chemistry of life 1,2,3 Flashcards
atoms are
units of matter
nucleus of atoms consists of
neutrons and protons
what orbits the nucleus of atoms
neg charged electrons
in a neutral atom
electrons= number of protons
energy is
the ability to do work
potential energy
the energy matter stores due to its position or location
greater the distance electrons have from the nucleus the greater their
potential energy
shell diagram
2 electrons in first shell then 8 then 8
outermost shell electrons are valence electrons
atomic number is number of electrons
atom with complete valence shell is
unreactive or inert
cation
atom that loses valence electrons and become pos charged
anion
atom that gains electrons to complete valence shell and becomes neg charged
covalent bonds
2 atoms share a pair of valence electrons
ionic bonds
transfer of electrons between pos charge and neg charge form ionic bond
compounds which form ionic bonds are
salts
hydrogen bonds
weak bond
H atom attached to an EN atom by a polar covalent bond is shared with another EN atom through weak electrical attraction
water’s cohesive forces are due to it’s
H bonds with other water molecules
any molecule or atom that has polarity will
attract water molecules and thus will dissolve in water (soluble)
van der waal’s interactions
similar to H bonds but are formed from non polar molecules where “hot spots” of pos and neg may transiently occur
hydrophobic interactions
non polar molecules do not mix readily w polar water molecules
ex fats and oils
cohesion of water that results in surface tension is due to
large proportion of water molecules being H bonded to their neighbours at any time
molecules in centre of drop of liquid are equally attracted to surrounding molecules and molecules at surface are drawn into centre way from air (they would rather interact with each other than with air) which creates surface tension
water has a high specific heat which means
amount of heat which must be absorbed / lost for 1 gram of a substance to raise/ lower its temp by 1 degree C and for water this is 1 calorie
why does temp of water NOT change as much as many other substances
because with water much of energy is used to break H bonds
solvent, solute
solvent ie the water
solute ie the substance that dissolves
form a solution
structural isomers
same formula but different structure
cis-trans isomers
differ in arrangement around a double bond
enantiomers
mirror images of each other
4 main classes of macromolecules
carbs
proteins
nucleic acids
lipids
cabrohydrates
- composed of C, H and O
- classified into:
- fibre
- starch
- complex sugars (polysaccharides)
- simple sugars (monosaccharides)
- most are ring structures
carbs for energy storage
- plant cells use polysaccharides for both storage (starch) and cell structure (cellulose)
- herbivore break down these plant polysaccharides for energy
- animal cells use polysaccharides for storage (glycogen) which can be catabolized through glycogenolysis to yield energy
proteins perform all essential functions for cells to stay alive including
- catalysis
- signalling
- structure
- energy/ gradient generation
essential vs non essential amino acids
essential need to be in diet, body cannot synthesize by itself
polypeptide chain
2 amino acids positioned so COOH group of one lines with amino group of other
dehydration rxn; peptide bond is formed between carbon and nitrogen
amino acid properties are from their various
side chains (R groups)
protein shape
- final shape important
- function of protein
- exposes binding sites
nucleic acids are
info carrying molecules
DNA –> RNA via transcription –> protein via translation
nucleic acids made up of
- high energy triphosphate
- sugar; either deoxyribose or ribose
- base; adenine, guanine, cytosine, thymine or uracil
A and T
C and G
pair through H bonds
A and T 2
C and G 3
are lipids soluble
no
lipid functions
crucial part of cell membranes
cell signalling
key energy storage reserve
most important lipids
fats, phospholipids, steroids
fats vs oil
solid vs liquid lipids
triglyceride consist of
glycerol backbone and 3 FA molecules
saturated vs unsaturated fats
saturated with H bonds ie no double bonds
essential fatty acids
- not synthesized by body
- necessary to prevent pathological conditions
- important in growth phase of children
- may protect against cardiovascular disease in adults
phospholipids make up all animal
cell membranes
how do phospholipids differ from fats
only 2 FAs bound to glycerol backbone, third carbon bound to a phosphate group
hydrophilic head; water soluble
hydrophobic tails
naturally form bilayers in water
cholesterol made where
liver
is cholesterol absorbed well in diet
no
where is cholesterol often found
in many animal cell membranes; influences membrane fluidity
what is the precursor molecule of all steroids
cholesterol
anabolism
energy is stored in cells or used to help build up and repair structures of body
catabolism
breakdown of body tissues into simples forms, which can then be used to create energy
by product of metabolism is
heat
endergonic rxns
absorb free energy (anabolic)
exergonic reactions
release energy (catabolic)
energy currency
ATP
high energy phosphate bonds store chemical energy
ato may be degraded to
ADP or AMP; releases phosphate groups and energy, energy used to drive metabolic processes, heat is also produced
ATP hydrolysis
- phosphate bonds are high energy
- Phosphate groups are neg charged; naturally repulsive
- in ATP they are held close together
- during hydrolysis this energy is released
- coupled w cellular reactions, enable the cell to do work
photosynthesis
- electromagnetic energy in light is captured in plants, produces ATP
- uses ATP plus H2O and CO2 used to generate glucose (sugar) and O2
- O2 is released
- glucose stored or used in cellular respiration
order of other sources of energy being used by body
- sugar reserves used first (glycogen), then fat reserves, then protein reserves (muscle)
- require catabolism to produce ATP
activation energy
energy investment required to reach unstable transition state
transition state
when molecules absorb this energy and become unstable, where bonds can break
how do enzymes lower Ea
by binding to its substrates forming a complex, converts the substrate into product
enzyme specificity
- high specificity w substrate
- 3D structure (from amino acid sequence) binds substrate in a highly specific active site
how is substrate held in active site of enzyme
weak H or ionic bonds
mechanisms enzymes use to lower Ea
- Two substrates are bound close together so they can react
- The enzyme can stretch the substrates towards their transition state form
- The active site may create a favorable microenvironment
- Direct binding of substrate to amino acids in the active site
what conditions do enzymes require to work at max efficiency
- sufficient substrate to saturate the active site
- physical environment at optimal pH and temp
- cofactors (inorganic molecules) or coenzymes (organic molecules) sometimes requires
competitive inhibitors
bind reversibly to an enzymes active site
non competitive inhibitors
do not bind to he active site, bind elsewhere and change enzymes shape, makes active site harder to access
how is control of metabolism by controlling enzymes achieved
- switching on/off genes encoding specific enzymes
- by regulatory molecules
natural regulators
- act like reversible competitive inhibitors
- allosteric regulation
what is a common allosteric inhibitor and activators to control enzymes
inhibitor; ATP
activator; ADP
what is one of the most common ways to regulate a metabolic path
feedback inhibition
- end product binds to one of the early enzymes in a metabolic path, prevents it from catalyzing, pathway switched off
localization of enzymes within the cell
enzymes are located in many different sites within cell
enzymes which catalyze steps in same path often located together
cellular respiration produces ____ and ____ and generates ____
H2O, CO2
ATP
oxidation
loss of electrons or increase in oxidation state
reduction
gain of electrons or decrease in oxidation state
3 stages in cellular respiration
- glycolysis
- Citric acid cycle
- electron transport chain and oxidative phosphorylation
glycolysis
- splits glucose into 2 3C compounds
- occurs in cell cytoplasm
- product is pyruvate
2 stages in glycolysis
energy investment and energy payoff; spend ATP to make ATP
does glycolysis require oxygen
no
is carbon released during glycolysis
no
where does pyruvate from glycolysis go
into the mitochondria, converted into acetyl-co-A and enters the citric acid cycle
where does CAC take place
mitochondrial matrix
CAC
- produces CO2 and NADH
pyruvate to acetyl coA involves what enzyme
pyruvate dehydrogenase (PD)
what 2 enzymes control pyruvate dehydrogenase (PD)
- pyruvate dehydrogenase kinase (PDK) phosphorylates PD and makes it inactive
- pyruvate dehydrogenase phosphatase (PDP) reverses actions of PDK and makes PD active again
at end of glycolysis and CAC what is a net gain of
4 ATP
most energy has been harvested as NADH or FADH2
where does ETC take place
in mitochondrial membrane
as electrons are passed down the ETC, H+ ions are
transported into the inter-membranous space
where can electrons enter the ETC
complex I or complex II, both of which feed to CoQ and then onto Complex III and so on
how does ATP synthase work
The ATP synthases uses that proton gradient as the
power force to phosphorylate ADP to ATP
H+ escape back into the inter membrane space through ATP synthase
ATP synthase uses the protons kinetic energy
Each member of the electron transport chain gets progressively more
electronegative
electrons from NADH and FADH2 are passed down the ETC in a series of
redox reactions
this pumps protons from mitochondrial matrix to the inter-membrane space
ATP synthase; concept of used H+ gradient to do work is called
chemiosmosis
ATP synthase structure
protein complex with 4 main parts, each part composed of multiple polypeptides, protons bind one by one to parts of the rotor, changes shape of rotor and causes it to spin, catalyses ATP synthesis
max amount of ATP generated during cellular respiration
30-32 molecules
strenuous exercise on ETC
- pH decreases; more acidic; effects complex I, less proton force generated
- temp increases; get leak in system and protons can cross back over without ATP synthase
electrons leaking from ETC can produce
reactive oxygen species such as superoxide and hydrogen peroxide; toxic but necessary signalling molecules
endurance rely on
aerobic metabolism, slower energy supply than anaerobic, but produces large amount of energy
mid distance rely on
initially rely on stored ATP and phosphocreatine in muscle, and then move into aerobic energy production
As they approach the final sprint, the oxygen supply
becomes inadequate compared to the metabolic demand. They gradually ramp up
anaerobic glycolysis,
sprinting relies on
anaerobic metabolism
Energy released from glucose
and stored glycogen (i.e.,
glycolysis)
Hydrolysis of phosphocreatine
stored in muscle cells (8‐10s
burst of max energy generation)
traditional view or metabolism
aerobic metabolism
is “good”, and anaerobic metabolism is ”bad” ie lactic acid is bad
lactic acid strength
weaker acid than any other intermediate of glycolysis so it actually increases pH of cell
lactate clamp experiments
nothing happened when lactate was forced to stay up
lactic acid overview
glycolytic fiber, and it’s producing glucose. At some point, you generate so much pyruvate it goes over into lactate, which then goes out into the bloodstream, through a monocarboxylate transporter. And then you’ve got your oxidative fibers. Highly oxidative fibers take lactate up, convert it back into pyruvate, and then passing it through their considerably larger supply of mitochondria, and making ATP with it through the krebs cycle.
At physiological pH levels, lactic acid is nearly complete dissociated into a lactate anion and hydrogen ion which are both removed from the muscles. Once in the blood, the free H+ is buffered by bicarb producing CO2 which is subsequently expelled during expiration. The lactate anion is reused in one of two ways. It’s either transported to metabolically active cells where it is converted back to pyruvate to be used for aerobic energy metabolism, or it’s transported to the liver for gluconeogenesis
Summary: lactate is a product of anaerobic metabolism. If the concentration in the blood is increasing, glucose is broken down and oxidized to pyruvate, and lactate is produced from the pyruvate faster than the capacity of clearance/consumption mechanisms.
Lactate shuffle
lactate going round the body not just accumulating
which of the following referring to inert atoms is false
The outermost shell always requires 8 electrons for stability
An atom with a complete valance shell is unreactive, or inert
An atom with an incomplete valence shells is unreactive, or inert
The first valence shell contains 2 electrons in its orbit
An atom with an incomplete valence shells is unreactive, or inert
Which of the following statements referring to chemically reactive atoms is FALSE?
The chemical properties of an atom depend on the number of valence electrons
An atom that loses its valence electrons becomes positively charged; this is known as a cation
An atom that gains electrons to complete its valence shell will be negatively charged; this is known as an anion
An atom with a complete valance shell is chemically reactive
An atom with a complete valance shell is chemically reactive
Which of the following statements regarding covalent bonds is TRUE?
2 atoms share a pair of valence electrons
Compounds which form covalent bonds are salts
If an electron is transferred, this is a covalent bond
Covalent bonds are formed from non-polar molecules where “hot-spots” of positive and negative may transiently occur
2 atoms share a pair of valence electrons
Which of the following statements BEST describes hydrogen bonds?
They are formed from non-polar molecules where “hot-spots” of positive and negative may transiently occur
A hydrogen atom attached to an electronegative atom (e.g., O or N) by a polar covalent bond is shared with another electronegative atom through a weak electrical attraction
They are formed where 2 atoms share a pair of valence electrons, and are a strong chemical bond
It is a strong chemical bond, which is formed between cations and anions
A hydrogen atom attached to an electronegative atom (e.g., O or N) by a polar covalent bond is shared with another electronegative atom through a weak electrical attraction
Which of the following statements regarding surface tension is FALSE?
Water molecules want to interact with one another rather than with air
Molecules in the centre of a drop of liquid are equally attracted to surrounding molecules
Molecules at the surface are drawn into the centre, away from the air-water interface
Molecules at the surface of a drop of liquid are equally attracted to surrounding molecules
Molecules at the surface of a drop of liquid are equally attracted to surrounding molecules
Many substances can dissolve in water. Which of the following is the CORRECT term to describe a liquid which is able to dissolve other substances?
solvent
Each carbon is a branch point with 4 possible options. Which of the following types of bonds is NOT formed by a single carbon to other atoms?
4 single bonds
2 single bonds and 1 double bond
1 double bond and 1 triple bond
1 triple bond and 1 single bond
1 double bond and 1 triple bond
Which of the following statements BEST describes cis-trans isomers?
Differ in arrangement around a double bond
Which of the following statements regarding proteins is FALSE?
All proteins are comprised of amino acids
Proteins have a rich and diverse array of functions
Essential amino acids are the amino acids that it is essential to have in the diet
The categorisation of essential versus non-essential amino acids is the same for all organisms
The categorisation of essential versus non-essential amino acids is the same for all organisms
A peptide bond is formed between the carbon and nitrogen atoms during which of the following types of reaction?
Dehydration reaction
Which of the following statements regarding side chains is FALSE?
The different properties of polypeptides are from their various side chains, or “R” groups
Non-polar side chains are hydrophilic
Polar side chains are hydrophilic
Electrically charged side chains are hydrophilic
Non-polar side chains are hydrophilic
Which of the following is NOT a property of phospholipids?
Phospholipids make up all animal cell membranes
Have 2 fatty acids bound to the glycerol backbone
Have a hydrophobic head
Naturally form bilayers in water
Have a hydrophobic head
Which of the following statements regarding ATP hydrolysis to ADP is TRUE?
Requires energy; obtains energy from catabolism
Requires energy; comes from glycolysis
Yields energy that is coupled in the cell to an exergonic reaction
Yields energy that is coupled to an endergonic, energy-consuming processes
Yields energy that is coupled to an endergonic, energy-consuming processes
Which of the following statements regarding ATP hydrolysis is FALSE?
Phosphate groups are negatively charged and are naturally repulsive. However, in ATP they are forced close together. On hydrolysis this energy is released.
ATP hydrolysis is coupled with reactions that are naturally exergonic
ATP hydrolysis is coupled with reactions that are naturally endergonic
ATP hydrolysis enables the cell to “do work”
ATP hydrolysis is coupled with reactions that are naturally exergonic
Activation energy is the:
Initial energy investment required to reach an unstable transition state, during a reaction
Which of the following statements regarding enzymes is FALSE?
Enzymes lower the activation energy barrier, decreasing the energy investment required in order for the reaction to proceed
Enzymes have high specificity with which they bind their substrates, due to the 3D structure of the active site
For an enzyme to work at maximum efficiency, there must be sufficient substrate to saturate the active site
Non-competitive inhibitors bind reversibly to the active site, mimicking the substrate
Non-competitive inhibitors bind reversibly to the active site, mimicking the substrate
Metabolism can be controlled through controlling enzymes. This can NOT be achieved by:
Switching on or off genes, which encode specific enzymes
Allosteric regulation. ATP is a common allosteric inhibitor.
Allosteric regulation. ADP is a common allosteric inhibitor.
Feedback inhibition. This is where the end product binds to one of the early enzymes in a metabolic path, preventing it from catalysing reactions.
Allosteric regulation. ADP is a common allosteric inhibitor.
Which of the following is NOT a product of cellular respiration?
Carbon dioxide
Glucose
ATP
Water
Glucose
Redox reactions are chemical reactions in which the oxidation state of substrates change. Which of the following statements is INCORRECT?
Oxidation is the loss of electrons, and is often achieved by losing electrons to oxygen
Oxidation is an increase in the oxidation state of a molecule, and is often achieved by sharing electrons with oxygen
Reduction is the gain of electrons, which is often achieved by gaining electrons from oxygen
Reduction is a decrease in the oxidation state of a chemical, which is often achieved by sharing electrons with hydrogen
Reduction is the gain of electrons, which is often achieved by gaining electrons from oxygen
Which of the following statements regarding glycolysis is TRUE?
It occurs in the mitochondrial matrix
Glycolysis is the splitting of glucose into 2 molecules of pyruvic acid (pyruvate)
The product of glycolysis is glucose
Glycolysis requires oxygen to occur
Glycolysis is the splitting of glucose into 2 molecules of pyruvic acid (pyruvate)
The main PRODUCT of the Krebs cycle that is used in the electron transport chain is:
NADH
Which of the following statements regarding the electron transport chain is INCORRECT?
The electron transport chain is a series of molecules embedded into the inner membrane of the mitochondria
As electrons are passed down the chain, H+ ions are transported into the intermembranous space
There are thousands of copies of the electron transport chain contained in each mitochondrion
As electrons are passed down the chain, H+ ions are transported into the mitochondrial matrix
As electrons are passed down the chain, H+ ions are transported into the mitochondrial matrix
Oxygen gets consumed at which complex of the electron transport chain?
Complex I
Complex II
Complex III
Complex IV
Complex IV
Which protein complex in the inner mitochondrial membrane is responsible for converting ADP and phosphate into ATP?
ATP Synthase
Strenuous exercise results in an increase in skeletal muscle temperature in horses. This has an effect on the electron transport chain. Which complex does it primarily have an effect on, and what is this effect
Complex I. Without complex I functioning properly, you get less proton force being generated.
Which of the following best describes in order from greatest to least, the aerobic contribution to overall energy production of these equine performance disciplines?
Endurance > Thoroughbred racing > Barrel racing
Which of the following intermediates of glycolysis is the WEAKEST acid?
Lactic acid
Which of the following statements referring to lactate is INCORRECT?
Oxidative fibres take lactate up and convert it back into pyruvate, which then passes into their considerably larger supply of mitochondria (than glycolytic fibres) to make ATP
Lactate is produced in glycolytic fibres, and passes out into the bloodstream through a monocarboxylate transporter
The liver takes up lactate and makes glucose through a process called gluconeogenesis
The concentration of lactate that you measure in the blood is the amount of lactate that the body is producing
The concentration of lactate that you measure in the blood is the amount of lactate that the body is producing
