exam 1: lecture 1 Flashcards
what 3 branches of study in cell biology a combination of?
Cytology
Biochemistry
Genetics
what is cytology
the study of cells
the beginning of cell biology
-an observation where it is just looking- not experiment or interaction.
not until biochemistry and genetics that there were interactions or experiments
what is cell biology?
a cell-level zoology
what does a zoologist do? study how the animal functions
-> cell biology is the same: how they move, make energy, reproduction, organelles, and different types of cells
micrometer
1/1,000,000th meter (million)
ex. bacteria (prokaryotes), nucleus, mitochondria
nanometer
1/1,000,000,000th meter (billion)
ex. mycoplasma, viruses, ribosomes,proteins, lipids, small molecules, atoms
uses electron microscope
number of electron in each shell orbital
1st: 2
2nd: 8
3rd:8
what is valence number
the number of electrons that are needed to fill the orbitals
what are covalent bonds
bonds that are made by sharing of electrons of molecules ( missing valence electrons)
-strong: takes energy to break (heat from fire, electricity)
the importance of carbon: organic chemistry
the study of all classes of carbon-containing compounds
the importance of carbon: biochemistry
the study of chemistry of living systems
what is the most important atom in biological molecules?
carbon
specific bonding properties of carbon account for the characteristics of carbon-containing compounds
bonding properties of carbon
carbon has 4 valance electrons, which means it can form 4 bonds
most likely to form covalent bonds with C,H,O,N,S
what is a covalent bond
the sharing of a pair of electrons
stable
why are strong covalent bonds necessary for life
high energy such as UV light is more hazardous to the molecules (nucleic acids are sensitive)
->the visible light is lower in energy than C bonds
=>visible light cannot break of he bond of covalent bonds
what are ionic bonds
weaker than covalent bonds
ions: imbalance between protons and electrons (have a charge)
cation: loss of electron (+) ~ Na+
anion: gain of electron (-) ~ Cl-
structure of sodium chloride
a crystal
how to break ionic bonds? water (the molecules will dissociate)
what are hydrogen bondings
The bonding of H with other charged atoms
ex.h2o
H has a smaller nucleus-spends more time around the oxygen
->uneven electrons sharing=> polar charged
what makes water molecules polar?
- unequal distribution of electrons
- geometry: bent, not linear
- the O atom has a slight negative charge that draws H atoms around it
what bonds water molecules tgt?
hydrogen bond
=1/10 as strong as covalent bonds
How are water molecules cohesive?
due to their polarity, they are attracted to each other as the electronegativity of oxygen draws other electropostive H nearby
what are the effects hydrogen bonds have on water
- surface tension
- boiling point
- specific heat
- heat of vaporization
- freezing point: salt content plays a role in water not freezing
what are the two weak molecular interactions
- van der waals
- hydrophobic interaction
what are van der waals interactions
the weak attraction between two atoms ONLY IF THE ATOMS ARE VERY CLOSE TGT AND ORIENTED CORRECTLY
-atoms that are too close will repel
-van der Waals radius: defines how close other atoms can come to it= the basis for space-filling models
=explains why molecules are certainly distanced
what are hydrophobic interactions
the behavior of nonpolar groups- will try to minimize contact with water
-> cause nonpolar groups to be found in the inside of a protein or a membrane
Building block of the cells
- sugars (carbohydrates)-> polysaccharides
2.fatty acids (lipids)-> fats, membranes - amino acids-> proteins
- nucleotides (DNA/RNA)-> nucleic acids
+WATER
why is water so important biochemically?
- Most nutrients are dissolved in water
- water heps the transport of food and wastes in/out of cells
- water is the medium for most reactions
- water makes up on avg. to 65-75% of a cell’s mass
How do hydrogen bonds make water a special molecule
- being able to form hydrogen bonds, this allows it to have a high boiling point and a low freezing point
->water freezes from the top down unlike other nonpolar molecules - its polarity makes it an excellent solvent
- can act as a donor of hydroxide (OH-) and hydrogen (H+)
H2O–dissociates–> H+ & OH_ - makes water an excellent temp. buffer
-small scaled: slow exchange of heat
-large scale: during the summer, water will stay cold for a while due to the cold climate of winter has heat is lost during the summer
How does water have high temp-stabilizing capacity
high specific heat
-> water changes temp slowly, protecting living systems from extreme temp changes
= without this, the energy released into cells would lead to overheating and death
water freezes from the topdown, but wy does ice float?
in ice, water molecules from a crystal lattice, which is less dense
in liquid water, no lattice forms, so liquid water is denser than ice
what is diffusion
the movement of molecules that goes to an area of high concentration to an area of low concentration
what is osmosis
the diffusion of water
principle 1: concentration is the amount of a particular molecules per set volume (200gm/L)
principle 2: more solute-> diluted water
-more stuff dissolved in water, the lower the concentration of water
hypotonic
“pop”
more solute inside-> water moving in
hypertonic
shrink
less solute inside->water moving out
Examples of homeostasis
water balance
regulations of ions
regulations of sugar levels
pH scale
7: OH-=H+
7-14: OH->H+ (base:10^14)
0-7: OH-<H+ (acid: 10^1)
Functions of Sugars (CHO)
1) nutrient for energy
2) nutrient storage
3) structural function in cell walls
4) signal transduction (recognition, transportation)
How many carbons monosaccharides have
3 or more carbons
(H have double the # of C & O)
the difference between glucose and fructose
same chemical formula
the difference is where the double bond is
how are macromolecules synthesized
- synthesized by the stepwise polymerization of monomers
- condensation (monomers are put tgt by losing water)
- activated monomers must be present- coupled with a carrier molecule
- energy for coupling is provided by ATP
- directionality-differs at each end
what is condensation
monomer in, water out
what is hydrolysis
water in, monomer out
what is a glycosidic bond
a covalent sugar bond that connects sugars
Beta glycosidic bond
galactose-glucose
cellulose
STRAIGHT-180 turns to each other
-> easy hydrogen bonding between monomers and its neighbors= stable structure & resistant to hydrolysis
alpha glycosidic bond
starch/glycogen
BEN-longer and father apart–> circular structure
glucose and fructose form what sugar
sucrose
What are storage polysaccharides?
starch in plant cells
glycogen in animal cells & bacteria
* consists of alpha units linked by alpha glycosidic bonds (1-4) [1-6: side chains)
storage polysaccharides: glycogen
in animals and bacteria
highly branched, the branches 8-10 unis
mainly in the liver (glucose) & muscle tissue (muscle contraction)
bacteria store glycogen as a glucose reserve
storage polysaccharides: starch
*glucose reserve in plants
*unbranched amylose (10-30%)
*branched amylopectin (70-90)- alpha 1-6 branches once every 12-25 units (longer than glycogen)
*starch grains in plastids
amyloplasts: starch storage
structural: cellulose
repeating monomers of beta units (1-4)
*chitin: cell walls of fungal cells and insects exoskeletons
functions of proteins (CHONS)
1) structrual- cytoskeleton
2) enzymatic activity
3) signal transduction functions
4) nutrient
what are 2 types of chemical in the cells
anabolic: to build
A+B-> AB
catabolic: to break down
AB-> A+B
enzymes
speed up chemical reactions @ low temp.
lowering activation energy
Lock and key model
have specificity between substrate and enzyme
proximity is important because if they’re close tgt, then they use less energy to “bang” them tgt
how are amino acids held together
by peptide bond with condensation (dehydration)
amino group (N terminus) to carboxyl group (C terminus)
peptide bond-stable and stiff
levels of protein structure
primary
secondary: motifs (substructure)
tertiary structure: final 3D structure (active site + substrate)
quaternary : multiple monomers join tgt
protein structure: primary
formal designation sequence
written from N-terminus to C-terminus
insulin: 1st to have its sequence known
–> 1 alpha + 1 beta subunit with 21 & 30 amino acids
“intra” vs “inter”
intra: w/in chain
inter: between 2 peptide chains
form by a disulfide bond (condensation/ dehydration)
what is the importance of primary structure?
genetically: specified by the order of nucleotides in mRNA
structurally: order + identity directs the formation of higher-order structures
protein structure: secondary
describes local regions that result from hydrogen bonding betwen NH and CO groups with the backbone
= result in alpha helix & beta sheet
secondary structure: alpha helix
spiral: peptide backbone with r group jutting out
3.6 aa per turn
hydrogen bond: NH group of one aa & the CO group of a second aa that is one turn away from the first
secondary structure: beta sheet
sheetlike conformation with “peaks” and “troughs”
r groups are on alternating sides
same polarity: parallel
opposite polarity: antiparallel
protein structure: tertiary structure
*depends on the interactions of the R-groups
not repetitive
*neither repetitive/easy to predict
—> the sum of hydrophobic residues avoiding water, hydrophilic residues interacting water, the repulsion of same charged residues, and attraction between oppositely charged residues
Tertiary structure: native conformation
most stable 3D structure
what are the two board categories?
1) fibrous
2)globular
Fibrous proteins
highly ordered, repetitive structure
ex.
fibroin of silk
keratin of hair and wool
collagen in tendons and skin
elastin in ligaments and blood vessels
globular proteins
folded in compacted structures
unique structure:
-alpha helical (ball & stick model)
-beta sheet (spiral & ribbon model)
-a mixture of both
What are the interactions that determine the tertiary structure of proteins?
1) hydrogen bond:
-between peptide groups
-side chains &peptide bonds
-between 2 side chains
2) hydrophobic interaction
-push h2o have hydrophobic chains near each other
3) ionic bond
4) disulfide bond
protein structure: quaternary structure
subunit interactions & assembly
–> multimeric proteins: multiple identical subunits
ex. hemoglobin
formation is spontaneous with the help of chaperone molecules
