Unit 3 AOS 1

Question 1

What are cells?

Answer 1

• Cells are the basic structural and functional units of life, and all living organisms are built of one or more cells.
• Cells constantly need to transport materials as they exchange ions with the extracellular environment, gain nutrients and remove wastes.
• Cells need to be small in order to maximise their surface area to volume ratio, allowing for the movement of ions, nutrients and wastes to occur quickly.
• Without a large surface area to volume ratio, cells will not survive.

Question 2

What is cell theory?

Answer 2

1. All organisms are composed of cells.
2. All cells arise from pre-existing cells (biogenesis).
3. The cell is the smallest living organisational unit.

Question 3

What are eukaryotic cells?

Answer 3

Cells within eukaryotes have a membrane-bound nucleus and other membrane-bound organelles.

Include plants, animals, fungi, and Protista.

Contain membrane-bound organelles and linear DNA

Question 4

What are prokaryotic cells?

Answer 4

Cells within prokaryotes lack a membrane-bound nucleus

Unicellular, smaller, and less complex.

Examples: Bacteria and Archaea.

Features: Single circular DNA, nucleoid, lacks organelles

Question 5

Similarities in both prokaryotic and eukaryotic cells

Answer 5

Plasma membrane, jelly-like cytoplasm, genetic material (DNA), and ribosomes.

Have DNA as their genetic material

Have cell membranes that selectively control the entry and exit of dissolved materials into and out of the cell

Use the same chemical building blocks, including carbon, nitrogen, oxygen, hydrogen and phosphorus, to build the organic molecules that form their structure and enable their function.

Produce proteins through the same mechanism (transcription and translation)

Use ATP as their source of energy to drive the energy-requiring activities of their cells.

Question 6

What are the organelles and their functions

Answer 6

Nucleus: Contains DNA, controls cell activities

Ribosomes: Synthesize proteins

Endoplasmic Reticulum (ER):
Rough ER: Transports proteins.
Smooth ER: Synthesises lipids

Golgi Body: Processes and packages proteins

Mitochondria: Energy release from organic compounds

Chloroplasts: Photosynthesis in plants

Lysosomes: Digest waste

Vacuoles: Storage, larger in plant cells

Question 7

What is the plasma membrane?

Answer 7

• The Plasma Membrane is a partially permeable boundary of a cell controlling entry to and exit of substances from a cell.
• The plasma membrane is the active boundary around all living cells, consisting of a phospholipid bilayer and associated proteins, that separates the cell contents from their external environment.

Question 8

Functions of the plasma membrane

Answer 8

The plasma membrane carries out several important functions for a cell. The plasma membrane:
1. is an active and selective boundary
2. denotes cell identity (which is vital in the immune response)
3. receives external signals
transports materials.

Question 9

What are the factors that affect a substance’s ability to cross a membrane?

Answer 9

1. molecular size
2. charge (positive or negative)
3. solubility in aqueous solution (hydrophobic/nonpolar, or hydrophilic/polar)
4. concentration gradient

Question 10

What is the difference between hydrophilic and hydrophobic

Answer 10

Hydrophilic (water-loving) molecules dissolve readily in water.

Hydrophobic (water-fearing) molecules are usually lipophilic (lipid-loving) and dissolve readily in organic solvents such as benzene.

Question 11

What is the difference between passive transport and active transport?

Answer 11

Substances can cross a membrane by several different methods

These can be passive (not requiring energy) or active (requiring energy).

Question 12

Passive methods include the following:

Answer 12

Simple diffusion is the means of transport of small lipophilic substances. Water can also move across the plasma membrane by diffusion; this is a special case of diffusion known as osmosis.

Facilitated diffusion involves protein transporters and is the means of transport of dissolved hydrophilic substances down their concentration gradients.

Question 13

Active methods include the following:

Answer 13

Active transport involves protein transporters known as pumps and is the means of transport of dissolved hydrophilic substances against their concentration gradients.

Bulk transport of macromolecules and fluid includes:
endocytosis (movement into the cell)
exocytosis (movement out of the cell).

Question 14

What is the structure of the plasma membrane?

Answer 14

1. Phospholipids - Various kinds of phospholipids are the main structural components of the plasma membrane. They are organised as two layers (leaflets).
2. Proteins - Some proteins are embedded in the plasma membrane; others are attached at the membrane surfaces.
3. Carbohydrate Groups - These are attached to some lipids, forming glycolipids, and to some proteins, forming glycoproteins. Both of these occur at the membrane surfaces.

Question 15

What is the fluid mosaic model?

Answer 15

The fluid mosaic model describes the structure of the plasma membrane. This model also applies to the membranes that form the outer boundary of cell organelles, such as the membranes that surround the cell nucleus and other cell organelles.

The fluid mosaic model proposes that the plasma membrane and other intracellular membranes should be considered as fluid layers in which proteins are embedded.

The term ‘fluid’ comes from the fact that the fatty chains of the phospholipids are like a thick oily fluid, and the term ‘mosaic’ comes from the fact that the external surface (when viewed from above) has the appearance of a mosaic because of the various embedded proteins set in a uniform background.

Question 16

What are phospholipids?

Answer 16

The plasma membrane consists of a double layer (bilayer) of phospholipids.

Each phospholipid molecule consists of two fatty acid chains joined to a phosphate-containing group.

The phosphate-containing group forms the water-loving (hydrophilic or polar) head of the molecule.

The fatty acid chains constitute the water-fearing (hydrophobic or nonpolar) tail of each phospholipid molecule.

Question 17

What type of proteins are found in the plasma membrane?

Answer 17

Proteins form the second essential part of the structure of the plasma membrane. Many different kinds of protein make up the plasma membrane.
They can be broadly grouped into:
1. integral proteins
2. peripheral proteins.

Question 18

What are integral proteins?

Answer 18

Integral proteins: Proteins that are embedded in the phospholipid bilayer.

→ They span the width of the plasma membrane, with part of the protein being exposed on both sides of the membrane

→ These proteins are described as being trans-membrane.

Question 19

What are trans-membrane proteins?

Answer 19

Trans-membrane proteins: Proteins that are embedded within and span the plasma membrane, allowing them to have parts exposed to both the intracellular and extracellular environment.

→ They serve many functions, including as transporters, receptors, channels and carriers.

Integral proteins can be separated from the plasma membrane only by harsh treatments that disrupt the phospholipid bilayer, such as treatment with strong detergents.

Question 20

What are peripheral proteins?

Answer 20

Peripheral proteins: Proteins that are anchored to the exterior of the plasma membrane through bonding with either lipids or integral proteins

Question 21

What are carbohydrates in the context of the plasma membrane?

Answer 21

Carbohydrate groups, such as sugars, are attached to the exposed parts of proteins on the outer side of the membrane, creating combinations called glycoproteins

Carbohydrates on the cell surface have many functions, including:
1. cell-to-cell communication
2. acting as receptors, distinguishing cells as ‘self’ (a feature that is vital in the immune system)

The prefix ‘glyco’ means sugar.
Sugars attached to a protein = glycoprotein
Sugars attached to a lipid = glycolipid

Question 22

How does cholesterol act in the plasma membrane?

Answer 22

1. At low temperatures, cholesterol molecules maintain the fluidity of the membrane by keeping phospholipid molecules separated and preventing the membrane from become too stiff.
2. At high temperatures, cholesterol stabilises the membrane by raising its melting point and preventing it from becoming excessively fluid.

Question 23

What are nucleic acids?

Answer 23

Nucleic acids are large biomolecules that store and transmit hereditary information.

They encode instructions for protein synthesis.

Nucleic acids are made up of sub-units known as nucleotides.

Nucleotides basic building blocks or sub-units of DNA and RNA consisting of a phosphate group, a base and a five-carbon sugar

Question 24

What are the two types of nucleic acids?

Answer 24

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

Question 25

What is DNA?

Answer 25

Deoxyribonucleic acid (DNA): Nucleic acid consisting of nucleotide sub-units that contain the sugar deoxyribose and the bases A, C, G and T; DNA forms the major component of chromosomes. → It is located in chromosomes in the nucleus of eukaryotic cells. It is the genetic material that contains hereditary information and is transmitted from generation to generation.

Question 26

What is RNA?

Answer 26

Ribonucleic acid (RNA): Nucleic acid consisting of a single chain of nucleotide sub-units that contain the sugar ribose and the bases A, U, C and G; RNA It is formed against a template strand of DNA.

Question 27

All nucleic acids are polymers made up of sub-units (or monomers) known as nucleotides. Each nucleotide has:

Answer 27

a 5-carbon (pentose) sugar a phosphate a nitrogenous base

Question 28

Differences between RNA and DNA

Answer 28

DNA Type of sugar: deoxyribose Nitrogen-containing bases: adenine, guanine, thymine, cytosine Number of strands: 2 RNA Type of sugar: ribose Nitrogen-containing bases: adenine, guanine, cytosine, uracil Number of strands: 1 - can fold onto itself

Question 29

What are the different forms of RNA

Answer 29

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

Question 30

What is messenger RNA and its function?

Answer 30

Messenger RNA (mRNA): Carries a copy of DNA sequence. It carries the genetic message from the DNA within the nucleus to the ribosomes, where the message is translated into a particular protein. Each group of three nucleotides in mRNA (known as a codon) provides the information for the addition of one amino acid. A special form of mRNA known as pre-mRNA is made through transcription in the nucleus.

Question 31

What is transfer RNA and its function?

Answer 31

Transfer RNA (tRNA): Reads and translates DNA information. molecules that carry amino acids to ribosomes that are free in the cytoplasm, where they are used to construct proteins. An anticodon (a set of three nucleotides) binds to the complementary codon on mRNA.

Question 32

What is a gene?

Answer 32

A gene is a region of DNA that may be translated into a polypeptide or an RNA molecule that can be functional, such as tRNA.

Question 33

What are two steps in gene regulation?

Answer 33

Transcription and translation

Question 34

What is transcription?

Answer 34

Transcription: The process of copying the genetic instructions present in DNA to messenger RNA (DNA to mRNA).

Question 35

What is translation?

Answer 35

Translation: The process of decoding the genetic instructions in mRNA into a protein (polypeptide chain) built of amino acids (mRNA to protein).

Question 36

What is a template strand?

Answer 36

Template Strand: One strand of a DNA double helix that is used to produce a complementary mRNA strand during transcription; sometimes called the sense strand. The complementary chain to this is sometimes called the non-template strand or the coding strand: one strand of a DNA double helix that is complementary to the template strand.

Question 37

What is RNA processing?

Answer 37

Another step, known as RNA processing, occurs between transcription and translation, in which pre-mRNA produced in transcription is processed and made into mature mRNA to be used in translation.

Question 38

What is RNA processing in Eukaryotes

Answer 38

The primary product of transcription is pre-mRNA, also known as the primary transcript. The sequence of bases in the pre-mRNA is complementary to all the DNA bases of a gene, both introns and exons. The primary mRNA transcript then undergoes a process termed RNA processing or post-transcription modification

Question 39

From DNA to mRNA: step by step

Answer 39

1. An enzyme, known as RNA polymerase (an enzyme that controls the synthesis of an RNA strand from a DNA template during transcription) 2. It attaches to a specific promoter sequence of DNA in the upstream region of the template strand. The double-stranded DNA of the gene unwinds and exposes the bases of the template strand. 3. The base sequence of the DNA template guides the building of a complimentary copy of the mRNA sequence. The RNA polymerase enzyme moves along the DNA template in a 3′ to 5′ direction. As it moves, complementary nucleotides are brought into place and, one by one, are joined to form an RNA chain. These new nucleotides are added onto the growing 3′ end of the mRNA strand. 4. After the RNA polymerase moves past the coding region and into the downstream region of the gene, transcription stops and the mRNA molecule (pre-mRNA) is released from the template.

Question 40

The bases in one DNA strand and complementary bases in an RNA strand as follows:

Answer 40

* A pairs with U * T pairs with A * C pairs with G * G pairs with C It is important to remember that in mRNA, there is no thymine (T). This is replaced with uracil.

Question 41

Process of Translation

Answer 41

The mRNA moves from the nucleus to the cytoplasm, where it attaches to sub microscopic organelles known as ribosomes The construction of a protein according to the coded instructions in mRNA involves the assembly of amino acid sub-units. The various amino acids are present in solution in the cytosol. The information in mRNA is present in coded form as sets of three bases or triplets. These triplets, such as AGG and UCU, are called codons. Most codons contain the information to add one specific amino acid to a protein chain. In addition, one codon (AUG) is a start translation instruction, and three different codons (UAA, UAG and UGA) are stop translation instructions

Question 42

From mRNA to protein: step by step

Answer 42

1. mRNA moves to the ribosome, where it is read in groups of three known as codons. Translation begins at the ‘start adding amino acids’ signal (AUG codon) 2. Each amino acid is brought to the mRNA on the ribosomes by a carrier molecule called transfer RNA (tRNA). At one end of each tRNA molecule are three bases that make up an anticodon. At the other end of a tRNA molecule is a region that attaches to one specific amino acid. The first amino acid to be added is methionine (met). 3. The ribosome continues to move along the mRNA and tRNA molecules to deliver the appropriate amino acid, determined by the code. As amino acids are added, they are joined by peptide bonds. 4. A codon representing STOP is reached (UAA, UAG or UGA) and the polypeptide is released from the ribosome.

Question 43

Characteristics of tRNA

Answer 43

* Each tRNA molecule consists of a single strand of 76 nucleotides coiled and paired with themselves. * At one end of each tRNA molecule are three bases that make up an anticodon. * At the other end of a tRNA molecule is a region that attaches to one specific amino acid. An enzyme, amino acyl tRNA synthetase, catalyses the linking of each amino acid to its specific tRNA carrier. As each codon is translated, the tRNA molecule with the complementary anticodon pairs momentarily with the mRNA.

Question 44

What is an anticodon?

Answer 44

anticodon is sequence of three bases in a transfer RNA molecule that can pair with the complementary codon of a messenger RNA molecule

Question 45

What is a codon?

Answer 45

codons are sequences of three bases in a messenger RNA molecule that contain information either to bring amino acids into place in a polypeptide chain or to start or stop this process

Question 46

What is the promotor region?

Answer 46

Promoter regions are sections of a gene that are found before the start triplet, at the 5' end of the site where transcription will begin. A promoter region: 1. Is the location where the RNA polymerase (the enzyme that initiates transcription) attaches to the gene 2. Identifies which DNA strand will be transcribed 3. Identifies where transcription of the gene will start 4. Identifies in which direction transcription will occur In many eukaryotic genes, the promoter region is coded for by the sequence of bases TATAAA, which is sometimes called the TATA box The CAT or CAAT box, located around 60 to 100 bases upstream of the transcription start site, is also part of some promoter regions.

Question 47

What is introns and exons?

Answer 47

1. Exons are regions of a gene that are usually ‘expressed’ as proteins or RNA. Exons come together to make up mRNA, which is then translated into proteins. 2. Introns are non-coding- , or intervening, regions of a gene. Introns are spliced out of the mRNA during the stage of gene expression called RNA processing. 3. There are no rules about the number of exons and introns in a gene. In the dystrophin gene, for example, 99% of its length is made up of introns.

Question 48

What is the structure of eukaryotic genes?

Answer 48

Eukaryotic genes all have a number of structural features in common, including: Promoter Regions: an upstream binding region for the enzyme that is involved in the encoding process (which is RNA polymerase). Stop and Start Triplet Sequences: regions where encoding DNA begins and ends for a specific gene Exons: DNA regions that are the coding segments Introns (or spacer DNA): DNA regions that are non-coding segments.

Question 49

Transcription occurs in three steps:

Answer 49

1. Initiation: Transcription factors combine with the region at the start of the gene, known as the promoter. 2. The promoter region contains specific nucleotide sequences (TATA box) that are recognised by an appropriate subunit of the enzyme RNA polymerase. In eukaryotic cells, transcription factors are required for RNA polymerase to attach to the DNA. 3. RNA polymerase then attaches to the promoter, unwinding and unzipping the DNA molecule by breaking the weak hydrogen bonds between the two strands to expose the bases

Question 50

What is elongation and what is the process?

Answer 50

Elongation refers to the process of lengthening a biological entity, such as a DNA, RNA, or protein chain, through the addition of nucleotides or amino acids 1. During transcription the RNA polymerase molecule covers a region of approximately 30 base pairs. Within this region, a segment of about 15 base pairs is uncoiled, this results in the formation of a transcription bubble. 2. As the RNA polymerase moves along the gene, DNA strands located behind the transcription bubble are coiled again. 3. The RNA polymerase moves along the DNA molecule, producing a strand of mRNA. It uses a strand of DNA as a template, attaching nucleotides (A, U,G, C) by complementary base pairing. 4. mRNA is always synthesised in the 5' to 3' direction, with new nucleotides added to end. The initial mRNA molecule transcribed is called a primary RNA transcript. The primary RNA transcript will then be processed into mature mRNA.

Question 51

What is termination and the process?

Answer 51

1. Transcription ends when RNA polymerase reaches the termination site of the gene. 2. This region contains a stop triplet code, which binds release factors that signal termination. 3. The RNA polymerase detaches, releasing the mRNA and allowing the DNA molecule to reform

Question 52

What happens during RNA processing

Answer 52

After transcription, the primary RNA transcript undergoes processing before it is translated. This stage of gene expression is called RNA processing and includes: 1. the addition of a 5' cap 2. the addition of a poly-A (adenine) tail 3. splicing (removal) of the introns (mRNA maturation)

Question 53

Explain 5' cap and poly-A tail

Answer 53

1. A cap consisting of a methylguanosine triphosphate molecule, called a 5‘ cap is added to the 5‘ end of the primary RNA transcript while it is been synthesised. 2. Once transcription has finished, a chain of up to 250 adenine nucleotides is added to the 3' end of the primary RNA transcript. This chain is called a poly-A tail. i. These modifications to either end of the primary RNA transcript increase its stability and prevent it from degrading. ii. Additionally, the 5' cap aids the binding of the ribosome to the mRNA at the beginning of translation

Question 54

What is the operator region?

Answer 54

* Operator regions are special sections found in prokaryotic genes. * An operator is found between the promoter and the gene being transcribed. * It is the binding site for repressor proteins. When a repressor (produced in another gene) binds to the operator, it prevents the RNA polymerase binding to the promoter, and thus transcription cannot be initiated.

Question 55

Gene Expression in Prokaryotes

Answer 55

In prokaryotes, there is no nucleus and ribosomes can begin translating a gene while it is still being transcribed.

Question 56

What is splicing?

Answer 56

1. Eukaryotic genes have protein-coding regions called exons and non-protein coding regions called introns. Exons carry the code for the protein, while introns are ‘intervening’ regions. 2. Most prokaryotes contain only exons and therefore the RNA processing described in this section does not occur in prokaryotes. 3. In eukaryotes, before a protein can be produced, the introns must be cut out of the primary RNA transcript to form the mature mRNA molecule. This process is known as splicing. 4. During splicing, a complex molecule composed of protein and RNA molecules, called a spliceosome, removes the introns from the primary RNA transcript and joins the exon sections together to make mature mRNA. 5. (Not all of the exons will necessarily be included, as you will see in the next section.) 6. The single-stranded mature mRNA molecule then exits the nucleus via a nuclear pore.

Question 57

Editing the Primary mRNA

Answer 57

Exons are spliced together to form the mature mRNA. There are several ways in which this is done. Introns might also facilitate recombination between exons of different genes. This may accelerate evolution. Alternative splicing is one reason why the 21000 genes of humans can produce so many more than 21000 proteins.

Question 58

Ribosomes & tRNA

Answer 58

Ribosome Comprises two subunits in which there are grooves where the mRNA strand and polypeptide chain fit in. The ribosomal subunits are constructed of protein and ribosomal RNA (rRNA). The subunits form a functional unit only when they attach to a mRNA molecule. tRNA molecule There is a specific tRNA molecule and anticodon for each type of codon. The anticodon is the site of the 3-base sequence that 'recognises' and matches up with the codon on the mRNA molecule.

Question 59

Process of Translation

Answer 59

1. Initiation: The first initiation stage of translation brings together mRNA, a tRNA bearing the first amino acid of a polypeptide, and the two ribosomal subunits. The small ribosomal sub-unit attaches to a specific nucleotide sequence on the mRNA strand just 'upstream’ of the initiation codon (AUG) where translation will start. The initiator tRNA, carrying methionine, attaches to the initiator codon. The large ribosomal sub-unit binds to complete the protein-synthesising complex. 2. Elongation: In the elongation stage of translation, amino acids are added one by one by tRNAs as the ribosome moves along the mRNA. There are three steps: 1. The correct tRNA binds to the A site on the ribosome. 2. A peptide bond forms between adjacent amino acids. 3. The tRNA at the P site is released. The tRNA at the A site, now attached to the growing polypeptide, moves to the P site and the ribosome advances by one codon. This step requires energy. 3. Termination: The final stage of protein synthesis (termination) occurs when the ribosome reaches a stop codon. A release factor binds to the stop codon and hydrolyses the completed polypeptide from the tRNA, releasing the polypeptide from the ribosome. The ribosomal units then dissociate so that they can be recycled.

Question 60

Something to remember about introns

Answer 60

Introns are transcribed but not translated

Question 61

Leader Region

Answer 61

Another region that is upstream of the coding region of some genes is the leader region. In prokaryotes, it tends to be small, but can be much longer in eukaryotes. Leader regions contain sections known as attenuators and as such are involved in a process of gene regulation called attenuation. This involves the formation of hairpin loops and the stalling and detachment of the ribosome and in turn RNA polymerase when the structural genes do not need to be transcribed and translated.

Question 62

What is a repressor?

Answer 62

Repressor: A protein produced by a regulatory gene that can bind to DNA and prevent transcription

Question 63

The Structure of Genes

Answer 63

The part of a gene that contains the coded information for making a protein is called the coding region of a gene. The regions on either side of the coding region of a gene are called flanking regions. The flanking region before the start of the coding region is called the upstream region. The flanking region after the end of the coding region is called the downstream region.