Lecture flashcards
The study of organisms too small to be seen with the human eye
Microbiology
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
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)
Microbiology born as a science in?
1674
- 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
Theory of Spontaneous Generation
The theory states that?
“organisms can arise from non-living matter”
The theory of spontaneous generation had its supporters and detractors. Detractors included?
– Francesco Redi
– Louis Pasteur
– JohnTyndall
* Each contributed to disproving the theory
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
- Italian biologist and physician
* Demonstrated maggots found on rotting meat came from eggs of flies landing on meat
Francesco Redi
- 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
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
Studied causative agents of disease
– Anthrax
– Examined colonies of microorganisms
Robert Kosh
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
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
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
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
Who was able to establish endospore role in disease transmission
Robert Koch
The Theory of Spontaneous Generation was disproved and the Golden Age of Microbiology was born
– Golden Age was from?
1854–1914
Golden age of microbiology.
Between ___ and ___ most disease-causing bacteria
were discovered
Between 1875 and 1918
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
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
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
Describe microbiologies role in bioremediation
Use organisms to degrade environmental waste. Degrade PCB’s, DDT, clean up oil spills and treat radioactive waste
Bacteria can synthesize numerous products such as?
– Ethanol
– Pesticides
– Antibiotics
– Dietary amino acids
Define genetic engineering
Introduce genes of one organism into an unrelated organism to confer new properties on the organism
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
More people died worldwide of what in the 1918 epidemic than died in WWI, WWII, the Korean War and the Vietnam war combined
Influenza
Modern sanitation, vaccination and effective antimicrobial treatments have reduced?
Incidences of the worst diseases
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
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
Define strain
Variations within a species. Not all organisms from the same species/types are necessarily the same
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
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
Most common cause of human infection. Members widely diverse
Bacteria
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
Archaea share a number of attributes with Bacteria
– Same shapes
– Multiply through binary fission
– Move by means of flagellum
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
Microbial world includes Eukarya which are
– Algae
– Fungi
– Protozoa
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
Fungi are diverse single celled and multicellular organisms: – Single-celled =
– Multicellular =
– Single-celled = yeast
– Multicellular = molds, mushrooms
Gain energy from organic materials. Found wherever organic materials are present
Fungi
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
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
Viruses contain a protein?
Coat surrounding nucleic acid. Essentially protein bag of nucleic acid
Viruses termed obligate intracellular parasites. They must have?
Host machinery to replicate. Inactive outside of host
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
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
Atomic number is?
The number of protons in the nucleus
What is atomic mass (atomic weight)?
The sum of masses of protons, neutrons, and electrons
Consist of a single type of atom
Element
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)
Atoms combine by sharing or transferring valence electrons, this is called?
Chemical bonds
Two or more atoms held together by chemical bonds
Molecule
A molecule composed of one or more elements
Compound
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.
Covalent bonds can be?
Polar or non polar
Universal solvent is
Water because of its polar property
Ionic bonds are formed by?
Gaining or losing electrons. Electrons completely leave first atom and become part of outer orbital of second atom.
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.
Charged atoms are attracted to each other & form a bond between ions
Ionic bond
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.
Important among weak forces holding biological molecules together
Ionic bonds
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).
Hydrogen bonds occur between molecules such as
Water and DNA
Weakest of the biological bonds
Hydrogen bonds
Constantly being formed and broken at room temp.
Hydrogen bonds
At room temp. the average lifetime of a single hydrogen bond is?
A fraction of a second
Large numbers of hydrogen bonds can?
Hold molecules together firmly (DNA)
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
Acidity is measured as?
pH
What is pH?
Defined as concentration of H+ ions. Potential Hydrogen
On a pH scale 0 is?
Highly acidic
On a pH scale 14 is?
Highly alkaline (basic)
Acidity is based on ionization of?
Water to H+ and OH- ions. When H+ and OH- ions are equal solution is neutral
High H+
Acid
High OH-
Basic
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-)
Certain enzymes require positively charged _____ for proper functioning
Ions
Negatively charged phosphate ions are essential in?
Energy metabolism
Small organic molecules act as?
Precursor metabolites. These are converted to the building blocks of macromolecules. Monomers: Nucleotides, amino acids, monosaccharides
Biological macromolecules are divided into 4 classes
1) Lipids
2) Polysaccharides (carbohydrates)
3) Proteins
4) Nucleic acids
Critical component of cell membranes
Lipids
Heterogeneous group of molecules, made up of different subunits
Lipids
Insoluble in water
Lipids
Smallest of the 4 macromolecules
Lipids
Lipids can be divided into two general categories
Simple lipids and compound lipids
Most important compound lipid
Phospholipid
Compound lipids contain
Fatty acids, glycerol and other elements
Phospholipid is made up of?
A phosphate and two fatty acids attached to a glycerol molecule
Phosphate head is?
Polar and soluble in water (hydrophilic)
Fatty acids are non-polar and
Insoluble in water (hydrophobic)
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
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)
Polysaccharides are?
Oligosaccharides are?
Monosaccharides are?
Poly-Large molecules made of carbohydrate molecules
Oligo- Short chains of carbohydrates
Mono- Single carbohydrate molecule
Monosaccharide are classified by?
The number of carbons in the molecule
The most common monosaccharides
Five and six carbon sugars
- Pentose (5C), ribose and deoxyribose
- Hexose (6C), glucose, fructose, and galactose
The carbohydrate disaccharides are produced by?
Joining two monosaccharides through dehydration synthesis
Most common disaccharide in nature is
Lactose and sucrose
Lactose is: glucose + galactose
Sucrose is: glucose + fructose
Less common disaccharide is
Maltose which is glucose + glucose
Proteins constitute over ___% of cell dry weight
50%
Proteins are made up of?
Amino acid subunits including the elements: carbon, hydrogen, oxygen, nitrogen, and sulfur
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
Proteins are composed of numerous combinations of ___ amino acids
20
A proteins function depends upon the?
Shape of the protein and the proteins shape depends on the sequence of amino acids
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
Proteins have 4 potential levels of structure
1) Primary
2) Secondary
3) Tertiary
4) Quaternary
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
Protein denaturation can be?
Reversible or irreversible. The environment determines reversibility
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)
Subunits of nucleic acids are
Nucleotides
Master molecule, determines specific properties of the cell
DNA
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
DNA in living organisms is a?
Double-stranded helical molecule. Hydrogen bonding between the nitrogenous bases
Three hydrogen bonds form between
C & G
Two hydrogen bonds form between
T & A (DNA) or between U & A (RNA)
DNA is double stranded in most cells and viruses.
Two strands are complementary and two strands are antiparallel
RNA is
Necessary for decoding DNA. The structure is similar to DNA
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
Characteristics of each cell is dictated by?
Information contained in DNA. DNA holds the master blueprint
All cell structures and processes directed by
DNA
Complete set of genetic information is referred to as?
Genome
Genome of all cells is composed of?
DNA. Some viruses have RNA genome
Functional unit of genome is?
The gene
Gene coes for?
Gene product which is most commonly protein
Study of transfer of genes is?
Genetics
Study of sequence of DNA is?
Genomics
Living cells must accomplish 2 general tasks to multiply
1) DNA replication
2) DNA expression
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
DNA is replicated to create?
Second copy of molecule which is identical to original
DNA replication is bidirectional
Replication begins at specific starting point and proceeds in opposite directions building from 5’ to 3’
DNA replication: Two strands are unwound and separated. The free, unbound nucleotides match up to the newly separated nitrogenous bases of the?
Parent strand
Also called template strand
Parent strand
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
In DNA replication, what happens to bases that are improperly inserted?
They are removed and replaced with the correct base
Newly added bases are added by the enzyme
DNA polymerase
DNA replication begins
At the origin (specific DNA sequence)
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
In DNA replication as nucleotides are added, the replication fork moves?
Down the parental (leading) strand
DNA pol requires an?
RNA primer to begin synthesis. RNA primers are laid down by primes.
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
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.
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
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
DNA replication is referred to as?
Semiconservative
Portion of DNA acts as template for?
RNA polymerase. Either strand of DNA can act as template.
RNA molecule that is produced is called?
Transcript. Numerous transcripts can be produced from one chromosome
Three different functional groups of RNA
1) Messenger RNA (mRNA)
2) Ribosomal RNA (rRNA)
3) Transfer RNA (tRNA)
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
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
What is gene expression translation?
The decoding of the mRNA sequence into the amino acid sequence of proteins.
What 2 additional RNA molecules are involved in translation?
Ribosomal RNA (rRNA) & Transfer RNA (tRNA)
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)
Site of translation
Ribosome
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)
What is a codon?
Three nucleotide sequence of mRNA
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
The sequence of codons determines the?
Sequence of amino acids in the protien
Translation has 3 steps
1) Initiation
2) Elongation
3) Termination
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
Start codon
AUG
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
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
Many organisms adapt to changing environments by?
Altering the level of gene expression. The mechanisms include signal transduction and natural selection
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
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
Before each cell divides is must?
Copy its genetic material in a process called DNA replication
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
DNA polymerase always begins a new strand by ?
Adding to an existing RNA primer that has been constructed first
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
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
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
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
Finishing replication: Growth of the leading and lagging strands continues on both sides of the replication bubble until?
There are two identical DNA molecules
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
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
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
What is the central dogma of genetics?
Transcription and translation
What are the 3 stop codons?
UAA
UAG
UGA
