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PhoenixxFire

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Converting content to exam-style questions (Biology)
« on: December 21, 2018, 01:17:07 pm »
+10

A key aspect of biology is the ability to answer questions in a succinct way whilst still providing enough information to get full marks. To do this, you need to know what the question is asking. Understanding the way questions are constructed to test specific knowledge will help you to understand the intent of the question, and therefore will help you to answer it.

You are welcome to write questions based on any of the content outlined in the biology study design however I will also be posting a summary of a topic at the start of each week, which you can use to make questions.

Your questions can be in any format that you might find in a SAC or exam, this includes multiple choice and short answer as well as other formats such as drawing/labelling diagrams and filling in flowcharts.

When writing your questions please also include the answer in a spoiler below it.

Week 1 content summary – Plasma membranes
All cells are enclosed in a plasma membrane, consisting primarily of a phospholipid bilayer.
When placed in water, phospholipids will spontaneously form a lipid bilayer, with the hydrophobic tails facing inwards, away from the watery solution, and the hydrophilic heads facing outwards, towards the watery solution.

Diagram of a phospholipid

The plasma membrane serves as a barrier to separate different environments in an organism. This is important for cell specialisation.
The fluid mosaic model describes the plasma membrane. It is fluid because the components of the membrane can move around, and mosaic because it is made of many different pieces.

Diagram of a plasma membrane

Some of the components found in plasma membranes are:
Glycoproteins: Markers for cell-cell communication.
Cholesterol: In cold temperatures it makes the plasma membrane more fluid, in hot temperatures it makes the plasma membrane more rigid. (In effect, it keeps the plasma membrane at a similar fluidity level regardless of external temperature that would otherwise affect it.)
Channel proteins and carrier proteins: Transmembrane proteins that allow facilitated diffusion and active transport across the plasma membrane to occur.

There are 3 types of passive transport across the plasma membrane.
Simple diffusion: The passive net movement of a solute from a region of high solute concentration to low solute concentration across a semi-permeable membrane.
Osmosis: The passive net movement of free water molecules from a region of low solute concentration to high solute concentration across a semi-permeable membrane.
Facilitated diffusion: The passive net movement of a solute from a region of high solute concentration to low solute concentration across a semi-permeable membrane via a protein channel.

Non-polar (hydrophobic) molecules, and small polar (hydrophilic) molecules (e.g. water) can cross the membrane via simple diffusion. Large polar molecules and charged molecules travel via facilitated diffusion. Any type of molecule that moves against the concentration gradient must travel via active transport.

Another type of active transport is bulk transport. Bulk transport involves the movement of large molecules into or out of a cell. There are two types of bulk transport – exocytosis and endocytosis

The export of proteins across the plasma membrane (exocytosis)

Proteins destined for export from the cell are transported to the golgi apparatus after synthesis. Here they are enclosed in a vesicle which travels to the plasma membrane. These vesicles fuse with the plasma membrane, releasing their contents into the extracellular environment.

Ribosome: An organelle made of protein and ribosomal RNA (rRNA). The site where polypeptides are synthesised.
Endoplasmic reticulum: A system of membrane-bound networks (channels). Allows molecules to be channelled around throughout the cell. The rough ER (rER) has ribosomes embedded in its surface, the smooth ER (sER) does not.
Golgi apparatus: In the Golgi apparatus, proteins are packaged ready for export (exocytosis) from the cell. The Golgi apparatus consists of a stack of flattened membrane-bound sacs.
Vesicle: A small sac made of a phospholipid bilayer.

Exocytosis

Cellular engulfment (endocytosis)
During endocytosis, a vesicle buds off from the plasma membrane, enclosing a substance from outside of a cell and bringing it into the cell. There are two types of endocytosis – pinocytosis and phagocytosis.

Pinocytosis: A type of endocytosis involving the engulfment and movement of liquid into a cell.
Phagocytosis: A type of endocytosis involving the engulfment and movement of solids into a cell.
« Last Edit: January 15, 2019, 04:25:30 pm by Joseph41 »
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Bri MT

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Re: Converting content to exam-style questions (Biology)
« Reply #1 on: January 07, 2019, 12:27:07 pm »
+5
Amazing work by PF (yet again)  :)


I'll contribute a question here:

The movement of carbon dioxide across the cell membrane:
a) is active and requires transport proteins
b) is active and requires channel proteins
c) is passive and requires channel proteins
d) is passive and does not require transport proteins

answer
The answer is d. carbon dioxide is a small neutral molecule which can diffuse across the cell membrane
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Erutepa

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Re: Converting content to exam-style questions (Biology)
« Reply #2 on: January 07, 2019, 03:32:16 pm »
+7
Just a quick couple of questions (I'll try to do more later)

A phospholipid is composed of:
A) a polar fatty acid tail and a non-polar phosphate-containing head
B) a non-polar fatty acid tail and a polar phosphate-containing head
A) a polar carbohydrate tail and a non-polar phosphate-containing head
B) a non-polar carbohydrate tail and a polar phosphate-containing head

answer
B: a phospholipid is composed of a non-polar fatty acid tail and a polar phosphate-containing head


The cytoplasm is:
A) the fluid part of the cell
B) the entire inside of a cell
C) the region of a cell from the nuclear membrane to the plasma membrane
D) the collecton of the cells organelles

answer
C: the cytoplasm is the region of a cell from the nuclear membrane to the plasma membrane. not to be confused with the cytosol which is the fluid part of the cell.
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Re: Converting content to exam-style questions (Biology)
« Reply #3 on: January 07, 2019, 03:53:16 pm »
+5
Choose the most suitable answer for the following question:

The organelle where protein synthesis is most likely to occur in a cell is:
a) Mitochondria
b) Smooth Endoplasmic Reticulum
c) Golgi Apparatus
d) Rough Endoplasmic Reticulum

Answer
d. The Rough Endoplasmic Reticulum is studded with ribosomes and is where protein synthesis can occur.

Draw a labelled diagram of the fluid mosaic model of the plasma membrane (2 marks)

Answer
Phosphilipids must be included and labelled as - hydrophilic phosphate head and hydrophobic fatty acid tail (or equivalents) - 1 mark

Each additional component is worth 0.5 marks each (maximum totalling 1 mark)
-Cholesterol
-Protein channel/protein carrier
-Glycoproteins
-Glycolipids
-Integral proteins
-Peripheral proteins



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Re: Converting content to exam-style questions (Biology)
« Reply #4 on: January 08, 2019, 04:06:00 pm »
+4
Animals with the greatest temperature tolerances possess the highest membrane cholesterol levels.
Q. State the function of cholesterol in the plasma membrane and thus explain why animals with greater temperature tolerance possess higher membrane cholesterol levels. (2m)

answer
1 mark for stating function. For example:
- membrane cholesterol functions to maintain membrane fluidity
or
 - membrane cholesterol function to counter the rigidity caused from low temperatures and the fluidization from higher temperatures.

1 mark for relating back to question prompt. For example:
Therefore, animals of greater temperature tolerances will possess greater membrane cholesterol levels to maintain an optimal fluidity in extremes of temperature.
« Last Edit: January 08, 2019, 04:08:51 pm by Erutepa »
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Re: Converting content to exam-style questions (Biology)
« Reply #5 on: January 08, 2019, 04:49:17 pm »
+3
Choose the most suitable answer for the following question:

Which term best describes the bulk transport of solids into a eukaryotic cell?
a) Endocytosis
b) Exocytosis
c) Pinocytosis
d) Phagocytosis

Answer
d. Phagocytosis. The questions asks specifically for the best answer with regards to solids entering a cell.


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Re: Converting content to exam-style questions (Biology)
« Reply #6 on: January 14, 2019, 02:43:34 pm »
+1
Week 2 content summary - Nucleic acids & proteins
DNA is degenerate/redundant. This means that an amino acid can be coded for by several different DNA triplets. DNA is universal. This means that it is the same in all species.
image
DNA strands run antiparallel. When a nucleotide is added by DNA polymerase, it can only be added to the 3’ (three prime) end. The ends are labelled 3’ or 5’ depending on the carbon number at that end.

image

Guanine: 3 bonds, 2 rings
Cytosine: 3 bonds, 1 ring
Adenine: 2 bonds, 2 rings
Thymine: 2 bonds, 1 ring
Uracil: 2 bonds, 1 ring
Bases can only bind to a base with the same number of bonds and a different number of rings.

There are 3 types of RNA. They are transferRNA (tRNA), ribosomalRNA (rRNA), messengerRNA (mRNA).
tRNA - Transfers amino acids from the cytosol to a ribosome.
rRNA - Makes up part of the ribosome, the site of translation.
mRNA - Carries a copy (transcription) of a genetic sequence to a ribosome for translation.

Polymer: A long molecule made by joining many simple molecules together. The small repeating molecules are called monomers.
Polypeptide chain: A polymer made of amino acid monomers.

The primary structure of a polypeptide is the sequence of amino acids that makes it up.
The charges of each amino acid decide whether the will be attracted to or repel each other.
The interactions of neighbouring amino acids in a chain result in the whole chain bending and flexing. This causes alpha-helixes and beta-pleated sheets to form. An Alpha helix looks like a corkscrew and a beta-pleated sheet looks like corrugated carboard. This is the secondary structure of a protein. Random coils (which form spontaneously) may also be considered part of this.
Other enzymes and chaperone proteins in the cell will take the polypeptide and bend and fold it into a highly specific 3D shape, to do a specific job. This is the tertiary structure of a protein. It is the tertiary structure of a protein that determines its function.
Some proteins have a quaternary structure which means they’re made of more than one polypeptide chain.

Condensation polymerisation: The bond between the carbon and oxygen break on one monomer, and between the nitrogen and hydrogen on another. The detached OH and H bond, creating a water molecule. The carbon from the first monomer then bonds to the nitrogen of the second monomer.

Gene expression: The process of transcribing and translating a genetic sequence (gene) into a gene product (usually a protein).
Triplet: A sequence of 3 DNA bases, that codes for an amino acid.
Codon: A sequence of 3 mRNA bases, that codes for an amino acid.
Anticodon: A sequence of 3 tRNA bases that codes for an amino acid. Complementary to a codon.

Transcription:
-RNA polymerase binds to the promotor region, upstream of the coding region of a gene.
-RNA polymerase copies the template strand of the DNA, within the coding region of the gene. It joins together RNA nucleotides, building in a 5’ to 3’ direction.
-When it reaches a terminator sequence, the RNA polymerase stops copying and releases the pre-mRNA strand.

Post-transcriptional modification / mRNA processing:
-Introns are spliced out, exons are joined together.
-A poly-A tail is added to the 3’ end
-A methyl cap is added to the 5’ end

Translation:
-Translation begins when ribosomal subunits bind to the 5’ end of a mRNA molecule.
-The first amino acid of a polypeptide chain will be added when the ribosome reaches a START codon.
-tRNA molecules bind to amino acids in the cytosol and transfer them to the ribosome.
-If a tRNA molecule’s anticodon is complementary to an mRNA’s codon, it will enter the binding site of a ribosome.
-The ribosome will then catalyse the formation of a peptide bond. The amino acid is joined to the growing polypeptide chain.
-This process continues until a STOP codon, where the polypeptide chain is released.
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Re: Converting content to exam-style questions (Biology)
« Reply #7 on: January 14, 2019, 03:12:10 pm »
+2
30% of the nitrogenous bases of the nucleotides in a certain double stranded DNA strand are Adenine.

What Percentage of the DNA strand contains the nitrogenous base Guanine
a) 30%
b) 70%
c) 35%
d) 20%

Answer
d. 20%. Adenine pairs with Thymine thus 30% of the bases are Thymine (as prompt states 30% is Adenine). This accounts for 60%. The remaining 40% is equally shared between Guanine and Cytosine thus 20% for Guanine.

Select the true statement.
a) The tertiary structure describes a protein that contains multiple polypeptides
b) During mRNA processing and modification a poly A tail is added to the 5'end of the mRNA
c) During mRNA processing and modification introns are spliced out and exons are joined together
d) Adenine is a pyrimidine

Answer
c. is correct
a. Multiple polypeptides = Quaternary structure
b. poly A tail is added to the 3' end of the mRNA. A methyl (guanosine) cap is added to the 5'end
d. The three pyrimidines are cytosine, uracil, thymine. The two purines are Adenine and Guanosine

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Re: Converting content to exam-style questions (Biology)
« Reply #8 on: January 14, 2019, 09:51:33 pm »
+2
Multple Choice

Question 1.
 A condensation polymerisation reaction
a) requires an input of water
b) releases water as a product
c) produces ATP
d) involve the breakdown of polypeptides
answer
B - A condensation polymerisation reaction releases water as a product

Question 2.
In post-transcriptional modification
a) mRNA is synthesized from DNA
b) RNA is converted into DNA
c) a 3' poly-A tail and a 5' methyl cap is added
d) a 5' poly-A tail and a 3' methyl cap is added
answer
C - In post-transcriptional modification  a 3' poly-A tail and a 5' methyl cap is added

Short Answer:

Question 3.
For the following sequence of DNA triplets:

 GCT AGG CGA GGA TCA

a) write the complementary:
  i) mRNA codons (1 mark)

  ii) anticodons (1 mark)

b) Using the mRNA codon chart provided, write the amino acid sequence coded for by the above DNA sequence (1 mark)
 

c) 'The genetic code is redundant/degenerate'. Explain what this means and provide and example (2 marks)

answer

a) i) CGA UCC GCU CCU AGU
    ii) GCU AGG CGA GGA UCA

b) Arg - Ser - Ala - Pro - Ser

c) 1 mark for explaining:
 - the genetic code is redundant/degenerate as multiple codons can code for one amino acid
or,
 - the redundancy/degeneracy of the genetic code refers to the fact that a specific amino acid can be coded for by multiple codons
or equivilant

1 mark for providing a valid example where multiple codons code for the same amino acid.

Question 4.
a) i) name the monomer/subunit of DNA (1 mark)
    ii) draw and label the monomer/subunit you have named (3 marks)

DNA can be transcribed to produce mRNA
b) describe this process of transcription (3 marks)

answer
a) i) nucleotide are the subunit of DNA
    ii) 1 mark for a accurate and labeled:
        - Phosphate group
        - deoxyribose sugar
        - nitrogenous base
        Drawing should resemble


b) 1 mark for all of
 - Transcription initiated when RNA polymerase binds to upsream promoter region
 - RNA polymerase reads template strand in 3' to 5' direction and synthesises mRNA complimentary strand in 5' to 3' direction
 - RNA polymerase reaches terminator sequence, ending stransciption and releasing mRNA
(note from me: this marking may be too hard, so please correct me)

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Re: Converting content to exam-style questions (Biology)
« Reply #9 on: January 22, 2019, 12:29:16 am »
+1
Week 3 content summary - Gene structure and regulation & biochemical pathways
Gene structure and regulation
Regulatory genes code for a gene product that is involved in the expression of other genes.
Structural genes code for a protein that is involved in everyday cellular metabolism.

Eukaryotic gene structure
Promotor: Where RNA polymerase and other transcription factors bind. Where transcription begins. 5’ end. Upstream of the coding region.
Enhancer and silencer: Responsible for increasing or decreasing the rate of transcription. A repressor protein will bind to a silencer or an activator protein will bind to an enhancer, which will decrease/increase the rate of transcription.
Insulator: Stops the RNA polymerase from continuing down the DNA strand to the next gene. Forces it to transcribe each gene separately.
After the RNA polymerase has run along the template strand and transcribed it we end up with pre-mRNA. The pre-mRNA contains the 5’ and 3’ Untranslated Region (UTR) and the Introns and Exons.
Then, during post transcriptional modification (pre-mRNA processing), the introns get cut out, leaving just the UTR’s and exons. A methyl cap is added to the 5’ end and a poly A tail to the 3’ end. It is now mature mRNA. It then leaves the nucleus and travels to a ribosome to be translated.
image

Lac operon
Lac: Has to do with the digestion of lactose.
Operon: Found in prokaryotic cells. Cluster of genes that have related functions. They are transcribed together.
Normally a repressor protein is attached to operator region (downstream of promotor), which means the genes cannot be transcribed when there is no lactose present.
When there is lactose, a molecule of it binds to the repressor protein, and changes the proteins shape so it can no longer attach to the operator region, this allows the genes to be transcribed.
Once all of the lactose is digested, the repressor protein goes back to its natural shape and fits back onto the operator, and stops further transcription.
image

Structure and regulation of biochemical pathways
Induced fit model: Enzymes changes shape slightly when it bonds with substrate/s which stresses chemical bonds and catalyses a chemical reaction.
Lock and Key model: Substrate/s fit perfectly into the active site of an enzyme, Like a key fits into a lock.
Catalyst: A molecule that speeds up a chemical reaction by reducing the activation energy required.
Biological catalyst: A molecule that catalyses a biologic reaction
Catabolic reaction: One substrate is broken down into two (or more) products.
Anabolic reaction: Two (or more) substrates are built up into one product.
Endergonic: Reaction that requires energy
Exergonic: Reaction that produces energy
Enzyme: A protein that catalyses a biological reaction, by lowering the activation energy required. It is not used up in the reaction.

Temperature:
Every enzyme has an optimal temperature where it works the best. Below this temperature it works slow, and above this temperature it can become denatured.

If the temperature gets to high the hydrogen bonds holding the protein in its tertiary (3D) shape break apart. Without its tertiary shape the enzyme cannot function correctly, due to its active site’s shape changing, and therefore no longer being able to bind its substrate. The enzyme is then said to be ‘denatured’. Even if the temperature is cooled down, the enzyme will not return to its original shape (permanent denaturation).

The warmer the environment is, the more the molecules in it move around, and therefore the more the substrate and enzymes interact. Therefore, the optimal temperature is a point just below the point where denaturation occurs. (There is a slight gap, as some enzymes denature first, causing the rate of reaction to slow before it stops all together).

pH:
Every enzyme has an optimal pH. If the pH goes above or below optimal, the rate of reaction will slow. In a natural environment it is extremely unlikely that the enzyme will denature due to an unfavourable pH, however it is possible if the enzyme is placed in an extreme pH (either acidic or basic).

Amount of substrate and enzymes: The rate of reaction will increase with the more substrate that is added, until all enzymes are working at maximum speed (they are said to be ‘saturated’).
The more enzymes that are present the faster the rate of reaction, until enzyme concentration is no longer the limiting factor.

Inhibition:
Competitive inhibitor: Inhibitor that binds to the active site of an enzyme and prevents substrate from binding, can be dislodged by changing environmental conditions.
Non-competitive inhibitor: Inhibitor that binds to a site other than the active site (called an allostatic site) and in doing so changes the shape of the active site slightly, preventing substrate from binding. Cannot be dislodged by changing environmental conditions.

The cycling of coenzymes
Cofactors: Help the substrate to fit better in the active site of the enzyme. Increases the rate of reaction.
Coenzyme: Organic cofactors. Damaged in the reaction. A new molecule is needed for each subsequent reaction.
ATP: Adenosine TriPhosphate. A type of coenzyme. An ATP molecule goes into the active site of an enzyme, the substrate/s come in and join/break and in the process the ATP is broken down into ADP.
ADP: Adenosine DiPhosphate. Broken down form of ATP.
NADH: Nicotinamide adenine dinucleotide. Energy carrier molecule involved in cellular respiration. It carries electrons to the electron transport chain, where they are broken off and used to power ATP synthesis.
NAD+: Unloaded form of NADH
NADP+/NADPH: Same as NAD+/NADH except with an additional phosphate. It is involved in photosynthesis.
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