is the central dogma of genetics?

Transcription and translation

178

What are the 3 stop codons?

UAA
UAG
UGA