Biological Chemistry Flashcards
What is the central dogma of biology?
A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein
What does DNA stand for?
Deoxyribonucleic Acid
What are nucleotides made up of?
phosphate group
sugar
base
How are nucleotides linked together?
By phosphodiester bonds
What is important about phosphate groups for structure and stability?
They are negatively charged
How do RNA nucleotides differ to DNA ones?
- the ribose backbone is far less stable due to self-cleavage
- RNA uses Uracil instead of Thymine to pair with Adenine
What can the R-group of amino acids be?
- hydrophobic and non-polar
- hydrophilic and polar
What are proteins?
They are polymers of amino acids joined by a planar peptide bond
What is the protein primary structure?
the linear sequence of amino acids in a peptide or protein
What is the protein secondary structure?
comprised of regions stabilised by hydrogen bonds between atoms in the polypeptide backbone
What are two protein secondary structures?
α-helices
β- strands
How are α-helices stabilised?
by H-bonds between NH of residue i and C=O of residues i-4
How are β- strands stabilised?
by H-bonds forming to parallel strands thus forming sheets
How are the side chains arranged in α-helices?
they point away from the helical peptide backbone
How are the side chains arranged in β- strands?
they stick above/ below the sheet
What is a protein tertiary structure?
it is the 3D shape of a protein
What is a protein quaternary structure?
the structure of proteins which are themselves composed of two or more smaller protein chains
What is glycogen?
a polymer of glucose and it is the primary energy storage in animal cells
What is cellulose?
a polymer of glucose and the main component of plant cell walls
Metabolism defined
the set of biochemical reactions to make or break compounds (such as glucose, produced by plants, broken down by humans)
What is glycolysis?
the catabolic process to break down glucose to produce Adenosine triphosphate (ATP)
What is gluconeogenesis?
the β process to produce glucose from smaller metabolites (usually a small-molecule intermediate molecule)
What makes up a lipid?
a strongly hydrophobic part (usually alkyl chains), and a highly polar or charged hydrophilic part
What can lipids be classified as due to their charactersitics?
amphiphiles
What are the most common lipids?
glycerophospholipids
Double-chain lipids
they are not soluble in water so form lipid bilayers - the basic boundary for all cells
What other lipids are key components of higher organisms’ cell membranes?
sphingolipids
Prokaryotes defined
a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles
Eukaryotes defined
organisms whose cells have a defined nucleus separated by a phospholipid bilayer containing the DNA
Why are Archaea classified as the third domain of life?
they look like bacteria, but they’re genetically closer to Eukaryotes
Gram positive bacteria
- they retain the violet Gram stain
Gram negative bacteria
- they don’t retain the violet stain and go pink or red in colour
What is the make-up of gram positive bacteria?
- they have a thick outer peptidoglycan layer
- inner phospholipid bilayer
- contain a lipid-glycan
What is the make-up of gram negative bacteria?
- outer lipopolysaccharide (LPS) layer
- outer cell membrane (phospholipid bilayer)
- thin peptidoglycan in the periplasm
- inner cell membrane enclosing the cytoplasm
What is the peptidoglycan?
It is made of two sugars:
- N-acetylmuramic acid (NAM)
- N-acetyl glucosamine (NAG)
They are cross-linked by a tetrapeptide.
Endosymbiosis
the process where one type of cells is engulfed and then continues living within the predator
What is the strongest evidence for endosymbiosis?
mitochondria and chloroplasts contain their own DNA distinct from nuclear DNA and more closely related to bacterial DNA
What are the basic components of eukaryotic bilayers?
- glycerolphospholipids (GPL) with different head groups
- sphingolipids
- cholesterol
The nucleus of a eukaryotic cell
- it is defined by the nuclear membrane bilayer membrane
- substances are controlled entering and leaving by the Nuclear Pore Complex
- the nucleus contains the DNA wrapped up in proteins (histone) to form chromatin
The Mitochondria
It is the main producer of ATP and it has its own DNA
What is the endoplasmic reticulum (ER)?
the sheet/ tube-like extensions of the nuclear envelope
What is the role of endoplasmic reticulum?
- to provide different micro-environments to enable specific metabolic pathway that would not be possible in the cytosol
- it also functions as a transport system to bring the right protein (enzyme) to its designation within the eukaryotic cell
Rough ER
located closer to nucleus and has many ribosomes (responsible for protein synthesis)
Smooth ER
closer to the cell membrane and responsible for lipid and steroid synthesis
- for transport
What is the golgi apparatus?
it helps process and package proteins into lipid vesicles to be secreted from the cell
- it contains the enzymes for glycosylation
- transport and secretion
What are microbodies?
small vesicles with micro-environment to enable specific reactions
What is a vacuole?
membrane-enclosed water-filled compartments
- storage of inorganic and organic compounds
Describe the geometry of the peptide bond
it is planar due to the double bond character (cis and trans configuration)
Shape of a bacillus
Rod shaped
What is Plasmodium?
unicellular eukaryotes that are obligate parasites of vertebrates and insects
Two key chemical differences between DNA and RNA?
- DNA contains deoxyribose which misses a OH group at the sugar phosphate backbone, RNA contains ribose.
- RNA uses Uracil instead of Thymine
Reasons why RNA is less stable than DNA
- self-cleavage by forming a cyclic phosphodiester
- thymine is more photostable than uracil due to its additional methyl group
- cytosine easily de-aminates to produce Uracil, which in RNA leads to mutation
- RNA cannot form regular B-form RNA due to additional OH group. B-DNA is generally more stable as bases are protected by negatively charged backbone
