Module 1 Flashcards
biochemistry is…
-the study of life at a molecular level
-the application of chem principals to explain bio
-the common set of reactions and pricipasl that underlies all living organisms
-the study of molecular logic of life
how are all living organisms simular
they are all remarkable uniform at a molecular level
all organism are uniform at a molecular level. all organisms use…
-a common repertoire of building blocks to create common categories of biomolecules
ie. (nucleic acid, proteings, polysaccharides, lipids)
-a common core essential biochemical prosess
living states can be considered from four different perspectives/foundations…
-chemical
-energy
-genetic
-evolutinary
are all living things made from simular ingredients
yes
what four elements account for all living things ingredients
carbon, oxygen, hydrogen, nitrogen account for 98% of most organisms (in order)
what accounts for most of the hydrogen in living things
water
what element are all life forms based
carbon
how do we accumulate our carbon
from air through plants
how do we accumulate our oxygen
from air
how do we accumulate our hydrogen
from water
why cant we get our nitrogen from air
because its in inert form N2
how do we accumulate our nitrogen
it comes from plants which extracts it from soil
what can nitrogen in soil limit
the growth of plants, limiting the amount of food we can produce
how much food could we grow with the amount of natural occurring nitrogens in the soil
enough food for 4 billion people
how would the sale value of the chemicals vs organs tissue biomolecs compare in the human body
the chemicals within the human body would cost less then a dollar but tissue, organs, biomolecs would cost around 45,000,000
carbon is versatile in terms of…
the number and variety of chemical bonds that it can form
when carbon is versatile in the shapes it can make it enables
creation of a wide array of complex molecs
ie. amino acids, sugars, nucleotides
after carbon what would be the next-best candidate as a chemical foundation for life
silicon
why is a carbon molecule better to be the foundation chemical for life over silicon
-carbon to carbon bonds are stronger then silicon to silicon
-more energy is released on the C to C bonds (more energy from C based nutrients)
-combustion products of carbon (CO2) are soluble and remain active in biosphere
how does the silicon combustion byproducts compare to the carbon combustion byproducts
-the SiO2 is insoluble and cannot be used again
-the CO2 is soluble and remains active in the biosphere (used by plants)
describe or draw a carbonyl (aldehyde) molecule function group
a C with a single bonded H and a double bonded O that attaches to a R group making a T shape
describe or draw a carbonyl (ketone) molecule function group
a double bonded C and O with two R groups on either ends creating a T shape
describe and draw a carboxyl molecule function group
a C attached to a double bonded O and a single bonded O- anion that attaches to a R group making a T
describe and draw a (alcohol) hydroxyl function group
a O and a H bonded together with an R group crating a liner molecule
describe or draw a amino function group
a N with two Hs and a R group
describe or draw a amido function group
a C with a N and a double bonded O. the N has two Hs
describe or draw a guanidino function group
-a N attached to a H and a c
-the C has a N and a double bonded N
-double bonded N has a H
-the single bonded N has two Hs
draw Imidazole function group
just draw then google it
describe or draw a sulfhydryl function group
a S and a H
what does the properties of a functional group determine
the properties determine the structure, function, and properties of the biomolecules
what does structure dictate
the function
molecules “do what they do” because of their structures
understanding the structure-function relationship of biomolecules allows one to…
predict molecular function, understand complex biology (and pathobiology, and rationale development of treatments
what is the conformation of a molecule
flexable spatial arrangement of atoms within a molecule
(can be changed without breaking covalent bonds)
(think paper plane you can change the shape with out breaking)
what is the configuration of a molecule
fixed spatial arrangement of atoms within a molecule (cannot be changed with out breaking covalent bonds)
(think cutting off your finger)
configuration is conferred by either…
double bonds
chiral carbons(C bonded to 4 groups)
what are geometric (cis-trans) isomers
they have the same chemical formula but differ in the configuration of groups with respect to a non rotating double bond
what a cis bonds
groups on the same side of the double bond
what is a trans bond
groups on the opposite side of a double bond
can cis and trans change between each other
no. they stay this way there is so spontaneous conversations
what is a chiral carbon
it has four different substituents attached
can chiral carbons be arranged in different ways
yes. two different ways in space
because chiral carbons can be arranged in different ways in space what does this lead to
two different stereoisomers that differ in there configuration
how are steroisomers different
they tend to be identical but their biological properties are distinct
what are stereoisomers
they are molecules that are meior images of each other and take up space differently (think hands)
how many amino acids have a cyro alpha carbon
19 out of 20
Why is sterospecifity important
it is apparent in the construction and interactions of biomolecules
How many stereoisomers are bio molecules constructed from
biomolecules are often constructed exclusively from one stereoisomer
ie. proteins are built entirely from L-amino acids
what is the interactions between biomolecules, small molecules and biomolecules like
they are stereospicific
what does synthesis of chemical compounds (ie drugs) have a result of all the chiral forms
a asymmetric mixture of the chiral forms
why do not all forms of chiral carbons work for drugs
because these forms may have different biological activities
ie. thalidomide has two chiral forms one causes birth defects the other prevents moring sickness
what are biomolecules offten
polymers of simple building blocks
interms of biomolecule complexity what is more complex the structure and function or the the precursor molecules
the structure and function of resulting molecules are more complex then there precursor molecules; the whole is greater then the sum
what are the three advantages to constructing biomolecules as polymers
simplicity- simple and conserved reactions for synthesis and degradation
recycling-biomolecules can be digested back to component building blocks which can be recycled
diversity-incredibly complex molecules can be granted
what are the four major classes of biomolecules
proteins
carbohydrates
nucleic acids
lipids
what is the basic structure of DNA
two complementary strands
what are the two DNA complementary strands made up of
each strands is a linear polymer of four different types of building blocks
in DNA what is it that encodes information
the liner sequence within the strands
the nucleotide structure of genes dictates the…
sequence of amino acids incorporated into the corresponding protein
the amino acid sequence of proteins dictates…
the structure of the protein
the structure of protein dictates…
the biological activity
what is transcription
transcription of DNA into complementary RNA
what is translation
translation of RNA on ribosome to polypeptide chain
what can random changes in genotype can result in…
changes in phenotype (observable characteristics)
when a random change in genotype occurs when is it selected for
if the change offers a survival advantage it’ll be selected for
when a random change in genotype occurs when is it selected against
if it disadvantages the organism it’ll be selected against
do we have all or original proteins
no proteins in you today are not the same ones you had within you a month ago
biochem reactions are…
steriospicific
what do amino acids have attached to them
a carboxyl groups + amino group
how do amino acids link together
link by carboxyl group of one amino acid to amino group of other
what are proteins made of
linear polymers of amino acids
how many amino acids are there
20
what makes each amino acid different
they differ in there R group chains (which are different shapes/configurations)
when amino acids have different R group chains what does this mean
it means they have different properties associated with them
what do the different properties of amino acids determine
how the strands interact with eachother
what happens when amino acids link together
they link together to form linear chains that fold into complex patterns with distinct biological activities
what is protein folding a characteristic of
the amino acids that determines how it will fold
what does the structure of a protein determine
biological activity
what happens when when you have changes with in the structure
you change the function
what can you look at on the the amino acids to predict the behavior of a protein
if the amino acids are polar or non polar (that is one of the main determinants of protein folding)
what kind of chains do amino acids make
they make linear chains
how are polysaccharides constructed
they are monosaccharides linked together to form linear or branched polymers
what important biological roles do higher order polysaccharides serve
roles including structural, energy storage, and cellular recognition
how do we link individual monosaccharides
they are linked together through glycosidic linkages (covalent linkages)
what can carbohydrates do that can lead to very complex structures
they can form more then one covslent linkage to other sugars (branch points)
what are some roles polysaccarides can play
they play a number of different roles such as energy storage, cellulose, joint lubricants
how is nucleic acids constructed
linear polymers of nucleotide building blocks
how many building blocks is there for DNA and RNA
5
what is nucleic acids involved in
all aspects of storage and utilization of genetic information
what are the 5 DNA/RNA buliding blocks
cytosine
uracil
thymine
adenine
guanine
how do nucleic acids link together and what shape is it
they use covalent linkages creating linear structures
how are nucleic acids bonded together
they are bonded with covalent phosphodiester bond
what are lipids
they are aggregates (rather then defined polymers) of building blocks
how do lipids serve
in energy storage, formation of membranes and signalling
what is the structure of lipids
they have a hydrophilic head and two hydrophobic tails
how are lipids bonded together
they are agrogating together through non covalent forces
they come together through hydrophobia
why are lipids different from other biomolecules
because they aren’t bonded through covalent linkages but rater they are aggregating together through non covalent forces
in lipids what are some concequences of not being linked together
lots of freedom of rotation
how are lipids diffrent then the other 3 biomolecules
they done come together through covalent linkages and instead they aggregated together through non covalent forces
what kind of structure can you build from lipids
structures that are consistant with there biological functions
what are the two basic classes of living organisms
prokaryotes and eukaryotes
how big are prokaryotes
around 1 micrometer (they are small)
what can prokaryotes do because of there rapid cell growth
because of there rapid they can adapt to there environmental conditions easily
what is contained with in a prokaryote cell
a single compartment, the nucleoid, which contains nucleic acid
other biomolecules (protein, metabolites, etc) in a complex, organized mix
what are prokaryotes
they are single celled organisms and one cell represents the entirety of the organism
ie.. bacteria
are there specialized cells when it comes to prokaryotes
no. one cell represents the whole organism (homogeneous soup of together)
what are some advantages associated with prokaryotes
they can very easily adapt to changing circumstances
(change rapidly as new pressures are introduced)
how quickly can prokaryotes devide
they can devide every 20 minutes
how big are eukeryotes
around 100 micro meters (large)
what kind of organisms do eukaryotes make up
multi-cellular organisms such as yeast, plants, fungi, vertebrates
what do eukaryotes make up to support specialized functions
organells (nucleus, mitochondria, etc)
what are some consequences associated with eukaryotes
much slower evolution and adaptation
how many eukaryotes and prokaryotes do we contain within our bodies
we have around 30 trillion eukaryotic cells
around 100 trillion prokaryotic cells
are the prokaryotes good for us
yes they are critical for our health
what does the bacteria in out guts do
they help digest food and maintain a functional immune system
what does out gut including microflora in it impact
our mental health, obesity and intelligence
what are some possible ways to influence the microbiota in us
diet, pro and prebiotic, and fecal transplants
if we put all the bacteria in our body how much we have
something the size of our brains (think of it as a extra organ)
what are the two experimental approaches of studying molecules
in vitro
in vito
what is in vitro
(in glass) studies behavior of molecules outside the context of the cell and organism
what is in vivo
(in the living) studies occur within the complexity of the cell or organism
why do experiments that are successful in vitro fail in vivo
because the behavior of molecules is context dependent
what is the ideal way of studying molecules
in there natural habitat
what are some pros associated with in vitro
you limit variables
what are some in vitro cons
sometimes isolating molecules makes them harder to study
what does the order of testing subjects go like
first mice then pigs then humans
what animal is most ideal to study to compare to humans
pigs
what are some pros and cons of experimenting on mice
pro: they are easy to keep
con: they have very different biological systems then humans
how must energy for life be obtained
from the environment
how much ATP does your body go through a day
about your body weight
what is the first law of thermodynamics
the amount of energy in the universe remains constant energy cant be created nor destroyed
how are cells highly effects transducers of energy
they convert the energy metabolized nutrients, or the energy of the sun, into work, heats or the generation of complex molecules
what is the second law of thermodynamics
the tendency in nature is toward even greater disorder: the total entropy of the universe if continually increasing
how do living systems and their biomolecules like to be interms of there organization
they require a high level or organization
what theory did willard gibbs develop
the theory of energy changes during chemical reactions
how did willard gibbs demonstrate that free energy (G) of any closed system can be defined in terms of
-enthalpy(H)
-entrophy(S)
-temperature
what is enthalpy (H)
reflects number and kinds of bonds
what is entrohpy (S)
the degree of randomness
what is the equation of the definition of energy
G=H-TS
what is the equation of free energy change
delta G = delta H - T delta S
if the delta G is is bigger then 0…
(it is +) (endergonic meaning it absorbs energy in the form of work)
it is a non spontaneous process, needs input of energy to proceed
if the delta G is smaller the 0…
(it is -) (exergonic meaning occurs with out the input of energy)
it is a spontaneous process, releases free energy which can be used to do work
for a spontaneous process for free energy, what is meant by spontaneous
it means nothing about the time frame. just that it wants to be like this (with out energy imput)
in spontaneous processes for free energy how long do they occur for?
it proceeds until equilibrium is reached
if the delta free energy is 0…
system is at equilibrium, there is no change in free energy in the system
what does G mean
free energy
what does H mean
enthalpy
what does S mean
entropy
how can cells drive thermodynamically unfavourable reactions
by coupling energy requiring (endergonic) to energy releasing (exergonic) reactions
if the sum of the free energy changes is negative the overall process is…
exergonic (spontanious)
ATP serves as the link between…
catabolic and anabolic rxns
the perpetunation of life requires that genetic info be…
-stored in a stable form
-expressed accurately in the form of gene products
-reproduce with minimal efforts
for many organisms DNA provides…
-the instructions for forming all other cellular components
-a template for producing of identical DNA molecules to be distributed to the progeny when the cell devides
DNA must be…
stable, usable, easy mechanism to make a copy
What is the monomer of nucleic acid
Nucleotides
