Unit 1: biochem Flashcards
what is an atom?
smallest particle of an element
what is an ion?
A positively or negatively charged atom
what is a molecule?
2 or more non-metals
what is a compound?
2 or more metals and non-metals
electronegativity?
atoms ability to attract electrons to itself
isotope?
a form of an element that differs in its number of neutrons
isomer?
A molecule that has the same composition as another , but a different arrangment of atoms
polymer?
A large molecule that is formed when monomers link together chemically in a chain. EX. starch
structural formula?
H-O-H
molecular formula?
H2O
structural isomers?
same atoms bonded differently
Ex. glucose and fructose
stereoisomers?
atoms bonded in the same way but arranged differently in 3-D space
what makes up 50-90% of nearly all organisms?
WATER!!
what type of covalent bond is water?
polar covalent(uneven sharing)
name the 7 unique properties of water
- Cohesion
- Adhesion
- High specific heat capacity
- High specific heat of vaporization
5.density
6.universal solvent - dissociation
cohesion?
As a result of hydrogen bonding water molecules tend to stick together
adhesion?
water molecules stick to other polar molecules
high specific heat capacity?
- water requires a large amount of energy transfer to produce a change in temperature
- protects cells from rapid temperature change and provides a stable environment for cell reaction
high specific heat of vapourization
- hydrogen bonding causes liquid water to absorb a lot of thermal energ and turn into water vapour
- we dispiate body heat by evaporation of water heat to cool down(sweating)
density
ice is less dense than liquid water(ice floats) due to its expansion upon freezing
universal solvent
many compounds readily dissolve in water
dissociation
water dissociates into ions
About 99% of the mass of most cells are made up of?
H,C,N,O
virtually all chemicals of life are?
C based
properties of carbon
- relatively light weight
- can make 4 bonds
what are functional groups?
groups of atoms with characteristic properties such as:polar and hydrophillic
linkages?
show the manner in which atoms of functiona; groups bond together in a molecule.
most important energy source for the body?
carbohydrates
what is the ratio of carbohydrates
1:2:1
what are carbs composed of?
single sugar molecules or chains
saccharide?
sugar (mono=1, di=2, poly= many)
common monosaccharides
glucose and fructose
common polysaccharides?
starch, glycogen, and cellulose
storage form of carbs in plants?
starch
forms cell walls in plants
cellulose
storage form in animals
glycogen
how are disaccharides and polysaccharides formed?
dehydration synthesis
glucose + glucose
maltose
gluctose + galactose
lactose
glucose + fructose
sucrose
composed of hydrogens carbon and oxygen?
lipids
more difficult to breakdown than carbs
lipids
what has more energy lipids or carbs
lipids (twice as much)
3 groups of lipids?
- fats, oils and waxes
- phospolipids
- steroids
functions of lipids
- aid in vitamin absorption
- insulate the body
- protect internal organs
- main components of cell membrane
most common form of lipids
triglycerides and are composed of a glycerol molecule and and 3 fatty acids
saturated fats?
have single bonds between carbon atom
EX. lard and butter
unsaturated fats?
have double bonds between at least 2 carbon atoms
Ex oil
A unique lipid?
cholesterol which is used to makes hormones in your body
Used to build cell structures and during chemical activities
protein
what are proteins composed of
hydrogen, carbon, oxygen, nitrogen and sometimes sulfur
what are protein subunits called?
amino acids
many amino acids joined together?
polypeptide
bonds holding amino acids together
peptide bond
how many amino acids are essential and why?
8, our bodies cannt synthesize them and we must get them from our diet
fatty acid?
A molecule that consists of a single hydrcarbon chain with a carboxyl group at one end
fat
a lipid that is made from 2 types of molecules: fatty acid and a glycerol molecule
69.5% ofour cells are made up of what
water
29.5% of our cells are made up what?
organic molecules
monosaccharides?
simple sugars, contain either a carbonyl aldehyde or carbonyl ketone and a hydorxyl functional group.
EX. glucose
disaccharides
2 simple sugars bonded together to form a glycosidic(ether linkage)
Ex. sucrose
polysaccharides?
monosaccharide polymer composed of monosaccharide subunits held together by glycosidic linkage.
EX. chitin, amylase, starch, cellulose
alpha glucose?
the OH lies below the plane of the ring
beta glucose
the OH lies above the plane of the ring
% chance of being an alpha or beta glucose
50%
glycerol?
3 carbon chains attached to a hydroxyl group
fatty acids?
hydrocarbon chains containing a carboxl group at one end
lipids are produced via what
dehydration synthesis between the hydroxyl group on the glycerol with the carboxyl group on the fatty acid.. producing an ester linkage
cholesterol
compact hydrophobic molecule containing 4 fused hydrocarbon rings and one hydroxyl functional group
most common organic molecule and most diverse
proteins
how many different amino acids
20
An amino acid has
- an amino acid
- carboxyl group
- hydrogen
- side chain(R group)
All 20 amino acids differ in what?
R group
peptide bond
formed by the joining of the amino end of one molecule to the carboxyl end of another via dehydration synthesis
4 protein structures?
primary, secondary, tertiary, quaternary
primary protein structure
the sequence of amino acids and a change can alter the proper functioning
secondary?
coiling and folding caused by hydrogen bonding between the R groups
tertiary?
A folded individual peptide, due to more bonding or repulsion between the R groups and the polypeptide and its environment
what are tertiary protein structures stabilized by
- hydrogen bonds
- ionic bonds
- disulfide bridges
Quaternary protein structure
formed by the interaction of 2 or more polypeptides
Ex. hemoglobin
DNA and RNA are what?
nucleotide polymers
DNA
deoxyribonucleic acid
RNA
ribonucleic acid
pyrimidines
are the nitrogenous bases with a single ring
purines
nitrogenous bases with double rings
what does RNA have that DNA doesnt
uracil
phosphodiester bonds
hold the phosphate group of one nucleotide and the hydroxyl group attached to the number 3 carbon of the sugar on the adjacent nucleotide
2 strands of DNA are held together by what
hydrogen bonds between the nitrogenous base on adjacent strands. ( can only run if one strand is upside down)
energy?
ability to do work
kinetic energy?
energy possessed by moving objects
potential energy?
stored energy as a result of an objects position
work?
the transfer of energy from one body to another
first law of thermodynamics
energy cannot be created or destroyed but only converted from one form into another
second law of thermodynamics
entropy(randomness/ disorder in energy or in a collection of objects),of the universe increases with any change that occurs
exogonic(exothermic) reaction
chemical reaction in which chemical potential energy is LESS THAN the energy of the reactants.
Ex. energy has been released
endergonic(endothermic) reaction
chemical reaction in which chemical potential energy is MORE THAN the energy of the reactants.
Ex. Energy has been absorbed
Anabolic reaction
- reactions that produce large molecules from smaller subunits
- Energy is absorbed
- Ex. anabolic steroids - building muscles
Catabolic reaction
- Reactions that break macromolecules into subunits
- Energy is released
- Ex. Digestion
spontaneous change
- occurs on its own once started
- does not require a continuous supply of energy
- Ex. once a match is lit it’ll continue to burn
non-spontaneous change
- cannot occur without the continual input of energy
- Ex. a boiling pot of water will not continue to burn if you take away its heat source
primary source of free energy in living cells
ATP
what does ATP stand for
Adenosine TriPhosphate
what is ATP composed of
the purine nitrogenous base: adenine, a ribose sugar and a chain of 3 phosphate groups
what is ATP a collection of
negative charges on the phosphate chain which make the terminal phosphate highly unstable
what type of bond is energy stored in
covalent bonds between the phosphates with the greatest amount of energy between the terminal and second phosphate
what does the free energy required from the many endothermic reactions that occur within a cell come from?
Hydrolysis(addition of water), with the aid of the enzyme ATPase, of the terminal phosphate from the ATP molecule
ATP + H20 yields?
ADP + Pi + energy
phosphorylation
transfer of the phosphate group
How much ATP does the body use each day?
an amount of ATP equal to its own mass every day.
What do catabolic processes do for ATP?
break down molecules to release energy needed to make ATP.
How do anabolic processes use ATP?
use ATP to build larger molecules from smaller ones.
How does the body turn ADP back into ATP?
The body adds a phosphate to ADP using energy from breaking down food.
name the 5 major biological reactions
- neutralization
- Redox
- hydrolysis
- condensation
- phosphorylation
neutralization reaction?
the reaction of an acid and a base to produce water and a salt
Ex. NaOH + HCl -> H2O + NaCl
what’s a buffer
made up of a weak acid and its salt or a weak base and its salt.
- resists pH changes by shifting equilibrium
human blood pH
7.4
redox (oxidation-reduction)
reactions involving a transfer of one or more electron from one one to another
oxidation
loss of electrons
reduction
gain of electrons
what is always lost or gained during oxidation and reduction?
energy
Hydrolysis reactions
- addition of water molecule ito 2
- catabolic process(breaking down)
- releases energy
condensation reactions(dehydration synthesis)
- removal of water molecules to bind 2 molecules together
- anabolic process(build)
- absorbs energy
when was the fluid mosiac model developed?
1972
what is the cell membrane made of
phospholipid bilayer
what is the cell membrane polar end attracted to
water
what happens to the nonpolar ends of the cell membrane
they are repelled
what is embedded in the cell membrane
protein
what do proteins serve in the cell membrane
can serve in communication, transport, or strcutral support
proteins and phospholipids can what?
float and move past each other
wheres the cytoskeleton
below the surface of the cell membrane and anchors part of the membrane
what does the membrane also contain
cholesterol
what does cholesterol in the cell membrane allow it do
allows it to function at a range of temperatures
as temperature increases in the membrane…
cholesterol maintains rigidity
as temperature decreases in the membrane…
cholesterol keeps the cell fluid
what type of permeable type is the membrane
selective permeable
what does selective permeable mean
allows only specific molecules to pass across
name 3 permeable characteristics
- small non-polar molecules
- small polar molecules(water)
- large nonpolar (hydrocarbon)
name 3 nonpermeable characteristics
- large polar molecules(sucrose, nucleic acids)
- ions(sodium, potassium)
- large charged molecules(proteins)
what is a special case in the permeable vs nonpermeable
WATER
Brownian motion
the randomness movement of particles
particle theory
- all matter is made up of particles
- there are spaces between these particles
- the particles are always moving(vibrating)
what’s passive transport
the movement of molecules across a semipermeable membrane that does not require the cell to expand any energy
state the types of passive transport:
diffusion, osmosis, facilitated diffusion
diffusion?
the movement of particles down a concentration gradient from an area of high concentration to an area of low concetration
what causes diffusion
molecular collisions
what will have more collisions? areas of high or areas of low concentration
areas of high
diffusion rates are effected by what?
temperature and pressure
what’s free to diffuse across a cell membrane
oxygen and carbon dioxide
what’s osmosis?
the diffusion of water molecules across a selectively permeable membrane from an area of high concetration to an area of low concetration
solute
substance which dissolve in water
(ex. salt)
solvent
substances which the solute is dissolve in
facilitated diffusion
method of diffusion used by molecules that are simply too large to pass through the membrane by diffusion
imbedded specialized transport proteins do what in facilliated diffusion
move the molecule across
transport proteins only do what?
only recognize and move one type of dissolved molecule( very selective due to their structure)
carrier proteins
only accept non charged particles
channel proteins
will accept charged particles
a positively charged channel with only allow what?
negatively charged ions to pass and vice versa
active transport
movement across the cell membrane that REQUIRES the cell to expend energy and moves particles against the concentration gradient
how does active transport differ from passive transport
does not move with the concentration gradient
what does the amount of energy the cell expends on depends on?
concentration gradient
whats an example of active transport
- kidney cells need to pump glucose and amino acids into the blood
- intestinal cells need to pump nutrients out of the intestine and into the blood
sodium-potassium pump
protein pumps found in the membrane can move substances against the concentration gradient
what do sodium potassium pumps utilize
energy from metabolism specifically in the form of ATP
where is the sodium potassium pump found in
animal cells(every cell in your body)
how does the sodium-potassium pump work
- 3 Na+ ions within the cell bond to the transporter protein at the same time as 2K+ ions bind to the outside of the cell
- this causes the protein to change shape
- its new shape forces the Na+ ions out and the K+ into the cell
- once released, the proteins changes back to its original shape
- a high concentration of Na+ builds up outside the cell
- Na+ diffuses back inside if it has bonded with a glucose molecule
- Na+ returns to the cell down the concentration gradient and this provides the mean for glucose to enter the cell
name the two subgroups of bulk active transport
endocytosis and exocytosis
endocytosis
active process by which cells ingest material
what’s a vesicle
membrane enclosed sac
name the two types of endocytosis
1.Phagocytosis
2. Pinocytosis
phagocytosis
movement of a large molecule into the cell
pinocytosis
transport of fluid droplets into the cell
exocytosis
active process by which cells export materials
what does exocytosis restore
the membrane removed by endocytosis
isotonic
water concentration inside the cell is equal to the concentration outside the cell
net movement of isotonic environments
0
hypotonic
water concentration outside the cell is greater than the water concentration inside the cell
net movement of hypotonic environments
outside to inside
hypertonic
water concentration inside the cell is greater than the water concentration outside the cell
net movement of hypertonic
inside to outside
plants in what environment have increased turgor pressure
hypotonic and its a sign of a healthy plant
what’s also known as plasmolysis
plants in a hypertonic environment and they will wilt and the cell membrane shrinks away from the cell wall
an enzyme is a what?
A protein
enzymes acts as what
A catalyst
catalyst
speeds up reactions without being consumed in the process
substrate
the reactant upon which an enzyme acts on
active sites
depressions on enzymes
induced fit
when substrate binds to the active site, the enzyme can make subtle changes in shape to accomodate the substrate
an enzyme can speed up a reaction by:
- causing stress on the bonds of the substrate by bending/stretching existing bonds
- transferring H+ and OH- ions to or from the substrate to aid hydrolysis and condensation reactions
- can accept electron forming a temporary bond, making the substrate less stable
- bring 2 substrates together in the correct orientation for reaction
factors affecting enzyme function
A) temperature
B) pH
c) concentration
as temperature increases
the activity of the enzyme also increases up to a certain critical temp beyond beyond which enzyme function is impaired
- too hot -> denatured
most human enzymes work best between
35-40 degrees celcius(close to human body temp)
most enzymes pH
usually between 6-8
whats an exception for enzyme pH
pepsin( the enzyme that digests protein in the stomach) works optimally at a pH of 2
increasing substrate concentration
increases the rate of reaction . becuase more substrate molecules will be colliding with enzyme molecules, so more product will be formed
increasing enzyme concentration
will increase the rate of reaction, as more enzmes will be colliding with substrate molecules
rate of reaction __ as substrate is used up
decreases
3 types of regulations of enzyme activity
A) inhibitors
B) activators
C) cofactors/ coenzymes
inhibitors
- shut down the action of the enzyme
2 types of inhibitors
i) non-competitive inhibitors
ii) competitive inhibitors
non-competiitve inhibitors
binds to locations other than the active site, called ALLOSTERIC SITES, thus preventing the substrate from binding to the active site by causing a conformation change that alters the active site so that its no longer an ideal receptacle for the substrate.
competitive inhibitors
bind directly to part of or entire active site by mimicking the shape of the substrate thus preventing the enzyme from accepting the substrate.
activators
bind to allosteric sites enhancing the activity of the activity of the enzyme by conforming the shape of the enzyme so that the receptacle is a better fit for the substrate
cofactors/ coenzymes
located in the active site of the enzymes, they attract electrons from the substrate molecule bonds causing them to break
cofactors
inorganic ions such as copper, zinc and iron
Coenzymes
Organic, nonproteins molecules
