MCAT BIO CH. 5 PART 1 Flashcards
What is a virus?
An obligate intracellular parasite
A vrirus can reproduce outside a cell. T/F
They are obligated to reproduce within (intra) a cell
What must occur for a virus to begin reproducing?
Commandeer the cellular machinery of the host and make copies of themselves
What is the definition of a virus to remember?
A virus is an obligate intracellular parasite that relies on host machinery whenever possible
Some viruses can store what?
ATP in their capsid
How is the viruses genome protected?
Nucleic acid genome packaged in a protein shell
A virus is inside its host cell. T/F
A virus is not inside a host cell, it contains only its genome
What type of nucleic acid do mature viruses have?
Does not contain nucleic acid other than its genome
What is a limiting factor of viral genomes? What size are viruses?
Size; small
What is a difficulty with the exterior protein shell of virus?
A rigid structure of fixed size that cannot expand to accommodate a larger genome
What is the likely result if a visa genome is tripled in size?
Viral genome will probably no longer fit within the normal viral structures
What is a bacteriophage?
Virus that infects bacteria
To adapt to size constraint, how has viruses adapted to?
Viral genomes have evolved to be extremely economical
What are the two adaptation for the viral genomes?
- Few genes
2. Encoding
What is the few genes adaptation fo viral genomes?
Viral genome to carry very few genes and for the virus to rely on host-encoded proteins for transcription, translation and replication
What is the encoding adaptation fo viral genomes?
Ability to encode more than one protein in a given length of genome
How can viral genomes encode more than one protein in a given length of genome?
Utilizing more than one reading frame within a piece of DNA so that genes may overlap with each other
What is capsid?
Protein coat surrounding the viral nucleic acid genome
What is used to classify viruses?
External morphology of the capsid
How is the capsid made?
From repeating patterns of only a few protein building blocks
How do helical capsid look? How do polyhedral capsids look like?
Helical capsids are rod-shaped
Polyhedral capsids are multiple-sided geometric
Which virus is commonly used in research and what is it?
T4 bacteriophage and its host is bacterium E. coli
What do tail fibers do for a virus?
Attach to the surface of the host cell
What do base plate do for a virus?
Attach to the surface of the host cell
What do sheath do for a virus?
Contracts using the energy of stored ATP and inject the genome into the host
The viral capsid is composed of….? The viral genome is composed of…?
proteins; nucleic acids
What do many animal viruses possess?
Envelope that surrounds the capsid
What is the envelope on animal viruses?
Membrane n the exterior of the virus derived from the membrane of the host cell
What does the envelope on animal viruses contain?
Phospholipids, proteins, carbohydrates, proteins encoded by the viral genome
What is budding based on animal viruses?
The process of acquiring envelope on the virus through the host cell membrane
How do some viruses leave their de-envelopped capsid inside the host cell?
By fusing their envelope with the host’s plasma membrane
What are naked viruses?
Viruses which do not have enveloppes
Which ones are naked viruses?
All phages and plant viruses
Why are phages and plant viruses are naked viruses?
Because they infect hosts with cell walls; when virus leaves the cell, the cell wall is destroyed and membrane ruptured
What is the first step in viral infection?
A virus binds to a specific receptor on the cell surface
What happens the virus binds to the cell surface receipt?
Virus all be internalized by either fusion or receptor-mediated endocytosis
Why might the antibodies to a viral capsid be ineffective in blocking infection?
It suggests that the virus is enveloped, so the antibody cannot reach its epitope on the capsid surface in infectious virus
From where do our immune system recognize for viruses?
The viral surface is also important for recognition by our immune system
Why can only specific species or specific cell types are susceptible to infection?
Only cells with a receptor that matches the virus will become infected
How do the viral genome produce energy and replicate?
Viral genome contains genes that redirect the infected cell to produce viral products
What is the first step to the bacteriophage life cycles?
Attachment or absorption
What is attachment or absorption based on bacteriophage life cycles?
Binding to the exterior of a bacterial cell in a process
What is the second step to the bacteriophage life cycles?
Penetration or eclipse
What is penetration or eclipse based on bacteriophage life cycles?
Injection of the viral genome into the host cell
Why is the second step to the bacteriophage life cycles also called eclipse?
Because the capsid remains on the outer surface of the bacterium while the genome disappears into the cell
After the penetration step, what two options can the phage follow?
- Lytic cycle
2. Lysogenic cycle
What happens as soon as the phage genome entered the host cell?
Host polymerases and/or ribosomes begin to rapidly transcribes and translate it
What is hydrolase?
A hydrolytic enzyme that degrades the entire host genome
Hydrolase is an example of what…?
An early gene
What is an early gene?
Genes that are expressed immediately after infection which includes any special enzymes required to express viral genes
How are multiple copies of the phage genome produced? What else is produced at the same time?
Using the dNTPs resulting from degradation of the host genome; abundance of capsid proteins
What do the capsid proteins do after an abundance of capsid proteins are made?
Each new capsid automatically assembles itself around a new genome
What enzyme is produced once each new capsid automatically assembled itself around a new genome?
Lysozyme
What is lysozyme an example of?
Late gene
What is the lysozyme?
Destroys bacterial cell wall
What happens when the lysozyme breaks the bacterial cell wall?
The host bacterium bust because osmosis is not counteracted by the protection of the cell wall
The lytic cycle is an efficient way to do what?
For a virus to rapidly increase its numbers
What is the problem with the lytic cycle?
All host cells are destroyed
What is a prophage?
Phage genome incorporated into the bacterial genome during lysogenic cycle
What is the host called after the prophage has occurred?
Lysogen
How is the prophage after it has occurred infiltrated the host genome?
Silent
Why is the prophage dormant?
Transcription of phage genes is blocked by a phage-encoded repressor protein
What does the phage-encoded repressor protein bind to?
Binds to specific DNA element in phage promoters
Every time the host cell reproduces itself in the lysogenic cycle….?
The prophage is reproduced too
What happens when the prophage becomes activated?
It removes itself from the host genome and enters the lytic cycle
What is excision?
The prophage removes itself from the host genome
Why is a downside from the lysogenic cycle?
When the viral genome activates, excising itself from he host genome may cause it to take part of the host genome along with it
What is transduction?
Codes for a trait that the new infected host did not previously possess
What is important about the tissue-specificity of animal viruses?
Due to the distribution of receptors necessary or absorption
Animal viruses enter the cells by what?
Endocytosis
What is endocytosis?
The host cell engulfs the virus and internalizes it
What happens once the animal virus is inside the hose?
Viral genome is uncoated
What does it mean when the animal virus is uncoated?
Its released from the capsid
If the animal virus doesn’t go through endocytosis, how does it get into the cell?
Fuse with the plasma membrane to release virus into the cytoplasm
What are the methods the animal virus can infiltrate the genome when its released into the cytoplasm?
Lytic cycle, productive cycle or lysogenic cycle
What is the productive cycle?
Similar to the lytic cycle but does not destroy the host cell
Why is the productive cycle possible?
The enveloped viruses exist the host cell by budding through the host’s cell membrane and becomes coated with the membrane in the process
How does budding not destroy the cell?
The lipid bilayer membrane can reseal as the virus leaves
What is provirus?
Analogous to a prophage, the dormant form of the viral genome
What does the + RNA Viruses must do?
Must encode RNA-dependent RNA polymerase and do not have to carry it
What is the structural component of + RNA virus?
A single stranded RNA genome
What is the simplest type of viral genome?
+ RNA virus
What is an + RNA virus?
A piece of single-stranded viral RNA which serves as mRNA
The viral genome acts directly as what, in the animal cell? (For + RNA virus)?
As mRNA
What does it mean when the genome is infective?
Injecting an isolated genome into the host cell with result in virus production
In order for the virus to replicate itself, one of the proteins it encode must be….?
An RNA-dependent RNA polymerase
What is the role of an RNA-dependent RNA polymerase protein?
To copy the RNA genome for viral replication
If a viral genome is (+) strand RNA, what is used as a template by the RNA-dependent RNA polymerase?
To make (+) strand copies of the genome, the virus needs the complementary strand as a template: (-) strand RNA
If the viral genome needs (-) strand, how does the dependent RNA poly do it?
Produces a (-) strand intermediate before generating new (+) strand genomes
What does the (-) RNA Viruses must do?
Must carry RNA-dependent RNA poly and encode it too
The genome of a (-) RNA virus is _____ to the piece of RNA that encodes viral proteins?
Complementary
What is the template for the viral mRNA production in (-) RNA virus?
The genome of a (-) RNA virus is the template for viral mRNA production
When the - RNA viruses enter the host cell, what happens?
Create a + strand from the - genome
What must the retroviruses do?
Encode reverse transcriptase
What is an important example of retrovirus?
HIV, AIDS and HTLV
What are retrovirus?
+ RNA viruses that undergo lysogeny
How do retrovirus integrate into the genome?
Integrate as proviruses
What must the retrovirus have in order to integrate DNA genome?
Must also be composed of double-stranded DNA
The retroviruses enter the cell as RNA, how can they be composed of double stranded DNA?
Must undergo reverse transcriptase to make an RNA template
How is reverse transcriptase accomplished?
By RNA-dependent DNA polymerase ended by the viral genome
Why is retroviruses not required to carry his enzyme?
The viral RA genome can be translated by host ribosomes; reverse transcriptase may be made after the viral genome
What are the three main retroviral genes?
- gag
- pol
- env
What is the gag retroviral genes?
Codes for viral capsid proteins
What is the pol retroviral genes?
Polymerase codes for reverse transcriptase
What is the env retroviral genes?
Envelope codes for viral envelope proteins
What does the Double-Stranded DNA Viruses must do?
Encode enzymes required for dNTP synthesis and DNA replication
What must the double stranded DNA Viruses include?
Genes for enzymes involved in deoxyribonucleotide synthesis and DNA replication
If retroviruses are added into the cellular genome and a reverse transcriptase inhibitor added to the cell; will the production of new viruses be blocked?
No; once the viral genome has integrated, transcription to produce viral mRNA and new viral RNA genomes does not involve reverse transcriptase
Why doesn’t RNA viruses carry around genes for enzymes possessed by the host?
Transcription is always occurring in all cells, so NTPs are always present
What is a factor likely to limit the size of RNA genomes?
The error rate in RNA synthesis is much higher than in DNA synthesis
What are subviral particles? What are examples?
Infectious agents are smaller and simpler than viruses; prions and viroids
How does prions don’t follow the Central Dogma?
Prions don’t have transcription and translation and have proteins being shaped based on other proteins (self-replicating)
What happens when normally folded proteins comes into contact with the prion?
The prion acts as a template and the shape of the born protein is altered
What are prions responsible for based on a class of diseases in mammals?
Transmissible spongiform encephalopathies (TSEs)
What are the TSEs responsible for causing?
Cause degeneration in the nervous system; misfiled proteins found in the nervous tissues and resistant to degradation
Wha is BSE referred to?
Mad cow disease
What is a common disease that is apart of the TSEs?
Bovine spongiform encephalopathy (BSEs)
What prion disease is similar to kuru?
Follows a similar transmission path in humans
Where were kuru found and why?
Certain tribes that ate body parts (including brain) to honor the dead
Prion disease are not genetically linked. T/F
False: genetically linked through mutations in the gene that codes for the prion protein
Are prion disease common? How can they arise other than inherited?
No, they are rare; spontaneous
How are prions characterized by?
By their very long incubation periods; leading to loss of coordination, dementia and death
What are the physical structure of Viroids?
Short piece of circular, single-stranded RNA with extensive self-complementarity
What is an ability of viroids?
Can base-pair with itself to create some regions hat are double-stranded
What do viroids lack?
Do not code for proteins and lack capsids
What are abilities of viroids?
- Catalytic ribozymes
2. Replicated, produce siRNAs that can silence normal gene expression
What does replication of viroid shares similarity to?
To the replication of RNA viruses
What does the viroid contain as enzyme to replicate?
RNA-dependent RNA polymerase
What does the viroid RNA-dependent RNA polymerase do?
Synthesizes a (-) strand
What is the (-) RNA strand circularized by, based on viroids?
RNA ligase
What is RNA ligase derived by in viroids?
Derived from the host
After the (-) is synthesized in viroid replication, what is it used for?
The round, rolling template to make more (+) copies that match the original RNA viroid sequence
What is an other option for viroid replication other than synthesizing a (-) strand?
Leaves (-) strand in a more linear state where it can still act as a template for (+) strand creation and then become circularized
What does the viroid do when the viroid hijack the cell’s DNA?
Viroids hijack the cell’s DNA dependent RNA polymerase and direct it to read RNA templates
Most of the diseases caused by viroids are found where?
In plants
What is the only human disease linked to viroids?
Is Hepatitis D
How can Hepatitis D viroid can only enter ____ if it contained ____?
Hepatocytes (liver cells); contained in a capsid with a binding proteins
What does successful Hepatitis D infection require?
Required confection with Hepatitis B from which it derives its capsid
What is the cell theory?
- All living organisms are composed of 1 or more cells
- Cells are the monomer for any organism
- New cells arise from pre-existing, living cells
The organism’s activity is determined by….?
The total activity of its cells
What are basic biochemical processes prokaryotes and eukaryotes both are able to carry out?
Photosynthesis, the Krebs cycle and oxidative phosphorylation to produce ATP
What is the primary feature of prokaryotes that distinguishes them from eukaryotes is what?
They do not contain membrane-bound organelles
What does prokaryotes means?
Before the nucleus
What groups do prokaryotes include?
Bacteria, archea and blue-green algae
What is another word for archea?
Extremophiles
What is another word for blue-green algae?
Cyanobacteria
What is taxonomy used for?
Used to determinate evolutionary relationship of organisms to one another
What is the largest taxonomic division?
Domain
What are the three recognized domain?
Bacteria, Archea and Eukarya
Which domains include prokaryotic organisms?
Domains, bacteria, and archea
How can each domains be divided?
Subdivided into kingdoms
What are the three well-recognized eukaryotic kingdoms?
Animalia, Plantae, and Fungi
What are single-celled eukaryotes called?
Protist
Which organelle is present in prokaryotic cells?
Ribosomes
How is the prokaryotic genome?
A single double-stranded circular DNA chromosome
Where is the prokaryotic genome not located?
Not in the nucleus
The prokaryotic genome has histone proteins. T/F
False: not associated with histone proteins
What are polyribosomes?
Many ribosomes translate a single piece of mRNA
In prokaryotes, can transcription and translation occur at the same time?
Yes; they are in the same location
What antibiotics are examples that interfere with bacterial translation without disruption human ribosome?
Streptomycin, tetracycline which bind only to bacterial ribosomes
What are plasmids?
A circular piece of double-stranded DNA which is much smaller than the genome
Which type of cells carry plasmids?
Prokaryotic cells
How are plasmids usually called?
Extrachromosomal genetic elements
What do the plasmids do?
Encode gene products
What is an example of what plasmids usually carry?
Antibiotic-resistance genes
What are antibiotic-resistance genes?
Genes that encode proteins which can break down antibiotics
What are plasmids usually capable of doing?
Capable of autonomous replication
What is autonomous replication is a plasmid?
A single plasmid molecule within bacterial cell may cause itself to be replicated into many copies
What are plasmids important for?
Encoding advantageous gene products and conjugation
What is conjugation?
Bacterial exchange of genetic information
What are the three bacterial shapes?
- Round
- Rod-shaped
- Spiral-shaped
What’s the proper name for round shape of bacterial shape?
Cocci
What’s the proper name for rod-shape of bacterial shape?
Bacilli
What’s the proper name for spiral-shaped of bacterial shape?
Spirochetes or spirilla
How do animal cells deal with osmotic pressure due to their lack of cell wall?
By continuously pumping ions across the cell membrane
Bacterial cells do not have a cell wall.
False: outside the lipid bilayer is a rigid cell wall
What is the bacterial cell wall composed of?
Peptidoglycan
What is peptidoglycan?
A complex polymer unique to prokaryotes
What does peptidoglycan contain?
Contains cross-linked chains made of sugars and amino acids
What amino acid does peptidoglycan contain and how do we know its a bacterial cell?
D-alanine, animal cells are L configuration
Where is the lysozyme located based on animals? Made by what type of viruses?
In tears and saliva; made by lytic viruses
How do peptidoglycan react to lysozyme?
Destroys the peptidoglycan in the bacterial cell wall,
What’s the result of a destroyed peptidoglycan?
Protoplast
What is the protoplast?
Osmotically fragile structure after peptidoglycan was destroyed
What method is used to classify bacteria? What does it use to classify?
Gram staining; extent to which bacteria turn color
What are the two gram staining groupings?
- Gram-positive
2. Gram-negative
What is gram-positive bacteria?
Cell wall stain strongly; a dark purple colour
What is gram-negative bacteria?
Stain weakly; a light pink color
What do gram-positive bacteria contain, based on cell wall?
Thick peptidoglycan layer outside of the cell membrane; no other beyond this
What do gram-negative bacteria contain, based on cell wall?
Thinner peptidoglycan layer in cell wall but have an additional outer layer containing lipopolysaccharides
What is periplasmic space?
Intermediate space in gram-negative bacteria between the cell membrane and the outer layer
What is usually found in periplasmic spaces?
Enzymes that degrade antibiotics
What is the outer membrane of the gram-negative bacteria made of?
Endotoxins
What can endotoxins affect in our body?
The immune system to have an extreme reaction and cause us to die
When do endotoxins cause the most trouble?
When many bacteria die and their disintegrated outer membranes are released into the circulation
What happens when many bacteria die and all their endotoxins go into circulation?
Immune system releases so many chemicals that the patient goes into septic shock
What is septic shock?
Which much of the aqueous protein of the blood is leaked into the tissues, causing dropping blood pressure
What type of chemical structure can endotoxins have?
Lipopolysaccharides, sugars bound to lipids
Which type of bacteria release exotoxins? Are they toxic?
Gram + and -; very toxic
How does the exotoxin help the bacterium?
Aid in compete again other bacterial species
What is a capsule?
Sticky layer of polysaccharide surrounding the bacterial cell or entire colony of bacteria
What’s another term for capsule?
Glycocalyx
What does the capsule aid the bacteria with?
To adhere to smooth surfaces such as rocks in a stream or lining of the human respiratory tract
What do the bacteria have for mobility?
Flagella
What are flagella?
Long, whip-like filaments known as flagella
Can viruses move via flagellar propulsion to find host cells?
No, they lack any means of energy production on their own
When is a bacterium considered motile?
Possess one or more flagella because its teironly means of bacterial locomotions
What does it mean for a bacteria to be monotrichous?
Flagellum located at only one end
What does it mean for a bacteria to be amphitrichous?
Flagellum located at both ends
What does it mean for a bacteria to be peritrichous?
They have multiple flagella
What are the major components of the flagellum?
Filament, hook and the basal structure
What is the structure of the basal structure?
Contains a number of rings that anchor the flagellum to the inner and outer membrane
What does the basal structure serve?
Serve to rotate the rod and the rest of the flagellum
What is the arrangement of the eukaryotic flagellum?
Contains a 9+2 arrangement of microtubules
What is the rotation of the rod powered by?
The diffusion of the H+ down the portion gradient generated across the inner membrane by electron transport
What is the process for the bacterial motion to be directed?
Chemotaxis
The connection between chemotaxis and flagellar propulsion is dependent upon….?
Chemoreceptors
Where are the chemoreceptors located and what do they do?
Chemoreceptors on the cell surface that bind attractants or repellents and transmit a signal to influence flagellar rotation
The response of flagellar rotation is dependent on what, in bacterial cells?
A change in concentration over time
What are pili?
Long projections on the bacterial surface involved in attaching to different surface
What is the sex pilus?
Special pilus attaching F+ (male) and F- (female) bacteria
What do sex pilus facilitate?
Facilitates the formation of conjugation bridges
What are fimbriae?
Smaller structures involved in adhering to surfaces, not locomotion nor conjugation
What are mesophiles?
Bacteria that favor mild temperatures; moderate temperature lovers
What are thermophiles?
Heat lovers bacteria
What are psychrophiles?
Cold lovers bacteria
How might a decrease in temperature increase the bacterial growth?
Colds lovers possess enzymes that are optimally active at low temperatures
Based on nutrition, how can bacterias be classified?
Their carbon source and their energy source
What are autotrophs bacteria?
Utilize CO2 as their carbon source
What are heterotrophs bacteria?
Rely on organic nutrients created by other organisms
What are chemotrophs bacteria?
Get their energy fro chemicals
What are phototrophs bacteria?
Get their energy from light
What are four types of nutrition that bacterias have?
- Chemoautotrophs
- Chemoheterotrophs
- Photoautotrophs
- Photoheterotrophs
What are chemoautotrophs?
Build organic macromolecules from CO2 using the energy of chemicals
How do chemoautotrophs obtain their energy, what reaction do they go through?
By oxidizing inorganic molecules ex. H2S
What are chemoheterotrophs?
Require organic molecules made by other organisms as their carbon source and for energy
What are humans, based the four types of nutrition?
Chemoheterotrophs
What are photoautotrophs?
Use only CO2 as a carbon source and obtain their energy from sun
What are plants, based the four types of nutrition?
Photoautotrophs
What are photoheterotrophs?
Get their energy from the sun but require an organic molecule made by another organism as carbon source
What media do bacteria usually grow in?
Agar
What is a plaque based on bacterial growth media?
A clear area in the lawn
What is a lawn based on bacterial growth media?
Dense growth of bacteria
How do plaques happen, based on growth media?
Result from death of bacteria and are caused by lytic viruses or toxins
What is minimal media?
Contains only glucose and agar
What is doubling time?
Amount of time required for a population of bacteria to double its number
What are auxotroph bacteria?
Bacterium which cannot survive on minimal medium because it can’t synthesize a molecule it needs to live
What do auxotroph bacteria need to grow?
Auxiliary trophic substances; substances added to survive
How do auxotrophy occur?
Mutation in a gene coding for an enzyme in a synthetic pathway
How would you denote a bacteria that can metabolize saccharide lactose? What about one that cannot?
lac+, lac-
What are obligate aerobes?
Bacteria which require oxygen
What are anaerobes?
Bacteria that do not require oxygen
What are the three subcategories in anaerobe metabolism?
- Facultative anaerobes
- Tolerant anaerobes
- Obligate anaerobes
What are facultative anaerobes?
Will use oxygen when around but don’t need it
What are tolerant anaerobes?
Can grow in absence or presence of oxygen but don’t use for metabolism
What are obligate anaerobes?
Poisoned by oxygen
Why can obligate anaerobes be poisoned by oxygen?
Lack certain enzymes necessary for the detoxification of free radicals which form when O2 is around
What is a harmful O2 by product?
O2^-
What is respiration?
Glucose catabolism with use of an inorganic electron acceptor such as oxygen
What is fermentation?
Glucose catabolism which uses a reduced by-product of glucose catabolism
What type of reduced by-product of glucose catabolism can be used by fermentation?
Lactate or ethanol
What is anaerobic respiration?
Glucose metabolism with electron transports and oxidative phosphorylation relying on an external electron acceptor OTHER than O2
Where are the electrons passed to in fermentation?
From NADH to pyruvic acid
What is a possible electron acceptor based on anaerobic respiration?
NO3^-
