2 molecular biology Flashcards
function of nuclear membrane/envelope
controls crossing of macromolecules and permit passing of smaller molecules. shields cell
function of nucleolus
helps in protein synthesis and production of lysomes
function of chromatin
genetic material that results in formation of chromsome
function of centrioles
creates and anchors microtubules
function of microtubules
pull apart in cell division to form chromosomes
function of mitochondria
site of aerobic respiration (ATP production)
function of plasma membrane
semi permeable and selective barrier surrounding cell
function of ribosomes
site of polypeptide synthesis and translation
function of golgi body
involved in sorting, storing, modification and export of secretory products
function of cytoplasm
provides support to organelles and site of chemical reaction
function of free ribosome
synthesise proteins
function of rough endoplasmic reticulum
protein synthesis and storage
function of smooth endoplasmic reticulum
synthesis and transport of lipids and carbohydrates
function of golgi body
helps modify proteins and package them into vesicles
function of lysosome
breakdown/hydrolysis of macromolecules
function of cytoskeleton
provides internal structure and mediates intracellular transport
function of nucleus
stores genetic material as chromosomes
what atoms is water made up of in what bonding
2 hydrogen and 1 oxygen, joined by covalent bonds
what makes water molecules polar
the oxygen nucleus is stronger and can attract more electrons. this means the oxygen atom will have a slight negative charge whilst the hydrogen atoms are slightly positive. this is called a polar covalent bond. as the two hydrogen atoms are on one side, and the oxygen is at the other, they have polarity.
what happens when cations and anions bond
they form an ionic bond
what happens when water molecules (which have partial charges) attract each other
due to the partial charges, the attraction is less, but still enough to have significant effects. the attraction between the molecules is called a hydrogen bond. (it is actually more of an intermolecular force than a bond.)
what does molecules being adhesive mean
they can stick to surfaces
what does molecules being cohesive mean
they can stick to eachother
is water adhesive, cohesive or both or none
both
why is water a stable environment to live in
because the water molecules can attract each other, it takes a lot of energy to heat and boil. this means it has a high specific heat capacity. it is also less dense than many other molecules when frozen, and will rise to the top instead of displacing the water below it.
what is a carbohydrate made up of
1 carbon atom, 1 oxygen atom and 2 hydrogen atoms
what is a carbohydrate of one unit
(this is a monomer) a monosaccharide
what is a carbohydrate of two units
(this is a dimer) a di-saccharide
what is a carbohydrate of many units
(this is a polymer) a polysaccharide
what are proteins made up of
carbon, hydrogen, oxygen, nitrogen and sometimes sulphur.
what are the building blocks (monomers) that make up proteins
amino acids or ‘mono-peptides’.
what is the basic structure of a protein
an amino group, a central carbon, a carboxylic acid and a variable R group (of which there are 20 types)
what is two amino acids joined together called
(a dimer) a di-peptide
what is many amino acids joined together called
(a polymer) a polypeptide
what do we call it when a long chain of amino acids fold up into a 3D structure
a protein
what are lipids
fats, oils or waxes
how are lipids different from other molecules
they are not polymers built out of monomers
what are lipids made up of
two distinct molecules:
glycerol
fatty acids
what is a glycerol molecule
a simple molecule with 3 carbons and 3 alcohol groups
what is a fatty acid
a chain of carbons and hydrogens with a carboxylic acid group. the length of the chain can vary from 4 - 28 carbons
what is a triglyceride
3 fatty acids and 1 glycerol
what was vitalism
the thought that living organisms could only be made of organic chemicals that could only be produced in living organisms
who disproved vitalism
german chemist fredrich wohler
how did wohler disprove vitalism
he synthesized urea artifically using silver isocynate and ammonium chloride. this was the first time that an organic compound had been synthesized artifically.
how many bonds does hydrogen make
one
how many bonds does oxygen make
two
how many bonds does nitrogen make
three
how many bonds does carbon make
four
what is the metabolism
all the enzyme catalysed reactions in a cell or organism. most pathways consist of chain reaction sor cycles of reactions
what is anabolism
the synthesis of complex molecules from simpler molecules.
what type of reaction is anabolic reactions
condensation because water is produced
what is catabolism
breaking down of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers. in hydrolysis reactions, water molecules are split.
chain of metabolism
inital substrate
—>
intermediate substance x 4
–>
end product
when are molecules polar
when the nucleus of one of the atoms is more attractive to the electrons than the other and so the electrons are not shared equally. this means part of the molecule has a positive charge and part has a negative charge.
are water molecules polar
yes
melting point of methane
-182
melting point of water
0
specific heat capacity of water
4.2 J per g per degree celsius
specific heat capacity of methane
2.2 J per g per degree celsius
latent heat of vapourization of methane
760 J celsius
latent heat of vapourization of water
2257 J celsius
boiling point of methane
-160
boiling point of water
100
why is waters mp and bp higher than methane
heat energy needed to break hydrogen bonds and allow water to change states.
why is the specific heat capacity of water higher than methan
hydrogen bonds restrict movement so more energy is stored by moving molecules of water than methane
why is the latent heat of vapourization of water higher than methane
much heat energy is needed to break hydrogen bonds and allow a water molecule to evaporate.
why do hydrophilic substances dissolve in water
because their ions/molecules are more attracted to water than to each other.
ions with positive or negative charges dissolve as
they are attracted to the negative or positive poles of water molecules
how does NaCl travel in the body
dissolved in plasma as it is soluble.
how do glucose and amino acids travel in the body
polar so can be transported dissolved in the plasma
how does oxygen travel in the body
non polar and dissolved amount in plasma is insufficent so red blood cells are needed with haemoglobin to which oxygen binds.
how do cholesterol and fats travel in the body
non polar and insoluble in water so transported in small droplets called lipoproteins. cholesterol and fats are inside, coated by phospholipids and proteins.
monosaccharides consist of
a single sub unit
monosaccharides contain
carbon hydrogen and oxygen in the ration 1:2:1
ribose
PHOTO
fatty acid
PHOTO
amino acid
PHOTO
alpha-d-glucose
PHOTO
beta glucose
PHOTO
starch
PHOTO
cellulose
orintation of glucose units alternates which makes the polymer straight and not curved, allowing cellulose molecules to be arranged in parallel with hydrogen bonds forming cross links. these have enormous tensile strength and are the basis of plant cell walls.
starch
helical shape as glucose subunits are in the same orientation. used in plants to stroe glucose in an insoluble form that does not cause osmotic problems. by making the glucose branched its easier to load or unload glucose more rapidlttwo types: amylose and amylopectin
amylose
only 1,4 linkages so is unbranched
amylopectin
1,6 linkages so is branched
linkage between glucose subunits
glycosidic bond
what is glycogen a branched polymer of
alpha d glucose
what is glycogen used for
by mammals to store glucse in liver and muscle cells. because glycogen is insoluble, large amounts can be stored but if it were glucose, it would cause water to enter the cells via osmosis and they would burst.
why cant hydrogen bonds form in cellulose
because the chains of alpha d glucose in starch and glycogen are helical, they cannot become aligned in a parallel array so hydrogen bonds do not form.
what abilities do hydrogen bonds mean water has
cohesiveness
adhesiveness
thermal properties
solvent properties
water moleule is
a polar molecuel made of 1 oxygen and 2 hydrogen atoms
polarity is
having positively and negatively charged areas because of uneven distribution of electrons.
negative pole is
area with more electrons, around the oxygen atom.
postitive pole is
area with fewer electrons, near the hydrogen atom nuclei.
hydrogen bond is
a weak bond formed between polar water molecules
why is cohesion high in water
because H bonds make water moleucules stick to eachother more strongly. it causes surface tension.
why is density lower in ice
because extra hydrogen bonds cause cold water molecules to move apart slightly
why does water havea high specific heat capacity
because some heat is used to break h bonds so more is needed to raise the temperature
why is water an excellent solvent
because polar molecuels dissolve so many substnaces
why is water being transparent useful
if the organism does photosynthesis e.g water plants
benefits of water being made of a polar molecule
it can form dipole dipole bonds
benefits of water polarity
things with a charge can dissolve in it like glucose and minerals
benefits of water having hydrogen bonds and high cohesion
water can stay together and it is a adv for plants as water can travel up the plant and draw up more water
why is it useful that ice has a lower density
doesnt crush marine enviornemtn
allows organisms to live on top
why is water having a high specific heat capacity useful
keeps environment stable
why is water a good coolant in sweat
each molecule has lots of heat energy
when it evaporates it takes the heat energy with it
which statae is methane in the earths atmosphere
gas
how might hydrogen bonds change the cohesion of water molecules compared to hydrogen molecules
greater cohesion between molecules, useful in blood, and in xylem tubes where water flows
if humans made sweat with methane how would it change the effectiveeness of sweating to cool the skin
methane would not take as much heat away as water when it evaporated because it has a low specific heat capacity
suggest why cytoplasm or blood made with water would be better for living things than cytoplasm or blood made from methane
A cytoplasm of water can dissolve lots of proteins, and salts which are essential for life. The reactions of metabolism happen in solution, and can’t happen unless they dissolve. Blood transports lots of substances including oxygen and nutrients, hormones and antibodies. Many of these molecules would not dissolve in methane.
what feature of carbon makes it most suitable as a basis for life
its bonding properties
what property of water accounts for its moderating effects on the earths atmosphere
thermal
what are the most frequently occuring elements in living organisms
nitrogen carbon oxygen and hydrogen
explain waters solvent properties
water molecule is polar
water forms hydrogen bonds with polar substances
positive pole attracted to negativ eions
(negative pole attracted to positive ions)
glucose dissolves because its polar
sodium chloride dissolves becuase ions are attracted to it
three uses of fat in the body are
energy store
insulation
keeps cholesterol under control
helps your body absorb soluble vitamins
name three types of dietary fat
trans/cis mono/poly un/sat urated fat
what is the difference between poly unsaturated nad mono unsaturated fat
poly: more than one double bond
mono: only one double bond
what is the cis formation of fatty acid
the carbons are on the same side of the C=C
what is the trans formation of fatty acid
the carbons are opposite eachother on the C=C
give reasons why the food industry makes trans fats
stores long time (easy and cheap)
deep frying
tastes good/pallitability
bulks up food and is useful
list some influences which trans fats has on the body and health
increases risk of heart disease
shortens lifespan
what are triglycerides
three fatty acids and one glycerol by condensation reactions so they have three hydrocarbon tails
fats and oils are trigylcerides
what are phospolipids
simialr to triglycerides but only have two fatty acids linked to glycerol, with a phosphate group instead of the third fatty acid. phospholipids are only partly hydrophobic and form the basis of membranes
what are steroids
all have a similar structure of four fused rings in the molecule. cholesterol, progesterone and estrogen are all steroids.
what are the parts to a fatty acid
an acidic carboxyl group
unbranched hydrocarbon chain
saturated hydrocarbon
all single bonds
unsaturated hydrocarbon
one or more double bonds
adv of using lipids instead of carbohydrates for long term storage
amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates.
fats form pure droplets in cells with no water, whereas each gram of glycogen is associated with two grams of water, so lipids are 6 times more efficient.
how to calculate bmi
(height in meters)sqaured
bmi of under 18.5
underweight
bmi of 18.5 to 24.9
normal weight
bmi of 25 to 29.9
overweight
bmi of 30 or more
obese
health issues of trans fats
coronary heart disease
health issues of saturated fats
coronary heart disease but could be correlated with low amounts of dietary fibre instead
alternatives to bmi
waist to hip ratio for men
Alpha d glucose
Used in the production of ATP in cells
Beta D glucose
Used to build cell walls in plants
Starch
Used as long term storage in plants
Ribose
Used as a component of DNA and RNA
Triglycerides
Used as long term storage in adipose tissue in animals
Steroids
Used as chemical messengers in the body, have a distinctive ring shape
Phospholipids
Major component of plasma membranes
Structural proteins
Proteins such as keratin and collagen form the structural framework of many parts of the body
Polypeptides
A sequence of amino acids that may make up a portion or a series of polypeptides can also make up a protein
DNA
Used to store genetic information
RNA
Used to create proteins at ribosomes using the information stored in DNA
Metabolism
All the enzymatic reactions that take place inside a living organism
Anabolism
Synthesis of complex molecules from simpler molecules, a process that requires the input of energy. Includes the formation of macromolecules from monomers by condensation reactions. E.g. protein and starch are made from amino acids, and glucose units.
Catabolism
The breakdown of complex molecules into simpler molecules and includes the hydrolysis of macromolecules into monomers. The breakdown of sugars (including glycolysis) or fats to release energy are all examples of catabolic reactions - where energy is released.
What is a hydrolysis reaction
Breaking of chemical bonds by addition of water molecules
What is a condensation reaction
Refers to the reaction in which two smaller organic molecules combine to form a larger molecule with the accompanied formation of water or some other simple molecule.
Metabolism =
Anabolism + catabolism
Urea formula
CO(NH2)2
what is the basic unit of a polypeptide
amino acid
what is an amino acid made up of
a carboxyl group (-COOH)
an amino group (-NH2)
are polypeptides the same thing as proteins
yes
compare proteins and peptides
peptides are smaller.
peptides are molecuels that consist of 2-50 amino acids.
proteins are polymers made up of 51 or more amino acids
how many amino acids are there
20
where does synthesis of polypeptides take place
ribosomes during translation
what are the peptide bonds between each amino acid a result of
a condensation reaction
how does a protein conformation happen
a change in the order of amino acids
how does sickle cell anemia happen
the glutamic acid is substituted by valine, structurally changing haemoglobin
what is the primary structure of proteins
the sequence of amino acids
what is the secondary structure of proteins
the folding of the chains on themselves to form pleated sheets or alpha helixes
what is the tertiary structure of proteins
when the polypeptide coils and folds to form a 3d shape
what is the quaternary structure of proteins
when proteins are made up of 2 or more polypeptide chains, and refers to the way the multiple subunits are held together in a multi-sub unit complex.
give an example of a protein with a quaternary structure
two alpha and two beta chains
what is the proteome
each organism’s unique set of proteins
what can proteome analysis be used for
medical research and cancer treatment, determining if a particualr chemotherapy will be successful
globular proteins
globe like proteins that play active roles in the cells metabolism. e.g haemoglobin
what do globular proteins consist of
complex polypeptide chains that can be linked to other chains to form large complex proteins.
why are globular proteins usually soluble
hydrophobic r groups are folded into the core of the molecule
fibrous proteins
long, threadlike,
why are fibrous proteins usually insolouble
usually made of long polypeptide chains where the hydrophobic r groups are exposed, making the molecule insoluble.
where are fibrous protiens often found
in structural parts of organisms, such as tendons and skin (collagen and keratin)
rubisco
globular
An enzyme involved in the fixation of CO 2 in chloroplasts.
insulin
globular
A hormone produced by the beta cells of the pancreas, which is involved in glucose uptake from the blood.
immunoglobin
globular
These are large Y-shaped proteins, also called antibodies, involved in fighting infections by specifically recognising and binding to antigen molecules.
rhodopsin
globular
A protein linked to pigment, found on the membrane of rod (photoreceptor) cells of the retina, where it allows very low light intensities to be detected.
collagen
fibrous
A structural protein, found in muscles, tendons and ligaments, where it gives tensile strength. It also occurs in skin and bones, where it prevents tearing and fractures, respectively.
spider silk
fibrous
A fibrous protein produced by spiders for their webs. It can be extended and is very resistant to breaking.
what is denaturation
how proteins lose their secondary, tertiary and sometimes quaternary structures. the hydrogen bonds between R groups are disrupted and active sites change shape, making the whole enzyme lose their enzymatic properties.
how do you denature proteins
expose it to higher temps
change the pH
what doesnt break during denaturaiton, allowing the primary structure to remain
the peptide bonds holding adjacent amino acids together.
what breaks the bonds between non adjacent amino acids or between the polypeptide chains of quaternary proteinjs
strong alkaline or acidic solutions
what do amino acids consist of
hydrogen
amine group
carboxyl group
r group or radical
proteome
all the proteins produced by the cell
what is a polypeptide
an unbranched chain of amino acids
chains of fewer than 40 amino acids are usually called
peptides
how are protein structures stabilised
intramolecular bonds (these cause denaturation if broken during high temps or
what do catalysts do
speed up chemical reactions without being changed themselves
what type of proteins are enzymes
globular
a reactant in an enxyme catalysed reaction is called a …
substrate
where do enzymes catalyse reactions
on the active site
when does catalysis occur
only when the substrates are in liquid so their mlecules are in continual random motion and there is a chance of collisions between the substrates and the actives ite on the surface of the enzyme
what is an enzyme product complex
when the substrate is binded to the enzyme. they are chemically attracted to eachother and fit together.
what reduces the energy needed to turn substrates into products
the binding of substrates to the active site
benefits of enzyme immobilization
catalysis can be controlled by adding or removing enzymes
enzyme conc can be higher
enzymes can be reused
enzymes are resistant to denaturation over high pH and temperature
enzymes do not contaminate products
what is enzyme immobilization
attatchment of enzymes to another material or into aggregations to restrict their movement
methods of enzyme immoblization
(adsorption) attachment to surfaces like glass
(alginate) entrapment in a membrane or a gel
(aggregation) by bonding enzymes together into particles of up to 0.1 mm in diameter
attraction stage
substrate moving towards enzyme
reaction stage
substrate-enzyme complex
release stage
products released and enzyme reverts to original shpe
compeitive inhibitor
competes for active site of enxyme
transition state
when the substrate is about to become a product
non-competitve inhibitor
attaches to the enzyme but not to the active site, which then changes due to the inhibitor squishing the enzyme round the sides as it joins. now the enzyme requires LOADS of potential substrate to hopefuly get a reaction
why do substrates bind and not bond
it is not permenant
what does collision theory require
particles must collide
sufficent energy
correct orientation
what do enzymes and substrates require for a successful collision and reaction
speed to have enough activation energy
orientation (so the substrate fits into the enzyme active site)
what do enzymes do
speed up reaction
dont get used up
dont alter end product
what is the induced fit model
the idea the enzyme isnt perfectly suited to the substrate but to the transition state. therefore the reaction will actually happen and the complexes wont just stay (the lock and key method)
factors affectign enzyme activity
temperature
pH
substrate conc
effect of temperature on enzymes
enzyme activity increases as temperature increases because collisions between substrate and active site happen more frequently at higher temperatures due to faster molecular motion.
at high temps enzymes are denatured and stop working. this is because heat causes vibrations inside enzymes which break bonds needed to maintain the structure of the enzyme
effect of pH on enzymes
enzyme activity is reduced as pH decreases from the optimum because the conformation of the enzyme is altered more and more. a certain pH the acidity (H+ ions interrupting bonds) denaturing the enzyme. above the optimum the alkalinity (OH- ions interrupting bonds) denatures the enzyme.
effect of substrate concentration
at low substrate concentrations, enzyme activity increases steeply as substrate conc increases as random collisions between substrate and active sites happen more easily. at higher substrate conc, most of the active sites are occupied, so raising the substrate conc has little effect on enzyme activity
how to design an enzyme activity - the independent variable
should be wide enough to show all trends, like pH 1-14
how to design an enzyme activity - the dependent variable
measurement you take to assess the rate of enzyme activity. could be time taken for a substrate to be used up or quantity of of a product. measurement should be quantitative and accurate. should be repeated for replicate results that can be compared to evaluate whether they are reliable.
how to design an enzyme activity - the control variable
are other factors that could affect enzyme actiivty. must be kept constant for valid results. eg temperature, time, etc
what is a limiting factor
somethign which affects the rate of reaction
what is transcription
copying the DNA by synthesising mrna from the dna base sequences
what is translation
interpreting the genetic code to synthesise proteins (more specifically polypeptide chains) on ribosomes
when does replication of a new dna molecule occur in the cell cycle
s phase
dna is normally supercoiled by being tightly wound around histones to form nucleosomes. the first step is to unwind the coils to make them accessible to enzymes. then
the enzyme helicase unwinds the double helix and seperates the two DNA strands by breaking the hydrogen bonds between the bases.
after helicase seperates the DNA strands, what happens
another enzyme (dna polymerase) can start making new strands of DNA using the two old parent strands as templates
what direction does DNA replication occur in
5’ to 3’
how/why is dna replication semi-conservative
because each daughter molecule formed contains one original strand from the old molecule and one newly synthesised strand
what did meselson and stahl do
culture e.coli bacteria in a medium where the only nitrogen source was 15N, thereby meaning the nitrogen in the bases was 15N.
they then transferred the bacteria abruptly to a medium with the less density 14N isotope.
a solution of caesium chloride was spun in a centrifuge at 45,000 revolutions per min or 24 hours. caesium ions are heavy, and sank, causing a gradient with caesium ions at the bottom.
substances centrifuged with caesium chloride solution becomes concentrated at its level of density.
they spun bacteria cultures at different times after the transfer to the 14N medium.
after one generation, the DNA was intermediate. after 2, there were two equal bands, one still 14N and 15N, and one at 14N density. eventually the 14N became stronger.
adenine pairs with
thymine (if not uracil)
guanine pairs with
cytosine
when does thymine become uracil
in rna
what is rna polymerase responsibile for
seperating the dna strands of the double helix as well as for joining the ribonucleotides together by phosphodiester/covalent bonds to form an mRNA strnad
the DNA strand that is not transcribed is called the..
sense strand. inactive. has same bases as mrna (complementary to the antisense strand) but with thymine not uracil
the DNA strand that is transcribed is called the…
antisense strand. active.
complementary to mrna strand and sense strand
how mant bases code for an amino acid
3
outlinethe process which results in the formation of a strand of mRNA. include details of how the genetic code is preserved.
mRNA is made through transcription.
the enzyme RNA polymerase adds the RNA nucleotides, whilst unzipping and zipping the DNA strands.
Adenine joins to Uracil and Cytosine joins to Guanine in the mRNA single stranded molecule.
the genetic code is preserved because the complementary bases pair up in a certain way. (more detail?)
what is translation
the synthesis of polypeptides on ribosomes according to the genetic code
mrna to polypeptide
what does a degenerate genetic code mean
some amino acids can be encoded by more than one codon. it is also universal, so the gentic information in bacteria is translated in the same way as that of any other organism.
AUG codon
met or start
what are the stop codons
UAA
UAG
UGA
where is the anticodon
on the trna
where is the codon
on the mrna strand
where is the peptide bond
between proteins, above the trna and mrna
where does intramolecular base pairing occur
between the strand of trna when folded into a molecule (kinda, see diagram)
where are amino acids joined together to make polyppetides
ribosomes
give three overall stages of protein synthesis
an amino acid binds to trna.
trna moves from a binding site on the ribosome.
the ribosome reaches a stop codon
describe the genetic code and its relationship to polypeptides
the genetic code undergoes transcription to form a single stranded mrna from the double stranded dna using complementary base pairing
adenine joins to uracil (as thymine is replaced in rna) and cytosine joins to guanine
translation involves trna moving along the mrna strand attaching amino acids to codons of 3 bases, in the ribosome.
each codon is one amino acid
when the trna comes to a stop codon, it terminates, leaving a polypeptide, which are joined in the golgi to become a protein.
each gene codes for a polypeptide.
explain what pcr is fundamentaly
the desired section of dna is placed in a reaction chamber that contains many free nucleoside triphosphates, primers that will allow replication to occur from the desired point.
a special heat stable version of dna polymerase called taq polymerase is used as it doesnt denature at high temps.
explain the process of pcr
dna is heated to break the hydrogen bonds that hold the double helix together. 98 degrees. then the short primer sequences will bond to complementary sequences in the dna sample.
this allows taq polymerase to replicate dna using the primer as a starting point. (have to add on to, cannot create nucleotides). repeated.
each time a cycle occurs, the amount of dna doubles, resulting in exponential growth. within a few hours, enough cycles of pcr have occurred to create billions of copies of the dna sequence.
3 stages of pcr
denaturation
annealing
extension
denaturation of pcr
temp is increased to 98 degrees to seperate dna strands
annealing of pcr
temp is decreased at 60 degrees to allow primers to base pair to complementary dna template.
extension of pcr
heat resistant taq polymerase replicated dna to build new dna strand
how many amino acids does insulin contain
51
a human cell and protein gene merge to make
a recombinant plasmid (with addition of plasmid) to a transgenic bacteria, to be grown in culture and then become insulin/human protein
a gene for a human protein is translated by using the same codons as…
a bacterial gene
waht are transgenic microorganisms
placing a gene from one organism into a different one by inserting a gene from another organism into the plasmid of their cells.
what are plasmids
small circular DNA molecules in some prokaryotic cells that dna be used as transfer molecules.
glucose + oxygen
carbon dioxide + water
C6H12O6 + 6O2
6CO2 + 6 H2O
cellular respiration def
the gradual and controlled release of energy by breaking down organic compounds to produce ATP
when is energy produced
when ATP is hydrolysed
what is the strucutre of ATP
adenine
ribose phosphate phosphate phosphate
where does glycolysis take place
in the cytoplasm
where does the krebs cycle and oxidative phsphorylation occur
mitochondria
glucose –>
lactate + 2ATP
glucose –>
ethanol + carbon dioxide + 2ATP molecules
uses of yeast
beer, wine, bread, cheese
define cell respiration
controlled release of energy from organic compounds to produce ATP
substrate used for aerobic resp
glucose or lipids
substrate used for anaeriobic resp
glucose only
products of aerobic resp
CO2 and water
products of anaerobic resp
humans: lactate
yeast: CO2 and lactate
when is anaerobic resp used
sprinting or weight lifting
how long can anaerobic resp be used
about 2 mins, after that hydrogen ion conentrations would make the pH of the blood too low, so aerobic cell resp must be used and high intensity exercise cant be continued
explain how yeast is used in bread
uses up all oxygen present, then produces ethanol and carbon dioxide, producing bubbles. when the dough is baked, ethanol evaporates.
explain how ethanol and the brewing and biofuel industries
yeast can be used to produce ethanol by fermentation. the yeast is cultured in a liquid containing sugar and other nutrients, but not oxygen so it respires anaerobically. the ethanol conc of the fluid around the yeast cells rises, and then becomes toxic so fermentation ends. most CO2 bubbles out into the atmosphere. beer, wine and other alcoholic drinks are brewed in this way. ethanol is also produced by fermentation for use as a fuel
what does glycolysis involve
glucose –> pyruvate.
produces 2ATP
substrate-level phosphorylation
where does glycolysis occur
cytoplasm
where does the krebs cycle occur
matrix, or mitochondria
what does krebs cycle involve
produces 4ATP, but uses 2 so net 2
substrate level phosphorylation
where does the electron transport chain and oxidative phosphorylation occur
cristae
what does the electron transport chian and oxidative phosphorylation invovle
30+ ATP
ATP synthase
oxidative phosphorylation
what does phosphorylation mean
adding a phosphate
Which chemical reaction is taking place when a dipeptide is converted to two amino acids
hydrolysis
Name the bond that forms when two amino acids react together in a condensation reaction.
Peptide bond
peptide bodn
The secondary structure involves the folding of the chains on themselves to form
pleated sheets or alpha helixes
A quaternary structure only occurs in proteins that are made up of…
two or more polypeptide chains and refers to the way the multiple subunits are held together in a multi subunit complex
examples of proteins with quaternary structure
hemoglobin and rubisco
why can hemoglobin be a quartnary stucture (roughly)
consists of four polypeptide chains
is hemoglobin globular or fiberous
globular
What does enzyme–substrate specificity mean
enzymes can only catalyse one type of reaction
exergonic
a reaction that involves a release of energy
endergonic
a reaction that involves an absorption of energy
Yogurt is tolerated better than milk by lactose-intolerant people because
lactase from bacteria in yoghurt helps digest the lactose
what do purines have
two rings in their structure
what do pyrimidines have
only one ring in their structure
which nucleotides are pyramidines
thymine
cytosine
uracil
which nucleotides are purines
adenine
guanine
what links nucleotides
phosphodiester bonds
when nucleotides are linked by phosphotidester bonds what is formed
polynucleotide
what does the phosphodiester bond link
the phosphate group attatched to the 5’ C of one sugar and the hydroxyl group attatched to the 3’ C of another sugar
what are the two strands of dna held together by
hydrogen bonds
how did crick and watson build upon rosalind franklins work
they used her dna x-ray diffraction patterns to deduce that dna molecules must have a regular double helix structure
how did crick and watson build upon chargraffs base ratio
they deduced complentary base pariing. thy then visualised it and saw how th emolecule looked/arranged.
where is the genetic material stored in eukaryotes
nuclues
where is the genetic material stored in prokaryotes
cytoplasm
when does dna replication occur
during the S phase of the cell cycle
when do number of chromosomes and genes change
doubles after dna replication.
dispersive replciation
patches of newly and original sytnhesised strands
conservative replication
one strand newly synthesised
one strand orgiinal
semi conservative replication
alternating original and newly synthesised
enzymes in dna replication»>
??
what does tna do in dna replication
bring amino acids to the ribosome
A unicellular organism that carries a specific gene from another organism is called a ______ organism
transgenic
which organelle is used in gene transfer
plasmids
glycolysis turns
glucose to pyruvate
where does glycoloysis take place
cytoplasm
where does krebs cycle take place
mitochondria, matrix
where does oxidative phosphorylation (electron transport chain) take place
mitochondria, inner membrane of the mitochondrial enevelope
where does lactatae producdtion occur
cytoplasm (of muscle cell)
What is the net yield of ATP produced by anaerobic respiration in yeast?
2 ATP molecules
why should you use a respirometer in a waterbath
to ensure theat temperature does not affect the pressure and hence volume of air in the system
what can alkaline solution be used for in a respirometer
absorb excess carbon dioxide
photosyntheiss equation
6CO2 + 6H20 (sunlight and chlorophyll) = C6H12O6 + 6O2
what is photolysis
the process by which water is split by light
photo - light
lysis - split
what does photolysis generate
hydrogen ions, electrons and oxygen
what are the electrons generated by photolysis used for
to generate ATP
what happens to the electrons and hydrogen ions produced by photolysis
used in the later stages of photosynthesis
what happens to the oxygen produced by photolysis
a waste product so diffuses out of the plant
what are the two stages of photosynthesis
light dependent reaction
light independent reaction
light dependednt reaction of photosynthesis
requires light
occurs on thylakoids
photolysis occurs now
light independent reaction of photosynthesis
no light requirement
occurs in the stroma of chloroplasts
involves carbon fixation to produce carbohydrates
what side of the chloroplast is light independednt
the side with the calvin cycle
what does the calvin cycle involve
carbon dioxide fixed using atp, electrons and ions.
controlled by rubusco.
produces glucose
which molecules of photlysis carry the energy needed to produce carbohydrates from carbon dioxide in the light independent reactions of the stroma
NADPH and ATP carry energy from the photolysis reactions to the stroma where carbon fixation takes palce
what is the action spectrum
shows the efficency of photosynthesis or the rate of photosynthesis achieved over the various wavelengths of light from the visible spectrum
what is the absorption spectrum
shows which wavelnegth of visible light is absorbed by a particualr photosynthetic pigment such as chlorophyll a or b measured by a spectrometer
EXAMPLE OF
ABSORPTION SPECTRUM
where should the peaks be in an absorption and action spectum
at approx 425nm in the blue region
at approx 670nm in the red region
the first peak is higher than the second peak
suggest why chlorophyll A absorption spectrum is not exactly the same as the photosynthesis rate
might be other active pigments for photosynthesis in the leaf
is photolysis anabolic or catabolic
anabolic (small molecules join to form large molecules)
calvin cycle equation
carbon dioxide + water –> carbohydrates + oxygen
what is a limiting factor
a factor that restricts the rate of reaction when present in a low amount
when is water a limiting factor
when the plant is able to die due to dehydration
how is light a limiting factor
photosynthesis operates via a certain number of photosystems that capture photons. if they are all occupied, the rate of reaction cannot rise anymore.
how is carbon dioxide a limiting factor
raw material in production of carbohydrates, in carbon fixation, in the light dependent reaction,
explain the plateau on the graph rate vs conc of carbon dioxide
once all the active sites of the enzymes involved in this cyclic process are occupied with a substrate, any further increase in carbon dioxide conc will not increase the rate
how is temperature a limiting factor
causes denaturation of enzymes past their optimum temp
what should you consider when investigating the effect of limiting factors on photosynthesis
plant choice (eg aquatic or terrestial. one may make data collection easier) finalise independent variabke how many levels of independent variable and how many repeats. think about accuracy (eg volume of gas produced oer counting bubbles)
What are the two main components of eukaryotic chromosomes
Store DNA in nucleus/chromosomes
Histone proteins
Summarize transcription
DNA molecule unzipped and unwound by RNA polymerase
RNA polymerase builds a mRNA molecule using the DNA as a template
mRNA leaves the nucleus through a nuclear pore.
Summarise translation
mRNA binds for a ribosome
tRNA molecules being amino acids to the ribosome
tRNA anticodon attach to the mRNA codons in the correct sequence to build the polypeptide
AA joined by peptide bonds
How does a gene in the nucleus make a protein in the cytoplasm
A gene is transcribed by rna CONTINUE
In 1828 Friedrich Wohler synthesised an organic molecule. This falsified the theory of vitalism. Which organic molecule did he synthesise?
urea
An amino acid consists of an amino group at one end and which group at the opposite end?
carboxyl
which feature distinguishes between glucose and ribose molecules
ribose has five carbon atoms while glucose has six
which property of water allows spiders to run across the surface of the water
cohesive properties
Water can easily dissolve mineral ions for transport around plants. This is a very useful property of water. What term is used to describe this property of being able to dissolve mineral ions for transport?
solvent properties
what is cellulose made of
long straight chains of beta glucose moelcules. these chains are joined by glycosidic bonds ot provide stability and strength to the molecule
which disaccharide is made up of glucose and fructose joined by a glycosidic bond
sucrose
what does rna and dna have between molecules within a nucleotide
covalent bonds
describe the nucleic acid backbone
Nucleic acids are composed of a backbone of sugar molecules and phosphate groups. The nitrogen bases are attached to the sugars.
what is the start codon of mrna
AUG. codes for the addition of methionine
first amino acid in every polypeptide is
methionine
Which enzyme is responsible for joining together the nucleotides of the new DNA strand during DNA replication?
DNA polymerase
Which enzyme is responsible for unwinding the DNA double helix in preparation for DNA replication?
helicase
Which enzyme is responsible for joining together the nucleotides of the new DNA strand during DNA replication?
DNA polymerase
which process occurs in both aerobi and anaerobic cellular respiration
electron transport chain
what is measured by a respirometer
rate of respiration
where does the krebs cycle occur
matrix in mitochondria
function of acetone in paper chromatography to separate photosynthetic pigments
It dissolves pigments, allowing them to travel up the paper strip.
difference between action and absorption spectrum
The action spectrum represents the rate of photosynthesis at each wavelength of light while the absorption spectrum shows the percentage of light absorbed at each wavelength.
carbon based compounds found in living organisms include:
lipids
carbohydrates
nucleic acids
proteins.
which macromolecuels contain carbon hydrogen and oxygen
all of them
which macromolecules also contain nitrogen
proteins and nucleic acids
which macromolecules contain phosphorus
some lipids
what is the ratio of hydrogen to oxygen in carbohydrates
2:1
what are nucleic acids
chains formed by nucleotides
Alpha-D-glucose and function
Used in the production of ATP in cells.
Beta-D-glucose
Used to build cell walls in plants.
starch function
used as long term storage in plants
ribose function
used as a component of dna and rna
triglycerides function
used as long term storage in adipose tissue in animals
sterioids function
Used as chemical messengers in the body, have a distinctive ring shape.
phospholipids
major component of plasma membranes
Structural proteins
Proteins such as keratin and collagen form the structural framework of many parts of the body.
enzymes
metabolic proteins that speed up chemical reactions in the body
polypeptides
a sequence of amino acids that may make up a protein or a series of polypeptides can also make up a protein
dna function
used to store genetic information
rna function
used to create proteins at ribosomes using the information stored in dna
saturated
contains no double bonds
unsaturated
contains double bonds
starch test
iodine solution, turns blue black
protein test
biuret solution. turns purple
carbohydrate test
benedicts solution. blue to orange or brick red
hydrolysis reaction
the breaking of chemical bonds by the addition of water molecules.
condensation reaction
refers to the reaction in which two smaller organic molecules combine to form a larger molecule with the accompanied formation of water or some other simple molecule.
how does water have solvency, cohesion and adhesion?
polarity
polarity of water
oxygen gains negative charge, hydrogens gain positive charge
benefit of water having cohesive properties
Allows water to be pulled up from the roots to the leaves of plants.
Permits insects, such as pond skaters, to walk/float on the surface of water to catch their prey.
benefit of water having adhesive properties
Capillary action generated by adhesive forces assists the pumping action of the heart to help blood move through blood vessels.
Adhesion of water molecules to the cell wall of xylem vessels helps water move against gravity from the roots to the leaves.
beneit of water having thermal properties
Evaporation of sweat from body surfaces involves heat loss, which brings about a cooling effect.
The high specific heat capacity of water makes aquatic ecosystems more stable than terrestrial.
benefit of water having solvent properties
Water dissolves mineral ions in the soil and transports it along xylem vessels from the roots to all parts of the plant.
Water in blood plasma dissolves a range of solutes and gases, which makes it possible for blood to transport nutrients and gases around the body
Water’s versatility (its ability to exist as a liquid, solid and vapour) makes water a universal solvent and medium for numerous biochemical reactions.
which molecules are found in blood
glucose (dissolves)
amino acids (if R group hydrophilic. if not, transported in lower conc of blood)
fats (lipoproteins)
cholesterol (lipoproteins)
main differences between water and methane
polar and non polar.
water has a much higher bp, mp, c and hvap
no of carbon atoms in a monosaccharide
3-7. carbons joined to a hydroxyl group
how are two monosaccharide monomers linked together
through a condensation reaction which forms a glycosidic bond producing a disaccharide, releasing one water molecule.
what is sucrose composed of
glucose and fructose
what is maltose composed of
2 units of glucose
what is lactose composed of
glucose and galactose
what is starch and glycogen and cellulose composed of
glucose
what gives starch its stickiness
amylopectin
how are tricglycerides formed
condensation reactions between one glycerol and three fatty acids, creating ester bonds
bent cis fatty acid
both hydrogens on one side, leading to a bent molecule
straight trans fatty acid
hydrogens on different sides of the carbon chain, leading to a straight molecule
what happens if one fatty acid in a triglyceride is replaced by a phosphate group (PO4)
produces a phospholipid
what is considered to be the good fatty acid
unsaturated cis
pros of lipids not carbs
stores double energy doesnt store 2g of water (like glycogen does per gram) less dense non polar excellent heat insulation waterproof
what are considered to be bad fatty acids
trans fats, and those rich in saturated fatty acids
BMI
weight
/
height squared
what changes in sickle cell anaemia
glutamic acid is substituted by valine, causing severe changes to the structure of hemoglobin
globular proteins
tend to play active roles in the cells metabolism. they conssit of complex polypeptide chains that can be linked to other chains to form large complex proteins. usually soluble in water because their hydrophobiv r groups are folded into the core of the molecyle, away from the surrounding water molecules
fibrous proteins
usually made of long polypeptide chains where the hydrophobic r groups are exposed, making the molecule insoluble. often found in structural parts of organims,s such as tendons and skin
what structures are lost in denaturation
secondary and tertiary. mor tertiary or quaternary hydrogen bonds between r groups of amino acids and amino groups of different groups are disrupted. active sites lost their shapes.
what type of protein are enzymes
globular proteins
how is induced fit possible
because of the flexibility of the protein molecules that make up the enzyme
industrial enzymes
industry
environment
agriculture
what is lactose
a naturally occuring disaccharide in dairy. lactase can break it down.
what happens if you are lactose intolerant
lactose intolerant people can eat food that has had the enzyme lactase added, which breaks down lactose into its constituent monomers, glucsoe and galactose
what are dna and rna composed of
a pentose sugar
phosphate group
nitrogenous base
what does dna contain that rna doesnt
DEOXYribose (sugar)
what is the formation of a new dna molecule called
replication
when does replication occur
during s pahse
what enzyme does the first step of dna replication
unwinding the coils to make the strands acccesible to enzymes is done by helicase by breaking hydrogen bonds between the bases.
what enzyme does the second step of dna replication
DNA polymerase starts making new strands of DNA using the two old parent strands as templates
what were the 3 ways dna replication could occur
dispersive
conservative
semi-conservative
what did mehlson and stahl find dna to be
semi conservative meaning it alternated between 14N and 15N
what is rna polymerase responsible for
seperating the dna strands of the dna helix as well as for joining the ribonucleotides together by phosphodiester bonds to form an mrna strand
which dna stand is the sense strand
the one NOT transcribed
is the sense or antisense strand complementary to the mrna molecule
the antisense strand
which end of the trna molecule is 3’
the longer end
what is the anticodon
the 3 bases where the amino acid attatches itself
where does translation take place
cytoplasm of the cell
in which order does translation occur in
5’ to 3’ direction
the genetic code is…
degenerate
universal
what does PCR allow
the rapid production of multiple copies of dna using TAQ dna polymerase
insulin function
regualtes glucose uptake and the conversion of glucose to glycogen in the liver
glucose undergoes glycolysis becoming
pyruvate
pyruvaate can undergo anaerobic or aerobic resp…
anaerobic would undergo fermentation to become lactate or ethanol and CO2
aerobic would undergo
where is the electront ransport chain
the inner membrane of the mitochondrial envelope
how much atp does anaerboci resp generate
2
why would you set up the respirometer in a water bath
to ensure temp does not affect pressure and hence volume of air in the system
which pigments capture photon
chlorophyll a and b
other pigments involved in phtoosynthesis
xanthophylls and carotenoids, reflecting yellow and orange light respectively
what is the calvin cycle
name for the light independent reactions: a cycle of chemical reactions where CO2 is assimilated to make sugars.
calvin cycle equation
CO2 + H20 –> carbohydrates + oxygen
benefits of thin layer chromatography
same principle as paper but the stationary phase is usually silica gel, aluminum oxide or cellulose instead of paper. it gives a better result as well defined and well separated spots are obtained
cell respiration def
the gradual and controlled release of energy by breaking down organic compounds to produce ATP ( Adenosine T ri P hosphate).
each 6 carbon glucose is gradually broken down into
6 CO2 molecules
what does an action spectrum record
the amount of photosynthesis at each wavelength
where is the oxygen we breathe in from
the water used in photolysis reactions
What is needed in photosynthesis to convert carbon dioxide into organic molecules
ATP and hydrogen from the splitting of water.
waht type of reaction is photosynthesis
anabolic
waht cuases oxygen in the first 2700 million years of earth
cyanobacteria
what could be the earleist occurance during dna replication
free nucelotides base pair to original polynucleotide
methane vs water, bp vs freezing pt
methane’s bp is well above the freezing point of water
From which molecule(s) is oxygen released into the air as a product of photosynthesis?
water only.
Oxygen is derived from the photolysis of water.
How is oxygen produced during photosynthesis?
Water molecules are split with energy from light. Photolysis of water yields oxygen. The energy that is needed for this process is supplied by photons harvested by the chlorophyll reaction centres.
Hemoglobin can transport oxygen through its unique conformation that is displayed through:
two alpha and two beta chains.
Whereas hemoglobin contains heme group, it is still composed of two alpha and two beta chains. This flexible structure gives it a great advantage in the process of oxygen transport throughout the human body, which renders answer #1 the only correct answer to the question.
Mangrove trees live in swamps and saline coastal waters. These are harsh conditions in which aerobic respiration in the roots is difficult. One of the adaptations of mangrove trees to their environment is vertical roots called pneumatophores that grow upward out of the mud and water to function as the site of gas intake. What gas will be absorbed by pneumatophores?
oxygen.
In swamps and saline coastal waters, oxygen cannot penetrate the muddy and saline soil. Pneumatophores, also known as aerial roots, are erect side branches of the horizontal roots of mangrove trees that grow out of the mud to obtain oxygen from the air. They allow aerobic respiration to occur in the oxygen-deficient environment.
what process happens in aerobic and anaerobic cellular respiration?
glycolysis
difference between absorption and action spectryum
The action spectrum represents the rate of photosynthesis at each wavelength of light while the absorption spectrum shows the percentage of light absorbed at each wavelength.
Why is the action spectrum for photosynthesis similar to the absorption spectra of photosynthetic pigments?
Only wavelengths of light absorbed by pigments can be used in photosynthesis.
The absorption spectrum shows the range of wavelengths of visible light absorbed by plant pigments. It is these wavelengths that determine the rate of photosynthesis shown in the action spectrum.
