biochemistry Flashcards
what is the other name for proteins? and what does this mean?
polypeptides- many amino acids
how many amino acids do we have?
20
how many essential amino acids and what does this mean?
9 essential- need to eat, we cannot make
ow many non-essential amino acids and what does this mean?
11 non-essential- body makes
how are amino acids joined?
by a condensation polymerisation reaction which forms a repeating backbone with alternating R groups.
chirality?
amino acids have a chiral carbon centre which means that the have 4 different environments all around- an amine, R, H, carboxy
what are the exceptions in amino acids?
glycine is not chiral
proline changes from the general structure (but still chiral)n
what is the basic end? acidic end?
- amine
- carboxy
how are amino acids categorised?
by the properties of the R group
non-polar
dispersion forces only
+ charge
has an NH3+, NH2+ or NH+
polar
has an OH, C=O
- charge
lost some H forming O-
what does it mean that amino acids can acid as buffers?
they have amphiprotic capacity- act as an acid or base, this leads to conjugate pairs
what aspects does a zwitterion have?
a positive (protonated) and negative (deprotinated) end
- neutral overall
- protonated end is basic and accepts H+ in acidic solutions
- deprotinated end is acidic and donates H+ in basic solutions
- therefore amphiprotic and acts as a buffer
important note in buffering?
R groups can participate
at pH 7?
always zwitterions because neutral
how are dipeptides formed?
water is expelled, allowing C=ONH (amide link or peptide link) to form
what if dipeptides are being broken down?
add water ands its hydrolysis
number of waters lost?
number of amino acids-1
working out number of possibilities
use factorials
how does hydrolysis work?
water is added, the amide link breaks
primary structure
bead chain of amino acids
- peptide bonds (covalent bonds)
secondary structure
hydrogen bonding occurs causing folding on b-sheet or a-helix
tertiary structure
- 4 different types of bonds (governed by R groups)
- dispersion
- ionic (charges)
- hydrogen
- disulphide (S-S)
order of strength
quaternary structure
- when more than one pp chain join together eg. ribosomes, antibodies, haemoglobin
protein function
structure- keratin transport- Hb toxins defence, immunology- antibodies enzymes- biological catalysts
what are enzymes and what do they do?
speed up reactions by lowering activation energy needed to break reactant bonds. this leads to energy conservation (more energy put into increasing collisions) and therefore ensures another energy pathway to be present
what does it mean that enzymes are specific?
an enzyme only functions on a specific substrate. this is linked to their 3D structure and active site (Complementary bonding)
how does the lock and key model work?
when the substrate (key) internal bonds releax, the activation energy is decreased and therefore bonds break more easily
enzymes can be reused
they are not consumed by a reaction
enzyme-substrate complex
when lock and key fuse
induced fit model
active site is modified to better fit the substrate
what are the set conditions under which enzymes function?
optimal conditions- pH and temperature
changes to these change bond types and disrupt 3D structure
less than optimum temperature
decrease kinetic energy, do not denature (not enough energy)
- hypothermia
greater than optimum temperature
denature, 3D structure destroyed, R groups cannot bind, pp chain undone, coagulation (clump)
- hyperthermia
what are coenzymes formed from?
vitamins we eat
what do many coenzymes work?
with a cofactor
what are cofactors?
metal ions (cations) or small organic molecules (not proteins)
what is 1 coenzyme function?
attach functional groups to the substrate- phosphorylation or methylation
- cofactor, coenzyme and substrate bind and coenzyme passed functional group onto the substrate
what is 2 coenzyme function?
carry electrons
- oxidation and reduction
- NAD+ and H+ and 2e- form NADH
- same with FAD+
- NAD and FAD are both oxidants
how does a coenzyme differ to an enzyme?
a coenzyme needs a cofactor to function
how does a cofactor work?
the coenzyme is inactive but when a cofactor binds, it becomes activated and can then bind to the substrate
what are carbohydrates made of?
CHO
what is the equation of carbohydrates?
Cx(H2O)y where x and y are equal
what are carbohydrates a source of?
energy
what are the three groups of carbohydrates?
- monosaccharides
- disaccharides
- polysaccharides
what are monosaccharides?
- one sugar
- simple sugars
- glucose, galactose, fructose
glucose and galactose are isomers and hexose
fructose is pentose
they are highly soluble due to hydrogen bonding
what are disaccharides?
- 2 sugars added together
- condensation reaction
- bind 1 to 4 (horizontal) and water is expelled
what are polysaccharides? what are the types?
- many sugars
- continued condensation reactions
- starch, cellulose, glycogen
what is starch? what are the types? how does bonding occur? solubility?
polymer of glucose, stored in plants in the leaves and seeds
amylopectin- soluble in water due to its branching structure which exposes OH
- has bonding 1 to 4 horizontal and 1 to 6 vertical
amylose- insoluble in water as OH are not exposed
- only 1 to 4 bonding
what is cellulose? humans? bundle parallel?
polymer of beta glucose (humans have alpha). The humans don’t have enzymes to break it down, fibre
have 1 to 4 bonding and 1 to 6 bonding to form parallel lines
what is glycogen? bonding?
a polymer of glucose. it is in excess in humans in liver and muscle cells
mainly 1 to 4 bonding (glycosidic linkage) but also some branching with 1 to 6 glycosidic links
what are glycosidic links?
C-O-C also called ether links and can be 1 to 4 or 1 to 6
how does hydrolysis of sugars occur?
water is added and an enzyme breaks glycosidic link
what is GI?
- glycemic index
- a way of rating CHO food
- rates on affect on Blood Glucose Level over a period of time, namely 2 hours
- rates food on how quickly it releases the energy it contains
low GI
long time to release energy
what is biological availability?
how readily available the energy is in the food we eat
what are lipids?
fats
- ester
what are triglycerides?
3 glycerol fatty acids (carboxylic acids)
how do glycerols and fatty acids form to made a triglyceride?
glycerol and three fatty acids join by condensation reactions, expelling 3 waters and creating an ester link
how are triglycerides broken down?
add water
polarity of fatty acids? implications?
long hydrocarbon chains that are non-polar. therefore when moving in the blood stream, the lipids need the help of bile
what is bile?
a lipoprotein that is a surfactant- chemical that has a non polar nd and a polar end
looks like a circle (polar) with a zig zag end (non-polar)
how does the fatty acid travel with bile?
in the middle with the polar circles pointing out as they travel through the polar environment
what are the physical states of lipids?
solid- butter, lard, wax
liquid- oil
what are the chemical structures of lipids?
- saturated: no C=C bond, ane
- unsaturated: C=C bond, ene
can be polyunsaturated or monounsaturated
what do saturated and unsaturated fatty acids look like?
saturated are straight
unsaturated have a kink
comparing butter and oil?
butter is saturated and therefore has a higher boiling point because with no C=C there are lots of H to engage in dispersion forces and therefore more intermolecular bonding and more energy to overcome
oil is unsaturated and has a lower BP. this is because of less H atoms to dispersion force because of double bonds. therefore less energy to overcome and therefore less heat needed to overcome
what is the general structure of fatty acids?
alpha end COOH and omega end CH3
how do you determine whether a fatty acid is unsaturated and how many C=C bonds it has?
ignore COOH
subtract CH3
use CxH2x formula
if number of hydrogens is not equal, it is unsaturated
subtract hydrogens present from those of CxH2x
divide that number by 2 which will give the number of C=C bond
what is a cis-fatty acid?
Hs on the same side of the C=C bond and therefore chain has a large kink
trans-fatty acid?
Hs are on opposite sides of the C=C bond and there is a smaller kink due to this, they can stack which causes health issues
omega 3 fatty acids?
first double bond is on the 3rd carbon from the end
omega 6 fatty acid?
the first double bond is on the 6th carbon from the end
