Biochemistry Flashcards
Kinetic Energy
energy in motion
Potential energy
stored energy
Examples of kinetic energy
- Electrons moving along ETC
- Myofilament sliding during contraction
- Blood flowing through vessels
Examples of potential energy
- The H+ gradient that builds in the space btwn the inner and outer membrane of the mitochondria
- Energy from ATP stored
- Pressure gradient generated from a systolic contraction of the heart
1st Law of Thermodynamics
In a closed system, energy cannot be created or destroyed
Apply the 1st Law to Phys
Instead of creating new energy, energy is converted to other forms through chemical reactions
2nd and 3rd Law of Thermodynamics
Entropy will increase in a closed system and reach a constant value at absolute zero
Apply the 2nd and 3rd Laws to Phys
There is no perfect energy conversion. Some of the energy in ATP drives the Na/K ATPase but some that energy is given off as heat.
People are not closed systems. They eat food and take in oxygen.
Hydrogen bonds
weak bond because they are easily and rapidly formed and destroyed under normal physiological conditions).
Hydrogen has attraction between hydrogen and oxygen or nitrogen because of uneven distribution of electrons
Ionic bonds
- Electrostatic attractions btwn cations and anions
- Dissociate in water.
- NaCl has an ionic bond that permits it to dissociate in water.
- Body fluids are solutions of ions
Covalent bonds
- Bond through shared electrons
- Strongest bonds
- Store the most energy
- Their formation require enzymes to form and/or break
- Metabolism is regulated through the regulation of enzymes
Free radical
- Have an unpaired electron in the outer shell
- It is not necessarily charged, but it is reactive
- . It can be formed where there are high levels of oxygen, and it will react with proteins, fats, and DNA.
How are free radicals both beneficial and harmful?
- beneficial because they are important biological signaling molecules that protect against disease and play a pivotal role in the benefits of exercise.
- harmful because they will react with proteins and fats, causing DNA mutations and destruction of cell membranes.
Polarity
the separation of an electric charge, leading to a molecule or its chemical groups having an electric dipole moment with a negatively charged end and a positively charged end.
Examples of polar molecules
water
ethanol
ammonia
Examples of non-polar molecules
oxygen, methane, and the noble gases
Characteristics of polar molecules
- Polar molecules are highly water soluble and therefore are able to form hydrogen bonds
- The polarity influences its function in the cell because water participates in chemical reactions through hydrolysis and dehydration synthesis
pH
measure of hydrogen ion concentration.
It is the negative log of H+ concentration in molars. As H+ ion concentration increases, pH decreases
Protonation
the association of H ion with other molecules
Rltsp of pH and protonation
Side chains tend to be ionized at physiological pH. If there is a more acidic environment, then protonation of a carboxyl group may occur.
Amino groups tend to be protonated at physiological pH. However, if the pH becomes quite alkaline, then the protonation could be lost.
Amino acids
Amino acids have a repeating structure. They have a central carbon, a carboxyl (acid) group, an amino group, a hydrogen, and a remaining group
Primary structure
The sequence of amino acids in a polypeptide chain. Determines how a protein will fold.
Secondary structure
Secondary structure refers to a local, folded structure that forms within a polypeptide due to interactions between atoms of a backbone.
Tertiary structure
Tertiary structure refers to an overall 3-dimensional structure of a polypeptide.
Quaternary structure
Quaternary structure of a protein refers to proteins which are made up of multiple, polypeptide chains.
Enzymes
globular proteins that function as biological catalysts
very specific. For example, kinases are a group of enzymes that add a phosphate group.
How enzymes work
They increase reaction rates by increasing the frequency of collisions, decreasing the activation energy and providing correct orientation
Enzymes and cell metabolism
Biological regulation of reactions occurs through regulating enzymes and sometimes through cofactors like Ca2+, Mg2+, and vitamins.
Carbohydrates for nutrition purposes
- Hexoses are important energy source
- Glucose is essential for the brain. It is broken down via glycolysis and then further via the Krebs cycle to produce ATP
- Glycogen is a reservoir of available energy stored within bonds of individual glucose monomers. Hydrolysis of glycogen leads to the release of glucose monomers in the blood, preventing blood glucose levels to reach dangerously low levels.
Hexoses
glucose, galactose, fructose
Carbohydrates for structure
sugars added to lipids make glycolipids and sugars added to proteins make glycoproteins, which helps to generate a more complete structure in the cell membrane.
Triglyceride
Three fatty acids covalently bonded to a glycerol backbone.
- High density energy storage molecule
- Hydrophobic
Phospholipids
- similar to TGLs
- Have fatty acid tail, but only 2 and the glycerol backbone includes a polar group such as a choline or inositol
- Main component of bilayer
- Amphipathic which is why they form bilayers spontaneously
- major component in surfactant
Steroids
4 ring cholesterol derivatives
- These molecules modify the stiffness of lipid bilayers.
- Function as hormones, e.g. estradiol, cortisol, vitamin D etc.
Saturated TGLs
All single bonds within their carbon chains (these are easier to convert to cholesterol).
Unsaturated TGLs
As double bonds are added, the molecules are unsaturated. Omega three fatty acids have a double bond at the end of the fatty acid chain.
How are high energy compounds essential for cell physiology? Give examples
Needed to help the cell function, produce ATP, protection, respiration, and regulation
Examples: ATP, NAD and FADH (H+ carrier), coenzyme A (carrier in the Kreb cycle), and creatine phosphate (substrate phosphorylation).
