Med Biochem L1 - The Foundations of Biochemistry Flashcards
Biochemistry describes …
in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms
The smallest cells, certain bacteria known as …
mycoplasmas
Mycoplasmas are … nm in diameter and have a volume of about 10^-14 mL
300
A single bacterial ribosome is about … nm
20
Similarity between bacterial cell and animal cell
They have cytoplasm, plasma membrane, ribosomes
Differences between bacterial cell and animal cell
1) Bacterial cell is 1 micrometer;
Animal cell is 50 micrometer.
2) Bacterial cell has nucleoid;
Animal cell has nucleus, nuclear membrane, membrane-bounded organelles.
Presence of nuclear membrane: … and …
Eukaryotes and Prokaryotes
According to the evolutionary phylogenetic relationship: …, …, and …
Bacteria, Archaea, and Eukarya
Phototrophs
trap and use sunlight
Chemotrophs
derive their energy from oxidation of chemical substances
Lithotrophs
minerals
Organotrophs
organic matter
Autotrophs
can synthesize all of their biomolecules from CO2
Heterotrophs
need preformed organic nutrients for synthesis of their biomolecules
Cyanobacteria is
photoautotroph
Humans are
chemoheterotrophs
Both bacteria and archaea are
prokaryotes
… organisms derive energy from the transfer of electrons from fuel molecules to oxygen within the cell
Aerobic
… obtain energy by transferring electrons to nitrate (forming N2), sulfate (forming H2S), or CO2 (forming CH4)
Anaerobic
Many organisms that have evolved in anaerobic environments are … anaerobes: they die when exposed to oxygen.
Others are … anaerobes, able to live with or without oxygen.
obligate;
facultative
Oxidation = …
Lose electron
Both aerobic and anaerobic organisms …
burn fuel molecules to produce energy.
“Burn” means oxidation; Fuel molecules are oxidized, which means “lose electrons”.
So, some substances should take the electrons, which means “reduced”.
In aerobic organisms, for example, …
Glucose + O2 = CO2 + H2O
(Electrons are transferred from glucose to O2)
Anaerobic organisms also need an oxidant. In this case, the oxidant is not …, but …
not O2;
but nitrate, sulfate, CO2 etc
Prokaryotic cells have:
1) Cell membrane;
2) Cytoplasm;
3) Nucleoid;
4) Pili;
5) Flagella.
Eukaryotic cells have a variety of organelles:
1) Nucleus;
2) Mitochondria;
3) Endoplasmic reticulum and Golgi complexes;
4) Peroxisomes;
5) Lysosomes;
6) Vacuoles (in plants);
7) Chloroplasts (in plants).
Peroxisomes:
long chain fatty acids are oxidized
Lysosomes:
filled with digestive enzymes to degrade unneeded cellular debris
Vacuoles (in plants):
store organic acids
Chloroplasts (in plants):
synthesis of ATP
Cell membrane …
… has a lipid bilayer structure;
… mainly composed of phospholipids;
… also has proteins
Cell membrane occupies about 50% of cell membrane volume and perform various biological activities: …, …, … .
1) Integral proteins;
2) Peripheral proteins;
3) Lipid-anchored proteins.
Integral proteins:
Proteins that pass through or inserted into the cell membrane and have a hydrophilic cytosolic domain.
(Ion channels, proton pumps, receptors)
Peripheral proteins:
Have transient interactions with cell membranes.
(Some enzymes and hormones)
Lipid-anchored proteins:
Proteins that form a covalent bond with one or several lipid molecules in the cell membrane (G proteins)
(Mitochondria)
Inner membrane contains …
electron transport circuits and proteins for oxidative phosphorylation
Mitochondria has its own …
DNA
Rough Endoplasmic Reticulum - …
Main protein synthesis site
Smooth Endoplasmic Reticulum (planar cytoplasmic reticulum) - …
site of lipid synthesis and drug metabolism
Ribosomes - …
structures that synthesize proteins
The main components of the endomembrane system are … (5)
endoplasmic reticulum;
Golgi apparatus;
vesicles;
cell membrane;
nuclear envelope.
(Cytosol)
Substances other than the nucleus and organelle as part of the …
cytoplasm
Glycogen:
A polymer of glucose that is abundant in muscle and liver cells and, when necessary, breaks down glycogen into glucose for use in various organs (glycogen granules)
Lipids:
Stored mainly in adipocytes in the form of triglycerides and present in the form of lipid droplets in various cells
Crystals:
Located everywhere in the cell and thought to be a crystalline form of a specific protein
Pigment:
Melanin in skin and hair, etc
The cytoskeleton is divided into … (3)
microfilaments (actin filaments);
intermediate filaments;
microtubules.
Actin filaments
- finest fiber
- present in muscle cells
- cytokinesis, amoeboid movement, cell motility, cell shape endocytosis, exocytosis, cell contractility, mechanical stability
Microtubules
- thickest fiber
- it has a structure with a hole in the middle
- contributes to maintaining cell structure
- composes cilia and flagella
- providing a platform for intracellular movement
- mitotic spindle during cell division
Intermediate filaments
- not involved in cell movement
- contributes to maintaining structure by providing mechanical strength of cells or tissues
- Growth delay - the average height of a 10-year-old is similar to that of a 3-year-old child;
- Death of cardiovascular disease, usually around the age of 13;
- Structural protein lamin A cannot be converted from precursor to active form.
Hutchinson-Gilford progeria syndrom
- Acute visual loss due to optic nerve damage;
- Caused by a point mutation in mitochondrial DNA
Leber’s hereditary optic neuropathy
- Severe muscular weakness in early neonatal period;
- Caused by mutations in genes for peroxisome proteins
Zellweger spectrum syndrome
Lysosomal storage disease: ex, …
1) Gaucher’s disease;
2) Niemann-Pick disease;
3) Tay-Sachs disease;
4) Hunter syndrome
There is a striking similarity between yeast and human/other animals when …
it comes to glucose break down
The current understanding that all organisms share a common evolutionary origin is based in part on this observed universality of chemical intermediates and transformations - …
Biochemical Unity
Elements:
basic components that no longer break down into other substances
Compound:
A substance composed of two or more elements (the element loses its original properties and acquires new properties)
Mixture:
A state made up of two or more subtances without chemical bonding between them
Atom:
The most basic chemically indivisible particle
Molecules:
A substance composed of one or two or more atoms, which is a basic particle that exhibits the intrinsic properties of a substance
Trace elements:
present in small amounts in cells, but essential for life as they could be co-factors of enzymes or participate in enzymatic reactions
Three-dimensional structure of carbon bonds:
Four single bonds around carbon form a terahedral structure, C-C single bonds are freely rotatable, C=C double bonds are short and non-rotatable, and planar structures
Cells contain a group of small molecules that are converted by enzymes =>
metabolome (collection of low molecular weight metabolites produced by the cell during metabolism)
Macromolecules are the main constituents of cells =>
proteome (complete set of proteins expressed in the organism/cell);
genome (complete set of genetic material)
Stereochemistry = …
the arrangement of molecules’ atoms in 3D space
Carbon-containing molecules exist as … = molecules with the same chemical bonds and the same chemical formula but different configurations (the fixed spatial arrangement of atoms)
stereoisomers
Stereoisomers cannot …
convert into each other without breaking any bonds
Isomers are …
molecules or polyatomic ions with identical molecular formulas
Isomers:
1) Positional;
2) Geometric;
3) Optical isomers
Positional isomers:
same carbon skeleton and the same functional groups
Geometric isomers:
- Different arrangement of substituents attached to non-rotatable double bonds;
- Melting point, boiling point, solubility, crystal structure, biological role, etc. are different;
- The cis and trans isomers fall into this category.
Optical isomers
- Chiral atom/chiral center: when all surrounding covalent members are different;
- If there is one chiral carbon
Two non-overlapping, mirror images of isomers:
Enantiomers
(Enantiomers have the same physical and chemical properties, opposite directions of rotation of polarized light, and different specificities in enzymatic reactions)
A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called …
chiral centers
Chiral molecule:
Rotated molecule cannot be superimposed on its mirror image
Achiral molecule:
Rotated molecule can be superposed on its mirror image
… if they are mirror images
Enantiomers
… if they are not mirror images
Diastereomers
The configuration is (R) ( Latin …, ‘right’ )
rectus
[Clockwise (R)]
The configuration is (S) ( Latin …, ‘left’ )
sinister
[Counterclockwise (S)]
Molecular Conformation - …
the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom rotation about single bonds.
Configuration and conformation are important in biological interactions of:
- reactant with its enzyme;
- hormone and its receptor on cell membrane surface;
- antigen and antibody.
Usually only one form exists in living organisms, not both at the same time
Racemic mixture is …
a 50:50 mixture of two enantiomers.
Because they are mirror images, each enantiomer rotates plane-polarized light in an equal but opposite direction and is optically inactive. If the enantiomers are separated, the mixture is said to have been resolved.
Types of non-covalent interactions in aqueous solutions:
- hydrogen bond
- ionic interactions
- hydrophobic interactions
- van der Waals interactions
Hydrogen bonds in water molecules
A weak bond caused by the electrical force between oxygen in one water molecule and hydrogen in a neighboring water molecule.
Characteristics of hydrogen bonding
- much weaker than covalent bonds;
- breaks and forms constantly
- hydrogen bonds are formed between F, O, and H in polar solute and the hydrogens attached to F, O, and N on another molecule nearby
Water is a … solvent, solute is hydrophilic
polar
When the donor-hydrogen-acceptor is in … , its attraction is strongest
a straight line
Water is … with non-planar compounds and does not dissolve => hydrophobic
immiscible
When water is mixed with bipolar compouds, it forms …
micelles.
Buffer solutions …
maintain a stable pH by neutralizing added acids or bases.
Dynamic steady state:
A -> B -> C
Equilibrium:
A <=> B
Types of thermodynamic systems:
Isolated system;
Closed system;
Open system.
Isolated system:
Both matter and energy cannot be exchanged with the outside
Closed system:
Only energy can be exchanged with the outside
Open system:
Both energy and material can be exchanged with the outside
