Whole Biology 3/4 Flashcards

PAIN

How to draw an amino acid? (monomer of a POLYPEPTIDE)

N: 2 H's attached

C: H and R attached

C: Carboxyl group attached

What is the difference between mRNA, tRNA and rRNA?

mRNA:

• Carries the genetic code from DNA to the ribosome. Contains codons that specify amino acids.

tRNA:

• A clover shape like RNA molecule that holds an amino acid

  Brings amino acids to the ribosomes (they're specific to the amino acid that they're bringing)

  has the ANTICODON

rRNA:

• a structural component of the ribosome.

What is a Gene Degenerate?

More than 1 triplet of codons, codes for the same type of amino acid molecule.

If it only codes for 1, then its unambiguous.

Universal code means that each triplet codes for the same amino acid in all organisms

What is a codon?

group of 3 mRNA bases

(start codon is AUG - methionine)

What is a mutation, and what do they do?

Summary of Transcription

RNA polymerase binds to the gene at the promoter region.

RNA polymerase unwinds and unzips DNA

RNA polymerase attaches complementary RNA nucleotides to the bases on the DNA template strand.

RNA polymerase joins nucleotides together (phosphodiester bonds), forming an mRNA strand.

When RNA polymerase reaches the terminator sequence it stops transcribing.

mRNA & RNA polymerase detaches from the DNA and the DNA rewinds and forms double helix.

Summary of RNA processing

1. Introns are cut out, and Exons are spliced together

2. a 5' methyl cap gets attached to the 5' end of the pre-mRNA.

3. a Poly-A-Tail gets attached to the 3' end.

4. pre-mRNA now gets called mRNA

Summary of Translation

mRNA attaches to a ribosome. First tRNA matching the start codon AUG complementary base pairs with the mRNA in the P site of the ribosome.

The ribosome reads mRNA in triplets (codons) in the 5' to 3' direction.

tRNA molecules with complementary anticodons bind to codons in the A site of the ribosome. Each tRNA carries a specific amino acid.

The ribosome forms peptide bonds between amino acids.

Ribosome moves in the 5' to 3' direction by one codon. The polypeptide chain elongates.

When a stop codon is reached, the polypeptide is released.

What is the promoter region of the gene?

A non-coding DNA sequence located upstream (5') of a gene's transcription start site that acts as the binding site for RNA polymerase in transcription.

what is the TRP process for HIGH levels of trp?

1. At high levels of trp, the ribosome doesn't have to pause at the attenuator sequence.

2. a terminator hairpin loop is formed.

3. This terminator hairpin loop causes the ribosome to finish translation prematurely, and causes everything to disocciate

4. Thus, transcription and translation stop.

what is the TRP process for LOW levels of trp?

1. At low levels of trp, there will be limited numbers of available tRNA molecules carrying the trp amino acid.

2. Once the ribosome reaches the attenuator sequence in the DNA (trp codon), and translation stalls.

3. RNA polymerase continues to transcribe, and the antiterminator hairpin loop is formed.

4. This allows transcription to continue through to the structural genes, producing a complete mRNA transcript

What is a way of reguation of the trp operon? (way 1)

Repression

1. 2 trp molecules attach to an inactive repressor protein

2. this activates the repressor protein, by changing its conformational shape

3. Prevents RNA polymerase from binding to the promoter region, by binding to the operator region

4. Thus, represses transcription of the structural genes

What is a way of reguation of the trp operon? (way 2)

Attenuation

1. When trp is abscent, none binds to the repressor protein

2. The repressor protein is NOT activated.

3. RNA polymerase can bind to the promoter region and transcribe the structural genes

4. Thus, producing enzymes required to synthesise tryptophan.

Where does regulation and attentuation occur?

The leader region. Regulating before reaching the structural genes.

What can affect the genome and proteome?

The environment can affect the function of both the genome and proteome

What is the difference between primary, secondary, tertiary, and quaternary protein structure.

What is denaturation?

When the bonds in a protein are disrupted or broken, it will no longer be able to carry out its function.

Whats the difference between structural genes and regulatory genes?

Structural genes code for proteins that have a specific structure or function in the cell

Regulatory genes regulate the expression of other genes

explain the term 'gene regulation'

Gene regulation describes any mechanism that acts to increase or decrease the production of specific gene products (DNA or RNA) in the cell.

What are all the necessary organelles in a cell needed for protein synthesis?

Nucleus:

• Where transcription occurs

Ribosomes:

• primary site for protein synthesis

• translation occurs here

RER:

• proteins are folded into their correct shape

Golgi apparatus:

• receives the proteins from RER, makes final modifications, sorts them, and packeges them into vesicles.

transport / secretory vesicles:

• They transport proteins

Whats the difference between intracellular and extracellular enzymes?

Intra:

Made inside the cell, and remain there to control metabolism.

Extra:

Made inside the cell, but achieve theor effect outside the cell.

Photosynthesis equation?

6CO2 + 12H2O --> C6H12O6 + 6H2O + 6O2

top of the arrow: 'light energy.'

bottom of the arrow: 'chlorophyll'

respiration is just opposite equation.

What are coenzymes and what are the roles?

Non-protein organic substances that are required for enzyme activity.

They act as carrier or transfer molecules in many metabolic reactions (e.g: ATP, NADH, NADPH)

Why is biochemical pathway regulation essential?

1. to prevent waste of resources, such as ATP

2. prevent the build up of potentially harmful products

3. preservation of energy

What are competitive inhibitors?

Molecules that have a similar shape to the enzymes substrate. This means that they take residence into the active site, and thus, the substrate cannot enter the active site, and thus the enzyme cannot catalyse the reaction.

What are non-competitive inhibitors?

They are molecules that bind to non competitive binding sites on an enzyme.

This changes the 3 dimensional shape of the active site, and thus the substrate can no longer bind.

Therefore the reaction cannot be catalysed.

What are the inputs and outputs of the light dependent reaction?

Inputs:

• light energy

• water

• ADP + Pi

• NADP+

Outputs:

• Oxygen gas

• ATP

• NADPH

It occurs in the thylakoid membranes of the chloroplast

What is The Process Of the Light-Dependent Reaction?

1. Sunlight energy is absorbed by the chlorophyll in the thylakoid membranes of the chloroplasts.

2. This turns electrons into a high energy state

The high energy electrons are passed down a series of electron carriers.

3. This energy splits water into oxygen gas as a waste product, and H+ to be pumped into the thylakoid via hydrogen pumps.

4. The passive transport of H+ back into the stroma via ATPase, that converts ADP and phosphate into ATP.

5. The electrons are paseed along with H+ to load NAP+ into NADPH.

Inputs and outputs of light independent reaction?

Inputs:

• ATP

• NADPH

• CO2

Outputs:

• ADP + Pi

• NADP+

• Water

• Glucose

It occurs in the stroma of the chloroplast.

Depends not on light, but on ATP and H+ (which is carried by NADPH). Both of which are produced in the light dependent reaction.

What is The Process Of the Light-Independent Reaction / Calvin Cycle?

1. CO2 is fixed by the enzyme Rubisco in a process called carbon fixation.

2. The resulting molecules are reduced using ATP and NADPH to form G3P.

3. Some G3P are used to synthesise glucose, while the rest regenerates RuBP, allowing the Calvin cycle to continue

4. After 6 cycles of the calvin cycle, one glucose is produced.

How do C4 plants maximise photosynthesis?

C4 plants separate the initial carbon fixation from the remainder of the Calvin cycle in photosynthesis between cells.

Initial carbon fixation occurs in a mesophyll cell whilst the remainder of the Calvin cycle takes place in a bundle-sheath cell.

This separation allows for a high concentration of CO2 around Rubisco, encouraging it to bind CO2 rather than O2, which decreases photorespiration and increases photosynthesis.

What occurs in Glycolysis?

Occurs in the cytoplasm, and is the anaerobic process where a glucose molecule (6C) is broken down into 2 pyruvate molecules (3C).

This process yields 2ATP and NADH.

what occurs in the Krebs cycle?

In the mitochondrial matrix, the Krebs cycle processes the pyruvate into the coenzyme Acetyl-CoA to release CO2.

As the molecules get converted into another, H+ ions are released and are used to load NAD+ and FAD into NADH and FADH2

2ATP are produced.

What occurs in the electron transport chain?

In the cristae of the mitochondria, electrons from NADH and FADH2 are passed along a series of hydrogen pumps to pump H+ out of the matrix, and into the cristae.

The H+ move passively back into the matrix via ATPase, which results in the production of 26-28 ATP.

Finally, the electrons are passed to oxygen, where they react with H+ to form water.

What are the inputs/outputs of Glycolysis?

Inputs:

• Glucose

• 2 ADP + Pi

• 2 NAD+

Outputs:

• 2 Pyruvate

• 2 ATP

• 2 NADH

What are the inputs/outputs of Krebs Cycle?

Inputs:

• pyruvate

• Acetyl CoA

• 4 NAD+

• FAD

• ADP + Pi

Outputs:

• 3 CO2

• Aceytl CoA

• 4 NADH

• FADH2

• 2 ATP

What are the inputs/outputs of ETC?

Inputs:

• 10 NADH

• Oxygen

• 2 FADH2

• 26-28 ADP + Pi

Outputs:

• 10 NAD+

• 2 FAD

• H2O

• 26-28 ATP

What are the outputs of anaerobic respiration in animals and plants/yeast?

Animals:

• Lactic acid

Plants/yeast:

• CO2 + ethanol

Why is built up pyruvate bad during anaerobic respiration?

The buildup of pyruvate will inhibit the process of glycolysis. This is because tissue require a constant supply of energy, and the buildup of pyruvate will remove supplies of NAD+, which are required for the reactions to continue

What are the inputs and outputs of anaerobic respiration?

Inputs:

• Glucose

• 2 ADP + Pi

Outputs:

• 2 ATP

lactic acid in animals and CO2 + ethanol in plants/yeast.

What are C3 plants?

C3 plants carry out the entire Calvin Cycle in a single mesophyll cell during the day. They are the most common but are inefficient in hot weather because their stomata must stay open to let $CO_2$ in, which causes them to lose a lot of water.

What happens in C4 plants?

Carbon fixation is physically separated as PEPCase fixes CO2 in mesophyll cells, then pumps it to bundle-sheath cells where the Calvin Cycle occurs.

This creates a high-CO2 environment for Rubisco, effectively eliminating photorespiration in hot climates.

What happens in CAM plants?

CAM photosynthesis is common in plants that live in arid temperatures.

The stomata in CAM plants only open during the night to collect CO2.

In the mesophyll cells, the enzyme PEPCase catalyses the conversion of CO2 into malic acid, which is stored during the day.

during the day, malic acid is transported into chloroplasts where it is used to produce CO2 for photosynthesis.

What are the graphs for rates affecting photosynthesis? (apart from temp)

plateau, when a limiting factor comes into play.

What is the difference between C4 and CAM plants?

[Talk about carbon fixation]

C4 photosynthesis seperates carbon fixation from the remainder of the Calvin cycle over space, between a mesophyll cell and a bundle-sheath cell.

Conversely, CAM photosynthesis separates these two steps over time, between day and night with the use of a vacuole

How do C4 plants maximise photosynthesis?

C4 plants separate the initial carbon fixation from the remainder of the Calvin cycle in photosynthesis between cells.

Initial carbon fixation occurs in a mesophyll cell whilst the remainder of the Calvin cycle takes place in a bundle-sheath cell.

This separation allows for a high concentration of CO2 around Rubisco, encouraging it to bind CO2 rather than O2, which decreases photorespiration and increases photosynthesis.