Exam 2 Flashcards
Endocytosis
A form of active transport in which a cell transports molecules (such as proteins) into the cell (endo- + cytosis) by engulfing them in an energy-using process.
…the uptake by a cell of material from the environment by invagination of its plasma membrane; it includes both phagocytosis and pinocytosis.
Phagocytosis
A form of endocytosis in which the cell membrane actively engulfs large particles or cells into vesicles. A phagocyte is a cell specialized for doing this.
Pinocytosis
The engulfment, or endocytosis, of liquids by extensions of the cell membrane.
Receptor-mediated endocytosis
a process by which cells absorb metabolites, hormones, other proteins - and in some cases viruses - (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being absorbed.
Metabolism
the sum of the chemical reactions in an organism
Catabolism
the breakdown of complex molecules in living organisms to form simpler ones - energy releasing process.
Anabolism
the synthesis of complex molecules in living organisms from simpler ones - energy using process
Catabolic reactions
breakdown of a molecule - release energy
Ex. Glycolysis -> Glucose
Anabolic reactions
synthesis of molecules - use up energy
Ex. Gluconeogenesis
What catalyzes chemical reactions in organisms and are important in metabolism?
Enzymes (proteins)
Are enzymes used up in chemical reactions?
no
Chemoheterotrophs
organisms that obtain energy by the oxidation of electron donors in their environments. (take organic matter and process it)
Enzymes
biological catalysts - represent the “workhorses” of the cell - speed up reactions
List 4 important enzymes.
NAD+ NADP FAD Coenzyme A (all capture electrons)
What factors influence enzyme activity?
temperature
pH
substrate concentration
enzyme concentration
Coenzymes
a nonprotein compound that is necessary for the functioning of an enzyme (NAD+; carriers of electrons)
Oxidation
the removal of electrons
Reduction
the gain of electrons
Redox reaction
an oxidation reaction paired with a reduction reaction
Glycolysis
(The oxidation of glucose to pyruvic acid; produces ATP and NADH.) An aerobic and anaerobic pathway which breaks down one molecule of glucose into two molecules of pyruvate. (overall generates little ATP!)
- Oxidation of glucose
- Cytosolic (occurs in the cytosol)
- Can occur with or without O2
in biological systems, the electrons are often associated with what?
hydrogen atoms
Biological oxidations are often what?
dehydrogenations
What are the possible fates of glucose through glycolysis?
Glucose -> pyruvate
Pyruvate -> ethanol or lactate (fermentation - low O2)
Pyruvate -> CO2 + H2O (complete oxidation - with O2)
What is the chemical formula for glucose? How many carbons does it have?
C6H12O6 (6 Carbons)
What happens during the preparatory stage of Glycolysis?
- 2 ATP are used
- Glucose is split to form 2 Glucose-3-phosphate
What happens during the energy-conserving stage of Glycolysis?
- 2 Glucose-3-phosphate oxidized to 2 Pyruvic acid
- 4 ATP produced
- 2 NADH produced
What is produced after the preparatory stage and energy-conserving stage of Glycolysis?
- 2 Pyruvate
- 2 ATP
- 2 NADH
What are the general functions of Glycolysis?
- Provides ATP energy
- Generates intermediates for other pathways including Pyruvate dehydrogenase which leads to the Krebs Cycleo
What tissues are associated with glycolysis (sources of ATP)?
- RBC’s - energy
- Skeletal muscle - energy during exercise
- Adipose tissue - source of glycerol-P and acetyl-CoA
- Liver - source of glycerol-P and acetyl-CoA
How can you slow down a pathway?
- Competitive inhibition - blocks the substrate from binding to the active site of the enzyme (a form of enzyme inhibition where binding of the inhibitor to the active site on the enzyme prevents binding of the substrate and vice versa. Most competitive inhibitors function by binding reversibly to the active site of the enzyme.)
- Feedback inhibition - A cellular control mechanism in which an enzyme that catalyzes the production of a particular substance in the cell is inhibited when that substance has accumulated to a certain level, thereby balancing the amount provided with the amount needed.
- Allosteric regulation - the regulation of a protein by binding an effector molecule at a site other than the enzyme’s active site. The site to which the effector binds is termed the allosteric site.
Name three processes that breakdown carbohydrates to release energy.
- Glycolysis
- Krebs cycle
- Electron transport chain
Molecules of ATP produced by glycolysis (low O2) are produced through what?
substrate-level phosphorylation (simple fermentations)
What is Glycolysis called when O2 is present? What is the final acceptor? Does it produce more or less ATP than substrate-level phosphorylation?
Cellular respiration
O2 is the final acceptor
Produces LOTS of ATP - more
What are the four stages of metabolism?
- Glycolysis
- Intermediate step
- Kebs cycle (TCA)
- Electron Transport Chain
What happens during the Intermediate step?
conversion of of pyruvate into acetyl CoA by the pyruvate dehydrogenase complex (3 enzymes); Pyruvic acid (from glycolysis) is oxidized and decarboyxlated.
What is the net result of the intermediate step?
- generates Acetyl CoA
- lose CO2
- adds thioester group
- NADH
How much ATP and NADH is produced per glucose molecule after the intermediate step? How much ATP and NADH is produced net after this step?
2 ATP and 4 NADH per glucose molecule produced by this step
Net (2 glucose molecules): 4 ATP and 8 NADH (4 from the intermediate step + 1 from each of the 4 pyruvates - 2 pyruvates from each molecule of glucose)
What happens during the Krebs cycle?
Acetyl CoA condenses with oxaloacetate to generate a six carbon intermediate (citric acid) that is acted upon by the enzymes which comprise this pathway. (oxidation of acetyl CoA produces NADH and FADH2 and little ATP)
Krebs Cycle is also known as what?
Citric Acid Cycle - a metabolic pathway that forms part of the break down of carbs, fats, and proteins into CO2 and H2O in order to generate energy.
Where does the Krebs Cycle take place?
in the mitochondria
How many carbons does acetyl CoA have?
2 carbons
How many carbons does oxaloacetate have?
4 carbons
How many carbons does citric acid have?
6 carbons
What is produced per each acetyl CoA (turn of the Krebs cycle)?
3 NADH
1 FADH2
1 ATP
About how much ATP is 1 NADH equivalent to?
About how much ATP is 1 FADH2 equivalent to?
1 NADH = 3 ATP
1 FADH2 = 2 ATP
How much ATP, NADH, FADH2, and CO2 will you have total after glycolysis?
ATP - 2
NADH - 2
FADH2 - 0
CO2 - 0
How much ATP, NADH, FADH2, and CO2 will you have total after the intermediate step?
ATP - 0
NADH - 2
FADH2 - 0
CO2 - 2
How much ATP, NADH, FADH2, and CO2 will you have total after the Krebs cycle?
ATP - 2
NADH - 6
FADH2 - 2
CO2 - 4
How many turns of the Krebs Cycle are made per glucose molecule?
2
What is the Electron Transport Chain?
A series of membrane complexes act as oxidation/reduction centers and pass on the electrons donated by coenzymes NADH and FADH2. The energy released can be used to produce ATP by chemiosmosis by a process called oxidative phosphorylation.
How much ATP, NADH, FADH2, and CO2 will you have total after glycolysis, the intermediate step, and the Krebs cycle combined?
ATP - 4
NADH - 10 (each NADH = 3 ATP - +30ATP)
FADH2 - 2 (each FADH2 = 2 ATP - +4ATP)
CO2 - 6
How much ATP is produced from complete oxidation of 1 glucose molecule in eukaryotes?
36 ATP’s
Aerobic respiration
the final electron acceptor in the Electron Transport Chain is molecular oxygen.
A small amount of ATP is produced by what? A large amount of ATP (90%) is produced by what?
small amount - substrate level phosphorylation
large amount - oxidative phosphorylation “ATP synthase”
where does Glycolysis take place in Eukaryotes? in Prokaryotes?
Eukaryotes - cytoplasm
Prokaryotes - cytoplams
where does the Intermediate Step take place in Eukaryotes? in Prokaryotes?
Eukaryotes - cytoplasm
Prokaryotes - cytoplams
where does the Krebs cycle take place in Eukaryotes? in Prokaryotes?
Eukaryotes - Mitochondrial matrix
Prokaryotes - cytoplams
where does the ETC take place in Eukaryotes? in Prokaryotes?
Eukaryotes - Mitochondrial inner membrane
Prokaryotes - Plasma membrane
Four facts about Fermentation:
- releases energy from oxidation of organic molecules
- does not require oxygen
- does not use the Krebs cycle or ETC
- uses an organic molecule as the final electron acceptor
General definition of fermentation:
the chemical conversion of carbohydrates into alcohols or acids.
What does alcohol fermentation produce?
ethyl alcohol + CO2
What does lactic acid fermentation produce?
lactic acid
Bacterial growth
the process in which from a bacterial cell, two equivalent daughter cells are produced.
What are the four phases in which bacterial growth can be modeled?
- Lag phase
- Log phase (exponential phase)
- Stationary phase
- Death phase
On a bacterial growth curve, what is lag phase?
“adjusting” - very little or no growth; bacteria adapt themselves to growth conditions; individual bacteria are maturing and not yet able to divide.
On a bacterial growth curve, what is log (exponential) phase?
“healthy; rapidly dividing” - the number of bacterial cells doubles at a constant, exponential rate; individual bacteria are reproducing at their maximum rate - numbers increasing.
On a bacterial growth curve, what is stationary phase?
“amount replicated = dying bacteria” - population growth levels off as the rate of cell death equals the rate of cell division; growth rate slows due to depletion of nutrients - bacteria begin to exhaust the resources that are available to them.
On a bacterial growth curve, what is death phase?
more cells die than will grow and divide; characterized by a steady decline in population numbers from starvation and/or toxic concentrations; bacteria run out of nutrients and die.
What does a Bacterial Growth Curve look like?
(Vertical) Growth is shown as L = log (numbers) where number is the number of colony forming units per mL versus (Horizontal) T (time hr.)
What are different types of culture media?
Agar plates
semi-solid deeps
broths
slants
Culture medium
nutrients prepared for microbial growth
sterile
no living microbes
inoculum
introduction of microbes into medium
culture
microbes growing in/on culture medium
Properties of agar (5):
- complex polysaccharide
- used as solidifying agent for culture media in Petri plates, slants, and deeps
- generally not metabolized by microbes
- liquefies at 100 degrees celsius
- solidifies at about 40 degrees celsius
Chemically defined media
exact chemical composition is known
Complex media
exact chemical composition is not known - Extracts and digests of yeasts, meat, or plants (nutrient broth; nutrient agar)
Selective media
media designed to enhance the isolation procedure by inhibiting growth of some organisms while encouraging the growth of others.
What are some examples of selective media?
- mannitol salts agar - selects agains non-skin flora
- MacConkey agar - selects against gram-positives
- eosin-methylene blue agar - selects against gram-positives
- phenylethyl alcohol agar - selects against gram-negatives
Differential media
selective media that contains indicators to expose differences between organisms (make it easy to distinguish colonies of different microbes.)
- Differential media allow the growth of more than one microorganism of interest but with morphologically distinguishable colonies.
What component almost always make a medium differential?
a substrate
What makes a medium selective?
inhibitors
What is an example of a differential medium?
Columbia CNA - differentiates hemolytic from non-hemolytic organisms (is also selective for Gram-positive microbes)
bacterial colony
a population of cells arising from a single cell or spore or from a group of attached cells; often called a colony-forming unit (CFU)
What are the requirements for bacterial growth (7)?
- temperature
- pH (most bacteria grow between 6.5 and 7.5)
- osmotic pressure
- carbon
- nitrogen
- sulfur
- Phosphorous
How do cells divide?
binary fission
What are two ways to preserve bacteria cultures?
- deep-freezing (-50 to -95 degrees celsius
2. lyophilization (freeze-drying): Frozen (-54 to -72 degrees celsius) and dehydrated in a vacuum
What are three direct methods to measure microbial growth?
- Plate counts - counting plate colonies after a serial dilution is performed.
- Filtration (bacteria are retained on the surface of a membrane filter and then transferred to a culture medium to grow and subsequently be counted.
- Hemocytometer (counting bacteria directly)
What are the steps to a plate count?
- Perform serial dilutions of a sample
- Inoculate Petri plates from serial dilutions
- After incubation, count colonies on plates that have 25-250 colonies (CFU’s)
What is an indirect method to measure microbial growth (estimate bacterial numbers)?
Turbidity - using spectrophotometer
Taxonomy
a classification of organisms into groups based on similarities of structure or origin, etc.
genomics
an area within genetics that concerns the sequencing and analysis of an organism’s genome.
genome
the complete set of genes or genetic material present in a cell or organism - consists of DNA and RNA
gene
A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins.
genotype
the part (DNA sequence) of the genetic makeup of a cell, and therefore of an organism or individual, which determines a specific characteristic (phenotype) of that cell/organism/individual.
phenotype
the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
mutation
the changing of the structure of a gene, resulting in a variant form that may be transmitted to subsequent generations, caused by the alteration of single base units in DNA, or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes.
What is the Central Dogma of Molecular Biology?
It is the process by which the instructions in DNA are converted into a functional product. (“the flow of information in a cell”)
Explain the Central Dogma process.
The central dogma describes a two step process, transcription and translation by which the information in genes flows into proteins. (DNA - mRNA - Protein)
Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA) by the enzyme RNA polymerase.
Translation is the process in which cellular ribosomes create proteins. In translation, messenger RNA (mRNA) is decoded by a ribosome to produce a specific amino acid chain, or polypeptide.
What are the characteristics of DNA?
- double stranded
- anti-parallel
- made up of four nucleotides
- Each nucleotide is composed of a nitrogen-containing nucleobase—either cytosine (C), guanine (G), adenine (A), or thymine (T)—as well as a monosaccharide sugar called deoxyribose and a phosphate group.
What are the characteristics of RNA?
- single stranded
- transient
- mRNA serves as a template for ribosome’s to synthesize protein
- Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1’ through 5’. A base is attached to the 1’ position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U).
What is a virus?
a cellular parasite dependent upon cells to duplicate; infects cells and use the cells to make more viruses; cause disease in many organisms.
Why is a virus NOT a living organism?
It does not grow, have homeostasis, or metabolize
What are the parts of a Virion (virus particle)?
nucleic acid - DNA or RNA
Capsid - protein coat that surrounds the DNA or RNA in a virus
Lipid Membrane - a membrane around the capsid in many kinds of viruses; helps the virus enter cells
host specificity
the natural adaptability of a particular parasite to a certain species or group of hosts
What are three ways to identify viruses?
- Cytopathic effects (what does it do to a cell? lyse, agglutinate, etc)
- Serological tests - Test for virus (protein coat); test for exposure to virus by seeing if you made antibodies (ELISA)
- Nucleic acids - PCR (polymerase chain reaction) test
What are two methods of virus replication?
- Lytic Cycle - virus enters the cell, replicates itself hundreds of times, and then bursts out of the cell, destroying it. (virus reproduces using the host cell’s chemical machinery - the development of a bacteriophage)
- Lysogenic cycle - the virus DNA integrates with the host DNA and the host’s cell helps create more virus DNA. (virus reproduces by first injecting its genetic material into the host cell’s genetic instructions)
What are the stages of the lytic cycle?
- Attachment - phage attaches by tail fibers to host cell
- Penetration - Phage lysozyme opens cell wall, tail sheath contracts to force tail core and DNA into cell
- Biosynthesis- Production of phage DNA and proteins
- Maturation - Assembly of phage particles
- Release - Phage lysozyme breaks cell wall
What are the stages of the multiplication of animal viruses?
- Attachement - viruses attach to cell membrane
- Penetration - by endocytosis or fusion
- Uncoating - by viral or host enzymes
- Biosynthesis - production of nucleic acid and proteins
- Maturation - nucleic acid and capsid proteins assemble
- Release - by budding (enveloped viruses) or rupture
retrovirus
a class of enveloped viruses that have their genetic material in the form of RNA and use the reverse transcriptase enzyme to translate their RNA into DNA in the host cell.
What are prions?
Infections caused by proteis - short for proteinaceous infectious particle that lacks nucleic acid; believed to infect and propagate by refolding abnormally into a structure which is able to convert normal molecules of the protein into the abnormally structured form.
List some examples of human prion diseases:
- CJD (Creutzfeld-Jacob Disease)
- BSE (Mad cow disease
- GSS (Gerstmann-Straussler-Scheinke
- Kuru
List some DNA viruses and the illness they are associated with.
- Parvoviridae (human parvovirus)
- Papillomavirus (human wart virus)
- Molluscipoxvirus (smallpox, cowpox)
- Herpesvirus (cytomegalovirus)
- Hepadnavirus (hepatitis B virus - uses reverse transcription)
List some RNA viruses and the illness they are associated with.
- Enterovirus (include poliovirus)
- Rhinovirus (common cold)
- Rubivirus (rubella virus)
- Influenza viruses A and B
- Norovirus (causes gastroenteritis)
- Coronavirus (upper respiratory infections)
- Ebola and Marburg viruses
pathology
the scientific study of the nature of disease and its causes, processes, development, and consequences “study of disease”
etiology
the cause, set of causes, or manner of causation of a disease or condition “study of the cause of a disease”
Infection
the pathological state resulting from the invasion of the body by pathogenic microorganisms
Probiotics
Microorganisms that have beneficial effects on their host.
pathogenesis
development of disease
Disease
an abnormal state in which the body is not functioning normally
commensalism
one organism is benefited and the other is unaffected
mutualism
both organisms benefit
parasitism
one organism is benefited at the expense of the other
Koch’s Postulates
Criteria proposed by Koch for proving the pathogenicity of an organism (used to prove the cause of an infectious disease)
What are the criteria of Koch’s postulates?
- suspected causal organism must be constantly associated with the disease
- it must be isolate and grown in pure culture
- when inoculated into a healthy plant it must reproduce the original disease
symptom
any sensation or change in bodily function that is experienced by a patient and is associated with a particular disease
sign
a change in a body that can be measured or observed as a result of disease
syndrome
a specific group of signs and symptoms that accompany a disease
incidence
Fraction of a population that contracts a disease during a specific time
prevalence
Fraction of a population having a specific disease at a given time
endemic disease
an infectious disease that is present in the community at all times but normally at low frequency
epidemic disease
any infectious disease that develops and spreads rapidly to many people
pandemic disease
an epidemic occurring over a very wide area, crossing international boundaries and usually affecting a large number of people. global epidemic
transmission of disease - vehicle
transmission by an inanimate reservoir (food, water)
transmission of disease - vectors
arthropods, especially fleas, ticks, and mosquitoes
transmission of disease - mechanical
arthropod carries pathogen on feet
transmission of disease - biological
pathogen reproduces in vector
epidemiology
the study of the patterns, causes, and control of disease in groups of people.
Gram positive bacteria
Streptococcus, Staphylococcus, Enterococcus, Bacillus, Clostridium
Gram negative bacteria
Escherichia coli, Salmonella, Pseudomonas, Helicobacter, Moraxella
