Exam 2 Flashcards
Cytoplasm
The substance inside the plasma membrane
80% water plus carbohydrates, lipids, ions, and proteins (CLIP)
Cytoskeleton in cytoplasm; gives a cell its shape
Which of the following is common to all bacterial species?
Ribosomes, Plasma Membrane
Which of the following is the primary distinction (defining characteristic) between prokaryotic and eukaryotic cells?
Presence vs absence of a nucleus
In bacteria, the ribosomes subunits are:
30S, 50S
A compound that is transported through a membrane by a transporter protein without energy expenditure is called:
Facilitated diffusion
What part of the bacterial cell is targeted by beta-lactam antibiotics?
cell wall
Fluorescent
Some molecules have the ability to absorb light at one wavelength and emit at a different wavelength
These molecules are engineered into bacteria to aid in detection
Fluorescence microscopy: green squiggly lines
What is the defining difference between prokaryotic and eukaryotic cells?
Eukaryotes have a nucleus with DNA, prokaryotes don’t have a nucleus
Which of the following are examples of an anabolic process?
DNA replication, Transcription, Translation
Why: builds DNA, RNA, and protein(s)
Which of the following is found in/at the active site of an enzyme?
Competitive inhibitor, substrate(s), product(s)
Why: products are present at the active site, even if it’s just momentarily
Which of the following is involved in both cellular respiration and fermentation?
Glycolysis
Carbohydrate fermentation tests contain a _________that will change color to signify that fermentation has occurred
pH indicator
Why does enzyme activity decrease as temperature decreases?
Fewer interactions between substrate and enzyme
Which of the following statements most accurately describes the movement of water when a cell is placed in an environment with low solute concentration (e.g. pure water)?
Water diffuses into the cell due to the hypotonic environment, causing the cell to rupture
In the lab, you are inoculating a culture when you:
Transfer some bacteria into media
An experiment began with 5 bacterial cells and ended with 40 cells. How many generations did the cells go through?
3
Why: Start with 5 → 1 double = 10 → 2nd double = 20 (10 x 2) → 3rd double = 40 (20 x 2)
Which of the following statements about oxygen are true?
Oxygen is required by some bacteria (obligate aerobes)
Oxygen is toxic to some bacteria (anaerobes)
Some bacteria use oxygen as the final electron acceptor during cellular respiration
Some bacteria can break down oxygen and reactive oxygen species using enzymes
Which of the following approaches is based on probability/statistics and used for estimating bacterial counts for water safety?
Most Probable Number
Complex Media
Most often used
Supports the growth of many types of bacteria
Contains ingredients like yeast extract, meat extract, and protein digests
Chemical composition of ingredients isn’t defined – so media composition varies slightly from batch to batch
Defined Media
An alternative to complex media
Contains only ingredients whose chemical composition is defined
E.g. glucose, ammonium phosphate, sodium chloride, magnesium sulfate, potassium phosphate
Is more consistent from batch to batch
Only good for growing a certain kind of bacteria
Obligate aerobes
Require oxygen
Rely solely on respiration for energy
Facultative anaerobes
Can grow in the presence or absence of oxygen
Perform respiration when oxygen is present
Perform fermentation (or anaerobic respiration) when oxygen is absent
Anaerobes
Unable to use oxygen and most are harmed by it
Perform fermentation or anaerobic respiration
Microaerophiles
require oxygen concentration lower than air
Psychrophiles
microbes that grow best in cold temperatures
Mesophiles
microbes that grow best in moderate temperatures (including room temp and core body temp)
Thermophiles
microbes that grow best in hot temperatures
Acidophiles
microbes that grow best at low pH
Neutrophiles
microbes that grow best at neutral pH
most bacteria, especially human pathogens, are neutrophiles
human body is a neutral environment; bacteria have evolved to survive in a neutral pH
Metabolism
all chemical reactions within an organism
catalyzed by enzymes (-ase suffix)
Alkaliphiles
microbes that grow best at high pH
Catabolism
Release energy (break down complex molecules)
Ex. Glucose broken down → releases energy (ATP) for bacteria to use
Catabolic processes: Fermentation, respiration
Anabolism
require energy (building of complex molecules)
Energy is often stored in the form of ____
ATP
Lysozyme
Antimicrobial enzyme present in tears and saliva
Breaks the peptide bonds between NAG and NAM residues in peptidoglycan
Part of our innate immune system (kills bacteria non-specifically)
Beta-lactam antibiotics
Inhibits the enzyme (transpeptidase) that forms the peptide bridges in peptidoglycan
Includes penicillin, amoxicillin, etc.
The antibiotics we take allow the bacteria to be targeted
Peptide bridges never get formed → weak cell wall → cell susceptible; will die shortly after
Confocal microscopy
Type of fluorescence microscopy that captures multiple planes to produce a 3-dimensional image
Stack images on top of each other
Multicolored image
Fimbriae
Hairlike appendages (spiky looking) that allow for attachment
Important for biofilm formation, colonization within host
Typically many fimbriae on the cell surface (10’s -100’s)
Composed of the protein pilin that are stacked on top of each other
Pili
Involved in motility (gliding and twitching motility)
Conjugation (sex) pilus: a special type of pilus involved in DNA transfer from one cell to another
Pilus retracts, bringing the two cells in direct contact for DNA exchange
Only one pili per cell
Also composed of the protein pilin
Glycocalyx
General term for substance found external to the cell wall
Sticky and gelatinous layer
Made of polysaccharide (or sometimes polypeptide)
Two types: Capsule and Slime Layer
Capsule (type of glycocalyx)
Common to bacterial pathogens
Protects bacteria from phagocytosis
Phagocytes kill bacteria
Slime layer (type of glycocalyx)
Produced by bacteria in nature
Protects them from their environment; not hiding
Sterilization
Removing/destroying all microbial life
Not practical or necessary in everyday life
Disinfection
Destroying harmful microorganisms
Disinfectants are applied to surfaces (inanimate objects)
Not safe on skin
Practical in everyday life
Ex. Formaldehyde, Bleach, Phenol
Antisepsis
Destroying harmful microorganisms from living tissue
Are mild forms of disinfectants
Can be used on skin
HAI: Hydrogen peroxide, Alcohol, Iodine
Media
Also called growth media or culture media
(singular: medium)
Collection of nutrients used to grow bacteria in the lab
Inoculate (verb)
The process of transferring microbes into media
“I collected some bacteria with a sterile loop and inoculated the media.”
Placing inoculated media at an appropriate temperature for growth (often uses an incubator)
“After inoculating, the media is incubated at 37C overnight.”
Culture
The practice of growing microbes in the lab (verb)
“Today in lab, we cultured E. coli on agar plates.”
Microbes grown in the lab (noun)
“When I arrived in lab, I looked at our culture from the previous class.”
“Today in lab, I inoculated media with E. coli and incubated it to generate a culture.”
Osmotic pressure
results when a solute is at different concentrations inside and outside the cell
Hypertonic environment
higher solute concentration outside the cell
Hypotonic environment
lower solute concentration outside the cell
Isotonic environment
equal concentration inside and outside of cell
Halophile
Microbe that thrives in high salt environment
Even as high as 30% (for comparison, ocean water is ~3%)
Allosteric Inhibition
Inhibitor binds the enzyme at another location, causing a conformational change and loss of the active site
Causes protein to change shape → changes active site shape
Allosteric site: somewhere other than the active site
Strepto
When the cells divide, they multiple next to each other in the same plane
Why it’s a chain
Staphylo
Sarcinae: plane of division changes each time, so it forms a cluster
Active Transport
Substances move from low to high concentration; work against concentration gradient
Requires a transporter protein and energy (ATP)
Cell Wall
Prevents osmotic lysis (cell bursting from osmotic pressure) and protects the cell membrane from environmental stressors
~99% of bacterial cells have a cell wall, but some don’t
Made of peptidoglycan (in bacteria)
Enrichment culture
A selective medium that is used to increase the number of only certain bacteria (to enrich for them)
E.g. a bacterium that is present in small number within a soil or fecal sample
Interested in one type of species in soil sample → use selective media to grow just that species
Turbidity
The cloudiness of a bacterial culture
Is proportional to the number of cells in the culture
Measuring Turbidity
Use a spectrophotometer to quantify turbidity
A beam of light is passed through the bacterial suspension to a light-sensitive detector
Light does or doesn’t get blocked by culture
Live and dead cells block light
Absorbance (or optical density, how much light gets blocked by cells in sample) is measured
Not # of cells and not if they’re dead or alive
Ionizing radiation
X-rays, gamma rays, electron beams
High energy
Ionizes water to form reactive oxygen species (ROS) that wreak havoc
Nonionizing radiation (UV)
Doesn’t penetrate surfaces
Sporulation
endospore formation; process of forming an endospore
Electron Microscopy
Uses electrons instead of photons (light)
The shorter wavelength of electrons gives greater resolution
Used for images too small to be seen with light microscopes, such as viruses
B/W image; impart color after
2 types: TEM + SEM
Germination
Re-activation of endospore to vegetative state
Senses better conditions → reactivates
Transmission (TEM)
Electrons pass through ultrathin sections of a specimen
Internal structures can be seen; image of inside of cell
Scanning (SEM)
Electrons scans the surface of an entire specimen
External structures (ex. cilia) and topography can be seen
Bacteria often use _____________ as their primary energy source
carbohydrates (sugars)
Proteins and lipids are also commonly used as energy sources, but sugars are preferred
Selective media
Designed to suppress the growth of certain bacteria (and encourage the growth of others)
Salts and dyes are often included to inhibit the growth of certain bacteria
E.g. Bismuth sulfite agar is used to select for Salmonella typhi because bismuth sulfite inhibits the growth of most other bacteria
Something is included in the media so that only certain bacteria can grow and others can’t
Radiation causes _________
Mutations (changes in DNA sequence)
After many mutations have accumulated, some (by chance) will have been lethal
Cell not able to reproduce
Lag Phase
Bacterial cells first placed in a new environment; first must ‘prepare’ for growth before reaching a max growth rate
First phase
Before log phase
No increase in population
Log phase (or exponential growth phase)
Period of unconstrained growth
Growth during this phase is exponential
When plotted on a log scale it appears as a straight line with the greatest slope
After lag phase
Stationary Phase
Follows log phase
The number of new cells being generated will soon match the number of cells dying → plateau/equilibrium
Death Phase
After awhile, cell death will outweigh cell division
Follows stationary phase; downward slope
Microbial death is exponential [like growth]
Direct microscopic count
Put sample on hemocytometer
Channels for sample to be injected onto, cover slip put on top
Look at cells under microscope with grid to count cells in each grid area
Apply equation to find total # of cells
Bacteria reproduce through ______________
binary fission
The bacterial cell gets larger, its genome is replicated, and it splits into two
Not mitosis, not meiosis (those are eukaryotic processes)
Generation time
The amount of time it takes for a bacterial cell to reproduce/to double
Some take <20 minutes (in the lab), others take >24 hours
Peptidoglycan
Chain of alternating sugar residues:
N-acetylglucosamine (NAG)
N-acetylmuramic acid (NAM)
Chains are linked by polypeptide ‘bridges’: Green/blue balls: peptides (linked amino acids)
Structure wraps around the entire cell like a net
Ribosomes
Complex that synthesizes/make proteins (translation)
All cells have ribosomes; bacteria have 70S ribosome
Made of protein and ribosomal RNA (rRNA)
70S Ribosome
50S + 30S subunits
50+30=80, not 70
S = different unit that isn’t an additive property
Measure of how quickly molecules get centrifuged
Human Ribosome: 40S + 60S, 80S complex
Photoautotroph
get their carbon from CO2 and energy from light
Chemoautotroph
get their carbon from CO2 and energy from chemicals
Chemoheterotroph
get their carbon from organic compounds and energy from chemicals
Photoheterotroph
get their carbon from organic compounds and energy from light
Flagella
Primary mechanism of motility in bacteria
Allows movement toward nutrients or away from danger; sense environment (taxis)
Composed of protein (several including the monomer flagellin)
The flagella rotates, driven by a molecular motor, propelling the bacterial cell through the environment
Flagella proteins are H antigens and distinguish among strains (e.g., Escherichia coli O157:H7)
H: refers to type of flagella (ex. Type 7)
Different bacteria have different arrangements of flagella
Not all bacteria have flagella
Lipopolysaccharide (LPS)
3 parts:
Lipid A – anchors LPS into the outer membrane
Core polysaccharide – bottom part of tail, connects lipid A to O polysaccharide
O polysaccharide – chain of sugars that protrude from the cell, targeted by the host immune system (O antigen), outer part of tail
Some bacteria have a shorter version of LPS – called lipooligosaccharide (LOS)
Porins
proteins embedded within the outer membrane that form channels and control entry/exit of molecules
Passive Transport
Substances move from high concentration to low concentration; both simple/facilitated follow the concentration gradient, happens automatically so long as the molecule is small and uncharged
No energy expended [for simple or facilitated]
2 types: Simple + Facilitated
Simple diffusion
Type of passive transport
Small, uncharged molecules can pass directly through
Facilitated diffusion
Ions and large/charged molecules pass through a transporter [protein]
Driven by the concentration gradient
Nucleoid
where the DNA is found
somewhere in the cytoplasm
Bacterial chromosomes
circular thread of DNA that contains the cell’s genetic information
Plasmids
Extrachromosomal (not apart of chromosome) genetic elements
Carry non-essential genes; Essential genes are on chromosome
Give bacteria extra abilities (ex. antibiotic resistance, production of toxins) –> Specialty genes
Look like rings
How does temperature impact the rate of catalysis?
Faster reaction at high temperatures
Increase the likelihood of interaction between the substrates/enzyme; substrate is hitting active site more often
Slower reaction(s) at low temperatures
Microbial growth
the growth of bacterial population (number of cells)
not the size of cells
Microbes’ physical and chemical growth requirements
Physical (TOP): temperature, osmotic pressure, pH
Chemical: Nutritional requirements (carbon, oxygen, etc)
If bacteria have _______ _________, they will continue to divide at a maximum growth rate
abundant resources
Eventually, resources will become depleted and the growth rate will slow
Most probable number (MPN)
Used to determine if a water sample is safe to drink
Determines how much bacteria is in sample
Doesn’t tell you how much total bacteria is present, only coliform (type of bacteria)
Low temperature has a _________ effect
bacteriostatic (prevents the growth of bacteria)
Refrigeration
Slows growth of most microbes (not psychrophiles that grow fast at low temps)
Most human pathogens do not grow well at low temperatures; why we store food in fridge
Listeria is an exception; can still grow at low temperatures
Freezing
Stops growth completely [while frozen] until thawed
An effective method of storing microbes long-term
Microbes are still there, but don’t grow while in freezer
Start growing when taken out of freezer
Helpful in laboratory setting to work with bacteria in the future/again
How is disinfection and antisepsis often achieved using chemicals?
Alters membrane permeability
Damage proteins (enzymes)
Damage nucleic acids (DNA)
Blood agar
A differential medium that contains blood cells that can be lysed by certain bacteria – leading to zones of clearing (hemolysis)
Tests if the bacteria being tested lyses the red blood cells
Autoclave
Steam under pressure
121°C at 15 psi for 15 min
Kills all organisms/microbes and endospores
Pasteurization
Reduces number of microbes
High-temperature short-time (HTST): 72°C for 15 sec
Thermotolerant organisms survive
Used in beverages (milk, juice)
Heat as a sterilizer
Autoclave
Pasteurization
Moist heat
Flaming (dry heat sterilization)
Moist heat
Coagulates/denatures proteins
Boiling
Mannitol Salt Agar (MSA)
Both selective and differential media
How is MSA selective?
It contains a high concentration of NaCl (salt), which inhibits the growth of most bacteria (except Staphylococcus spp; Staphylococcus species)
How is MSA differential?
Contains mannitol (a sugar alcohol) that some Staphylococcus spp ferment while other don’t
The products of mannitol fermentation are acids, which drop the pH of the media
MSA plate contains a pH indicator → low pH turns the pH indicator (included in the media) from red to yellow
Yellow = bacteria can ferment mannitol
Enzymes
Position substrates in a way that favors their conversion into products
Are almost always proteins
Can be recycled
Have specificity for certain substrates
Binding occurs in the active site (opening)
Active site is formed based on protein folding (interaction between amino acids that make up the protein)
Chemical reaction only occurs if substrate fits into active sit
Improper protein folding → wrong active site formed → chemical reaction can’t occur
Filtration
Passage of substance through a screen like material
Vacuum line speeds up the process; pulls liquid through faster
Used for heat-sensitive materials (Ex. Sterilize antibiotics; antibiotics can’t contain bacteria and can’t be heated)
Membrane filters remove microbes > 0.22 μm
Smaller pore sizes are needed to filter out viruses and small bacteria
This is how viruses were first discovered; they would pass through filter
High-efficiency particulate air (HEPA) filters:
Pore size down to 0.01 μm
Can filter viruses if small enough
Since:
The cell wall is essential for bacterial viability
And it is composed of peptidoglycan, which is unique to bacteria
Then…
it is an easy target for killing bacteria [without harming our own cells]
competitive inhibition
Inhibitor binds to the active site, preventing the substrate from binding
Cell can make an inhibitor; prevents cell from carrying out reaction
Gram positive cells
Stain purple because the primary stain (crystal violet) forms a crystalized complex (when iodine is added) within their thick peptidoglycan cell wall
Complex isn’t washed out by the decolorizer (alcohol)
Stain is stuck in the thick cell wall
Gram negative cells
Thin peptidoglycan cell wall → does not retain the crystalized complex and loses its purple color when washed with decolorizer
Counterstain imparts a pink color to the Gram negative cells.
Describe the cell wall in gram positive cells
Thick, multiple layers of peptidoglycan
Exposed to the environment, located outside the cell membrane
Peptidoglycan layers held together by teichoic acid and anchored to cell membrane by lipoteichoic acid
Only gram positive bacteria have teichoic acid because gram negative don’t need it; thin layer so not much to keep together
Describe the cell wall in gram negative cells
Thin, single layer of peptidoglycan
Contained within the periplasm
Lipopolysaccharides (LPS) found on outer membrane’s outer leaflet
Stack: (sandwiches peptidoglycan)
Outer Membrane
Peptidoglycan (thin)
Plasma Membrane
periplasm
the space between the plasma membrane and outer membrane [in gram negative cells]
Why do only gram negative bacteria have LPS?
gram positive bacteria don’t have an outer membrane
What do all bacterial cells have?
70CNP:
70S Ribosome
Cytoplasm
Nucleoid containing DNA
Plasma membrane
Eukaryotic cells
DNA contained with a nucleus (defining difference)
Larger in size; why Hooke could see plant/animal cells but not bacterial cells
Multiple linear chromosomes, in pairs (diploid) or more copies (polyploid)
DNA wrapped around histones
Divides by mitosis
Organelles (e.g. ER, Golgi, mitochondria, chloroplasts)
Polysaccharide cell walls, when present;
Plants have cell walls made of polysaccharides
Animal cells don’t have cell walls
Prokaryotic cells
Lack nucleus (defining difference)
Smaller in size
Single circular chromosome (haploid)
No histones
Divides by binary fission
No organelles
Bacteria: peptidoglycan cell walls
Archaea: pseudomurein cell walls
Peripheral proteins
Sit on cytoplasmic membranes surface
Project either on the inside or outside
Integral and transmembrane proteins
Penetrate the membrane, span the membrane
Wedged into the membrane
Cytoplasmic Membrane
Also called ‘cell membrane’ or ‘plasma membrane’
Separates outside of cell and inside of cell
Semi-permeable membrane that encloses the cytoplasm; Allows the passage of some molecules, but not others
Made primarily of phospholipids; 2 leaflets
Also contains proteins: Peripheral + Integral and transmembrane
Differential media
Designed to distinguish between bacteria based on the observable characteristics when grown on media
pH indicator included to indicate if a provided substrate is metabolized to acids/bases; pH indicator changes color based on pH changes
Something is included in the media so that anything that grows looks different
A colony forms when…
a single bacterial cell is deposited onto an agar plate and divides repeatedly until visible by the naked eye
Colonies are obtained using the…
Streak plate method
Starts as mixed culture → streak plate → get isolated colonies of each type (pure cultures of each type of bacteria)
Effectiveness of treatment for killing microbes depends on:
Number of microbes
Environment (organic matter, temperature, biofilms)
Time of exposure
Microbial characteristics; Alcohol doesn’t kill some microbes
Disinfect for a longer period of time = more killing of microbes
If bacteria needs energy eventually but wants to be efficient in breaking down sugar→
respiration
If bacteria needs energy ASAP →
fermentation
Reactive oxygen species (ROS)
Group of compounds derived from O2 that damage cells’ macromolecules (protein, DNA)
Ex. hydrogen peroxide (H2O2) – can be broken down by the enzyme catalase
So that H2O2 doesn’t cause damage to the cell
Bacteria in presence of oxygen can tolerate it b/c of catalase
Purpose of liquid (broth) for growing microbes
When shaken in broth, all cells in the culture experience the same environment conditions (homogeneous)
We need to provide appropriate _______ to grow bacteria in the lab
nutrients
Purpose of solid (agar) for growing microbes
On the surface of an agar plate, bacterial cells can be separated from one another so that isolated colonies can develop after incubation
Agar is a non-nutritious solidifying agent; doesn’t serve as food to the microbes
Carbohydrates/sugars can be broken down by bacteria through 2 routes:
cellular respiration + fermentation
Cellular respiration
Requires O2 as final electron acceptor (only performed by aerobic bacteria)
Allows the cell to get as much energy as possible from the sugar it’s breaking down
Fermentation
No O2 requirement
No Krebs cycle or electron transport chain
Both respiration and fermentation start with __________
glycolysis
Explain the process/steps of respiration
- Glycolysis
- Krebs cycle (aka citric acid cycle)
- Electron transport chain (oxygen as final acceptor; aerobic)
An isolated colony represents a _____ __________
pure culture
pure culture
the entire population of cells arose from a single cell
Acid-Fast Cell Walls
Similar to gram-positive cell walls
Complex cell walls containing mycolic acid that imparts waxy character
Only a few bacteria: Mycobacterium spp., Nocardia spp.
Don’t stain well with Gram stain; inconsistent
Stain with carbolfuchsin (pink, with heat)
Some bacteria have no cell wall (Mycoplasma spp)
Endosymbiotic theory
Larger microbial cell engulfed smaller bacterial cell, developing into the first eukaryotes
Instead of eating and destroying the bacterial cell, it keep it around and when the larger cell divided, each of the two cells received the bacteria as well → bacterial cell was a source of energy to the larger cell
Ingested photosynthetic bacteria became chloroplasts; harvest energy from light
Type of cell engulfed took light and turned it into energy
Ingested aerobic bacteria became mitochondria
Today, if we take human cells and separate the mitochondria, the mitochondrial DNA looks like…
Bacterial DNA → strong evidence that what we call mitochondria today was its own independent bacteria 3 billion years ago
Chloroplast DNA looks like bacterial DNA, not plant DNA
Strengthens endosymbiotic theory
First eukaryotes evolved how many years ago?
2.5 billion
Life arose as simple organisms how many years ago?
3.5 to 4 billion
Explain how too much heat damages enzymes
Too much heat can damage enzymes → denature
A protein is a chain of amino acids held together by strong covalent bonds (peptide bonds)
A protein folds into a distinct conformation (3D structure) due to hydrogen bonds between non-adjacent amino acids
Heat can break the weak hydrogen bonds, causing the protein to misfold
A misfolded protein is no longer functional
After each generation, the cell population doubles in number.
Population size can be calculated using:
Ng = N0 * 2^g
g = the number of generations
Ng = the number of cells after g generations
N0 = the number of cells initially
Quantitative Plate Count
Determines # of live cells in a given sample; population density
2 indicators of a positive fermentation test:
color change (red to yellow), bubble in Durham tube
pH
A measure of H+ (hydrogen ion concentration) (and consequently OH-) in a solution
On a log scale
A solution with pH 6 has 10x the [H+] than pH 7
Each unit is a 10 fold difference in H+ concentration
Most proteins fold at neutral pH
Too low or too high pH → enzymatic activity drops
Affects the folding of proteins and efficiency of enzymes
Protein = amino acids linked together
Each amino acid has charges
pH affects the charge of amino acids in proteins, which affects protein folding
How to carry out MPN
Grab 15 separate tubes with broth
Into 5, transfer (ex.10mL) water in
In the next 5, transfer a smaller amount of water (ex. 1mL)
In the next 5, transfer even smaller amount (ex. 0.1mL)
Testing: the larger amount of sample being tested/added, the more likely bacteria is in sample
If so, tube contains some kind of nutrients for bacteria to grow
Yellow = bacterial growth
Example of rows: 5-3-1
Take those 3 numbers, look at table; shows MPN of bacterial per ___ mL is ___ bacteria
Which of the following can be used as antiseptics?
hydrogen peroxide, alcohol, iodine
What of the following is achieved using an autoclave?
Sterilization
Central Dogma
The flow of genetic information
Information is stored within DNA, converted into RNA, then used to produce proteins
In the central dogma, information is stored within ______
DNA
Genetics
The study of heredity – how traits are passed on
Was a field before DNA was discovered
Today, genetics refers to the study of genes and DNA, including:
how DNA stores information
how the information stored within DNA is ACCESSED
how DNA is replicated
Genes
segments of DNA that encode functional products, usually proteins
Genome
All the genetic information in a cell
Includes all chromosomes and any other forms of DNA (e.g. plasmids)
Chromosomes
Large pieces of DNA that store essential genetic information
Humans: 23 pairs of linear chromosomes
Bacteria: typically 1 circular chromosomes (many exceptions though)
DNA Structure
Double helix
Backbone consists of deoxyribose-phosphate
Two strands are held together by hydrogen bonds between complementary bases:
A-T (2 H bonds)
C-G (3 H bonds)
Strands are antiparallel; 5’ and 3’ ends
Order of the bases forms the genetic instructions of the organism
Semiconservative replication
Each new double-stranded DNA molecule contains one original (conserved) strand and one new strand
Because the bases along the two strands of double-helical DNA are complementary…
one strand can act as a template for the production of a new strand
Helicase
Enzyme that separates the DNA strands – unzips DNA
Breaks the hydrogen bonds between base pairs (denatures the DNA)
Reveals the bases so the strand can be used a template for the synthesize of a new strand
Forms a replication fork
DNA replication involves the coordination of many ____________
enzymes
As the helicase ‘unzips’ the DNA, __________ proteins bind the single-stranded DNA
stabilizing
Prevents degradation of the ’unzipped DNA’
Replication fork
One fork moves in a clockwise direction, another fork moves counter-clockwise
Where DNA replication is occurring
Formed by helicase
RNA primase
Enzyme that synthesizes a short RNA primer that is complementary to the sequence of the template strand
The RNA primer is single-stranded (and will eventually get replaced)
The RNA primer is needed because DNA polymerase can’t initiate DNA synthesis on its own
DNA polymerase
Adds nucleotides to the growing DNA strand
Uses RNA primer as reference point
Reads template in the 3’ → 5’ direction
Synthesizes DNA in the 5’ → 3’ direction
Moves away from helicase
After the DNA polymerase begins synthesizing DNA, the RNA primer is removed by ______
RNase
DNA Ligase
glues together Okazaki fragments in the DNA
Why does the lagging/leading strand situation exist?
DNA polymerase can only read in 3’ to 5’ and synthesize in ‘ to 3’
The field of genetics includes (select all that apply)
the study of heredity
how DNA stores information
how the information stored within DNA is accessed
how DNA is replicated
DNA replication is semi-conservative meaning that …
Each double-stranded DNA molecule contains one original strand and one new strand
Which of the following enzymes are involved in DNA replication?
Helicase, RNA primase, DNA polymerase
Which of the following accurately describes the movement of DNA polymerase during replication of bacterial DNA?
DNA polymerase only reads the template strand in the 3’ to 5’ direction
Which of the following statements about the lagging strand are correct?
DNA synthesis on the lagging strand results in the production of Okazaki fragments
DNA polymerase on the lagging strand moves away from the helicase
Disk-Diffusion Method
Evaluates efficacy of chemical agents
Filter paper disks are soaked in a chemical and placed on a culture lawn
Measure the zone of inhibition (ZOI) around the disks
Larger ZOI → more effective
Testing ability of chemical to kill the bacteria on the plate
Why does DNA replicate?
It wants to divide so the DNA has to be copied so that each cell has a copy of the DNA
Leading Strand
Synthesized continuously
DNA polymerase moves toward the helicase
Lagging Strand
DNA is synthesized in short patches (Okazaki fragments)
DNA polymerase moves away from helicase
