Quiz 1: Lecture Info Flashcards
How many more bacterial cells are in the body than human cells?
10x more
Why are we primarily composed of water?
Ancestors originated in water
Water is a great solvent for chemical reactions
How do cells compartmentalize?
Cells organize biochemical reactions to occur in specific compartments
Right chemicals at right concentrations in right places
What is used to assemble macromolecules?
Basic building blocks of life
What does the study of biochemistry show?
How collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the chemical and physical laws that govern the nonliving universe
The Molecular Logic of Life
biochemistry describes in molecular terms the structure, mechanisms, and chemical processes shared by all organisms and provides organizing principles that under lie life in all it’s diverse forms
Why do all organisms share the same chemical principles?
Evolution connects these organisms
All organisms derived from a single common ancestor
What is unique about bacterial cell membranes?
they can have multiple membranes with the cell wall in-between
What is the bacterial cell wall made out of?
peptidoglycan
What is the plant cell wall made out of?
cellulose
How do antibiotics work?
cell wall in gram negative bacteria is made out of peptidoglycan
transpeptidase enzyme synthesizes the cell wall
tanspeptidase enzyme is blocked by penicillin
without cell wall, water flows into the hypertonic cell environment and cell lysis occurs
B-lactamase
An enzyme that breaks down penicillin
Bacteria have evolved to share this gene through plasmids
Plasmids are passed through conjugation``
MRSA
methicillin-resistant staphylococcus aereus
tougher to treat than most strains of staph because resistant to many commonly used antibiotics
Chemotrophs
derive their energy from the oxidization of chemical fuel
Phototrophs
trap and use sunlight
Autotrophs
synthesize all of their biomolecules directly from CO2
Hetereotrophs
require some performed organic nutrients made by other organisms
How would we describe humans mode of nutrituion?
Chemoheterotrophs
How would we describe cyanobacteria’s mode of nutrition?
Photoautotrophs
Synergy
the whole is greater than the sum of its parts
This can be applied to biological systems
Ex: neurons don’t do much on their own but come together to create the complex brain
Emergent property
a novel property that arises at a specific level of organization
ex: life (novel property) emerges at the level of a cell but is not found in any simpler levels
What type of experiments were used to determine the content of cells in the 20th century?
centrifugation
separates different contents of the cell based on weight
Reductionist science
Breaks a system into little parts to see how they work and interact with eachother
What is bigger a nanometer or a micrometer?
Micrometer
How many nanometers is 1 micrometer?
1000
There are a 1000 nanometers in 1 micrometer
What elements are humans composed of? (in order from greatest amount to least)
Oxygen, carbon, hydrogen, and nitrogen
What structure does carbon typically make?
tetrahedral structure with bond angle of 109.5º
able to rotate around single bonds
What are biomolecules derivatives of?
Hydrocarbons
Stereoisomers
molecules with the same chemical bonds and same chemical formula but different configuration
Configuration
the fixed spatial arrangement of atoms
to change configuration need to break a bond
R-configuration
clockwise
S-configuration
counterclockwise
How is conformation different from configuration?
can’t go from one configuration to another without breaking a covalent bond
can change conformation by rotating around bonds
What is available chemical energy of a cell determined by?
the concentrations of ATP and NAD(P)H available
Catabolism
extracting energy from bonds and converting to ATP
breaking down things to liberate energy
Anabolism
using ATP and NAD(P)H to perform biochemical work
putting things together
Free energy
the energy available to do work
Exergonic reactions
occur with -G
energy is released, reactions are spontaneous
Endergonic reactions
occur with +G
energy needs to be put in to occur
does not happen spontaneously
How can you make a reaction occur spontaneously overall?
Combine exergonic and endergonic reactions
Does the universe tend to go to higher or lower entropy?
Higher entropy
More disorder
Why does ATP want to lose a phosphate?
all the negatively charged phosphates in ATP make it somewhat unstable with high energy
Is it exergonic or endergonic to break apart ATP?
exergonic
Why is water a polar molecule?
Oxygen is electronegative and pulls electrons towards it creating a partial negative charge
Hydrogen gains a partial positive charge
Hydrogen bonds
occur between partial negative oxygen and partial positive hydrogen on separate molecules
Why do polar and charged biomolecules dissolve in water?
Water’s partial charge interacts with charges on molecules to separate them
These changes are also energetically favorable
Flickering clusters
Water exist in a cluster for a picosecond and then change
Hydrogen bonding constantly changing
How many water molecules will hydrogen bond together?
3-4
What properties does hydrogen bonding give water?
High cohesion
High specific heat and heat of vaporization
Ice is less dense than water
Why is ice less dense than water?
Water molecules freeze in an orientation that makes them further apart in ice
Polar molecules
typically have oxygen or charged
differences in electronegativity
Nonpolar molecules
typically have long chains of hydrocarbons
maybe have one or two carbonyls or ethers, but no charges
Amphipathic molecules
have hydrocarbon chains but also charges/large polar regions
Why do hydrophobic, nonpolar molecules conjugate around eachother?
When water is organized around a hydrophobic molecule it has less entropy. Water would rather be free to move. Minimizes water having to be caged around hydrophobic molecules and increases the amount of entropy.
4-types of noncovalent bonds
van der Waals interactions, H-bonds, ionic bonds, hydrophobic interactions
Hydrophobic interactions
occur from being pushed away from water, not that they are actually attracted to eachother
van der Waals interactions
random variations in the positions of the electrons around one nucleus may create a transient electric dipole, which induces a transient, opposite electric dipole
these two dipoles weakly attract eachother and bring the nuclei closer together
In biological systems are ionic bonds are
weaker than covalent bonds since occuring in aqueous environment that will pull them apart
Ionic bonding
refers to the complete transfer of valence electrons
Osmosis
water movement across a semipermeable membrane driven by differences in osmotic pressure
Isotonic
solutions of osmolarity equal to that of a cell’s cytosol
Hypotonic
solution of osmolarity less than that of a cell’s cytosol
inside of cell is more concentrated
water moves into the cell
Hypetonic
solution of osmolarity more than that of a cell’s cytosol
outside of cell is more concentrated
water moves out of the cell
How does water act as a weak acid?
Gives up a H+ proton
What is Keq?
ratio of products to reactants at equilibrium
Keq=[products]/[reactants]
Proton hopping
short “hops” of protons between a series of hydrogen-bonded water molecules result in an extremely rapid net movement of a proton over a long distance
Triprotic acids
can lose multiple protons
as they lose more protons, the molecule becomes more negative and pH increases
Equilibrium constant (Ka)
describes the tendency of an acid to dissociate
What does a higher Ka mean?
Higher Ka means a stronger acid
What does a lower pKa mean?
lower pKa means a stronger acid
Buffer
mixture of weak acids and their conjugate base
Henderson-Hasselbalch equation
pH = pKa + log[A-]/[HA]
can use when you have a buffer
Why do enzymes have an optimal pH at which they can work?
as we change pH, we change the charge of molecules in the enzymes
these changes can help make reactions occur
At low pH there are more…
positive charges
At high pH there are more…
negative charges
Dynamic equilibrium
the rate of the forward and reverse reaction is the same, so overall concentrations are unchanging
True or false organisms are at equilibrium with the environment
False
If an organism was at equilibrium with the environment, they would be dead
Osmosis
bulk flow of water through a semi-permeable membrane into an aqueous compatment containing solute at higher concetration
Osmolarity
measure of solute concentration
number of osmoles per liter of solution
osmole=amount of solute that dissolves to form one mole
Tick borne encephalitis virus
virus is engulfed by the cell and stuck in a lysosome
pH of lysosome is 4.5-5
the virus has a histidine with a pKa of 6, so at this pH histidine has a positive charge
the positive charge interacts with the negatively charged membrane and inserts genetic information into the cytoplasm of the cell
Hydrophobic interactions in DNA
nitrogenous bases are hydrophobic so they conjugate in middle of DNA
negatively charged phosphate backbone sticks outwards towards aqueous environment
What has signal recoginition particle receptors?
endoplasmic reticulum
Where are large numbers of histones?
nucleus
What is considered to be the postmaster of the cell?
golgi apparatus
What’s bigger amino acid or sucrose?
Sucrose is larger
What’s bigger bacterial cell or mitochondria?
Bacterial cell
