Basics of biochemistry and physiology Flashcards
What is biochemistry?
the study of the molecular basis of life
What is an ion?
An ion is an electrically charged atom or molecule formed by the loss or gain of one or more electrons
How many electrons can each ring in an ion hold?
Each ring of an atom has a maximum number of electrons that it can hold
-The first (inner) ring can only hold two electrons
-The second level can hold eight
-The third can hold 18
-The fourth holds 32, …
What is a cation?
-positive charged ion – Na+
-If an atomic shell has lost electrons, there will be more protons than electrons, giving the ion a positive charge, one for each unbalanced proton
what is an anion?
-negative charged ion – Cl-
-If electrons are added to a shell, there will be more electrons than protons and the ion will be negatively charged, one for each extra electron
What are cations and anions also called ?
-Such substances are also called electrolytes because they facilitate conductance of electrical current
>The electrostatic attraction between +ve & -ve ions brings the particles together and creates an ionic compound, such as sodium chloride – NACL (salt)
what are common ions in the body and cochlea ?
common ions in the body and cochlea include Na+, K+, and Cl+
what is a molecule ?
It is the smallest unit of a pure substance that has all of the properties of that substance
what is a molecule made up of ?
It is made up of two or more atoms linked by a chemical bond
what is a radical?
-if its outer shell is not full it will be chemically unstable
-This type of uncharged atom is called a radical
what happens if there are too many radicals ?
too many free radicals damage other molecules over time, producing among other things, some aging effects and probably some cancers
what is a compound?
-A compound is the combination of < 2 elements with a chemical union
-These elements combine in a reproducible way
-They can be converted into simpler forms by chemical means
what is a mixture ?
-It consists of two or more different elements and/or compounds physically intermingled
-It can be separated into its components by physical means
-It often retains many of the properties of its components
what is an example of a mixture ?
Ex salt and water
Ex. like a cocktail (a mixture of things)
what is a non-uniform mixture?
-Consists of two or more substances without fixed proportions and without chemical bonding
-Chemical DON’T bond
-Each substance keeps its original properties
what is an example of a nonuniform mixture ?
oil and water
what is the hierarchy in the levels of organization ?
-Atomic (smallest)
-Molecular
-Cellular
-Tissue
-Organ
-Organism (a form of life, for e.g., an animal)
-Population
-Ecosystem (largest)
what does chemistry deal with?
-Identification of the substances of which matter is composed
-The investigation of the properties of substances
-The ways in which substances interact, combine, and change
-The use of these processes to form new substances
What is the structural formula of a chemical compound?
-The structural formula of a chemical compound is a graphical representation of the molecular structure showing how the atoms are arranged
What is a protein structure?
-A protein structure is the biomolecular structure of a protein molecule
-proteins are polypeptides sequences formed from the building blocks of many amino acids
What is a chemical bond ?
-A chemical bond is an attraction between atoms that allows the formation of chemical substances containing two or more atoms
What are different types of bonds ?
1)Covalent bonds
2)Non-covalent bonds
what are examples of non covalent bonds?
-Electrostatic bonds (ionic)
-Hydrogen bonds
-Hydrophobic attractions
-van der Waals bonds
what is a covalent bond?
-BONDING B/W NONMETALS
-It results from the sharing of a pair of electrons between two atoms on different molecules
How are molecules held together in chemical bonds?
-The molecules are held together by the mutual affinity for their shared electrons
-Example: Carbon (C) and Oxygen (O) = Covalent bond
-Covalent bonds are the force that hold together proteins, carbohydrates, and lipids
what is the most stable type of bond?
-It is the strongest and most stable type of chemical bond because the energy required to break these bonds is so great, which often makes these bonds irreversible
are covalent bonds involved in drug receptor interactions?
NO!! COVALENT BONDS ARE NOT INVOLVED IN DRUG RECEPTOR INTERACTIONS
What is a hydrogen bond?
-It is a special type of force between a positive hydrogen atom and an electronegative atom, such as oxygen, nitrogen, or sulfur
-A hydrogen bond alone is weaker than covalent and ionic bonds
-When atoms are close together, and several bonds are formed it increases the strength of the bond
Molecules attached to hydrogen atoms are attached directly to?
-Any molecule which has a hydrogen atom attached directly to an oxygen or a nitrogen is capable of hydrogen bonding
-one of them has to be a hydrogen, the other can be anything else
-Such molecules will always have higher boiling points than similarly sized molecules that do not have an -O-H or an -N-H group
-The hydrogen bonding makes the molecules “stickier”, and more heat is necessary to separate them
How do hydrogen bonds perform critical functions in the body?
-Holding the two strands of the DNA double helix together
-Holding polypeptides together
-Helping enzymes bind to their substrate
-Helping antibodies bind to their antigen
-Helping transcription factors bind to each other
-Helping transcription factors bind to DNA
what are ionic bonds?
-BONDING B/W METALS AND NONMETALS
-These are electrostatic bonds between two ions of opposite charges
-It is the transfer of > one electrons from a metal onto a non-metal
how do ionic bonds work?
-Atoms with an excess of electrons (-vely charged atom) are attracted to atoms with a deficiency of electrons (+vely charged atom)
-For example
>Sodium (Na) (alkaline metal) and Chlorine (Cl) = Ionic Bond
>Chlorine atom takes an electron from the sodium atom converting the atoms into ions (Na+) and (Cl-), which are now held together by their opposite electrical charge
What bonds are stronger?
-These bonds are stronger than hydrogen but weaker than covalent bonds
what bond is effective in attracting drug molecules toa receptor site
An ionic bond is the most effective force in attracting drug molecules to a receptor site
What are Van der Waals bonds?
-Molecules can attract each other at moderate distances and repel each other at close range
-These bonds are residual attractive/repulsive forces between molecules or atomic groups that do not arise from a covalent bond, or electrostatic interaction of ions, or ionic groups with one another, or with neutral molecules
-These areas interact with transient areas of opposite charges on another molecule
-The bigger the atom or molecule the bigger the Van der Waals’ force
-These attractive forces are collectively called van der Waals forces
When are van der waals bonds ideal to have?
-They are the most common bond between atoms
-They are weaker than covalent, ionic, or hydrogen bonds
-These forces operate only when molecules pass very close to each other
-They provide a weak force for some drugs and their receptors
What is oxidation and reduction ?
-Oxidation and reduction or Redox reactions are a family of reactions that are concerned with the transfer of electrons
Redox reactions are a matched set of?
-There is no oxidation reaction without a reduction reaction happening at the same time
What does oxidation and reduction refer to?
-Oxidation refers to the loss of electrons, while reduction refers to the gain of electrons
-Each reaction by itself is called a half-reaction, simply because there need to be two half-reactions to form a whole reaction
All metal atoms are characterized by?
-All metal atoms are characterized by their tendency to be oxidized, losing one or more electrons, forming a positively charged ion – the cation
–The electrons lost by the metal are not destroyed but gained by the non-metal, which is said to be reduced
—-As the non-metal gains the electrons lost by the metal, it forms a negatively charged ion, – the anion
What is oxidative stress?
-All forms of life maintain a reducing environment within their cells
–Oxidative stress is a disturbance (imbalance) between the production of reactive oxygen species – ROS (includes free radicals and peroxides) produced by most body reactions, and a biologic system’s antioxidant defenses, which would allow it to easily repair the resulting damage
—-Disturbance in this redox environment results in excess ROS that can damage components of cells, including proteins, lipids, and DNA
What are the evil twins?
-oxidative stress and inflammation are two processes believed to go hand in hand (the two evil twins!), they result in:
*The aging process
*Neurodegeneration
*Diseases such as:
-diabetes
-some cancers
-atherosclerosis
-Parkinsons
-Alzheimers
Severe oxidative stress may cause?
-cell death by necrosis
-passive, accidental cell death with subsequent inflammation
What can moderate oxidation trigger?
-Apoptosis
-Active, programmed cell death that avoids eliciting inflammation
-Cell suicide
Are reactive oxygen species harmful?
-Reactive oxygen species (ROS) are not always harmful and can be beneficial, such as
–ROS is used by the immune system to attack and kill pathogens
–ROS is used in cell signaling
Even though Reactive oxygen species aren’t harmful, why should it be prevented ?
-But overproduction of ROS must be prevented to prevent cell damage
-There are natural antioxidants that occur in the body as well as antioxidants obtained from food and vegetables
What is Glutathione ?
-Glutathione is a naturally produced antioxidant found in plants, animals, fungi, and bacteria that protects cells from toxins such as free radicals
-Reduced glutathione (GSH) has a strong electron-donating character
-reduces ROS
-As electrons are lost, the molecule becomes oxidized
-All cells in the body are capable of producing glutathione, but synthesis in the liver is essential
-Glutathione is an important protector within the auditory-vestibular system
-New otoprotective drug therapies are designed to promote actions of glutathione
-IT’S A NATURAL ANTIOXIDANT
What harmful stimuli will inflammation respond to?
-Inflammation is part of the complex biological immune response of vascular tissues to harmful stimuli such as
-pathogens (bacteria and virus )
-Physical trauma
-Chemical trauma
What does inflammation respond to ?
-It is a necessary response that allows the body to destroy invading organisms and repair itself (wound healing)
-In some disorders, the inflammatory process, which normally is self‐limiting, becomes continuous and chronic inflammatory diseases might subsequently develop
What is Chronic Inflammation ?
-It is a pathological condition characterized by continued active inflammation response and tissue destruction
Chronic inflammation induces what?
-The chronic inflammatory process induces oxidative stress and reduces cellular antioxidant capacity
-it induces the oxidative stress because inflammation leads to cell death which then leads to oxidative stress
-Overproduced free radicals react with cell membrane fatty acids and proteins impairing their function permanently
-In addition, free radicals can lead to mutation and DNA damage
What risk factors of chronic inflammation?
-Risk factors of chronic inflammation, to name a few, include
-Hypoxia (COPD?), obesity, hyperglycemia, and smoking
-There is now general consensus, that chronic inflammation can be a predisposing factor for some cancers and accelerated aging
-It is also believed to play a serious role in a wide variety of age-related diseases including
-diabetes, cardiovascular and autoimmune disease
What are cardinal signs of inflammation ?
1)Redness
-Vasodilation
-Increased blood flow
2)Swelling
-Edema, caused by accumulation of fluid outside blood vessels
3)Heat
-Increased blood flow to the area
-Fever is brought about by chemical mediators of inflammation and contributes to the rise in temperature at the injury site
4)Pain
-Distortion of tissues caused by edema
-Chemical mediators of inflammation such as prostaglandins
5)Loss of function
-Because of pain or severe swelling that prevents movement
What are enzymes?
-Enzymes are catalysts that speed up chemical reactions in the cells
-ALMOST ALL ENZYMES ARE PROTEINS
-Organization of proteins into the 3-D structures results in an enzyme that can do action
What happens in enzymatic reactions?
-Molecules at the beginning of the process are called substrates
-The enzyme converts substrates into different molecules, and these are called the products
-An enzyme must briefly unite with at least one of the reactants
——-
-The set of enzymes made in a cell determines which metabolic pathways will occur in that cell
-how is the enzyme going to bring about its action
-Enzymes end in …ase, of the name of compounds that they act on
-For examples: Collagenase, lactase, acetylcholinesterase
How do enzymes and substrates interact with each other?
look at study guide
What molecules might affect enzyme activity?
-Inhibitors are molecules that DECREASE enzyme activity
-many drugs and poisons are enzyme inhibitors
-Activators are molecules that INCREASE enzyme activity
Enzyme activity might be affected by what else ?
-Temperature, chemical environment (e.g. pH), and the concentration of the substrate
When might enzymes be used commercially ?
-In the synthesis of antibiotics
-Household products use enzymes to speed up biochemical reactions
-Enzymes in biological laundry detergent break down protein or fat stains on clothes
-Enzymes in meat tenderizers break down proteins making the meat easier to chew
What is a receptor ?
-A receptor is a protein molecule embedded in the cell surface or in the cytoplasm, which allows for communication between the cell and the world outside the cell
What do the receptors allow ?
-The receptor allows extracellular molecules such as hormones, neurotransmitters, toxins, or drugs to attach to it resulting in a change in the cell function
-These extracellular molecules are also called ligands
-ligands are chemicals that are not within the cell and it always attaches to a receptor
This binding occurs by (the question below)
How does receptor-ligand binding occur ?
-The receptor-ligand binding occurs by ionic bonds, hydrogen bonds, and van der Waals forces
-Some ligands (including drugs) just block receptors without resulting in any response
-For example, calcium channel “blocker” drugs act like plugs and are often used to treat hypertension
What are hormones ?
-A hormone is a chemical substance, usually a peptide or steroid, produced and released by one set of cells and conveyed by the bloodstream to another to effect physiological activity, such as growth or metabolism
-Hormones are powerful and only a small amount of a hormone is required to alter cell metabolism
-Hormones also are chemical messengers that transports a signal from one cell to another
-All multicellular organisms produce hormones
What type of reactions (fast or slow) are hormones producing?
-Hormones cause reactions that are slower than those associated with neurotransmitters
-Synthetic compounds also can act like hormones in the body
-Examples of hormones include
-Thyroid hormone, cortisol, estrogen, and testosterone
What is a neurotransmitter?
-A neurotransmitter is a chemical messenger that carries, boosts, and modulates signals between neurons and other cells in the body
What are neurotransmitters released from?
-In most cases, a neurotransmitter is released from the axon terminal after an action potential has reached the synapse
-The neurotransmitter then crosses the synaptic gap to reach the receptor site of the other cell or neuron
-In a process known as reuptake, the neurotransmitter attaches to the receptor site and is reabsorbed by the neuron
What are neurotransmitters affected by?
-Neurotransmitters are affected by disease or drugs, which can cause different adverse effects on the body
-Diseases such as Alzheimer’s and Parkinson’s are associated with deficits in certain neurotransmitters, for example
How do we classify neurotransmitters?
-Neurotransmitters can be classified by function
-Excitatory neurotransmitters:
-These neurotransmitters have excitatory effects on the neuron
-These increase the likelihood that neurons will fire an action potential
-Major excitatory neurotransmitters include epinephrine and norepinephrine
-Inhibitory neurotransmitters:
-These neurotransmitters have inhibitory effects on the neuron
-They decrease the likelihood that neurons will fire an action potential
-Major inhibitory neurotransmitters include serotonin and GABA
-Some neurotransmitters, such as acetylcholine and dopamine, can have both excitatory and inhibitory effects depending upon the type of receptors that are present
What are the functions of different types of neurotransmitters?
1)Acetylcholine:
voluntary movement of the skeletal muscles (via the sympathetic pathways)
2)Norepinephrine:
wakefulness or arousal - via the sympathetic pathway
3)Dopamine:
voluntary movement and motivation, “wanting”, pleasure, associated with addiction and love
4)Serotonin (5-hydroxytryptamine or 5-HT):
memory, emotion, wakefulness, sleep and temperature regulation (association with depression?)
5)Gamma-aminobutyric acid (GABA):
inhibition of motor neurons; major inhibitory neurotransmitter in the central nervous system
6)Glycine:
spinal reflexes and motor behavior
7)Glutamate:
excitatory stimulation
What is neuromodulators:
-A neuromodulator is a substance, other than a neurotransmitter, released by a neuron and transmitting information to other neurons, thereby altering their activities
-They help modulate the action of the neurotransmitter
What do neuromodulators produce?
-Neuromodulators produce a more diffuse response, and are released throughout the central nervous system
Neuromodulators play a role in?
-Sensory transmission, especially in pain
-substance P modulates pain
-Dopamine and nicotine are involved in addiction
What are local chemicals?
-Some organs can secrete chemicals that work close to them
-These chemicals work locally and are not released into the systemic circulation and include
-Histamine and prostaglandins
What is histamine?
-Organic nitrogenous compound involved in local immune responses - Which are active in allergies
What are prostaglandins ?
-A group of hormone-like lipids compounds made at the site of tissue damage or infection
-They are involved in dealing with injury and illness, controlling processes such as:
-Inflammation
-Blood flow
-Formation of blood clots
-Induction of labor
Why do we study pharmacology?
-Adverse drug reactions that can affect auditory-vestibular systems
-Hearing loss
-Tinnitus
-Vestibular dysfunction (for several drug classes)
-Vertigo, dizziness, disbalance, ataxia, and abnormal eye movement
-Cognitive issues
-Confusion, short- and long-term memory deficit, delirium, & dementia, which may affect processing of auditory information and poor WRS
-Combination of the above symptoms
What questions should we ask to begin a pharmacological case history?
-What medications are you currently taking (dose and frequency)?
-What condition is this medication being taken for?
-How long have you been taking these medication(s)?
-Important to remember that over-the-counter (OTC) and herbal medications/supplements can also cause adverse auditory-vestibular effects so ask about those as well
-Also, many drugs can cause neurological side effects that may further complicate the clinical presentation and testing
