Lectures 1 & 2: Basics of Biochemistry and Physiology Flashcards
1
Q
Biochemistry
A
study of molecular basis of life
“study of chemical substances and processes of living matter”
2
Q
biochemistry can explain processes within other life science disciplines such as:
A
- biotechnology and bioinformatics
- cell biology and signaling
- development and disease
- energy and metabolism
- genetics
- molecular biology
- plant biology
pharmacology and ototoxicity
3
Q
What is an ion?
A
electrically charged atom or molecule formed by the loss or gain of one or more electrons
4
Q
The first inner ring can only hold
A
two electrons
5
Q
the second ring can only hold
A
eight electrons
6
Q
the third ring can only hold
A
18 electrons
7
Q
the fourth rings holds
A
32 electrons
8
Q
if atomic shell has lost electrons
gives what charge?
A
there is more protons than electrons
ion has positive charge (one for each unbalanced proton)
9
Q
cation =
A
positive charged ion
10
Q
if atomic shell has added electron
A
there will be more electrons than protons
ion will have negative charge (one for each extra electron)
11
Q
anion =
A
negative charged ion
12
Q
why are substances also called electrolytes?
A
facilitate conductance of electrical current
13
Q
the electrostatic attraction between positive and negative ions brings the particles together and creates an
A
ionic compound (such as sodium NACL)
14
Q
Molecule
made up of:
A
smallest unit of a pure substance that has all of the properties of that substance
two or more atoms linked by chemical bonds
15
Q
the number of protons in the nucleus of the atom is equal to
A
the atomic number
16
Q
radicals (uncharged atom)
A
least reactive when outermost electron shell is full
-uncharged atom (equal number of electrons and protons) may have balanced charges
if outer shell is not full = chemically unstable
17
Q
to many free radicals damage other molecules over time producing among other things
A
some aging effects and probably some cancers
18
Q
Compound
A
combination of <_ 2 elements with a chemical union
combine in reproducible way
ex: H20
19
Q
mixture
A
two or more different elements/compounds physically intermingled
can be separated into its components by physical means
ex: salt and water
20
Q
non uniform mixture
A
consists of two or more substances without fixed proportions and without chemical bonding
each substance keeps its original properties
EX: water and oil
21
Q
in biology structures exist at all levels or organization ranging from hierachy of
A
atomic
molecular
cellular
tissue
organ
organism
population
ecosystem
22
Q
higher level structure is composed of multiple copies of a
A
lower level structure
- organism consist of: atoms/molecules/cells/ and tissues
23
Q
chemistry is the branch of science that deals with
A
1) identification of substances of which matter is composed
2) investigation of properties of substances
3) ways in which substances interact, combine, and change
24
Q
structural formula of a chemical compound is
A
graphical representation of molecular structure showing how the atoms are arranged
25
protein structure is the
biomolecular structure of a protein molecule
proteins are polypeptides sequences formed from the building blocks of many amino acids
26
chemical bond is an attraction between atoms that allows
the formation of chemical substances containing two or more atoms
27
different types of bonds
covalent
non covalent
- electrostatic bond (Ionic)
hydrogen
hydrophobic
van der waals
28
Covalent bonds (bonding between NON METALS) results from
sharing of a pair of electrons between two atoms on different molecules
29
covalent bonds molecules are held together by
mutual affinity for their shared electron
ex: Carbon and Oxygen = covalent
30
covalent bonds are the force that hold together
proteins, carbohydrates, and lipids
31
what is the most strongest and stable bond?
covalent because energy required to break bonds is great so makes bonds irreversible
NOT involved in drug receptor interactions
32
Hydrogen bonds
force between a positive hydrogen atom and electronegative atom (Oxygen/nitrogen/sulfur)
33
a hydrogen bond alone is weaker than
covalent and ionic bonds
34
any molecule which has hydrogen atom attached directly to an oxygen or a nitrogen is capable of
hydrogen bonding
35
molecules with hydrogen atom will always have
higher boiling points (-O-H/ -N-H)
36
hydrogen bonding makes molecules
stickier and more heat is required to seperate them
37
Hydrogen bonds critical functions
- holding two strands of DNA double helix together
- help enzymes bind to their substrate
- help antibodies bind to antigen
- help transcription factors bind to eachother
- help transcription factors bind to DNA
38
Ionic bonds = Bonding between METAL and NONMETALS, electrostatic bonds between two ions of
opposite charges
39
ionic bond is transfer of
_> one electrons from a metal to non metal
40
ionic bonds
- atoms with excessive electrons (- charged atom) are attracted to
atoms of deficiency of electrons (+ charged atom)
ex: sodium (Na alkaline metal and Chlorine (CI) = ionic bond
41
ionic bonds are stronger than
hydrogen but weaker than covalent
42
what is the most effective force in attracting drug molecules to receptor sites
ionic bonds
43
Van der Waals bonds
molecules can attract each other at moderate distances and repel each other at close range
44
Van der Waals bonds are residual attractive/repulsive forces between
molecules or atomic groups that do NOT arise from covalent bond or electrostatic interaction of ions or ionic groups with one another or with neutral molecules
45
Van der Waals bonds areas interact with transient areas of
opposite charges on another molecule
46
bigger the atom or molecule the
bigger the Van der Waals force
47
attractice forces called van der waals forces are
most common bond between atoms
weaker than covalent, ionic, or hydrogen
- forces operate only when molecules pass very closely to each other
- provide weak force for some drugs and their receptors
48
oxidation and reduction (redox) are a family of reactions
concerned with transfer of electrons
49
redox reactions are a matched set meaning
there is no oxidation reaction without reduction reaction happening at the same time
50
oxidation refers to the ____
while reduction refers to ____
loss of electrons
gain of electrons
each reaction by itself is called hald reaction bc need to be two half reactions for a whole reaction
51
what are all metal atoms characterized by ?
tendency to be oxidized
losing one or more electrons
forming a postively charged ion (cation)
52
electrons lost by the metal are not destroyed but
gained by the non metal which is said to be reduced
53
as the non metal gains the electrons lost by the metal it forms
a negatively charged ion (anion)
54
what is oxidative stress?
disturbance (imbalance) between production of reactive oxygen species - ROS (includes free radicals and peroxides) produced by most body reactions and a biologic systems antioxidant defenses which would allow it to easily repair the resulting damage
55
disturbance in redox environment results in excess ROS that can
damage components of cells, including proteins lipids and DNA
56
oxidative stress and inflammation are two processes that go hand in hand resulting in
aging process
neurodegeneration
disease
- diabetes
- cancers
- atherosclerosis
- parkisons
- alzheimers
57
severe oxidative stress may cause cell death by
necrosis
58
necrosis
passive, accidental cell death with subsequent inflammation
no damage to surrounding cells
59
moderate oxidation can trigger
apoptosis
60
apoptosis
active, programmed cell death that avoids elicitng information
61
Reactive oxygen species (ROS)
used by immune system to attack and kill pathogen
cell signaling
62
Why must overproduction of ROS be avoided
to prevent cell damage
63
glutathione is
naturally produced antioxidant found in plants, animals, fungi, and bacteria that protects cells from toxins like free radicals
64
1) reduced glutathione has a strong
2) as electrons are lost
3) all cells in body are capable of producing glutathione but
4) glutathione is important factor in
5) new otoprotective drug therapies are designed
1) electron donating character
2) molecules become oxidized
3) synthesis in liver is essential
4) protector within auditory vestibualr system
5) designed to promote actions of glutathione
65
inflammation is part of biological immune response of vascular tissues to harmful stimuli such as
pathogens
physical trauma
chemical trauma
66
inflammation is necessary response that allows body
to destroy invading organisms and repair itself
67
inflammatory process (self limiting) can become continuous and
chronic inflammatory diseases might develop
68
chronic inflammation characterized by
continued active inflammation response and tissue destruction
69
what does chronic inflammatory process induce
oxidative stress and reduces cellular antioxidant capacity
70
overproduced free radicals react with
and can lead to
cell membrane fatty acids and proteins imparing their function permanently
lead to mutation and DNA damage
71
Risk factors of chronic inflammation are
Hypoxia (COPD)
obesity
hyperglycemia
smoking
72
chronic inflammation can be predisposing factor for some
cancers and accelerated aging and wide variety of age related diseases such as
diabetes
hypertension
cardiovascular
autoimmune diseases
73
cardinal signs of inflammation
redness
swelling
heat
pain
loss of function
74
vasodilation
increased blood flow
redness
75
edema caused by accumulation of fluid outside blood vessels
sweling
76
increased blood flow to area
fever is brought about by chemical mediators of inflammation and contributes to the rise in temperature at the injury site
heat
77
distortion of tissues caused by edema
chemical mediators of inflammation such as prostaglandins
pain
78
because of pain or severe swelling that prevents movement
loss of function
79
what are enzymes
catalysts that speed up chemical reactions in cells
(proteins)
80
molecules at the beginning of the process called
substrates
81
enzymes converts substrate into different molecules and these are called
products
82
an enzyme must briefly untie with
at least one of the reactants
83
set of enzymes made in a cell determines
which metabolic pathways occur in that cell
84
enzymes end in ase of the name of compounds they act on
collagenase
lactase
85
enzyme and substrate can have specific shapes such that an enzyme may be specific for a specific substrate, if enzyme and substrate dont match
NO reaction will occur
enzyme can slightly modify its shape to accomodate several substrates
86
enzyme activity can be affected by other molecules
inhibitors
activators
inhibitors = molecules decrease enzyme activity
activators= molecules that increase enzyme activity
87
enzyme activity also affected by
temperture
chemical environement
and concentration of substrate
88
receptors are ?
many receptors span the cell membrane
protein molecule embedded in the cell surface or cytoplasm and allows for communciation between the cell and the world outside cell
89
receptor allows extra cellular molecules such as
hormones, neurotransmitters, toxins, or drugs to attach to it resulting in a change in cell fucntion
90
extracellular molecules also called
ligands
91
receptor ligand binding occurs by
ionic bonds/hydrogen
and van der waals forces
92
what is a hormone?
chemical substance usually a peptide or steroid produced/released by one set of cells and conveyed by the blood stream to another to effect physiological activty such as growth or metabolism
93
horomones are powerful and only a small amount of hormone is required to
alter cell metabolism
94
hormones are chemical messengers that transports
a signal from one cell to another
95
what produces hormones ?
all multicellular organisms
96
hormones cause reactions that are slower than those associated with
neurotransmitters
97
hormone examples
throid
cortisol
estrogen
testosterone
98
a neurotransmitter is a chemical messenger that carries boosts modulates signals between
neurons and other cells in the body
99
process known as reuptake
neurotransmitter attaches to receptor site and is reabsorbed by neuron
100
neurotransmitters are affected by disease and drugs
diseases like Parkinson's or Alzheimer's
dopamine deficiency in parkinsons
acetylcholine deficiency in Alzheimer's
101
epinephrine and norepinephrine
excitatory effects on the neuron
increase likelihood neurons will fire an action potential
excitatory neurotransmitters
102
serotonin and Gaba
inhibitory effect
decrease likelihood of action potential
inhibitory neurotransmitters
103
voluntary movement of the skeletal muscles
acetylcholine
104
wakefulness or arousal
norepinepherine
105
voluntary movement and motivation wanting pleasure associated with addiction and love
dopamine
106
memory emotion wakefulness, sleep temperature regulation (associated with depression
serotonin
107
inhibition of motor neurons major inhibitory neurotransmitter in the central nervous system
GABA
gamma aminobutyric acid
108
spinal reflexes and motor behavior
glycine
109
excitatory stimulation
glutamate
110
neuromodulator is
substance released by a neuron and transmitting information to other neurons altering their activities
111
neuromodulator produce a more diffuse response and are released through
central nervous system
112
neuromodulator plays role in sensory transmission (pain)
substance P modulates pain
dopamine and nicotine are involved in addiction
113
local chemicals
work locally and are not released into systemic circualtion
114
local chemicals include
histamine
prostaglandins
115
histamine
organic nitrogenous compound involved in local immune responses (allergies)
116
prostaglandins
hormone like lipid compound made at site of tissue damage or infection
deal with injury
- inflammation
- blood flow
- formation of blood clots
- induction of labor
117
AUD ~2000 drugs and 400 side effects impact audiologic and vestibular system
hearing loss
tinnitus
vestivualr dysfucntion
cogntive issues
combination
118
case history questions
what medication are you currenly taking (dose and frequency)
what condition is medication for
how long have you been taking these medications
