Biochemistry A Flashcards
Metabolism
An organism’s net sum of reactions, the result of enzyme catalyzed biological pathways
Catabolic Reactions
Breaking down complex polymers into monomers, releases energy
Anabolic Reactions
Monomers are synthesized to form a polymer, requires energy
Examples of Anabolic Reactions
Photosynthesis, DNA replication, protein synthesis
Condensation Reaction (Dehydration Synthesis)
Two molecules covalently bonded to each other through the loss of water
Hydrolysis Reaction
A covalent bond is broken through the addition of water
Carbohydrates
Carbon, hydrogen and oxygen in a specific ratio. Categorized as monosaccharides, disaccharides and polysaccharides.
Carbohydrates Functions (2)
Provide energy storage and building blocks of life
Prefix in front of -ose indicates…
Number of carbon atoms in each molecule, e.g. triose has three carbon molecules
Monossacharides
Simple ring shaped sugar molecule, basic unit of carbohydrates
Isomers
Have the same formula but are structurally different, e.g. glucose, fructose and galactose
DIssacharides
2 monosaccharides bonded by a glycosidic bond
Sucrose
Fructose + glucose
Lactose
Galactose + glucose
Maltose
2 glucose molecules
Polyssacharides
Long chains of three or more monosaccharides
Starch in plants and glycogen in animals are responsible for …
Energy storage
Cellulose in plants and chitin in fungi and arthropods are responsible for forming…
Structure
Cellulose
Plant source, beta glucose subunit, 1 - 4 bonding, no branching
Starch: amylose
Plant source, alpha glucose subunit, 1 - 4 bonding, no branching
Starch: amylopectin
Plant source, alpha glucose subunit, 1 - 4 and 6 bonding, branching evry 20 subunits
Glycogen
Animal source, alpha glucose subunit, 1 - 4 and 6 bonding, branching every 10 subunits
Lipids
Carbon, hydrogen and oxygen atoms in an unfixed ratio. Can be phospholipids, triglycerides, steroids, and waxes.
Types of Lipids
Phospholipids (only lipid that contains phosphorus), e.g. lecithin, plasma membrane structure
Triglycerides: fats, oils, long term energy storage
Steroids: cholesterol, testosterone and estrogen: membrane component and sex hormones
Waxes: cuticle: protective covering
Five functions of lipids
Cell membrane component, long term energy storage, insulation, organ cushioning, structural component of hormones
Structure of a triglyceride
1 glycerol molecule, fatty acid chains
Ester Linkage
Binds the glycerol molecule to the hydrocarbon chains
Lipids are differentiated based on the level of…
Hydration of the carbon atoms in the fatty acid chain
Saturated Lipids
All carbons have the maximum number of hydrogen atoms
Monounsaturated
Only one double bond between carbons
Polyunsaturated
More than one double bond
Why are saturated lipids less healthy than unsaturated lipids?
Saturated lipids are harder to break down and absorb because they tend to be solid at room temperature by forming London dispersion forces that are difficult to break apart completely. The bends in unsaturated lipids help membrane fluidity and prevent stacking
Hydrogenation
Make a lipid more solid (creation of saturated lipids)
Cis vs trans fats
Cis lipids have hydrogens on the same size, causing kinks. Trans fats have hydrogens on opposing sides, resulting in a linear chain.
Why are trans fats desirable?
They are more stable at higher temepratures, last longer and taste better
Protein
Polymer made of amino acids constructed by nitrogen, carbon, hydrogen, oxygen and sulfur atoms. Structured as polypeptides
Amino acids are formed by an …
Amino group, a carboxyl group, a hydrogen atom and a random group
The R (variant) group of an amino acid determines…
The physical and chemical properties of the amino acid.
Essential vs Nonessential Amino Acids
9 essential obtained from food, 12 nonessential made by cells
Dehydration Synthesis for forming Peptide Bonds
The carboxylic acid loses an oxygen atom, and the amine loses two hydrogen atoms
Primary Protein
A chain of amino acids held together by peptide bonds that form between an amino group and a carboxyl group
Secondary Protein
Amino acids linked together by hydrogen bonding. Alpha helices and beta pleated sheets form
Alpha Helix
Hydrogen bonding between amino acids some distance apart, forming a spiral
Beta Pleated Sheet
Hydrogen bonding between opposing amino acids of a chain , resulting in kinks
Tertiary Protein
Attractions form between alpha helices and beta pleated sheets to form a 3D shape. Bound together by disulfide bridges, ionic interactions, hydrophobic interactions, intermolecular forces.
Quaternary Protein
Multiple tertiary protein clusters bound together: multi - subunit. Contains more than one AA chain.
Fibrous Proteins
Only found in animals, form long protein filaments, usually structural proteins, generally water - insoluble due to the hydrophobic R groups sticking out. Example: collagen
Globular Proteins
Compact and rounded, generally soluble due to the hydrophobic groups clustered inside, can form dipole - dipole bonds
The Proteome
An organism’s entire set of proteins
How are proteins made?
DNA are transcribed into mRNA, which are translated into polypeptides, which are modified into proteins
One gene can code for x polypeptide
More than one
Compare the size of the proteome and the genome
The proteome is much larger
3 possible ways in which one gene can code for more than one polypeptide
1, Genes may be alternatively spliced
2. Genes encoding non mRNA sequences may be transcribed but never translated
3. Genes may be mutated (contain a different base sequence) and produce a different polypeptide
6 Functions of Proteins
- Structure: collagen muscles
- Enzymatic (catalysts for all biochemical reactions)
- Messaging (protein hormones)
- Transportation (channels and carriers)
- Defense as antibodies
- Emergency energy source
Protein denaturation occurs when … structure(s) are lost
Secondary, tertiary and quaternary
Deviations from the x or y cause protein denaturation
Optimal pH or temperature
Effects of Protein Denaturation
H bonds lost, active sites lose their shape, enzymatic properties lost
Examples of Proteins
Rubisco, insulin, immunoglobulin, rhodopsin, collagen, spider silk
Protein Denaturation: Temperature
Large rises of energy change the interactions between the aminoi acids. Peptide bonds remain intact, conserving the primary structure
Protein Denaturation: pH
Break the bonds between nonadjacent bonds
Purpose of having an activation energy
Preventing random reactions from occuring
Enzyme Catalyzed Catabolic Reaction
The substrate enters the active site, forming an enzyme - substrate complex. Degradation occurs, breaking down the substrate into smaller counterparts before it leaves the enzyme
Changes in energy level during a catabolic reaction
Reactants have more energy than products, resulting in a net energy release (negative value)
Enzyme Catalyzed Anabolic Reaction
Reactants have less energy than products, resulting in the need to input energy (positive value)
The active site lowers the activation energy by…
Orienting the substrate correctly and covalently bonding to the substrate
2 models proposed for substrate - enzyme binding
Lock and key and induced fit
The Lock - and Key Model
Enzymes are very rigid and specific to only one type of substrate
The Induced Fit Model
The enzyme undergoes some conformational change to mold to the substrate, more flexible and increases efficiency by increasing the reactivity of the substrate. The enzyme is still highly specific but not just to one
Types of Enzyme Regulation
Competitive and non - competitive inhibition
Competitive Inhibition
A competitve inhibitor, a molecule that competes for the active sites, is structurally and chemically similar to the substrate and blocks the active site. If it stays permanently, the reaction doesn’t occur; if it stays temporarily, the reaction is slowed down
Example of Competitive Inhibition
Heavy metal poisoning: mercury and iron
Non - competitive (allosteric) inhibition
A molecule binds to the enzyme on an allosteric site, causing a conformational change to the active site
Increasing the concentration of the substrate only increases the possibility of the reaction occuring if the inhibitor is…
Competitive
Graph of substrate concentration against rate of reaction for a normal enzyme, competitve inhibitor and a noncompetitive inhibitor
Competitve inhibitor: curve is slower than normal enzyme but plateaus with the normal enzyme. Noncompetitive: curve is slower than competitive inhibitor and plateaus lower.
End Product Inhibition of Isoleucine
Threonine is the initial reactant. In the first step, threonine is converted into an intermediate compound by the enzyme threonine deaminase. It is catalyzed by multiple different enzymes to become intermediate molecules until it becomes isoleucine, the end product. As isoleucine levels rise, it binds to an allosteric site on threonine deaminase to inhibit it.
Purpose of end product inhibition
To ensure that the reaction only proceeds when end product is low
Benefits of enzymes in industry
Speed up reactions, display great specificity, cost - effective
Challenge of using enzymes in industry
Removing the enzyme once the desired compound is synthesized
Immobilized Enzymes
Enzymes that are held by a container attached to a support over which a substrate is passed through and converted into desired products
Applications of Enzymes in Industry
Biofuels (decomposing carbohydrates), medicine (diagnosis), biotechnology (gene splicing), food production (beer and dairy products), textiles (fibers), paper (wood)
Advantages of Immobilized Enzymes
Resuable, the ability to immediately terminate a rearction by removing the enzymes, the ability to stop random reactions from initiating, enzymes are stable, products don’t contain the enzymes, low energy requirement
Production of Lactose - Free Milk
Milk containing lactose is pour into immobilize lactase, converting lactose into glucose and galactose
Water vs Methane
Water has higher melting and boiling points, higher cohesion (H bonding). Methane is nonpolar while water is polar. Methane is tetrahedral, water is bent. Water can dissolve nutrients; dissolution necessary for metabolic reactions to start: not possible with methane
Water Properties
Cohesion and adhesion (sticking to its own molecules and other molecules through hydrogen bonds), high surface tension (H bonds form spherical shape with strong collective force to minimize area to volume ratio), high specific heat capacity due to large quantity of energy needed to disrupt H bonds, ionic and polar (universal solvent)
Water’s Cooling Effect
High latent heat of vaporization: cools skin during evaporation by taking heat with it
Urea’s Chemical Composition
Co(NH2)2
Properties of Urea
Non - toxic, highly soluble organic compound, used to excrete potentially toxic nitrogen, shows that the synthesis of organic compounds from inorganic molecules is possible, disproved the theory of vitalism
Solubility of Biological Molecules Found in Blood
Glucose: polar. Lipid: nonpolar, transported by lipoproteins. Amino acids: depends on R group and size, transported in lower concentrations if hydrophobic. Oxygen: needs hemoglobin, soluble in small amount. CO2 and NaCl both soluble.
