CHAPTER 2-nucleic acids

Question 1

Role of proteins in the body:

Answer 1

1. Can we antibodies produced by the immune system to defend against foreign pathogens
   2.Can be hormones released by the endocrine glands to signal between different cells, or cause stimulation or inhibition eg. insulin or ca
2. Can serve as structural proteins, providing strength, support and protection eg.hair(keratin))and nails
3. Cytokines-

Question 2

Different protein structures with examples

Answer 2

1.A primary structure is a polypeptide chain of amino acids held together by peptide bonds

A secondary structure is a polypeptide chain folds and coils, forming hydrogen bonds between the amino acids, resulting in the formation of alpha helices and beta pleated sheets. eg. alpha helix coil andbeta pleatde sheets

. 3. Tertiary structure:
A tertiary structure refers to the 3D functional shape of a protein and is formed when secondary structures further fold by forming interactions and bonds between the amino acids and the R group. eg. myglobin

Quaternary structures are formed when two or more polypeptide chains with tertiary structures join together and not all proteins will have a quaternary structure. eg. insulin

Question 3

Where are primary structures formed and how are they formed

Answer 3

Primary structures are formed when amino acids are joined together through a condensation polymerisation reaction

Primary structures are produced in the ribosomes through translation

Question 4

Types of interactions of tertiary structures include:

Answer 4

Disulphide bonds: strong covalent bonds between 2 sulfur atoms-found in tertiary and quaternary structures.

Weak hydrogen bonds or ionic bonds–play a critical role in maintaining the proteins shape and flexibility-secondary, tertiary and quaternary structures.

Hydrophobic interactions-Hydrophobic interactions occur when non-polar amino acid side chains cluster together away from water, helping to stabilize a protein’s folded structure in tertiary and quaternary structures.

Question 5

what protein structuresare functional and what are not

Answer 5

primary and secondaryare notfunctional proteins

tertiaryu and quatneryar are functional

Question 6

how can a protein structures change eg. via folding

Answer 6

The folding of a protein is dependent on thesequence of amino acids in a primary structure-one change in the amino acid can cause a different protein or the protein may not be functional at all.

Due to the degeneracy of the genetic code, multiple codons can code for the same amino acid, so a silent mutation will result in the same protein being made and no functional change.

If a nonsense mutation occurs, which is where this can result in the protein no longer functioning, due to the codon turning into the stop codon, which means translation ends early and the protein is short.

If a missense mutation occurs, then a different protein will be produced.

Proteins can also be denatured when subjected to high temperature or extreme pH, levels.— Denaturation works due to the unfolding of a protein structure, resulting in the loss of function and is irreversible.

Question 7

How do proteins strucutures change when subjected to high temperatures or pH

Answer 7

Proteins can also be denatured when subjected to high temperature or pH, levels.— Denaturation works due to the unfolding of a protein structure, resulting in the loss of function and is irreversible.

Question 8

What are amino acids,

what is the chemical structure of amino acids,

whatelemetns are amino acids made up of

and what are thedifferent types of amino acids

Answer 8

Amino acids are monomers of proteins(they make up proteins)

Chemical structure of amino acids:
COOH-carboxyl group
NH2- amino group
R group- whichdetermines hte type of amino acid

the elements amino acids are made up of are Carbon, hydrogen, oxygen, nitrogen and someitms sulfur

There are 20 differnety amino acids, but 9 are essiental because their not produced by the body so ists essinteal to be consumed thru diet

Question 9

What are R groups and explain hydrophobic and hydrophilic R groups

Answer 9

Each R group has its own chemical properties whicheffect how differnet mino aicds interact with eachother.

Hydrophobic R groups will interact wit hydrophobic R groups eg, alanine whereas hydrophilic R groups will interact with hydrophilic R groups eg. tyrosine

Question 10

How are proteins formed, explain the sythensis of proteins

Answer 10

Amino acids are joined togheter via peptide bonds in a condensation polymerisation reaction.

This involves the removal of water.

A polypeptide chain forms a primary structuer of a protein

Question 11

nucleotides; what are they made up of,

differneceof the 5 carbonsugar in RNA vs DNA

what is the structure,

what nitrogenous bases are they made of

Answer 11

Nucleotides are made up of a phosphate group(PO4^3-)

structure:
Five carbon sugar is deoxyribose in RNA and ribose in DNA

the 1’ end attaches to the nitrogenous base

The 3’ and 5’ end attached to the phosphate group

nitrogneosu bases:
Adenine, thymine, cytosine and guanine in DNA but adenine uracil cytoisne and guianine in RNA

Question 12

What are nucelic acids, DNA, Anabolic reactions, Catabolic reactions, monomers, polymers, condensation, a condenstation polyermisationreaction, triplet, transcription and translation

Answer 12

Nucleic acids are organic macromolecules consisting of repeating nucleotides-the two types of nucleic acids are RNA and DNA.

DNA is the genes that carry the instructions to make proteins, is found in the nucleus of eukaryotes and in humans DNA is packaged into 46 chromosomes, each containing thousands of genes.

Anabolic reactions are where simple molecules combine to produce complex molecules eg. in the liver, glucose molecules store extra glucose as glycogen or in photosynthesis, where CO2 and water form the complex molecule, glucose.

Catabolic reactions are where larger molecules are broken down into simpler molecules by releasing chemical energy eg. aerobic and anaerobic respiration, glycolysis is a catabolic reaction because glucose is broken down into pyruvate, producing ATP and NADH.

Monomer are atoms or small molecules that bond together to form more complex structures such as polymers

Polymer is a large molecule, made of smaller units called monomers, bonded together in long chains.

Condensation refers to a process where two molecules join together and a water molecule is lost.

A condensation reaction occurs when two monomers combine to form a larger molecule, a polymer, creating a chemical bond, and a water molecule is lost in the process.

Triplet is a sequence of three nucleotides that codes for a specific amino acid during protein synthesis. In mRNA these triplets are called codons, whereas in tRNA, these triplets are called anticodons.

Transcription is a process involving RNA polymerase(enzyme) to create a pre-mRNA molecule in the nucleus. In this process complementary base pairing is used but Thymine is replaced with Uracil.

Translation Involves reading the mRNA molecule produced in transcription and producing a polypeptide chain of amino acids.

Question 13

codons vs anticodons

Answer 13

Codons are triplets of nucleotides found on mRNA that code for specific amino acids.

Anticodons are complementary triplets found on tRNA, which pair with the codons during protein synthesis to ensure the correct amino acid is added to the growing protein chain.

For example:
mRNA codon: AUG (codes for methionine)

tRNA anticodon: UAC (complementary to AUG, bringing methionine to the ribosome)

Question 14

Compare the structure of DNA and RNA:

Answer 14

DNA has 2 strands of multiple nucleotide chains that are antiparallel(5’ to 3’ in one direction and 3’ to 5’ in another direction)

The two chains are held together when hydrogen bonds form between the complementary nucleotide A-T and C-G

RNA is single stranded nucleic acid containing ribose sugar.

Thymine is replaced with Uracil.

DNA stores genetic material for a long period of time, whereas RNA transfers a copy of the DNA during translation to the ribosomes

Bases of DNA are A, T, C, G whereas in RNA, A, U, C, G

DNA has deoxyribose sugar whereas RNA has ribose sugar soto detmerine whehther a structuure is DNA or RNA, if it has an OH group its RNA if its just H its DNA

Question 15

mRNA, tRNA, rRNA:

Answer 15

mRNA are RNA molecules formed in the nucleus during transcription and carries genetic information from the nucleus to the ribosomes for translation(protein synthesis. In mRNA, 3 bases are read together and are known as a codon.
Once an mRNA molecule binds to the ribosomes, it is read and tRNA delivers individual amino acids to begin forming a polypeptide chain!

tRNA delivers individual amino acids to begin forming a polypeptide chain and is made up of three nucleotides and is known as an anticodon.

rRNA serves as the main structural component of ribosomes within a cell and rRNA folds into small subunits to make ribosomes.

Question 16

comparison of the strctures of RNA

Answer 16

mRNA contains codons, it is a single stranded, linear molecule–it also includes a 5’ cap and a poly A tail at the 3’ end of the eukaryotes which protects it from degrading and it aids in translation

tRNA contains anticodons, it is single stranded but has a clover leaf shape due to the hydrogen bonds between the complementary base pairs.
Does not have a poly A tail or a 5’ cap

rRNA is single stranded, but it folds into complex secondary or tertiary structures due to extensive internal base pairing.
Does not have a Poly A tail or 5’ cap.

Question 17

What is the process of DNA becoming a protein?

Answer 17

1. DNA is copied into an mRNA molecule in the nucleus via transcription.

2,The mRNA molecule undergoes some modification prior to exiting the nucleus to the ribosomes.

3,Once attached to the ribosomes, the mRNA strand is read and the corresponding tRNA molecule with a specific amino acid is carried to the ribosomes, forming a polypeptide chain of amino acids via translation.

4.The folding of the polypeptide chain occurs through the rough endoplasmic reticulum and is then exported through the vesicles.

Question 18

Universal and degeneracy

Answer 18

The genetic code is described to be both universal and degenerate.

Universal- nearly all organisms use the same codons to code for the same amino acid
Degenerate-multiple codons code for the same amino acid.

If a mutation occurs and the genetic code is degenerate, since the amino acid sequence will remain the same, the same protein is produced(the protein does not change).
ii

Question 19

Types of bonds:

Answer 19

1. Hydrogen bonds- bonds between the complementary nitrogenous bases- they are weak bonds and are broken down by the enzyme, polymerase
2. Peptide bonds- bonds between the carboxyl group of one amino acid and the amino group of another amino acid-joins amino acids together.
3. Phosphodiester bonds-bonds between the nucleotides

Strength: ranking-weakest to strongest.
Hydrogen bonds, peptide bonds and phosphodiester bonds—phosphodiester bonds are the strongest because they are covalent bonds that strongly link the nucleotides together in DNA and RNA backbone, providing stability and resistance to breaking compared to peptide or hydrogen bonds.

Question 20

THE STRUCTURE OF GENES:
what is the function of:

Promotor region
RNA polymerase
Start triplet
Template strand
Non template strand
DNA
exons
introns
termination sequence

Answer 20

1. Promotor region is where RNA polymerase binds to and is also known as the TATA box.

Start triplet-where RNA polymerase begins to copy the gene into an mRNA molecule.

RNA polymerase- an enzyme that copies the DNA strand to produce an pre-mRNA strand during transcription.

Template strand(
non-coding strand) is the strand of DNA to be copied as the strand of DNA is transcribed by RNA polymerase to produce a complementary pre-mRNA strand.–its always in the 3’ to 5’ direction

The non-template strand(coding strand)-always in the 5’ to 3’ direction it provides the information to code the protein for RNA polymerase but is not directly involved in transcription.

4. Exons are coding regions of the gene which are spliced togetherin RNA processing.
5. Introns are non coding regions of the gene which are removed during RNA processing.

The termination sequence is a sequence of DNA that signals the end of transcription.

Question 21

Compare promoter region and start triplet:

Answer 21

The promoter region is a specific sequence of DNA where RNA polymerase and transcription factors bind to initiate the process of transcription (copying DNA into mRNA). It does not directly participate in translation.

The start triplet (start codon) is a sequence of three nucleotides (usually AUG in mRNA) that signals the start of translation, where ribosomes begin to read the mRNA to produce a protein,.

Question 22

Gene expression and what does this process involve

Answer 22

Gene expression is the process by which the information stored in the gene is used to synthesize functional products(such as a protein or RNA)

Porces sinvovles;
transcription
RNA processing
translation

Question 23

Transcription define and steps

Answer 23

is a process involving RNA polymerase(enzyme) to create a pre-mRNA molecule in the nucleus. In this process complementary base pairing is used but Thymine is replaced with Uracil.

There are three stages of transcription:
1. Initiation:
Rna polymerase binds to the promoter region which signals to the weak H+
between the DNA to break. This unwinds the DNA strands.

Elongation:
RNA polymerase moves along the template strand of the DNA in a 3’ to 5 direction and adds complementary RNA nucleotides to produce a pre-mRNA molecule The premRNA is complemetnary to the DNA template strand and in premRNA, adenine binds with uracil, not thymine

Termination:
Transcription ends when RNA polymerase reaches the termination sequence. The pre-mRNA molecule released for processing is DNA molecule winds up and hydrogen bonds reform between the strands.

Question 24

What are transcription factors, how would you detemrine a strand is the template strand, does RNA polymeraese transcribe the TATA box.

Answer 24

Transcription factors are proteins that bind to the promoter region and control the functioning of RNA polymerase.

The template strand is the 3’ to 5’—- YOU NEED TO LOOK FOR A TATA BOX(promotor region) OR TAC also symbols start which suggests that it is the template strand/ the start of translation is occuring.

RNA polymerase does not transcribe TATA its just where it starts and also if transcription question has 4 marks, then you need to talk about RNA processing but if its 3 marks its just transcription

Question 25

RNA PROCESSING(processing of pre mRNA into mRNA)

Answer 25

1. Removing introns which are non-coding regions
2. Splicing exons(coding regions) of the mRNA molecule together
3. Adding a methyl cap to the 5’ end of the mRNA molecule. This allows it to bind to the ribosomes during translation.
4. Adding a Poly A tail to the 3’ end of the mRNA molecule. This stabilizes the molecule, preventing it from degrading.
5. Mature mRNA exits the nucleus to the ribosomes for translation.

Question 26

why does RNA processing only occur in eukaryotes, notin porkaryotes like bacteria, why do we only reove introns but not exons

Answer 26

1. RNA PROCESSING DOES NOT OCCUR IN PROKARYOTES(NOT EUKARYOTES) BECAUSE PROKARYOTES LIKE BACTERIA DO NOT HAVE INTRONS IN THEIR DNA.
2. Why do we remove introns and splice exons?
   Introns are non-coding regions of the gene, hence they do not contain information to build a protein, hence they are removed during mRNA processing to ensure accurate translation. Exons are coding regions of the gene that contain the necessary information for protein synthesis, and splicing the exons creates a mature mRNA molecule. Additionally, alternative splicing of the exons allows for different combinations of exons, increasing the diversity of proteins produced from a single gene.

Question 27

Alternative splicing

Answer 27

involves the splicing of pre-mRNA in different ways. This results in a different protein being produced.

Question 28

Translation define and steps

Answer 28

Involves reading the mRNA molecule produced in transcription and producing a polypeptide chain of amino acids.

Three stages of translation:
Initiation:
1.The 5’ end of the mRNA molecule attaches the ribosomes

2. The start codon(AUG) is read, then the tRNA molecule with the complementary

anticodon(UAC) binds to the ribosomes to deliver the amino acid to methionine.

Elongation:
1.The next codon is read and the complementary tRNA molecule delivers a specific amino acid to the ribosomes.

2. This amino acid will bind to the adjacent amino acid to form a peptide bond.

Termination:
Once the STOP codon is read, this signals the end of translation
There was no tRNA molecule that codes for the STOP codon
Instead, a release factor binds to the polypeptide chain of the amino acids for modification

Question 29

What is a release factor and why are they called a release factor

Answer 29

A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. They are named so because they release new peptides from the ribosome..

Question 30

What is gene regulation: and the types of genes involved in gene regulationas well as their functons

Answer 30

Gene regulation is the process in which the expression of a gene is activated or inhibited.

Regulatory genes are genes that code fora represosr protien, which influecnes the expression of structurla genesto turn genes on or off, increase or decrease the expresisionof a gene or control altneriaivt splcing
1. Turning genes on or off
2. Increasing or decrease the expression of a gene
3. Control alternative splicing

Structural genes are genes that code for proteins involved in the structure of the function of an organism such as enzymes, protein channels and hormones.

Question 31

Role of the following organelles in protein production: nucleus, ribosomes, rough endoplasmic reticulum, golgi apparatus, mitochondria (indirectly):

Answer 31

Nucleus: contains DNA, which is transcribed into mRNA, providing the instructions for protein synthesis.

Ribosomes: Site of protein synthesis where mRNA is translated into a polypeptide chain of amino acids.

Rough endoplasmic reticulum: Assists in protein folding and modification and transports proteins to the Golgi body.

Golgi body:
Modifies, sorts and packages proteins for secretions within the cell.

Mitochondria: Provides ATP needed for the energy-intensive process for protein production.

Trp operon- contains a series of genes involved in the production of the amino acid, tryptophan-used in protein production of E.coli

Question 32

What is the operator region:

Answer 32

is the DNA segment where the repressor molecule binds to the operon model. In the prokayotes operator region, it facilitates the binding of transcription factors and RNA polymerase for gene transcription.

Question 33

What happens if tryptophan levels are high vs low

Answer 33

-transcription of the trp operon structural genes is stopped(saves energy and prevents unnecessary production of tryptophan). Whereas, if tryptophan levels are low, transcription of the trp structural genes is initiated.

Question 34

Repression of trp operon

Answer 34

Tryptophan is present and binds to the repressor, cause a conformational shape change inthe repssor allowign
The active repressor binds to the operator region.
Hence, RNA polymerase is unable to transcribe the trp operon structural genes to make tryptophan.(no transcription)

Question 35

Expression of trp opreon

Answer 35

No tryptophan present so the repressor protein is inactive due to no tryptophan binding to it. This means that no repressor is bound to the operator region.
This allows RNA polymerase to transcribe the structural genes to make mRNA molecules to code and produce tryptophan.

Question 36

What is trp operon

Answer 36

trp operon is a group of genes that code through tryptophan. trp operon allows bacteria to converse energy if there is an over production of tryptophan.

note that trp operon is only found bacteria, not animals or eukaryotes.

Question 37

compare post transcriptionla modification(RNA PROCESSING) in prokayryoes like bacteria to eukaryotes like animals.

Answer 37

bacteria does not undergo post transcriptional modification and there are no introns and in bacteria transcription and translation occurs at the same, whereas in eukaryotes, post transcriptional modification occurs, introns exist and transcriptional translation do not occur at the same time.

Question 38

What happens if the operator region is blocked

Answer 38

The repressor binds to the operator region, blocking it (1 mark).
This prevents RNA polymerase from binding to the promoter or moving forward (1 mark).
As a result, transcription of the genes involved in tryptophan synthesis is stopped (1 mark).

Question 39

What is attenutation, why is the attenutator region held together by weakder hydrogen bonds, leader sequence containshow many domains and which are complementary, what codes for tryptophan

Answer 39

Attention is the second process of trp regulation in response to high tryptophan levels. (means attenuation is the second mechanism of trytpohna too high decrease)Attenuation is in response to the amount of tRNA-bound tryptophan(so more attenuation occurs if there are high tryptophan levels and vice versa).

Attenutatar region is held together by weaker hydrogen bonds Adenine and Uracil.

Leader section contains 4 domains, domain 1 and 2 are complementary(have complementary base sequencing) and domain 3 and 4 are complementary(have complementary base sequencing)

UGG codes for tryptophan

Question 40

when do we use attenutation and when we do we use repression which thres high levels of tryptophan

Answer 40

If tryptophan is attached to a tRNA molecule, then attenutation porcess is used

If tryptophan is not attached to tRNA molecule, then repression of trp operon ocucrs.

Question 41

Process of Attenuation of trp operon when tryptophan is present

Answer 41

1.RNA polymerase runs along the leader region and transcribes mRNA. At the same time, a ribosome translates the mRNA to create a polypeptide chain
.
2.When the ribosome reaches the UGG code for tryptophan, tRNA with tryptophan joins to the polypeptide chain

3.Once the ribosomes reach the STOP codon, RNA polymerase continues to read the DNA, however the ribosomes stop translating the mRNA.

4.This causes region 3 and 4 to pull and form an attenutator loop Therefore, RNA polymerase stops reading the DNA after the attenuated region.

Question 42

Process of Attenuation when tryptophan is absent:

Answer 42

1/ When tryptophan is absent, the ribosomes pause at the two tryptophan codons, waiting for tRNA carrying the tryptophan

2. This allows leader region 2 and 3 to pair to form an anti-attenutator loop, preventing region 3 and 4 from pairing. This prevents the attenuated region from pulling away.
3. This, also allows RNA polymerase to continue to transcribe the trp operon genes, thus making more tryptophan.

Question 43

What is exocytosis, what are the main organelles
responisble for modificaton, compare where transcription and translation occurs and packaging, what macromolecule does insulin belong to and what is the process of exocytosis

Answer 43

Exocytosis is a form of Bulk transport, where ATP is required to release the contents of the vesicle from a cell.

*Main organelles responsible for modification and packaging:

Transcription occurs in the nucleus and translation occurs in the ribosomes.

*Rough ER – modification of protein
*Golgi apparatus – package proteins into vesicle

polypeptide

Process includes:
1. Vesicle being transported to the plasma membrane
2.Vesicle fusing with the plasma membrane
3. Contents released from the cell into the extracellular environment.

Question 44

key parts of a plasmid and function

Answer 44

orgin of rpelication
promotor region
antbitoic resistnace gene which is reuqired because when we grow bacteria on agar, we want to knwo whcih ones survive.

reporter gene