Proteins Flashcards
4 categories of bio molecules
- Proteins
- Carbohydrates
- Lipids
- Nucleic acids
Protein functions
structural support, storage, transport, cellular communications, movement and defense against foreign substances.
Amino acids
General structure:have an amino group,have a carboxyl group
Bioactive Amino Acids
- Tryptophan is a precursor of the serotonin neurotransmitter.
- Tyrosine is a precursor of the dopamine neurotransmitter.
- Aspartate, glutamine, glycine are precursors of nucleotides.
- Arginine is a precursor of nitric oxide.
Precursor meaning
A substance from which another is formed
Peptide bonds
Binding occurs between the amino group of one amino acid and the carboxyl group from another amino acid.
= Condensation reaction or dehydration synthesis
Cysteine
Sulfhydryl (SH) group of cysteine is highly reactive Reversible oxidation that forms a disulfide bond
Types of peptides
Dipeptide 2 Aa
Tripeptide = 3 aa and so on.
Oligopeptides = <25 aa residues
Polypeptides = >25 aa residues
Proteins are oligomers containing 50 or more aa residues.
Role of peptides
Insulin (two polypeptides, 21 and 10 aa)
Glucagon (29 aa)
Oxytocin (9 aa)
Primary structure of proteins
the number and sequence of amino acids in a protein
Primary structure is determined by inherited genetic information
Secondary structure of Proteins
The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of
the polypeptide backbone.
Typical secondary structures are:
1) a coil called an helix.
2) a folded structure called a pleated sheet.
3) Tertiary structure
Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents
Hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals, covalent bonds (disulphide bridges)
4) Quaternary structure
Quaternary structure results when two or more
polypeptide chains form one macromolecule.
- Collagen is a fibrous protein consisting of three polypeptides coiled like a rope.
- Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains.
Results of change in primary structure
▪ A slight change in primary structure can affect protein structure and ability to function
▪ Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
What determines protein structure
▪ In addition to primary structure, physical and chemical conditions can affect structure.
▪ Environmental factors: pH, salt concentration, temperature can cause proteins to unravel (denaturation).
▪ A denatured protein is biologically inactive
How is protein structure determined
▪ X-ray crystallography.
▪ Nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization.
▪ Bioinformatics is another approach to prediction of protein structure from amino acid sequences
The Roles of Nucleic Acids
▪ There are two types of nucleic acids ▪ Deoxyribonucleic acid (DNA)
▪ Ribonucleic acid (RNA)
▪ DNA provides directions for its own replication (Dr Zubko).
▪ DNA (genes) directs synthesis of messenger RNA (mRNA) which controls protein synthesis.
▪ This process is called gene expression: transcription and translation.
What are the 3 stages of transcription
Initiation
Elongation
Termination
Steps in trasncription
Hydrogen bonds (between DNA bases) break;
(Only) one DNA strand acts as a template; (Only) one DNA strand acts as a template;
(Free) RNA nucleotides align by complementary base pairing;
(In RNA) Uracil base pairs with adenine (on DNA) OR (In RNA) Uracil is used in place of thymine;
RNA polymerase joins (adjacent RNA) nucleotides;
(By) phosphodiester bonds (between adjacent nucleotides);
Pre-mRNA is spliced (to form mRNA) OR Introns are removed (to form mRNA);
Molecular components of initiation
• Promoter: DNA sequence where RNA polymerase attaches. TATA box in Eukaryotes.
• Transcription factors: mediate binding of RNA polymerase II.
+
• RNA polymerase II: pries the DNA strands apart and links together the RNAnucleotides.
• Transcription initiation complex (RNA polymerase II + transcription factors).
Molecular components of Elongation
▪ RNA polymerase unwinds the DNA double helix, 10
to 20 bases at a time. Links RNA nucleotides.
▪ mRNA is complementary to the DNA template strand.
▪ Nucleotides are added to the 3′ end of the growing RNA molecule
▪ Transcription rate of 40 nucleotides / s in Eukaryotes.
▪ RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine
Termination of transcription
▪ Bacteria: polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification.
▪ Eukaryotes: RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides after this poly-A sequence / tail.
RNA processing in eukaryotes
1) Both ends of the primary transcript are altered.
2) Interior sections of the molecule can be excised and
the remaining parts spliced together
3) Enzymes in the eukaryotic nucleus modify pre-
mRNA.
ALL OCCUR IN THE NUCLEUS OF THE CELL
Alteration of mRNA ends
-5′ end receives a modified nucleotide 5′ (prime) cap
-3′ end has a poly-A tail
-modified guanine nucleotide added to the5 end
-50-250 adenine nucleotides added to the 3 end
Why?
- Facilitate the export of mRNA to the cytoplasm.
- Protect mRNA from hydrolytic enzymes.
- Assist ribosomal attachment to the 5′ end
RNA splicing
Only exon are expressed and translated to amino acids
Splicing remove introns and joins exons creating an mar molecule with a continuous coding sequence
Spliceosome
Large rna protein complex that catalyses the remove of introns
Function of introns
▪ Some contain sequences that may regulate gene expression.
▪ Some genes encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing.
▪ This is called alternative RNA splicing Which means…
Number of different proteins an organism can produce is much greater than its number of genes
Codons: Triplets of Nucleotides
▪ Gene to protein is based on a triplet code: a series
of nonoverlapping, three-nucleotide words.
▪ The words of a gene are transcribed into three- nucleotide words of mRNA.
▪ These words are then translated into a chain of amino acids, forming a polypeptide.
tRNA
▪ tRNAs transfer amino acids to the growing polypeptide in a ribosome.
▪ RNA molecules, 80 nucleotides long.
▪ Flattened into one plane to reveal its base pairing.
Structure of tRNA
Clover shape
Amino acid attachment at the top
Anticodon at the bottom
Some hydrogen bonding
Steps of translation
(1) a correct match between a tRNA and an amino acid, performed by the enzyme aminoacyl-tRNA synthetase.
(2) a correct match between the tRNA anticodon and an mRNA codon.
Translation step by step
Amino acid and tRNA enter active site
Using atp synthethase catalyses convalescent bonding
Aminoacyl tRNA released
Structure and function of ribosomes
▪ Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis.
▪ The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA).
▪ Bacterial and eukaryotic ribosomes differ.
The have 2 ribaosomal subunits and 3 binding sites
3 stages of translation
1) Initiation
2) Elongation
3) Termination
Molecular Components of Translation
▪ mRNA
▪ tRNAs (with amino acid added)
▪ Ribosome (large and small subunits): made of protein and rRNA molecules.
▪ Translation factors
▪ Start codon (AUG)
▪ Stop codons
What happens at each stage of translation
1 initiation
>codon recognition
2 elongation
>peptide bond formation
>translocation
3 termination
>ribosome reaches a stop codon
>release factor promotes hydrolysis
>ribosomal subunits and other components dissociate
What happens to polypeptide chais after translation
Polypeptide chains are modified after translation (post-translational modification), maybe required for correct folding (tertiary structure etc). Glycosylation, acetylation, methylation etc.
Protein targeting to specific sites in the cell (use of signal peptide) such as the ER.
