Module 1: Introduction to Biochemistry Flashcards
(Chemical Foundations)
What is the Unity of Biochemistry?
all life may seem phenotypically different, but on molecular life there are a lot of similarities:
- use same building blocks to create common biomolecule categories (nucleic acids, proteins lipids, polysaccharides)
- Common biochemical processes
(Chemical Foundations)
What 4 common elements are all living organisms made from? And where do they obtain these elements from?
Carbon - get from air through plants
Oxygen - get from air
Hydrogen - get from water
Nitrogen - a lot exists in the air but in the form N2. So we have to get N from plants = which would only allow for 4 billion people. But Fritz Haber found a way to convert N2 → N : so no more restriction
These 4 make up for 98% of most organisms
(Chemical Foundations)
All known life is _____ based because . . . ? 2nd best option?
Life is carbon-based = carbon allows for great bonding versatility (1x/2x/3x bonds) that produces various C-C skeletons with an array of functional groups = these FG give biomolecules there biological & chemical characteristics.
2nd Best option is silicon-based life = since it also can have form 4 covalent bonds and there exists in abundance in Earth’s crust
(Chemical Foundations)
Why is life Carbon based as opposed to Silicon based?
Cuz a symbolic relationship is created between carbon-based life as CO2. Combustion products of carbon (CO2) are soluble and remain active in biosphere (recycle)
(Chemical Foundations)
What (3x) roles do Functional Groups determine?
F.G exist within biomolecules, their properties determine the structure, function, & property of the biomolecule
(Chemical Foundations)
What is the Structure-Function Relationship of Biomolecules and why is it important (3x)?
Biomolecules: structure dictates function, molecules do what they do because of their structure.
This allows us to:
- Predict molecular function
- Understand complex biology
- Rationale development of treatments
(Chemical Foundations)
What are the two broad categories of structure-function relationships?
Conformation & Configuration
(Chemical Foundations)
What is Confirmation? Example?
The flexible spatial arrangement of atoms in the molecule (can be changed without breaking bonds) (rotate the single bonds)
Ex: how a polypeptide chain folds
(Chemical Foundations)
What is Configuration? Example?
Fixed spatial arrangement of atoms within a molecule. Can’t be changed without breaking covalent bonds. These changes are more dramatic.
(Chemical Foundations)
What are the 2 sub-categories of configuration?
Double bonds and Chiral Centers
(Chemical Foundations)
Double bonds result in _______ ________: which create 2 sub-categories known as?
Result in geometric (cis-trans) isomers (different in configuration & biological properties but similar in chemical formula) creating:
- Cis-isomers
-Trans-isomers (more common in peptide bonds)
(Chemical Foundations)
2 __________ are created when chiral carbons are arranged in different ways?
- 2 stereoisomers (different in configuration and biological properties but similar in chemical formation) result
- L isomer
- D isomer
Define Stereochemistry.
Stereochemistry studies the spatial and 3D arrangements of atoms + molecules & their effect on the chemical rxn.
Define Biochemistry
Biochemistry is the study of life on molecular life.
Principals of chemistry applied to explain biology.
Explores chemical processes within and relate to living organisms
Explain how Stereochemistry relates to Biochemistry.
List 2 examples of how stereospecificity impacts biochemistry.
Construction & Interactions
Define “construction” in biochemistry.
Biomolecules are often constructed/made from one stereoisomer. Ex. proteins are always built from L-Amino acids.
Define “Interactions” in biochemistry.
Interactions between biomolecules, as well as between biomolecules & small molecules, are stereospecific.
So like the smallest change in spatial configuration result in completely different biological properties.
What are 3 advantages of constructing biomolecules as polymers?
Simplicity - since all the thousands of proteins inside us are made from the same blocks, it’s easier to work with (to break them apart and rebuild)
Recycling - we can reuse biomolecules by returning them to their building blocks. We recycle proteins in the biosphere. (ex. protein in brain is broken and rebuilt as protein for your liver
Diversity - limitless combinations result from the 20 amino acids. which allows us to build complex structures/molecules.
Explain how “Simplicity” is an advantage in making biomolecules as polymers.
Simplicity - since all the thousands of proteins inside us are made from the same blocks, it’s easier to work with (to break them apart and rebuild)
Explain how “Recycling” is an advantage in constructing biomolecules as polymers.
Recycling - we can reuse biomolecules by returning them to their building blocks. We recycle proteins in the biosphere. (ex. protein in brain is broken and rebuilt as protein for your liver)
Explain how “Diversity” is an advantage to constructing biomolecules as polymers.
Diversity - limitless combinations result from the 20 amino acids. which allows us to build complex structures/molecules.
How to biomolecules relate to the saying “the whole is greater than the sum of parts”?
Biomolecules are made of simple building blocks. But their structure & function is more complex than the precursor molecules.
Name the four major classes of Biomolecules
Proteins
Carbohydrates
Nucleic Acids
Lipids
Proteins are _____ polymers of _____ _____
Proteins are linear polymers of amino acids
What four things to all __ amino acids have in common?
All 20 have:
-alpha carbon bonded to
- Amino group (NH2)+
- Carboxyl Group (COO)-
- Hydrogen
How Peptide bonds form:
The ________ of one amino acid (covalently) links to the ______ of the next amino acids
The amino group of one amino acid (covalently) links to the carboxyl group of the next amino acids
How do amino acids differ? And how does this impact proteins?
Only the side chains of amino acids differ.
Different side chains = have different properties = which will fold differently = which decides the overall biological function of the protein.
[diff side chain = diff properties = diff fold = diff function]
What are the 3 main parts that make up nucleic acids?
5-carbon sugar
phosphate group
nitrogenous base
Nucleic acids are ____ polymers made out of building blocks called ________ that occur as either DNA or RNA.
Nucleic acids are linear polymers made out of building blocks called nucleotides that occur as either DNA or RNA.
What are the types of nucleic acids?
Main ones: DNA & RNA
Other ones: mRNA and rRNA
List the 5 different nucleotides
(C) Cytosine
(U) Uracil
(T) Thymine
(A) Adenine
(G) Guanine
what four nucleotides make up DNA?
(A) with (T)
(C) with (G)
what four nucleotides make up RNA?
(A) with (U) Urucil
(C) with (G)
Nucleic acids and proteins are similar cuz they both have . . . ?
Linear bonds
What are nucleic acids?
They are linear polymers of nucleotides that make up DNA and RNA
What are some functions of nucleic acids?
Involved in all aspects of storage & utilization of genetic info
How do lipids differ from the other 3 macromolecules?
Lipids are held together by non-covalent forces that allow for aggregation. They are aggregates rather than defined polymers of building blocks
This allows freedom of motion (Fluid mosiac model)
What are the parts of the lipid?
Hydrophilic head and hydrophobic tail
List 3 functions of lipids.
store energy
form membranes
signaling ?
Does our body have more prokaryotic or eukaryotic cells?
Prokaryotic, but they are smaller
List 2 functions of prokaryotes (in the gut?) ?
Bacteria in gut help digest food (ex.yugurt) and maintain immune system
Our 2nd brain ______ & our microflora may impact _____ health, _____ and _______
Our 2nd brain the gut & our microflora may impact mental health, obesity and intelligence
The _____ is linked with obesity, anxiety, depression
Microbiom
Type of ____ present in our body influence a lot of human _______
Bacteria & characteristics
List 3 possible ways to influence the microbiota
Through diet
Pro/Prebiotics
Fecal transplants
Define “In Vitro”
(in glass) study behavior of molecules (isolate in glass) outside the context of the cell organism
Define “In Vivo”
studies the behavior of molecules within (their living enviro) the context/complexity of cell
Failure in the translation of science is when . . . ?
When lab observations aren’t able to be applied to real life
Experiments which are successful in _____ often fail in _____
If it succeeded in vitro(glass) it often fails in vivo(living)
List pro & con of In Vitro approach
Pro: isolating the variable simplifies experiments
con: can’t observe the interaction of the molecules in its normal envro
List pro and con of In Vivo
Pro: Ideal approach, since we can observe molecules rxn & behavior while its under influence of its enviro
Con: Hard to maintain studies on large animals (ethics?)
How are the Laws of dynamics applied to Biochem?
Cellular energy conversions follow laws of dynamics
What is the currency of energy in our body?
ATP - u burn ur body weight in ATP/day
What is 1st law of thermodynamics?
Energy cannot be created or destroyed, just transformed
Amount of physical/chemical energy = constant , but its forms might change
Explain how cells follow the 1st law of Thermodynamics
Cells are highly effective transducers of energy (converts energy from one form to another)
List some examples of how cells follow the 1st law of Thermodynamics
Cells covert energy of metabolized nutrients & sun into = work, heat, generation of biomolecules
Explain the 2nd law of Thermodynamics.
Things naturally want to get more disorganized and disordered. And so disorder (entropy) of the universe is always increasing
Define Entropy (S)
Degree of randomness
lack of order or predictability; gradual decline into disorder. –> linked to 2nd lay of thermodynamics
Define Enthalpy (H)
is the energy associated with the bonds that are present - reflects the number of bonds
Unit of temp in Gibbs Free Energy?
K - Kelvin
What is Gibbs “Free Energy” (G) ?
Free energy (G) = Enthalpy (H) - [Entropy (S) x Temp (K)]
Free energy (G) = number/kinds of bonds - [degree of randomness x temp]
A value that describes how spontaneous a rxn is?
What does a positive change in free energy mean (+G) ?
It is a non-spontaneous process –> not a favored rxn
Needs input of free energy to occur
Endergonic
What does a negative free energy mean (-G) ?
RXN is a spontaneous process -> favored rxn
RXN releases free energy which is used to do work until equilibrium is achieved.
Exergonic - energy leaves rxn to power work?
*Spontaneous rxn = means rxn will occur without the input of energy. It doesn’t haven’t to occur instantly, it can span over years and still be spontaneous.
What does a free energy (G) of 0 mean?
system is at equilibrium, no further change in free change in the system
No specific advantage to either sides
What are proteins made of?
Amino acids (20)
How do cells drive thermodynamically unfavorable reactions?
By coupling energy rxn *endergonic” to energy releasing rxn “exergonic”
The common energy currency is _______ which acts as a link to________ and ________ reactions.
Currency is ATP, links catabolic to anabolic reactions
What are the 2 categories of energy in our body?
Catabolic and anabolic pathways
What are catabolic pathways?
They break things down (ex. proteins, food, etc. you consume) are produce energy
Energy producing and exergonic rxn
What are anabolic pathways?
They build things up (ex. create proteins within body), they require energy
Energy requiring and endergonic reactions
How does ATP link anabolic and catabolic reactions?
Catabolic rxn generate ATP and then this ATP is used to drive anabolic rxn
List 3 basic needs of genetic information in order for life to work
stable, usable, replicable
We need to be able to store DNA in a stable form (no break/change)
We need to be able to access it on an ongoing basis and express it accurately in the form of gene products
We need to be able to replicate our DNA every times cells grow and divide
