The relationship between nucleic acids and proteins

Question 1

Nucleic acids

Answer 1

Nucleic acids are biomolecules that are vital for the continuity of life and are made up of subunits known as nucleotides.
Nucleic acid is a polymer (Monomers build polymers)

Question 2

Structure of DNA

Answer 2

Nucleotides in DNA are arranged in a double helix. The two strands of DNA are antiparallel and are held together by hydrogen bonds between complementary nitrogenous bases.
5’ to 3’ means: can only add at 3’ end

Question 3

Messenger RNA

Answer 3

Carries the genetic message from the DNA within the nucleus to the ribosomes, where the message is translated into a particular protein.
→ shorter than DNA
→ Group of three nucleotides in mRNA are a codon

Question 4

Ribosomal RNA

Answer 4

A stable form of RNA found in ribosome

Question 5

Transfer RNA

Answer 5

tRNA are molecules that carry amino acids to ribosomes that are free in the cytoplasm, where they are used to construct proteins.
→ An anticodon binds to the complementary codon on mRNA

Question 6

Degenerative code

Answer 6

Some amino acids can code for more than one codon due to the universal code (same sequence of nucleotides for all organisms)
Genes are more tolerant to mutations
Advantage → Gene manipulation and therapeutic uses (eg: use of CRISPR, bio-tech, insulin being expressed through recombinant plasmid)
Disadvantage → easy for foreign DNA to be incorporated into a genome. (Eg: some viruses are able to hide in the genomes of host cells without being recognised as foreign.

Question 7

Gene expression

Answer 7

1. Transcription
2. RNA processing (eukaryotic cells in nucleus)
3. Translation
4. Post translational modification

Question 8

Transcription

Answer 8

Initiation - RNA polymerase binds to the promoter region to separate DNA sequence.
Elongation - The polymerase runs in a 3’ to 5’ direction and builds messenger RNA in 5’ to 3’ direction.
Termination - When a stop codon is reached, transcription stops and pre-mRNA molecule is released

Question 9

RNA processing (eukaryotic cells in nucleus)

Answer 9

Capping: The 5′ end of the pre-mRNA is capped with an altered guanine (G) base which protects the pre-mRNA from enzyme attack and contributes to its stability, helping it attach to the ribosome.
Adding a tail: A poly-adenine (A) tail, with up to 250 A’s, is added at the 3′ end of the pre-mRNA. The poly A tail contributes to the stability of the mRNA and facilitates mRNA export from the nucleus.
Splicing: The regions in the pre-mRNA that correspond to the introns are spliced and the remaining exons are joined together. (done by spliceosomes, which recognise specific base sequences at the ends of the introns)
Alternative splicing of pre-mRNA Sometimes, additional exons are removed by the spliceosomes to add further complexity to RNA processing and gene regulation, enabling one gene to produce a multitude of proteins if required.

Question 10

Translation

Answer 10

Initiation - Ribosome binds to mature mRNA structure
Elongation - mRNA structure goes through the ribosome and tRNA molecule carries an amino acid complementary to the anticodon creating a polypeptide chain (amino acids form peptide bonds)
Termination - ribosome reads a stop codon and polypeptide chain is released

Question 11

Post translational modification

Answer 11

Polypeptide chain gets folded in the rough ER (its secondary structure)
The folded protein is transported in a transport vesicle to the Golgi body for final packaging of the protein (completed 3D structure- either at tertiary or quaternary level)
Protein travels in a secretory vesicle to the plasma membrane.
With an input of ATP from the mitochondria, the vesicle fuses with the membrane and the protein leaves the cell by exocytosis.

Question 12

Exons

Answer 12

Exons contain the instructions that code for the amino acids in the produced protein. They are both transcribed and translated.

Question 13

Introns

Answer 13

Introns are interrupting segments that separate the exons. They do not contain instructions relating to the protein chain. They are transcribed in the nucleus but are cut out in RNA processing

Question 14

Promoter

Answer 14

The promoter is where RNA polymerase binds to initiate transcription. Without a functioning promoter region, transcription cannot be properly initiated.
Proteins called transcription factors can bind and regulate the expression of genes.
Also known as TATA box (rich in A and T’s)

Question 15

Operator

Answer 15

Are the binding sites for repressor proteins. When a repressor binds to the operator, it prevents the RNA polymerase binding to the promoter, and thus transcription cannot be initiated.
Found in prokaryotic genes between the promoter and the gene being transcribed.

Question 16

RPOS

Answer 16

Regulator, promoter region, operator region, structural genes

Question 17

Prokaryote

Answer 17

→ Repressor proteins bind to an operator
→ Gene regulation only occurs at transcriptional level
→ Gene regulation only occurs at cytosol
→ Only have exons
→ Structural genes for every operon region

Question 18

Eukaryotic

Answer 18

→ Regulatory proteins bind in an upstream region
→ Gene regulation occurs at transcriptional level, post-transcriptional modification, translational level
→ Gene regulation occurs at nucleus or cytosol
→ Have exons and introns
→ Have no operator region

Question 19

Both prokaryotic and eukaryotic

Answer 19

→ Have promoter regions to initiate transcription where RNA polymerase binds to
→ Have structural genes (exons) that code for biological proteins
→ regulation methods (molecules that activate or inhibit gene expression)

Question 20

Structural genes

Answer 20

Genes that produce proteins that become part of the structure and the functioning of the organism.

Question 21

Regulatory genes

Answer 21

Genes that produce proteins that control the action of other genes (active or inactive) Many of these act as DNA binding proteins, binding directly to sections on the DNA. Others act as signalling molecules, binding to receptors on the cell surface

Question 22

Trp operon

Answer 22

Tryptophan is an amino acid that the bacterium Escherichia coli (E. coli) is able to ingest from the surrounding environment. E. coli is able to synthesise tryptophan using enzymes encoded by five genes.

Question 23

Presence of trp (operator repressor)

Answer 23

1. Trp binds to repressor protein causing a configurational change in its shape allowing it to be active
2. Repressor can bind to the operator
3. Thus, RNA polymerase is unable to bind to the promoter and transcription does not occur as operon is off

Question 24

Low levels of trp (attenuation)

Answer 24

→ occurs when there is little trp left and is carried by tRNA molecule for translation (attenuation means slowing something down)
1. The ribosome will run past the ‘pause’ and stop when it gets to the stop codon. it now occupies a region of the leader that keeps 1 from binding to 2 and making a loop.
2. Therefore, the RNA polymerase gets further ahead of the ribosome and transcribes 3&4 which bind together forming a loop.
3. This will pull the attenuator away from the DNA.
4. Thus, the RNA polymerase comes off the DNA and does not transcribe the genes of the operon

Question 25

Absence of trp (attenuation)

Answer 25

1. The ribosome translates the mRNA but when it gets to the codons for trp, there is no tRNA with trp.
2. The ribosome waits and does not get to the stop codon.
3. Thus, the RNA polymerase transcribes domains 2&3 and they stick together creating a loop.
4. As 3 is stuck to 2, it can’t stick to 4. Therefore, it does not yank the messenger RNA away from the attenuator.
5. The RNA polymerase does not fall off the DNA and continues on transcribing the genes of the operon

Question 26

Amino acids

Answer 26

The R group variable determines the property of the amino acid (pos/neg charger, hydrophilic/phobic) Interactions between the different R groups determine how folding in the protein occurs.
–> is an amino group, carboxyl group, variable group and hydrogen group

Question 27

Condensation polymerisation (synthesis) and hydrolysis

Answer 27

The reaction that forms peptide bonds is condensation polymerisation where water is released. The reaction that breaks down peptide bonds is hydrolysis where water is required.
Both requires energy in the form of ATP

Question 28

Primary protein structures

Answer 28

Specific linear sequence of amino acids in the protein brought together as a polypeptide during translation in the ribosome.

Question 29

Secondary protein structures

Answer 29

Depending on R group, 3 different folds can occur
Alpha helix: single twisted strand. Help increase SA:V, can stretch / relax and contract - muscle fibres.
Beta-pleated sheets: staggered fold. Can stretch, maintains a structure / appearance surrounding
Random coiling: often the active site of an enzyme allowing a substrate to successfully bind

Question 30

Tertiary protein structures

Answer 30

The total irregular 3D folding held together by various bonds forming a complex shape. The tertiary structure depends on both the primary and the secondary structures. Bonds include:
hydrogen bonds, ionic attractions between charged R groups, interactions between hydrophobic R groups in the protein interior, covalent disulfide cross links.
These bonds differ in their strength and frequency. Disulfide bridges are the strongest bonds that can form in a tertiary structure.

Question 31

Quaternary protein structures

Answer 31

Made of more than a single polypeptide chain each with its own primary, secondary and tertiary structure. Those polypeptides are held together by hydrogen bonds and the mutual attraction between polar and amino acid side chains. Has a heavy and light chain

Question 32

Protome

Answer 32

The complete array of proteins produced by a single cell or organism in a particular environment

Question 33

Enzyme as catalyst in biochemical pathways

Answer 33

Catalysts are substances that speed up the rate of chemical reactions without the catalyst itself being used up in the reactions.

Question 34

Ribosome

Answer 34

Site of translation where amino acids join forming a polypeptide chain
Often attached to ER

Question 35

Rough ER

Answer 35

Consists of a system of membrane bound channels that transport substances within the cell
Through its network of channels the rough ER:
Folds proteins into their correct functional shape/ conformation
Assembles complex proteins by linking together several polypeptide chains eg. haemoglobin protein

Question 36

Golgi apparatus

Answer 36

Consists of stacks of flattened pockets (cisternae)
As proteins progress through the cisternae of the GA they are modified by enzymes that may add or remove components until the protein is in its mature form
It then packages proteins into vesicles for export from the cell through exocytosis

Question 37

Vesicles

Answer 37

Secretory vesicles break through GA
Are membrane bound and move to plasma membrane where they fuse with it and discharge protein contents to the exterior through exocytosis