Biochem & Meta Midterm Flashcards
7 conventional definitions of life
- Organization
- Reproduction
- Metabolism
- Growth
- Homeostasis
- Response to stimuli
- Adaptation
other proposed features of life
carbon-containing - chemical element that forms basis of life on earth
reliance on water - chemical substance needed for survival of all forms of life on earth
genetic information - uses DNA & RNA to store blueprint of organism
6 bio elements
hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur
What are the Shared Molecular Characteristics?
- Life obeys the laws of thermodynamics
- ATP is the energy currency of life
- Life is composed of similar biological molecules
1st law of thermodynamics
energy can neither be created nor destroyed, it can only change from one form to another (energy from food is being transformed into chemical energy)
2nd law of thermodynamics
all processes increase entropy (disorder) (Biochemical application (catabolism): large food molecules = less entropy, are broken down into smaller molecules = more entropy)
Micronutrient
a nutrient required in small amounts
- all vitamins (A, B, C, D, E, K)
- microminerals - iron, copper, manganese, zinc
macronutrient
nutrient required in large amounts
- carbs, protein, lipids
- also some minerals - calcium, potassium, magnesium, phosphorous
what do vitamins do?
act as co-factors for enzymes, organic compounds that are only loosely bound to the enzyme during its reaction, but they are required for the enzyme to function properly
3 kinds of hydrocarbons
- Alkane: carbon-carbon bonds are all singe bonds
- Alkene: there is at least one carbon-carbon double bond
- Alkyne: there is at least one carbon-carbon triple bond
Prefix for # of carbons
meth - 1 eth - 2 prop -3 but - 4 pent - 5 hex - 6 hept - 7 oct - 8 non - 9 dec - 10
Naming branched alkanes
- Identify the longest linear carbon chain (parent chain)
- name parent chain using learn naming rules (prefix for number of carbons, suffix for alkane, “ene” “yne”)
- Number the carbons on the parent chain so side chains (branches) occur at the lowest possible numbers
- Name each side chain using linear naming rules and change the suffix from “-ane” to “-yl”
- List the side chain(s) before the parents chain and number them
9 functional groups
- alcohol
- ether
- amine
- aldehyde
- carboxylic acid
- ketone
- ester
- phosphate
- thiol
Alcohol -OH group
R-O-H
Naming: (# of C with -OH) - (parent chain name, suffix “ol”)
CH3-CH-CH3
|
OH
(1-propanol)
Rules for naming Hydrocarbons with functional groups
- functional groups have priority over side branches for numbering the parent chain
- determine the parent chain: longest chain that includes the carbon with the functional group (may not be the longest!!!)
- number and name the parent chain to give the lowest number to the carbons the functional group (even if this gives higher numbers to branches)
- if there are branches, number and name them, and place them before the parent chain, same as before
- follow the naming rules for the specific functional group
Ethers R-O-R group
naming: (name of each R group, “ane” replaced with “yl”) + suffix “ether”
Amines -N- group
3 possible types: Primary: one R group Secondary: two R groups Tertiary: three R groups *R group must have carbon bound to N
naming: (Name of R group, ane replaced with yl) + suffix amine
CH3-CH2-CH2-N-CH3
|
CH3-CH3
(ethyl methyl propyl amine)
Aldehydes -CO group
O
||
R-C-H
Naming: (parent chain name) + suffix “al” instead of “e”
O
|| CH3-CH2-CH (propanal)
- total # of carbons includes the C in the aldehyde groups
- aldehyde groups are always at the end of molecules and always contain carbon #1, so its unnecessary to indicate aldehyde location
Carboxylic acids -COOH group
O
||
R-C-OH
Because functional group contains C, R group does not HAVE to
Naming: (parent chain) + suffix "oic acid" instead of "e"
O
||
H-C-OH
(methanoic acid)
- total # of carbons includes the C in the carboxylic acid group
- always at the end of molecules and always contain carbon #1, so no need to indicate location (similar to aldehyde)
Ketones -COR group
O
||
R1-C-R2
Even though functional group contains C, both R groups MUST contain C, or else it would be an aldehyde or carboxylic acid
naming: (# of C with ketone) + parent name + suffix “one” replacing “e”
O
|| CH3-CH2-C-CH2-CH3 (3-pentanone)
Esters -COOR group
O
||
R-C-OR’
R’ group HAS to contain C
carboxylic acid + alcohol = ester + water
naming:
esters are named for the alcohol and the carboxylic acid which combined to make the ester
- name alcohol and replace the “ol” with “yl”
- name the carboxylic acid and place the “oic acid” with “oate”
- the ester name has alcohol first and carboxylic acid second (alphabetical does not apply here)
4 carbonyl compounds (contain C=O, double bond)
aldehydes
carboxylic acids
esters
ketones
Thiols -SH group
R-S-H
naming:
parent chain name + suffix thiol
- alkane name remains unaltered when adding “thiol” suffix (‘e” remains)
CH3-CH2-CH2-SH
(1-propanethiol)
Phosphate group
O
||
R-O-P-OH
|
O
R group will contain C
naming:
(R group name, “ane” replaced with “yl”) + suffix phosphate
O
||
CH3-O-P-OH
|
O
(methyl phosphate)
Enthalpy
- heat content of a molecule represented by H
- the change in enthalpy of biochemical reaction is represented by
ΔH: ΔH = H(final) - H(Initial)
when ΔH is neg = exothermic, spontaneous
if ΔH is pos = endothermic, non-spontaneous
Entropy
change in entropy is represented by ΔS
ΔS = S(final) - S(initial)
entropy can be lost (negative ΔS - less disorder) or gained (positive ΔS - more disorder) by a system
3 factors affecting entropy
- arrangement of molecules
- tightly packed arrangement = less entropy
- loose arrangement = more entropy - number of molecules
- more molecules = more entropy
- fewer molecules = less entropy - motion of molecules
- more motion = more entropy
- less motion = less entropy
degree Kelvin
degrees Kelvin is the SI unit of temperature: °K = °C + 273
Gibbs free energy (G)
combines the concepts of enthalpy (H) and entropy (S) into the term G (expressed as KJ/mol)
- ΔG = ΔH - TΔS
- T is temperature in degrees Kelvin
ΔG is also represented by
- ΔG = G(final) - G(initial)
Conditions that favour exergonic (spontaneous) reactions
reactions that have both:
- loss of heat (-ve ΔH) and gain of entropy (+ve ΔS) will be energetically favourable and will be spontaneous
if it isn’t clear whether reaction will proceed…
dependant on:
- temperature to be the factor
ΔG vs. ΔG°’
ΔG = Gibbs free energy
- max amount of energy available to do work
- represents what is actually happening in a living cell (conditions that are constantly changing, and impossible to measure)
ΔG°’ = Gibbs standard free energy
- measured under standard laboratory conditions
- usually ΔG°’ is given in biochem, since ΔG is hard to measure accurately in dynamic in vivo conditions
Gibbs standard free energy
ΔG = ΔG°’ + RTlnKeq
Keq = [product C][product D]
__________________
[product A][product B]
Uni vs bidirectional arrows
Uni: irreversible reaction, one-way
Bi: reversible reaction, operate in both directions
Problem: ΔG°’ is large & positive, non-spontaneous, energetically unfavourable
solution: using ATP hydrolysis to make reaction energetically favourable
ATP hydrolysis: exergonic, releases a lot of energy (-30.5 kJ/mol)
calories vs Joules
1 calorie = energy needed to increase temp of 1 gram (1ml) of water by 1°C
1 Joule = energy needed to lift 1 lb to a heigh of 9 inches
1 calorie = 4.184 J
5 Cal = 5kcal = 5000 calories = 20920 J = 20.8 kJ
easy question lol
cals of macros
- carbs - 4 cals
- protein - 4 cals
- lipid - 9 cals
- alcohol (ethanol) - 7 cals *fyi
Energy in food - Gross Energy (GE)
(GE) = total energy found in good
- useable - digestible, metabolizable
- non-useable - indigestible energy
GE is measurement of heat produced by combustion of food (as determined by comb calorimetry)
- also known as heat of combustion
Non-useable (indigestible) energy
Energy not used to do work 3 types
- fecal energy (FE): energy lost in feces
- Urinary energy (UE): energy lost in urine
- Gaseous energy (GasE): energy lost in gas
Gross energy (GE) = useable E + non-useable E
- Gross energy (GE) = useable E + (FE + UE + Gas E)
Useable (or digestible) energy
Metabolizable Energy (ME) = energy available to the organism to do work. Useable energy only
Energy used for 4 things: growth, cell/tissue maintenance and repair, activity (movement), and reproduction
- 4 cal/g protein, 4 cal/g carbs, and 9 cal/g lipid are metabolizable energy values
- ME = GE - (FE+UE+GasE)
Energy Out
- Energy expenditure (measured in calories over 24 hrs)
- Energy expenditure (in 24 h) = BMR + activity + thermic effect of food
BMR
BMR (basal metabolic rate) = BW (lbs) x 10 cal/lb/24h
- energy needed for the very basic functioning of vital tissues (e.g. heat, brain, liver, kidneys)
- affected by: age, sex, genetics, training status, health, etc.
standardized condition for measure:
- at rest, awake
- temperature neutral environment
- post-absorptive state (fasting)
Activity level
"inactive" = BMR x 20% light = BMR x 30% moderate = BMR x 40% high = BMR x 50%
Thermic effect of food
Thermic effect of food (TEF) = food intake (in cal) x 10%
- energy needed for digestion of food eaten
- rough approximation
- in reality, TEF is different for each macronutrient (protein > carb > fat)
Obesity
How to define obesity
- BMI = weight (kg) divided by height (metres)^2
3 factors contributing to obesity epidemic:
- intake of fast food
- intake of added sugar (sweetened beverages)
- large portion sizes
the number of protons, neutrons, and electrons is usually equal to…
the atomic number of the atom
of electrons in first, second, and third orbital
- first orbital can contain 2 electrons
- second and third, 8 electrons each
- atoms attempt to have their outermost electron orbital filled
- when orbital is half filled or more, atom attempts to gain electrons
- when less than half filled, it attempts to lose electrons
# of bonds formed for: carbon hydrogen oxygen nitrogen phosphorous sulfur
carbon - 4 hydrogen - 1 oxygen - 2 nitrogen - 3 phosphorous - 3 sulfur 2
Types of chemical bonds:
intra vs intermolecular
intra: bonds within a molecule (covalent, ionic)
inter: bonds between molecule (hydrogen, van der waals, hydrophobic)
relative chemical bond strength (high to low)
covalent ionic hydrogen van der waals hydrophobic
Covalent bonds (electron sharing)
sharing of electron pair between bonded atoms (stable & strong)
Ionic bonds (electron transfer)
- one or more electrons removed from one atom and added to another atom
- results in +ve and -ve ions (bond is based on attraction between oppositely charged ions
Hydrogen bonds
(important role for DNA, amino acids, etc. /technically strong when there’s a lot)
only 5-10% strength of covalent bond
Van der Waals forces
- force generated by any two molecules with electron shells that are almost touching
- temporary situation, since electrons are always moving in orbit
- electrostatic attraction between opposite charges similar to hydrogen bonds though weaker
Hydrophobic force
hydrophobic (non-polar) molecules don’t interact well with water and tend to seek each other out and avoid water (eg. waxes, fatty acids, oils, alkanes (greasy things)
Electronegativity:
- ability of an atom to attract electrons
two atoms in a bond can exert different forces on the electron pair
- high electronegativities exert a strong attraction on electrons
- low electronegativities exert a weak attraction on electrons
Result: unequal sharing of electrons between atoms
- electrons spend more time closer to the atom with the higher electronegativity
Bonding between atoms with electronegativities
- 0 - <0.4 = non-polar covalent (equal sharing)
- 0.4 - <2.0 = polar covalent (unequal sharing)
- 0.4 - <1.1 (slightly polar covalent)
- 1.1 - <2.0 (highly polar covalent)
- > or = to 2.0 = ionic (full transfer/stealing)
Polarity vs electronegativity
electronegativity:
- ability of an atom to attract electrons
Polarity:
- charges in a bond or molecule resulting from unequal sharing/stealing of electrons
- amount of bond polarity is proportional to the difference in electronegativities of the atoms forming the bond
ionization of water
there is a measurable tendency for the hydrogen ion to jump to an adjacent water molecule
acid and bases
acid: ac as proton donor
bases: act as proton acceptor
structural isomer
differing bonds between atoms even though the total number of atoms of each element are identical
spatial isomer
- same bonding arrangement between atoms, but a different spatial arrangement
- i) enantiomers - mirror images
- ii) diastereomers - non-mirror images
- iia) cis/trans isomers (oriented either on same or opposite side of double bond)
- iib) epimers (spatial positioning different at only one atom)
