Part 1 Flashcards
A molecular description of the structures, mechanisms, and processes of living things.
Definition of biochemistry
- primary function: chemical reactions and structural components
- Monomer: amino acid
- polymer/macromolecule: protein or peptide/polypeptide
protein
-primary function: genetic information
- monomer: nucleotide
- polymer/ macromolecule: RNA/ DNA
nucleic acids
-primary function: energy storage/membranes
- monomer: lipids
lipids
-primary function: energy
- monomer: monosaccharide
- polymer/macromolecule: polysaccharide
carbohydrates
maintaining a steady-state with the environment, even when faced with external challenges.
homeostasis
an organic molecule that includes carbohydrates, protein, lipids, and nucleic acids.
biomolecules
- defines the periphery of the cell
- composed of lipid and protein molecules
- thin, flexible, hydrophobic barrier around the cell
- contains embedded transport proteins, receptor proteins, and membrane enzymes
Plasma Membrane
internal volume enclosed by the plasma membrane; composed of cytosol and organelles
cytoplasm
(an aqueous solution) highly concentrated solution: contains enzymes RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions
cytosol
the site of protein synthesis
ribosomes
organic compounds required by many enzymes for catalytic activity
coenzymes
small molecules that are intermediate products of biochemical processes that take place in living organisms
-(such as amino acids, lipids, peptides, nucleic acids, carbohydrates, vitamins, and minerals)
metabolites
contains all of the cell’s chromosomes, which encode the genetic material.
nucleus
complete set of genes, composed of DNA
genomes
organisms whose cells contain a nucleus and other membrane-bound organelles.
eukaryotes
a microscopic single-celled organism that has neither a distinct nucleus with a membrane nor other specialized organelles
Prokaryotes
plentiful supply of O2; organisms transfer electrons from fuel to O2 for energy
Aerobic
devoid of O2; organisms transfer electrons to nitrate, sulfate, or CO2 for energy
Anaerobic
Mitochondria
the site of most of the energy-extracting reactions of the cell
polymers that are assembled from relatively simple precursors: proteins, nucleic acids, polysaccharides
macromolecules
long polymers of amino acids; can function as enzymes, structural elements, signal receptors, transporters
Proteins
polymers of nucleotides; store and transmit genetic information
- DNA and RNA
nucleic acids
polymers of simples sugars:
- energy-rich fuel stores
- rigid structural components of cell walls
- extracellular recognition elements that bind to proteins on other cells
polysaccharides
stereoisomers that are mirror images of each other
enantiomers
system exchanges both energy and matter with its surroundings
open system
one reactant is oxidized (loses electrons) as another is reduced (gains electrons)
oxidation-reduction
represents the randomness or disorder of the components of a chemical system
entropy
negative is spontaneous/ exergonic, positive is non-spontaneous/ endergonic
Gibbs Free energy
a state in which opposing forces or influences are balanced.
equilibrium
proteins that help speed up metabolism, or the chemical reactions in our bodies.
enzymes
greatly enhance reaction rates of specific chemical reactions without being consumed in the process
catalyst
The breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy
catabolism
synthetic pathways that require the input of energy
anabolism
Is most often single-stranded and has a backbone made of alternating phosphate groups and the sugar ribose,
RNA
the molecule that carries genetic information for the development and functioning of an organism.
DNA
unmutated cells
Wild Type
changes in the nucleotide sequence of DNA
- changes the instructions for a cellular component
- can be beneficial
mutation
members of the same protein family
homologs
Why don’t nonpolar compounds dissolve in water?
Nonpolar compounds do not dissolve in water due to thermodynamically unfavorable conditions (enthalpic and entropic problems)
biomolecule containing both hydrophobic and hydrophilic regions
amphipathic molecules
water flowing to areas of high concentration from areas of low concentration (not the size the quantity)
osmosis
not net water movement
isotonic
Cell in solution: water moves out and cell shrinks
hypertonic
Cell in solution: water moves in creating outward pressure; cell swells, may burst
hypotonic
What happens when a molecule ionizes?
gains or loses electrons; usually and equilibrium process but sometimes all or nothing with strong acids/ bases
any process by which electrically neutral atoms or molecules are converted to electrically charged atoms or molecules (ions) through gaining or losing electrons.
ionization
Strength of a chemical bond A-B
the energy required—an endothermic process—to break a bond and form two atomic or molecular fragments, each with one electron of the original shared pair
bond dissociation energy
electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another
hydrogen bond
water loving; describe compounds that dissolve easily in water; generally charged or polar compounds
hydrophilic
water fearing; non polar molecules such as lipids and waxes
hydrophobic
contain regions that are polar (or charged) and regions that are non-polar
amphipathic
distance-dependent weak attractions and repulsions between transient dipoles
Van der Waals / London dipersion forces
gives the position of equilibrium for the generalized reaction
- defined in terms of the concentrations of reactants and products at equilibrium
equilibrium constant / Keq
figure expressing the acidity or alkalinity of a solution on a logarithmic scale on which 7 is neutral, lower values are more acidic and higher values are more alkaline.
- Defined by the expression: -log[H+]
pH
used to differentiate between strong and weak acids. The acid dissociates more as the Ka increases. Strong acids must therefore dissociate more in water. A weak acid, on the other hand, is less likely to ionise and release a hydrogen ion, leading to a less acidic solution.
acid dissociation constant
- analogous to pH and defined by the equation:
=log 1/Ka or =-logKa - the stronger the tendency to dissociate a proton, the stronger the acid and the lower its ___
pKa
aqueous systems that tend to resist changes in pH when small amounts of acid or base are added
- consists of a weak acid (proton donor) and its conjugate base (proton acceptor) or vice versa
buffer
describes the shape of the titration curve of any weak acid
Henderson-Hasselbach
What are some functions of a protein?
transport, structure, channels, enzymes, signaling
Which amino acid is achiral?
glycine
Which amino acids are non polar and have aliphatic R groups?
glycine, alanin, proline, valine, leucine, isoleucine, methionine
Which amino acids are aromatic?
phenylalanine, tyrosine, tryptophan
Which amino acids are non charged polar (polar, uncharged R groups)
Serine, threonine, asparagine, glutamine, cysteine
Which amino acids positively charged?
Histidine, arginine, lysine
Which amino acids are negatively charged?
aspartate, glutamate
What are the two ionizable groups on every amino acid and what is the possible third?
the amino group and carboxylic acid group and possibly the side chain
a dipolar ion that has equal number of negative and positive charges
zwitterion
the pH when the overall charge is 0 (less soluble, proteins and amino acids alike have a pI
Isoelectric Point
water is released when we form a peptide bond between amino acids from the OH on the carboxy acid and the hydrogen connected to the nitrogen of the next amino acid
condensation reaction
homologs within an organism
paralogs
homologs among species
orthologs
What is the resonance imply in a peptide bond?
implies rigidity for the backbone
a collection of proteins that share >25% identical sequence (share common structure and function)
protein families
What is the blood buffering system?
bicarbonate system
When an amino acid is part of a polypeptide that amino acid is called a _____
residue
naturally occurring variation in an aa sequence in a population or organism
polymorphism
