Introduction to Biochemistry Flashcards
Carbon can form 4 _____ bonds
covalent
the less oxidised the molecule the ____ energy contained in the bonds.
more
alkane (in fats) has ____ energy in its bonds than carbon dioxide (final product of catabolism)
more
what is the glycosidic bond in lactose?
galactose beta 1-4- glucose
what is the glycosidic bond in maltose?
glucose alpha 1,4 - glucose
what is the glycosidic bond in sucrose?
glucose alpha 1,2 - fructose
what is the glycosidic bond in cellobiose?
glucose beta 1-4- glucose
carbs are made of carbon, hydrogen and oxygen in a ___:___:___ ratio
1:2:3
what is the free energy equation involving enthalpy and entropy
ΔG = ΔH – TΔS
for a process to occur delta G must be _____
negative
an endothermic process with a negative ᐃS can never be _______, for example photosynthesis.
spontaneous
ΔG = (energy of the ______) – (energy of the ______)
ΔG = (energy of the products) – (energy of the reactants)
exergonic reactions are reactions in which the total free energy of the product(s) is _____ than the total free energy of the reactant(s)
less
exergonic reactions can occur +_____
spontaneously
endergonic reactions are reactions in which the total free energy of the product(s) is ____ than the total free energy of the reactant(s)
more
endergonic reactions cannot occur _____. They need an Input of _____ to proceed.
spontaneously, energy
what is the equation for delta G for a given reaction
ΔG = ΔGo’ + RTln([C][D]/[A][B])
what is R
the universal gas constant
what is T
the absolute temperature
what is ΔGo’
the change in free energy under standard conditions
ΔG is related to the point of equilibrium: The further towards completion the point of equilibrium is, the ____free energy is released
more
ΔG values near ___ are characteristic of readily reversible reactions.
zero
When the system is at equilibrium, forwards and backwards reactions are balanced:
ΔG = 0 and therefore
ΔGo’ = -RTlnKeq
Keq = [C][D]/[A][B]
(substrate and product concentrations at equilibrium)
reactions with a negative delta Go, i.e. reactions going from high energy reactants to low energy products, are ______
favourable
What about reactions with a positive delta G - it all depends on the initial concentrations of the _____
reactants
what is the effect of increasing [A][B] relative to [C][D] do the delta G ?
- [C][D]/[A][B] becomes smaller than 1
- the ln of a number smaller than 1 is negative!
many cellular processes are unfavourable and are driven by ____ to highly favourable processes
coupling
the breakdown of ATP is a very ____ delta G
negative
The negative charges close together in ATP put a ____ (electrostatic repulsion) on the molecule that makes it less ____ than ADP
strain, stable
the phosphate parts of ATP are anhydride bonds. These are ___ energy bonds. So when they break energy is _____
high, released
what are the two ways to make ATP?
- using creating phosphate
2. using 2 ADP
what is glycolysis ?
Initial breakdown of glucose for the generation of ATP
Reactions close to equilibrium (ΔG close to 0) are not used as _____ points
control
hydrogen bonds tend to be ____ in form
linear
amphipathic molecules form ____ in water
micelles
Proteins and polypeptides in humans are made up from ___ different __-amino acids
20, L
what is the one exception to the L amino acids?
glycine - it has two of the same group
all amino acids contain an α-carbon bonded to …. 4 things
an amino group (-NH2)
a carboxyl group (-COOH)
a hydrogen (-H)
a side chain (-R)
D and L form AAs are _______
stereoisomers
what are the 4 groups of AAs
- non polar, hydrophobic
- polar, uncharged
- acidic
- basic
what are the characteristic chains on - non polar, hydrophobic ?
mainly hydrocarbons
what are the characteristic chains on - polar uncharges?
mainly carbonyl and hydroxyl groups, NH
what are the characteristic chains on acidic aas?
carboxyl grop
what are the characteristic chains on basic AAs?
ammine
NH3 and
what is a peptide bond the linkage of?
CO and NH groups with the removal of water
peptides have a direction , what is it?
from N terminal residue NH3+ to the C-terminal residue COO-
peptide bonds have a partial ___ bond character
double
____ bonds are planar
peptide
Acids are molecules which can ____ a proton (hydrogen ion, H+)
donate
Bases are proton _____
acceptors
H+ conc of 10 -7 has a pH of 7, what is the pH of a H+ conc of 10 -6
6
the henderson -hasselbach equation Connects the __ of a weak acid with the __ of a solution containing this acid
Connects the Ka of a weak acid with the pH of a solution containing this acid
what is the quation?
pH = pKa + log[A-/HA]
the H-H equations lets us calculate the properties of _____ solutions
buffer
When the concentration of acid is equal to the concentration of conjugate base: pH = ____
pKa
at their ____value buffers tend to resist a change of pH upon addition of moderate amounts of acid or base
pKa
Amino acids without charged side groups exist as _____ in neutral solution
zwitterions
The pH at which a molecule has no net charge is called the —_______ pH, pI
isoelectric
The ends of proteins can be ____- and therefore proteins can act as _____
ionised, buffers
give an example of a protein buffer?
haemoglobin in blood
Proteins can act as buffers because each protein molecule is both a weak _____ and a weak _____. The weakly acidic carboxylic acids counteract ____ pHs while the weakly basic amino groups can counteract ____ pHs.
Proteins can act as buffers because each protein molecule is both a weak acid and a weak base. The weakly acidic carboxylic acids counteract rising pHs while the weakly basic amino groups can counteract falling pHs.
polypeptides can rotate around the angles between, which two things in the chain?
the α carbon and the amino group
the α carbon and the carboxyl group
what is the secondary structure of a protein?
Hydrogen-bonded three-dimensional arrangements of a polypeptide chain
secondary structure considers only the ____ of the polypeptide
backbone
what are the three types of secondary structures?
alpha helix
beta strands and sheets
triple helix
Alpha helix is where the ___ group of one amino acid forms a hydrogen bond with the __group of an amino acid four residues away
-C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away
how do proline residues break alpha helices?
Prolines in alpha helices after the first turn (4th residue) cause a kink in the helix.This kink is caused by proline being unable to complete the H-bonding chain of the helix
beta sheets can run in a _____ or anti_____ direction
parallel
what amino acids occur at turns in the strands? 2
glycine and proline
beta sheets can be in a zig zag shape in which case they are called Beta ____ sheets
pleated
Different ______ structure elements can occur within one protein
Example: _______ ______
Different secondary structure elements can occur within one protein
Example: phosphoglycerate kinase
collagen triple helix is a component of ___ and _____ tissue
bone and connective
collagen triple helix is made of Three ___-handed helical chains twisted around each other form a ____-handed superhelix
Three left-handed helical chains twisted around each other form a right-handed superhelix
tropocollagen is a repeating sequence of X-Y-Gly in all strands
X=
Y=
X = any amino acid Y = proline or hydroxyproline
in collagen triple helix there are inter-chain h bonds involving _____ and______
hydroxylysine and hydroxyproline
______ of collagen occur with age
crosslinking
scurvy results in weakened collagen, how?
- the enzyme which hydroxylates proline requires ascorbic acid (vitamin C)
- dietary deficiency of vitamin C results in reduction in hydroxyproline
results in weakened collagen
the tertiary structure of a polypeptide is held together by interactions between the ____ chain - the ‘R’ groups.
side
what are fibrous proteins?
Contain polypeptide chains organized approximately parallel along a single axis
fibrous proteins are ____ in water and dilute ___ solutions
insoluble, salt
give some examples
- keratin of hair and wool
- collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels
what are globular proteins
Proteins which are folded to a more or less spherical shape
globular proteins tend to be ___ in water and salt solutions
soluble
in globular proteins most of their polar side chains are on the o____ and interact with the aqueous environment by _____ _____ and___-_____ interactions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
give 2 examples of globular proteins
myoglobin and haemoglobin
give 5 examples of the bonds/forces stabilizing tertiary structures
- Covalent disulphide bonds
- Electrostatic interactions = salt bridges
- Hydrophobic interactions
- Hydrogen bonds
- Complex formation with metal ions
______ side groups are normally located on the outside of proteins
Charged (polar) side groups are normally located on the outside of proteins
interact with water
Amino acids with hydrophobic side-chains tend to cluster in the ____ of globular proteins
centre
sickle cell anaemia results from a signle nucleotide sequence meaning that there is a change of ___in the proteins
shape
Sometimes folding process is aided by other specialised proteins. what are these called/
chaperones
Detergents, urea, guanidine hydrochloride can disrupt _______ interactions
hydrophobic
myoglobin contains a _____ haem group
prosthetic
haemoglobin is composed of __ alpha and )___ beta subunits
2
how many haem groups are there in haemoglobin?
4
