CHAPTER 2-nucleic acids Flashcards
Role of proteins in the body:
- 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 - Can serve as structural proteins, providing strength, support and protection eg.hair(keratin))and nails
- Cytokines-
Different protein structures with examples
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
Where are primary structures formed and how are they formed
Primary structures are formed when amino acids are joined together through a condensation polymerisation reaction
Primary structures are produced in the ribosomes through translation
Types of interactions of tertiary structures include:
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.
what protein structuresare functional and what are not
primary and secondaryare notfunctional proteins
tertiaryu and quatneryar are functional
how can a protein structures change eg. via folding
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.
How do proteins strucutures change when subjected to high temperatures or pH
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.
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
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
What are R groups and explain hydrophobic and hydrophilic R groups
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
How are proteins formed, explain the sythensis of proteins
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
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
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
What are nucelic acids, DNA, Anabolic reactions, Catabolic reactions, monomers, polymers, condensation, a condenstation polyermisationreaction, triplet, transcription and translation
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.
codons vs anticodons
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)
Compare the structure of DNA and RNA:
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
mRNA, tRNA, rRNA:
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.
comparison of the strctures of RNA
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.
What is the process of DNA becoming a protein?
- 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.
Universal and degeneracy
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
Types of bonds:
- Hydrogen bonds- bonds between the complementary nitrogenous bases- they are weak bonds and are broken down by the enzyme, polymerase
- Peptide bonds- bonds between the carboxyl group of one amino acid and the amino group of another amino acid-joins amino acids together.
- 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.
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
- 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.
- Exons are coding regions of the gene which are spliced togetherin RNA processing.
- 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.
Compare promoter region and start triplet:
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,.
Gene expression and what does this process involve
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
Transcription define and steps
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.
What are transcription factors, how would you detemrine a strand is the template strand, does RNA polymeraese transcribe the TATA box.
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
