BIOCHEM Lecture 1 Flashcards
What are the types of chemical bonds
covalent, ionic, and hydrogen bonds
Covalent bonds
- when 2 atoms share one or more pairs of electrons
- attain stable electron numbers in their outermost shells
- very strong; takes energy to break
- very stable under physiological conditions
- can be single, double or triple
Define electronegativity
- attractive forces that an atomic nucleus exerts on electrons
- depends on number of protons and distance between the nucleus and electrons
nonpolar covalent bond
electrons shared equally
polar covalent bond
unequal sharing of electrons bc one atom has greater electronegativity
Ionic bonds
when one atom is more electronegative than the other - complete transfer of electrons may happen
What do ionic bonds result in
two ions with will outer shells
what is an ion
electrically charged particles formed when atoms lose or gain electrons
cations
positive
anions
negative
ionic attractions
bonds formed by electrical attraction of positive and negative ions
What is the arrangement of ions in a solid
ions closer together and ionic attractions are strong
what is the arrangement of ions in water
ions further apart and attraction is much weaker
Hydrogen bonds
- form within or between molecules with polar covalent bonds
- weak electrical attractions between partially negative charges atom and partially positively charged atoms
amino acids make…
proteins
Rank bonds in order
covalent > ionic > hyrdogen
nucleotides make..
nucleic acids
monosaccharides make…
polysaccharides
glyecerol and 3 fatty acids make
lipids
what are the functional groups present in an amino acid
amino group and carboxyl group
How do monomers join
by dehydration synthesis or condensation reactions
What is organizational order of a cell
atoms –> molecules –> macromolecules –> organelles –> cell
What is the hierarchy of organization is a cell structure
chemical/molecular –> cell –> tissue –> organ –> organ system –> organisms
prokaryotes
single celled organisms that include bacteria and cyanobacteria
eukaryotes
- well defined nucleus surrounded by nuclear membrane
- can be singles celled or multicelled
function of nucleus
location of main genome - site of most DNA and RNS synthesis
function of mitohcondrion
site of energy yielding oxidation reactions - has its own DNA
function of chloroplast
site of photosynthesis in green plants and algae - has its own DNA
function of golgi
continuous membrane throughout the cell; rough part studded with ribosomes
lysosome
membrane enclosed sacs containing hydrolytic enzymes
peroxisomes
sacs that contain enzymes involves in metabolism of hydrogen peroxide
cell membrane
separates cell contents from outside world; includes organelles and the cytosol
central vacuole
membrane enclosed sac (plant cells)
what is the chemical structure of water
- sharing of electrons b/n one oxygen and two hydrogen atoms
- bonding electrons shared unequally
- attraction b/n partially negatively charged oxygen atom and partially positively charged hydrogen atom
What are some unique structures of water
- polar molecule
- forms hydrogen bonds
- tetrahedral shape
How many hydrogen bonds can water be involved in
4
Hydrophillic interactions
“water loving”
- polar molecule that interacts with water
- weak attraction of hydrogen bonds
Hydrophobic interactions
“phobia of water”
- nonpolar molecule that aggrgates with other nonpolar molecules
- hydrocarbon molecules
What is a solution
produced when substance is dissolved in a liquid
Substance in a solution is solute or solvent?
solute
liquid is solute or solvent in a solution
solvent
in an aqueous solution, what is the role of water
water is the solvent
Where do most biochemical reactions occur
in aqueous solutions
What type of substances tend to dissolve in water?
hydrophillic
Define amphipathic molecules
both polar and nonpolar character
- interaction b/n nonpolar molecules is very weak; van der Waal interaction
Micelle
spherical arrangement of organic molecules in water solution
What is the arrangement of molecules in a micelle
- hydrophobic parts buried inside the sphere
- hydrophobic parts on surface of sphere and in contact w water in the environment
how do acids interact when dissolved in a solution
release H+
how do bases act when dissolved in a solution
accept H+
How does a strong acid act in water
ionizes fully in water
HCL ==> H+ + Cl-
How does a weak acid act in water
not all acid molecules dissociate into ions
How does a strong base act in water
fully ionizes in water
How does a weak base act in water
can accept a H+ ion
True or False: acid- base reactions may be reversible
True
When is ionization irreversible
ionization of SA and SB
Higher the Ka..
stronger the acid
Lower the pKa…
stronger the acid
Define pH
-log
What does the Henderson-Hasselbalch equation teach us
when concentrations of weak acid and conjugate base are equal - pH of solution equals pKa of weak acid
when pH < pKa…
weak acid predominates
when pH > pKa…
conjugate base predominates
What is a buffer
solution whose pH resists change upon addition of acid or base
What does buffer consist of
weak acid and conjugate base
What is the purpose of a buffer
helps maintain stable pH
Hyperventilation can result in increase blood pH which leads to..
respiratory alkalosis
Hypoventilation can result in decreases blood pH which leads to..
respiratory acidosis
What is CA
carbonic anhydrase - catalyzes the formation of carbonic acid from water and carbon dioxide
What is CAI
carbonic anhydrase Inhibitors - control aqueous humor production and lower IOP (intraocular pressure)
What determines the identity of an amino acid
the R group
Every amino acid is chiral except which one
glycine
Peptide bond
amide bond between the alpha - carboxyl group of one amino acid and alpha amino group of another amino acid
What process forms peptide bonds?
through the process of dehydration synthesis
What does glutathione consist of
- gamma, Glu, Cys, Gly
Properties of glutathione
tripeptide with unusual gamma carboxy peptide bond linkage
- important reductant in cells - helps protect proteins from oxidative damage
Where does glutathione play an essential role
lens, cornea, retina, and other ocular tissue
Polymers are formed through what type of a reaction
condensation reaction
Polymers are broken into monomers through what reaction
hydrolysis reaction
Primary structure
polypeptide strand
Secondary structure
helix and pleated sheet - 3 polypeptide strands
tertiary structure
helix and pleated sheets folded into 3D shape
Quatenary structure r
relationship of several folded polypeptide chains forming a protein
When can proteins be denatured
when proteins encounter hostile environments such as temp and pH
Hydrolysis during denaturation destroys which structure
primary - digestion of a protein
Globular proteins
- compact, tightly folded
- soluble in water and salt solutions
- most enzymes
example of a globular protein
hemoglobin
fibrous proteins
long fibers or large sheets
- mechanically strong
- insoluble in water and dilute salt solutions
- play important role in structural roles
examples of fibrous proteins
keratin, collagen
Triple Helix of Collagen
- 3 polypeptide chains in triple helix
- strands held together by hydrogen bonding
- collagen helices become cross linked by covalent bonds formed b/n Lys and His residues
Vitreous humor
makes up semiliquid gel
Cornea
forms lamellae in corneal stroma
sclera
lens capsule and blood vessels
retina
ocular basement membranes
what does collagen in eye do
- Forms and maintains tissue structure
- scaffoldinf and adhesion
- sustains shape
- provids strength
- maintains transparency
Ehlers Danlos syndrome
mutations affecting structure or assembly of different collagen types
Crystallins
- predominant structural, water soluble proteins in the lens
- contains significant amounts of Cys and Met
- alpha, beta, and gamma crystallins with subunits and subtypes
- maintain elongated shape of lens fiber cells and lens structure
- affects refractive index and transparency of lens
What kind of bond within and between crystallin protein
disulfide bonds
what happens when crystallin is oxidized
protein shape is altered with exposes Cys sulfhydryl groups
what is a senile cataract
high molecular weigh aggregates are formed which reduces the integrity and clarity of the lens
Hemoglobin
-tetramer of two alpha chains and two beta chains
- each chain has 1 heme group - hemoglobin can bind up to 4 molecules of O2
-
What is function of hemoglobin
to transport oxygen
What are antibodies
two identical heavy chains and two identical light chains held together by disulfide proteins
- glycoproteins
what are the binding sites for antibody on antigen called
epitopes
PrPc
normal cellular prion protein on cell surface
PrPSc
scrapie protein
