Biochem revision - Week 3 Proteins and Enzymes Flashcards
How are proteins created? (basic)
- DNA is transcribed into mRNA
- mRNA is translated into proteins
What is the general structure of a protein building block? i.e an amino acid
A carbon atom with four groups attached: amino group, carboxyl group, hydrogen, and a variable group/side chain that determines the protein’s ID
What are the building blocks of proteins and what are the linkages called?
Amino acids. They are covalently joined by peptide bonds. The part of the amino acid participating in the peptide is called a ‘residue’
What are the 4 building structures of proteins?
- Primary structure - is the base determinant of protein shape and function (amino acid sequence/chain)
- Secondary structure - peptide fold in complex ways due to hydrogen bonds
- Tertiary structure - conformation of the entire polypeptide chain stabilized by hydrogen bonds, electrostatic bonds, Van der Whaals interaction, Disulfide bonds and Hydrophobic interaction
- Quaternary structure - two or more polypeptide chains linking via interactions in tertiary structure
What is denaturation and how does it occur?
Modifying the molecular structure of a protein through breaking weak linkages or bonds (i.e hydrogen bonds)
Ex. heat or acidity
What are enzymes made of and what are their three main features?
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
What is the small surface area of attraction referred to on an enzyme? How does an enzyme interact with things in this area?
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
What is a co-factor?
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
What are the three factors that effect enzyme rctns?
- Substrate availability - speeds up rctn to a certain point
- Enzyme concentration - increased [enzyme] = increased rctn rate
- Temperature and pH - denaturation @ certain point
What are the three kinds of cofactors and which is the most common?
- Coenzymes - organic compound often derived from vitamins
- Metal cofactors - metal ions
- Metalloenzymes - metal ions embedded in organic compounds (e.g Heme)
The most common is a metal cofactor
What is a nucleotide and what are its building blocks?
Nucleotides are the building blocks of DNA and RNA and they are made up of:
- A sugar
- A base
- A phosphoryl group
What are the two subgroups of nucleotide bases which are contained in each?
Purines (2-ring) : adenine and guanine
Pyrimidines (1-ring) : thymine (uracil in RNA) and cytosine
What makes up DNA and RNA? How are these bonds joined?
Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are biopolymers of nucleotides. These nucleotides are joined by phosphodiester bonds
What is the difference between a nucleotide and a nucleic acid?
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
What are the variable groups in DNA/RNA?
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
What are the structures of DNA and RNA?
DNA - Secondary structure/double helix of two polynucleotides wrapped around each other with complimentary base pairing via hydrogen bonds
RNA - Primary structure/single stranded
How is DNA stored? i.e flow of genetic information
Base pairs - DNA double helix - Histones - Chromatin - Chromosomes
When does replication occur? What are the four steps to DNA replication?
During mitosis. Only occurs once in the cell’s lifetime.
- Separation of strands. HELICASE breaks hydrogen bonds to ‘unzip’ DNA molecule
- Primer binding. A small strip of RNA PRIMER created by primase, is complementary to the template strand and is base paired to it.
- Elongation. DNA POLYMERASE adds complementary base pairs to the template strand in the 5’ to 3’ direction.
- Termination. EXONUCLEASE removes the primers and the bases are then re-added to complete a new DNA double helix
Describe the process of transcription of a DNA template to a mRNA molecule
- 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
- TRANSCRIPTON FACTORS bind to promoters and attract RNA POLYMERASE
- 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 - Messenger RNA (mRNA) is formed from DNA template strand (antisense strand)
What base pair is switched out in RNA?
thymine is replaced with uracil
What is mRNA splicing?
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
What is translation and where does it occur?
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.
What is the process of translation?
- mRNA transcribed in the nucleus is brought outside into the cytoplasm
- 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.
- 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’.)
- 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)
- Proteins have specific peptide sequences that can guide then to a specific location within the cell:
- Cell release (Insulin, adreneline)
- Traffic to a specific organelle or cell membrane
What is a codon?
A codon is a sequence of three nucleotides that code for a specific amino acid
What is Van der whaals principle?
What is a Disulfide bond?
What is a hydrophobic interaction?
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
