Chapter 1 - The Chemical Basis of Life (3)

Question 1

Functions of proteins

Answer 1

enzymes = mediate chemical reactions in organisms
structure = used as building material
hormones = released by glands to cause an effect elsewhere in the body
antibodies = produced by immune system which target pathogens for destruction
transport = pump molecules against a concentration gradient
recognition = identify cells to your immune system

Question 2

Structure of proteins

Answer 2

highly organized, complex molecules
their structure is described using up to 4 different levels of scrutiny
1 has the smallest scope
4 has the largest scope

Question 3

Primary structure

Answer 3

the order of amino acids
met, val, leu, ala, try
all amino acids have the same structure
20 different amino acids for each position in a protein allows for an almost infinite number of possible sequences
the variety leads to a diverse structural and functional importance

Question 4

Alpha helix

Answer 4

a common, stable and strong helical arrangement
stabilized by hydrogen bonds between a carbonyl oxygen and the amide hydrogen four amino acids down the chain
R-groups project outward from helix
the ends are created due to L-proline, which makes the structure very stiff
eg. keratin

Question 5

Beta-pleated sheet

Answer 5

different sections of a polypeptide lie side by side
stabilized by hydrogen bonds
adjacent R-groups alternately project above and below the sheet, and therefore do not get in the way of the structure
eg. silk

Question 6

Tertiary structure

Answer 6

overall, complex structure of a polypeptide
maintained by intermolecular attractions
disulphide bridges between cysteines can link distant regions of a polypeptide
polar and charged R-groups are attracted by water and clump together in hydrophobic pockets, but are unable to associate with lipids in membranes
bulky R-groups distort secondary structures such as alpha-helices
the R-group of proline is bonded twice, the inflexibility disrupting alpha-helices

Question 7

Protrusions and pockets

Answer 7

protrusions = allow protein to interact with complementary pocket of another protein
pockets = provide attachment points for prosthetic groups and coenzymes

Question 8

Quaternary structure

Answer 8

interaction between polypeptide and either other polypeptide(s) or prosthetic group(s)
the forces holding subunits together are the same as those that cause tertiary structure
disulphide linkages
hydrophilic and hydrophobic interactions
hydrogen bonding between subunits

Question 9

Fibrous proteins

Answer 9

typically rod shaped
alpha-keratin
found in hair, fingernails, wool
characterized by long polypeptide chains with an uninterrupted alpha helix
beta-keratin
found in spider webs and silk
secondary structures consists of beta pleated sheets

Question 10

Globular proteins

Answer 10

typically fold into compact spherical or oblong forms
maximizes the number of hydrogen bonds with water
hemoglobin
consists of 4 globular subunits, each with a heme prosthetic group
binds oxygen in blood cells
myoglobin
single globular polypeptide with an associated heme subgroup
binds oxygen in muscle cells

Question 11

Thermodynamics

Answer 11

the study of energy transformations
first law = energy cannot be created or destroyed, only converted from one form to another
second law = during energy conversions, some of the energy is lost as heat, which increases the entropy of the molecules in the universe

Question 12

Second law of thermodynamics

Answer 12

making ice cubes increases the entropy of the universe
even though water molecules are more orderly in cubes, the energy used by the freezer wasted energy
this is why there is no such thing as a perpetual motion machine

Question 13

Exergonic reactions

Answer 13

same as exothermic, but occur at body temperature, can use enzymes
overall net release of energy
reactants have less bond energy, but more potential energy than the products
self-sustaining reactions (energy released acts as activation energy for other reactions)
eg. respiration

Question 14

Endergonic reactions

Answer 14

same as endothermic, but occur at body temperature
require an overall input of energy
reactants have more bond energy but less potential energy than the products
not self-sustaining (requires continuous activation energy)
eg. photosynthesis

Question 15

Metabolism

Answer 15

catabolic reaction = breaks down larger molecules to smaller ones, exergonic
anabolic reaction = builds larger molecules from smaller ones, endergonic
metabolism = total sum of the catabolic and anabolic reactions

Question 16

Role of enzymes

Answer 16

molecules often don’t react unless they are activated (generally with heat)
this is the activation energy
enzymes decrease the activation energy of chemical reactions so they can occur at body temperatures

Question 17

Lock and key model

Answer 17

enzymes have a unique 3D shape which is complementary to the shape of specific substrates
only the correct substrates bind to the active site of the enzyme
the enzyme flexes, stressing bonds and causing new ones to form
products leave the active site
some enzymes can also put things together

Question 18

Induced fit model

Answer 18

enzyme normally exists in an inactive form
as substrates bind to the active site, enzyme is induced to achieve optimal fit
since the active site is not exclusively configured until after induction, enzymes have the ability to bind to several substrates

Question 19

Competitive inhibition

Answer 19

caused by a molecule which is similar to the substrate

binds to the active site, preventing the substrate from binding

Question 20

Non-competitive inhibition

Answer 20

caused by the binding of a molecule to a region other than the active site of an enzyme
changes the shape of the active site, preventing the enzyme from functioning

Question 21

Allosteric regulation

Answer 21

form of non-competitive inhibition
consists of two or more subunits whose shapes can be altered by activators or inhibitors to allosteric sites
activator or substrate binds with the enzyme in active site, locking it in active form
inhibitor binds in allosteric site, locking it in inactive form

Question 22

Feedback inhibition - one enzyme

Answer 22

a product produced by an enzyme can inhibit its activity
when product is in abundance, it binds competitively with the active site
as the product is used up, it diffuses away and the enzyme is free to produce more product, maintaining the concentration
excess of product leads to a slow diffusion, acting as competitive inhibitor

Question 23

Feedback inhibition - metabolic pathway

Answer 23

the end product of the pathway binds at an allosteric site on the first enzyme of the pathway
this shuts down the entire pathway, minimizing the intermediate products

Question 24

Low temperature and enzyme activity

Answer 24

substrates diffuse into the active site very slowly
products diffuse away slowly, interfering entry of new substrates
enzyme is very stiff

Question 25

High temperature and enzyme activity

Answer 25

substrates diffuse into active site faster
products diffuse away faster
enzyme is more flexible

Question 26

Denaturation

Answer 26

at excessively high temperatures, the enzyme’s activity increases a lot
this affects the intermolecular attractions and disulphide bridges and the enzyme can no longer maintain its tertiary structure
the enzyme is denatured and rendered useless

Question 27

Lowering pH and enzyme activity

Answer 27

adds protons to neutral amino or charged carboxyl groups
previously neutral amino groups become positive
previous charged carboxyl groups become neutral

Question 28

Raising pH and enzyme activity

Answer 28

removes protons
charged amino groups become neutral
neutral carboxyl groups become charged

Question 29

pH and enzyme activity

Answer 29

altering the charge of the R-groups affects their intermolecular interactions with water and other parts of the enzyme
this therefore changes the tertiary structure of the enzyme
each enzyme has a different optimal pH

Question 30

Redox reactions

Answer 30

in metabolic processes, molecules or atoms often lose their high potential energy electrons to a different atom or molecule
the transfer of such excited electrons is called a redox reaction, as reductions and oxidations always happen together

Question 31

Electron donors and acceptors

Answer 31

electron donors = 
are oxidized in a redox reaction
are reducing agents
electron acceptors = 
are reduced in a redox reaction
are oxidizing agents

Question 32

Electron carriers

Answer 32

NADH = mitochondria, becomes NAD+
FADH2 = mitochondria, becomes FADH
NADPH = chloroplasts, becomes NADP