+++Bio Lec. Final+++ Flashcards

All virus has 2 parts: 1-Nucleic acid which varies virus to virus. 2-Capsid (protein coat and made of capsomeres) every virus has this.

Some animal viruses have an envelope (made of phosphate lipids).

Glycoprotein (identity)

Dependent on host.

Inside the cell.

Virus lives off something else (host). Host has an negative effect to virus and virus gain from host.

Receptors on host match the receptors on virus. (lock & key)

The Lytic Cycle- reproductive mechanism for bacteriophages. (bursting)

1-Phage binds to host cell: Host cell is going to be bacteria. Phage is specific for a species of bacteria. Receptors on host cell are going to be specific for virus (host and virus fit together like a lock and key).

2-Phage DNA enters host cell: capsid stays outside and inject DNA into host cell. The bacteria DNA is cut up and destroyed.

3-Phage DNA and protein production: Bacterial cell and virus use bacterial enzymes and ribosomes to do DNA replication and translation in order to make more viral DNA and capsomeres.

4-Self assembly of phages.

5-release of phages: bacterial cell bursts and releases the phages, phages infect more bacterial.

The ending result is host cell death.

Lysogenic Reproductive Cycles- another reproductive mechanism for phages, not all phages can do this cycle (specific).

1-Phage binds to bacterial cell and injects DNA

2-If the bacteria undergo the lysogenic cycles phage DNA intergrates into a bacterial chromosome. Resulting to a Prophage.

Prophage: bacterial chromosome that has viral DNA inside of it.

3- Bacterial cell reproduces by binary fission (clones).

Resulting to a population of bacteria infected with the prophage.

The Lysogenic Cycle provides protection for viral DNA when the environment is not hospitable. If the environment improves, phage DNA can remove itself from the bacterial chromosome and the phage enters into the Lytic Cycle.

Virulent Virus

Temperate phage

DNA animal viruses reproductive cycle:

1-Virus binds to host cell (specificity between the receptors on host and viral capsid/ envelope/ glycoproteins).

2-Whole virus enters into host cell and then virus disassembles.

3-Virual DNA uses host enzymes, machinery to do two things 1-make copies of the viral DNA, 2- Viral DNA then is used to do transcription and translation (to make capsid proteins).

4- Self assembly of virus and leave by bursting the cell or bud off from the cell (which does not kill cell). The benefit of bursting is that your immune system is recruited. When virus buds away from cell your immune system is not recruited.

RNA animal virus reproductive cycle:

• Binds to host cell (specificity between the receptors on host and viral capsid/ envelope/ glycoproteins).
• The capsid and nucleic acid (RNA) enter into the cell and the envelope is left externally.
• The capsids and RNA is dissembled within cell.
• The viral RNA (genome) is transcribed using RNA primase resulting of a copy of the viral RNA.
• Two strands. One strand is used to replicate RNA. (goal is to make lots of copies of genetic information). Other strand is used in translation to make capsid proteins.
• Virus self assembles. If glycoproteins are present virus makes virus glycoproteins, moves to the ER (rough), then goes to Golgi and lastly to the surface of the plasma membrane.
• The virus exits the cell. When exiting the cell, the virus steals the plasma membrane of cell and makes the plasma membrane it’s envelope with viral glycoproteins.

Reproductive Cycles of Retroviruses-

1. Binds to host cell (specificity between the receptors on host and viral capsid/ envelope/ glycoproteins). HIV binds to T4 cells.
2. The capsid and nucleic acid (RNA) enter into the cell and the envelope is left externally.
3. The capsids and RNA is dissembled within cell.
4. Viral RNA converted to DNA by reverse transcriptase. Resulting to viral RNA and a copy of viral RNA in DNA format.
5. DNA virus is copied (double stranded molecule), viral DNA inserts into the host’s chromosome (which is hidden from immune system).
6. Transcription, translation happens resulting to capsid proteins are made and reverse transcriptase.
7. Virus self assembles. If glycoproteins are present virus makes virus glycoproteins, moves to the ER (rough), then goes to Golgi and lastly to the surface of the plasma membrane.
8. The virus exits the cell. When exiting the cell, the virus steals the plasma membrane of cell and makes the plasma membrane it’s envelope with viral glycoproteins.

Retroviruses

Reverse transcriptase

RNA animal viruses

DNA Animal Viruses

Viroids- small infectious RNA particles (are only made up of RNA) that infect plants.

The plant is infected by the viroid in terms of growth. Viroids do not replicate within plant. Viroids just interfere with plants transcription and translation rate.

Prions- small infectious particles / infectious, abnormal proteins that cause brain disorders/disease. Prions are abnormal proteins that covert normal proteins into abnormal resulting to aggregates of abnormal proteins in the brain. Have a long incubation time and results may not show up to 10 years. Example: mad cow disease, kuru (tripe that eats dead).

Bacteriophage,

phages

Tissue trophism

Host range

host range,

Tissue Trophism

Photosynthesis

Leaves- the place where photosynthesis occurs.

Structure of a leaf:

Upper epidermis: Top of leaf.

Found in-between epidermises-

Spongy mesophyll: open space

Palisade mesophyll: main site of photosynthesis / chloroplast.

Vain: contains xylem (water conducting tissue, water only move in one direction: root> stem>leaf.) and phloem (sugar conducting tissue).

Lower epidermis: Bottom of leaf. Contains stomata and guard cells. Stomata are opens that allow gas exchange to take place; carbon dioxide going into the leaf and oxygen exits the leaf. Guard cells are located around the stomata and regulate gas exchange.

Chloroplast: Outer and Inner membrane, Stoma (where DNA, ribosome, proteins are found), Thlakoid (membrane sacs that contain pigments). Grana is a stack of thylakoids.

Solar energy/Chemical energy + Carbon dioxide + Water = glucose sugar + oxygen gas

or

Energy + 6CO2 + 6HO2 > C6H12O6 + 6O2

glucose sugar and oxygen gas

Carbon dioxide + Water

Oxygen

A set of reactions which are used to remove electrons from water which are then used to turn carbon dioxide into organic compounds.

Stage 1. Light Reactions: reactions that capture light energy and convert light energy into chemical energy. The type of chemical energy that is produced is ATP, and the type of electron carrier produced is NADPH. Process occurs in the thylakoids and requires pigments (pigments are found in thylakoids).

Stage 2: Calvin Cycle: Does not require light / solar energy. Uses carbon dioxide, ATP and NADPH to make sugar. The Calvin Cycle occurs in the stroma.

The Calvin Cycle.

Pigments: capture solar energy from the visible light spectrum.

Electromagnetic Spectrum: Visible light spectrum: what we see as colors with our eyes (ROYGBIV).

Violet 380nm, Indigo 450nm, Blue 500nm, Green 550nm, Yellow 600nm, Orange 650nm, and Red 750nm

Shorter wavelength= Higher energy

Longer wavelength= Lower energy

Pigment Absorption spectrum: each pigment will have a different absorption peak.

Pigments

Chlorophyll b and Carotenoids

expand

different absorption peaks

Chlorophyll a

Green (because that is the color being reflected).

Abortion beak

Light Reactions: occurs in the thylakoids (membrane sacs), captures solar energy by using pigments and converts solar energy into chemical energy (ATP and NADPH).

Thylakoid membrane has two photosystem structures called PS2 and PS1.

Photosystem: is a collection of pigments (mostly chlorophyll a) and proteins.

There are two parts of the photosystem.

Part 1. Light harvesting complex and Part 2. Reaction center.

1. Light harvesting complex: pigments that capture light energy and transfer light energy to the reaction center.
2. Reaction center: A pair of chlorophyll a molecules that are going to lose electrons.

Light Reactions

PS2 and PS1

Photosystem

There are two parts of the photosystem.

Part 1. Light harvesting complex and Part 2. Reaction center.

1. Light harvesting complex: pigments that capture light energy and transfer light energy to the reaction center.
2. Reaction center: A pair of chlorophyll a molecules that are going to lose electrons.

Step 1. Photons (packets of energy) from the visible light spectrum (solar energy) is going to strike a pigment in the light harvesting complex.

Step 2. When the pigment catches the solar energy the electrons in the pigment will move to a higher energy level and when doing so energy is released. When the energy is release, the released energy is going to excite the next pigment in the light harvesting complex.

Step 3. When the next pigment is excited it causes another electron in the “next pigment” to move to a higher energy level. The electron of the pervious excited pigment returns to the original energy level.

Step 4. Step 2 and step 3 repeat until the energy excites the reaction center (chlorophyll a molecules) which cause electrons to be lost from chlorophyll a molecules. These electrons go to the primary electron acceptor.

Step 5. When an electron is lost from a molecule it must be replaced. The electrons that are lost from the reaction center in the photo system (PS2) are replaced by the splitting of water. The electrons from water go into the reaction center and the protons from the water go into the thylakoid space and oxygen is released as oxygen gas (CO2).

Step 6. Electrons in the primary acceptor go into an electron transport train (a collection of proteins were electrons enter and move down the chain of proteins of least electronegativity to more electronegativity).

PS2

Step 1. While PS2 is generating PS1 is generating. Photons (packets of energy) from the visible light spectrum (solar energy) is going to strike a pigment in the light harvesting complex.

Step 2. When the pigment catches the solar energy the electrons in the pigment will move to a higher energy level and when doing so energy is released. When the energy is release, the released energy is going to excite the next pigment in the light harvesting complex.

Step 3. When the next pigment is excited it causes another electron in the “next pigment” to move to a higher energy level. The electron of the pervious excited pigment returns to the original energy level.

Step 4. Step 2 and step 3 repeat until the energy excites the reaction center (chlorophyll a molecules) which cause electrons to be lost from chlorophyll a molecules. These electrons go to the primary electron acceptor.

Step 5. Electrons that are lost by PS1 are replaced by electrons from the electron transport chain of PS2.

Step 6. Electrons from PS1 reaction center go to the electron proton chain and a molecule named NADP+ which picks up electrons and protons and turns into an electron carrier called NADPH.

PS1

Step 7. (continued from light reactions) Electron transport chain of PS2 sets up a proton gradient. Hydrogen Ions from broken down water assist in forming the proton gradient.

Protons enter the thylakoid space which created a high concentration on protons. These protons move though ATP synthase and ATP is formed. ***Only in PS2 is ATP made***

Photosynthesis- The thylakoid space and Cellular Respiration- inner membrane of mitochondria.

PS2

Step 1. Carbon fixation: CO2 (carbon dioxide) enters from the air into stroma and it will combine with ** RuBP resulting to an unstable 6-carbon molecule.

Step 2. 6-carbon molecule is split into 2-3 carbon molecules. These 3 carbon molecules will undergo a series of chemical reactions. These reaction use ATP and NADPH to make G3P.

Step 3. G3P goes through a series of reactions that converts it to RuBP.

an unstable 6-carbon molecule

Chemical reactions which use ATP and NADPH to make G3P.

is used to make sugar, and the regenerating RuBP

NADPH and ATP

stroma

sugar