Topic 2 2.2

Question 1

Proteins

Answer 1

. Made up of one or more polypeptide chains
. Made up of monomers called amino acids
. All contain carbon, oxygen, hydrogen and nitrogen
-> sometimes also contain sulfur

Question 2

Structure of amino acids

Answer 2

Amino acids have a carboxyl group (COOH), an amine group (NH2) and a carbon containing R group
-> the R group is also known as the variable group as its the part of the amino acid structure that varies depending on the type of amino acid

Question 3

Formation of polypeptides

Answer 3

Polypeptides are formed when more than two amino acids are linked together by peptide bonds through a condensation reaction where a molecule of water is formed
-> the peptide bond forms between the carbon of the carboxyl group and nitrogen of the amine group

Question 4

structural levels of protein: primary

Answer 4

The order of amino acids in the polypeptide chain
-> this is determined by the order of bases in mRNA which was determined by the order of bases in DNA -> bonds form between the carboxyl and amine groups of the amino acids

Question 5

structural levels of protein: secondary structure

Answer 5

Hydrogen bonds form between the amino acids in the polypeptide chain making it coil into either a B-pleated sheet or an a-helix
-> bonds form between the carboxyl and amine groups of the amino acids

Question 6

structural levels of protein: tertiary structure

Answer 6

3D folding a polypeptide caused by bonds/interactions between the variable groups of different amino acids
-> the order of amino acids in the primary structure determine the types of variable groups and so the types of bonds/interactions formed and therefore the different folds in the tertiary structure
-> bonds form between the variable groups
. Eg: ionic bonds, hydrogen bonds, disulfide linkage and hydrophobic interactions

Question 7

structural levels of protein: quaternary structure

Answer 7

The way polypeptide chains are assembled together in a protein that is made up of more than one polypeptide

Question 8

Globular protein

Answer 8

General structure: round, compact proteins made up of multiple polypeptide chains
Properties: soluble proteins that are easily transported in fluids due to hydrophilic parts facing outwards of molecule and hydrophobic parts facing inwards
Uses: enzymes, hormones and antibodies
Examples: haemoglobin -> transports oxygen in the blood (soluble) through a haem group (made of iron) attached to each chain which binds to oxygen

Question 9

Fibrous proteins

Answer 9

General structure: made up of long, insoluble polypeptide chains tightly coiled forming a rope shape
Properties:
. Strong, fibrous proteins due to strong bonds between chains called cross-links
. Insoluble proteins due to hydrophilic parts facing inwards of molecule and hydrophobic parts facing outwards
Uses: connective tissue
. Eg: collagen -> forms connective tissue in animals in artery walls, tendons and ligaments

Question 10

Enzymes

Answer 10

. They are globular proteins
. They act as biological catalysts -> they spread up metabolic reactions without being used up
. Each one catalyses one reaction where the substrate has a complementary shape to their active site to form an enzyme-substrate complex
-> an enzymes active site. Is highly specific due to the folding of the polypeptide chain in the tertiary structure which is determined by the enzymes primary structure
. They can be intercellular where they catalyse reactions inside cells or extra cellular where they are produced and secreted from cells by exocytosis to catalyse reactions outside cells
EG: intercellular: DNA polymerase
EG: extracellular: amylase

Question 11

Mechanism of action in enzymes

Answer 11

Enzymes speed up reactions by lowering the activation energy
. Build up enzymes -> active site holds the two molecules close together and in the correct orientation reducing any repulsion between the molecules so they can bond more easily
. Build down enzymes -> active site puts a strain on the bonds in the substrate so bonds break apart easily

Question 12

Effect of mutation of mechanism of action in enzymes

Answer 12

A change in the base sequence of DNA -> change in sequence of amino acids -> change in sequence of R group -> different bonds in the tertiary structure-> change in the shape of active site making it no longer complementary to the substrate so reaction wont take place

Question 13

Factors that affect rate of enzyme controlled reactions

Answer 13

. Enzyme concentration
. Substrate concentration
. PH
. Temperature

Question 14

DNA and RNA basics

Answer 14

Are Both types of nucleic acids
. DNA: stores genetic information -> instructions and organism need to grow and develop
. RNA: transfers genetic information from DNA to ribosomes

Question 15

Structure of DNA and RNA

Answer 15

DNA and RNA are polynucleotides made up of monomers called mononucleotides that are made up from:
. A PENTOSE SUGAR:
- DNA: deoxyribose sugar -> one oxygen atom less
- RNA: ribose sugar
. AN NITROGENOUS BASE:
- DNA: adenine + thymine + cytosine + guanine
- RNA: adenine + uracil + cytosine + guanine
. A PHOSPHATE GROUP

Question 16

Forming polynucleotides

Answer 16

The mononucleotides in a polynucleotide are joined by phosphodiester bonds between the phosphate group of one mononucleotide and the sugar of another through a condensation reaction (water is a product) catalysed by the enzyme DNA polymerase
-> DNA has two polynucleotide strands
-> RNA has one polynucleotide strands

Question 17

DNA double helix structure

Answer 17

1. Two DNA polynucleotides strands join together by hydrogen bonds between bases
2. Each base can only join with one particular partner -> complementary base pairing
   
   • adenine + thymine (A+T) -> 2 hydrogen bonds
   • cytosine + guanine (C-G) -> 3 hydrogen bonds
3. Two antiparallel polynucleotides strands twist to form the DNA double helix

Question 18

Gene: sequence of bases on a DNA molecule that codes for a sequence of amino acids

Answer 18

Gene: sequence of bases on a DNA molecule that codes for a sequence of amino acids in a polypeptide chain (protein)
-> each amino acid is coded for by sequence of three bases (a codon/triplet) where this codon signals where translation (protein synthesis) should begin and through start and stop codons

Question 19

Types of RNA: messenger RNA (mRNA)

Answer 19

. Made in nucleus during transcription
. Three adjacent bases are called a codon
. Carries genetic code from DNA in the nucleus to the cytoplasm where its used in translation

Question 20

Types of RNA: transfer RNA (tRNA)

Answer 20

. Found in cytoplasm
. It has an amino acid bonding site on one end and sequence of three bases at the other end called an anticodon
. Carries amino acids that are used to make proteins to the ribosomes during translation

Question 21

Genetic code

Answer 21

Sequence of codons (three bases) in DNA or mRNA which codes for specific amino acids
Example: 12 bases code for 4 amino acids

Question 22

Characteristics of the genetic code

Answer 22

. Universal -> every living organism has the same method of genetic coding
. Degenerate -> often more than one codon for the same amino acid
- example: AAT and AAC code for leucine
. Non-overlapping -> each triplet is discrete
- example: GUC and UCA give two distinct triplets

Question 23

Transcription

Answer 23

Process of copying the DNA code and taking it to the ribosome through the use of mRNA
-> this ie because DNA is too large to leave the nuclear envelope in which it’s contained (Nucleus)

Question 24

Process of transcription

Answer 24

1. DNA helicase (enzyme) breaks apart the hydrogen bonds holding the DNA strands together revealing the template strand
2. Free RNA nucleotides align with the template strands and bond with the bases on it forming hydrogen bonds through complementary base pairing
3. RNA polymerase (enzyme) moves along DNA separating the strands and assembling the mRNA strand where the RNA nucleotides are joined together by phosphodiester bonds through a condensation reaction
   -> the DNA strands recoil back into a double helix one RNA polymerase has passed by
4. When RNA polymerase reaches a stop codon it stops making mRNA and detaches from the DNA and so the mRNA strand exists and moves from the nucleus through a nuclear pore into the cytoplasm where it attaches to a ribosome

Question 25

Translation process

Answer 25

1. The mRNA attaches to ribosome in the cytoplasm and transfer RNA (tRNA) carry specific amino acids to which they’re attached to towards the ribosome
   2.tRNA molecule with an anticodon that’s complementary to the start codon on the mRNA attaches itself to the mRNA by complementary base pairing forming hydrogen bonds
2. A second tRNA molecule attaches itself to the next codon on the mRNA in the same way forming hydrogen bonds and the two amino acids attached to the tRNA are then joined together by a peptide bond through a condensation reaction and so the first tRNA moves away leaving behinds its corresponding amino acid
3. Ribosome continues to move along the next codons producing a chain of linked amino acids (a polypeptide chain) until the ribosome reaches a stop codon on the mRNA chain and so the polypeptide chain moves away from the ribosome