Biochemistry Flashcards
What are the pyrimidines?
Single ring structures such as C, T, U.
Which are purines?
Double ring structures such as G and A.
What is the difference between Uracile and Thymine in terms of structure?
Thyminine has an extra ch3 on the econd C after the sugar
Hat are the building blocks of DNA?
Nucleotides.
What are the three components of a nucleotide?
Base, sugar and a phosphate group.
What is a nucleoside?
Its a base plus a sugar group.
What’s the difference between Ribose and Deoxyribose?
Deoxyribose is included in DNA and as an H group on the second carbon while Rybose is in RNA and has a OH group on the second carbon.
In which carbon does the base and the phosphate group bind to?
The base binds on the first carbon while the phosphate group on the fifth.
How do nucleotides form bonds between them to form a single strand?
Two phosphates leave the nucleotide and the one remaining binds with the sugarof the other on its 3’ carbon. The leaving of phosphates is called hydrolisis.
How do bases bind?
G binds with C and T binds with A. That is because AT pair form 2 hydrogen bonds while GC pair forms 3 hydrogen bonds. The bond length is equal and its a hydrogen bond.
What are the three characteristics of DNA strand pairing?
They are complementary, antiparallel and pairing.
What are the three types of double stranded DNA, what are their characteristics and what causes them?
It’s A-DNA which is broad, B-DNA which is the most common and Z-DNA which is narrow. These three types of DNA are pendent on sequence, temperature and ionic conditions.
What are the three function of DNA OR RNA?
DNA could be used as energy carrier because of the three phosphates, also, it is a great information carrier for organisms and RNA catalyses reactions such as as the hammerhead ribozyme which cuts RNA messages.
What are the forming molecules of Proteins?
Amino acids.
What is the difference between polymers and polypeptides?
Polypeptides are polymers of proteins. Polymers can be polysaccharides (sugars) or polypeptides (proteins).
What’s the variety of macromolecules (polymers)?
Macromolecules differ a lot between cells, even more within a species and even more between species.
How Are macromolecules synthesised and how are produced?
Synthesis occurs through condensation (anabolism) while break down occurs through hydrolysis (catabolism). Both form metabolism.
Name three structural proteins.
Collagen fibroin and keratin
Name two storage proteins.
Casein (milk) and Ovalbumin (egg).
What type of proteins are hexokinase and amylase?
Enzymes.
Name three transport proteins.
Haemoglobin, Myosin (muscle) and sodium-potassium protein
Name three receptor proteins.
Rhodopsin in the eye, antibodies for antigens and Acetylcholine in nerve cells.
Name one hormone.
Insulin.
Name two toxins.
Cholera toxin and Botox.
What’s the primary structure like?
It’s a linear chain of amino acid residues.
What does the primary structure of a protein determine?
It’s properties.
Which type of amino acids form proteins?
L-amino acids (laevo).
What are the two types of protein structure in the secondary structure category?
It can be either a-helix or b-pleated sheet.
What are b-turns?
They are turns of the backbone that let the protein sequence make an abrupt turn.
In what terms do side chains differ from each other?
In charge, hydrophobic character, size and shape and reactivity.
What are the four characteristics of Glycine (Gly or G)?
It has the smallest side chain (H),
It’s not chiral,
It is usually found in u-turns of the backbone,
It can help the backbone form hinges that change the relative position of the chain
What are the main characteristics of Proline (Pro or P)?
It’s bulky because of it’s side chain (circle),
It makes a rigid peptide chain with limited flexibility,
It cannot fit in a helix
It can form a more open helix (collagen).
What’s the main characteristic of Cystein (Cys or C)?
It cross links with other Cystein residues making the protein even more rigid.
How does the cross link occur between Cystein residues ?
When the SH of the one side chain comes in contact with another SH, the hydrogens leave forming H2 and yield a S-S bond.
What are motifs and how do they affect proteins?
Motifs are clusters amino acids that have different properties because of the amino acids they contain. For instance, they could be polar, negatively/ positively charged, hydrophobic/philic .
How do the properties of different amino acids affect the protein way of folding?
Hydrophobic residues tend to bury inside the structure while hydrophilic amino acids are found on the surface of the protein. This way a tertiary structure is formed having a 3D shape.
How are disulfide bonds broken or formed?
By reducing them(broken down) or oxidising them.
Describe the pattern that collage follows based on its shape.
It’s a pattern of 1 Glycine every three residues. Also, Proline is really common.
What happens to proteins that are adapted in hydrophobic environments such as a membrane?
The folding rules change and hydrophobic residues are found on the outside and hydrophilic residues on the inside.
What are the two types of protein structure in the secondary structure category?
It can be either a-helix or b-pleated sheet.
How are quaternary proteins folded?
They are dimers of amino acids that bind one to each other forming a big protein. However, the properties of the protein are determined from the sequence of the primary structures of the protein.
What are b-turns?
They are turns of the backbone that let the protein sequence make an abrupt turn.
How other factors such as charge may affect the structure of the protein?
If for example one part of the chain includes a positively charged amino acid, it would be attracted by a positively charged atom such as Ca+. Hence, the shape will change.
In what terms do side chains differ from each other?
In charge, hydrophobic character, size and shape and reactivity.
What are the four characteristics of Glycine (Gly or G)?
It has the smallest side chain (H),
It’s not chiral,
It is usually found in u-turns of the backbone,
It can help the backbone form hinges that change the relative position of the chain
What is the use of a detergent in protein separation?
The function of a detergent is to separate the proteins from membranes. A detergent can be ionic or apolar depending on the proteins that we want to separate.
What types of separation are there available?
Gl filtration (separation by size), affinity chromatography (antibodies), separation by charge, and with the use of salt/ pH/ hydrophobicity/ temperature (physicochemically separated).
What are the main characteristics of Proline (Pro or P)?
It’s bulky because of it’s side chain (circle),
It makes a rigid peptide chain with limited flexibility,
It cannot fit in a helix
It can form a more open helix (collagen).
What are the analytical methods of separation of proteins?
SDS-Page which is based on the size of the protein applying charge,
Based on the isoelelectric point of the protein using either an ampholite solution. Also, we can combine the two methods on an SDS-page.also, with the used of mass spectroscopy based on the relative molecular weight.
What’s the main characteristic of Cystein (Cys or C)?
It cross links with other Cystein residues making the protein even more rigid.
How does the cross link occur between Cystein residues ?
When the SH of the one side chain comes in contact with another SH, the hydrogens leave forming H2 and yield a S-S bond.
Further more ways of analysing a separated protein?
NMR- analysis, enzyme related function, look up on databases based on the SDS-Page.
What are motifs and how do they affect proteins?
Motifs are clusters amino acids that have different properties because of the amino acids they contain. For instance, they could be polar, negatively/ positively charged, hydrophobic/philic .
How do the properties of different amino acids affect the protein way of folding?
Hydrophobic residues tend to bury inside the structure while hydrophilic amino acids are found on the surface of the protein. This way a tertiary structure is formed having a 3D shape.
How are disulfide bonds broken or formed?
By reducing them(broken down) or oxidising them.
Describe the pattern that collage follows based on its shape.
It’s a pattern of 1 Glycine every three residues. Also, Proline is really common.
