Biochem revision - Week 3 Proteins and Enzymes

Question 1

How are proteins created? (basic)

Answer 1

1. DNA is transcribed into mRNA
2. mRNA is translated into proteins

Question 2

What is the general structure of a protein building block? i.e an amino acid

Answer 2

A carbon atom with four groups attached: amino group, carboxyl group, hydrogen, and a variable group/side chain that determines the protein’s ID

Question 3

What are the building blocks of proteins and what are the linkages called?

Answer 3

Amino acids. They are covalently joined by peptide bonds. The part of the amino acid participating in the peptide is called a ‘residue’

Question 4

What are the 4 building structures of proteins?

Answer 4

1. Primary structure - is the base determinant of protein shape and function (amino acid sequence/chain)
2. Secondary structure - peptide fold in complex ways due to hydrogen bonds
3. Tertiary structure - conformation of the entire polypeptide chain stabilized by hydrogen bonds, electrostatic bonds, Van der Whaals interaction, Disulfide bonds and Hydrophobic interaction
4. Quaternary structure - two or more polypeptide chains linking via interactions in tertiary structure

Question 5

What is denaturation and how does it occur?

Answer 5

Modifying the molecular structure of a protein through breaking weak linkages or bonds (i.e hydrogen bonds)

Ex. heat or acidity

Question 6

What are enzymes made of and what are their three main features?

Answer 6

Enzymes are made up of proteins and have three main features:

a) Speed up rctns. Enzymes decrease the amount of ‘free energy for activation’ needed during the transition state

b) Display high specificity i.e each enzyme catalyzes one, or a group of rctns involving substrates that have something in common like a chemical bond or group

c) Their catalytic power is regulated i.e the speed of a rctn is subject to a variety of factors

Question 7

What is the small surface area of attraction referred to on an enzyme? How does an enzyme interact with things in this area?

Answer 7

The active site

Either ‘lock and key’ model or the ‘induced-fit’ model in which the enzyme undergoes a conformational change on interaction with substrate

Question 8

What is a co-factor?

Answer 8

A non-protein chemical entity like a metal ion or organic compound that is needed to be present for an enzyme to catalyze a rctn

Question 9

What are the three factors that effect enzyme rctns?

Answer 9

1. Substrate availability - speeds up rctn to a certain point
2. Enzyme concentration - increased [enzyme] = increased rctn rate
3. Temperature and pH - denaturation @ certain point

Question 10

What are the three kinds of cofactors and which is the most common?

Answer 10

1. Coenzymes - organic compound often derived from vitamins
2. Metal cofactors - metal ions
3. Metalloenzymes - metal ions embedded in organic compounds (e.g Heme)

The most common is a metal cofactor

Question 11

What is a nucleotide and what are its building blocks?

Answer 11

Nucleotides are the building blocks of DNA and RNA and they are made up of:

• A sugar
• A base
• A phosphoryl group

Question 12

What are the two subgroups of nucleotide bases which are contained in each?

Answer 12

Purines (2-ring) : adenine and guanine

Pyrimidines (1-ring) : thymine (uracil in RNA) and cytosine

Question 13

What makes up DNA and RNA? How are these bonds joined?

Answer 13

Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are biopolymers of nucleotides. These nucleotides are joined by phosphodiester bonds

Question 14

What is the difference between a nucleotide and a nucleic acid?

Answer 14

A nucleotide is a monomer that when connected in series by phosphodiester bonds is referred to as a nucleic acid (polymer)

DNA and RNA are nucleic acids

Question 15

What are the variable groups in DNA/RNA?

Answer 15

The only variable groups in DNA and RNA are the bases

So in order to describe the primary structure of DNA, the base sequence must be reported

Question 16

What are the structures of DNA and RNA?

Answer 16

DNA - Secondary structure/double helix of two polynucleotides wrapped around each other with complimentary base pairing via hydrogen bonds

RNA - Primary structure/single stranded

Question 17

How is DNA stored? i.e flow of genetic information

Answer 17

Base pairs - DNA double helix - Histones - Chromatin - Chromosomes

Question 18

When does replication occur? What are the four steps to DNA replication?

Answer 18

During mitosis. Only occurs once in the cell’s lifetime.

1. Separation of strands. HELICASE breaks hydrogen bonds to ‘unzip’ DNA molecule
2. Primer binding. A small strip of RNA PRIMER created by primase, is complementary to the template strand and is base paired to it.
3. Elongation. DNA POLYMERASE adds complementary base pairs to the template strand in the 5’ to 3’ direction.
4. Termination. EXONUCLEASE removes the primers and the bases are then re-added to complete a new DNA double helix

Question 19

Describe the process of transcription of a DNA template to a mRNA molecule

Answer 19

1. PROMOTORS are DNA base sequences that ‘signpost’ for where transcription should start. Promoters attract transcription factor proteins. It is a docking site for RNA polymerase
2. TRANSCRIPTON FACTORS bind to promoters and attract RNA POLYMERASE
3. Enhancers, lying far away from the transcription start site (either upstream or downstream), attracts the transcription
   factor complex, thus making contact and activating the RNA polymerase. RNA polymerase adds ribonucleotides one after
   another opposite the bases of DNA
4. Messenger RNA (mRNA) is formed from DNA template strand (antisense strand)

Question 20

What base pair is switched out in RNA?

Answer 20

thymine is replaced with uracil

Question 21

What is mRNA splicing?

Answer 21

Introns (non-coding regions of mRNA) are excised from the mRNA transcript and the remaining exons form mature mRNA

Alternate mRNA splicing can account for different isoforms of proteins ex. tropomyosin of smooth or skeletal muscle

Question 22

What is translation and where does it occur?

Answer 22

Translation is the pairing of anticodons with codons by the ribosome to code for proteins, in other words, the formation of a polypeptide chain (protein) from a mature mRNA transcript.

It occurs in the cytosol once mature RNA (mRNA) is transported out of the nucleus.

Question 23

What is the process of translation?

Answer 23

1. mRNA transcribed in the nucleus is brought outside into the cytoplasm
2. mRNA attaches to a ribosome and is ‘read’ (by the small subunit of rRNA/ribosome) and decoded where then the large subunit binds to tRNA molecules (anticodons) and its corresponding amino acid to the mRNA codons.
3. These amino acids then form peptide bonds, building a sequence of amino acids or a polypeptide chain\

(The amino group of the second amino acid attacks the carboxyl group and removes its tRNA attachment, forming a peptide bond and elongating. This continues until the ribosome reads a ‘stop codon’.)

4. Once formed, the endoplasmic reticulum contains various proteins that fold the protein to form its tertiary structure. The Golgi apparatus then governs post-translational modifications (e.g glycosylation, phosphorylation)
5. Proteins have specific peptide sequences that can guide then to a specific location within the cell:
6. Cell release (Insulin, adreneline)
7. Traffic to a specific organelle or cell membrane

Question 24

What is a codon?

Answer 24

A codon is a sequence of three nucleotides that code for a specific amino acid

Question 25

What is Van der whaals principle?
What is a Disulfide bond?
What is a hydrophobic interaction?

Answer 25

Van der whaals principle states that a non-covalent attraction can occur due to the movement of ions in atomic or molecular orbitals

A disulfide bond is a bond formed between the sulfhydroryl groups of two amino acids of cysteine

A hydrophobic interaction is when hydrophobic side chains of amino acids come together in a folded protein due to a mutual repulsion of surrounding water