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199 Cards in this Set

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name the 4 most abundant elements in the human body
Nitrogen
Carbon
oxygen
hydrogen
List the essential elements other than N,C,O & F.
Sodium (Na)
Potassium (K)
Magnesium (Mg)
Calcium (Ca)
Phosphorus (P)
Sulfur (S)
Chlorine (Cl)
Atomic weight?
protons + neutrons
Term for atoms tendency to establish completely full outer energy levels?
Octet Rule
sharing electrons between atoms forms _______ ?
Covalent bonds
strongest bond?
Covalent
Bond formed by the transferring of electrons?
Ionic bonds
Bond due to molecular polarity?
Hydrogen bonds
a force due to fluctuating electrical charges?
Van der Waals Attraction

Includes :dipole-induced dipole,
induced dipole-induced dipole.
and
dipole-dipole
term for the repulsion force from water?
hydrophobic forces
forces that are weak in water, but in the absence of water are very strong (as in salt).
Electrostatic attraction
functional group name for OH
Hydroxyl
functional group name for O=C
Carbonyl
functional group name for
O=C-OH
Carboxyl
functional group name for
H-N-H
Amino
functional group name for
O
O-P-O
O
phosphate
functional group name for
S-H
Sulfhydryl
functional group name for
H
H-C-H
Pyruvate
How do Ketones differ from aldehydes?
In ketones the carbonyl (C=O) is placed between two carbons rather than at the end of a carbon skeleton (with a Hydrogen)
functional group that features a carbonyl group (C=O) bonded in between two other carbon atoms?
Ketone
eg: acetone is most common
Functional group in which a carbonyl group is bonded between the end of a carbon skeleton and a hydrogen.
Aldehyde

*many fragrances are aldehydes.
term for adding a phosphate to a substrate-
Phosphorylation
Term for adding a carboxyl group to substrate?
Carboxylation
Term for removal of carboxyl?
De- carboxylation
Term for removal of a hydrogen from substrate?
De- hydrogenation
Term for removal of amino group from substrate?
De-amination
4 Major types of macromolecules in cells?
1. polysaccharides
2. fats/lipids
3. proteins
4. nucleic acids
Monosaccharide containing an aldehyde group?
Aldose
Eg: glucose
Monosaccharide containing a ketone group?
ketose
Eg: fructose
similarity and difference between fructose and glucose?
both are 6 carbon sugars

Different STRUCTURES:
Fructose is in the ketose group (contains C=O)
Glucose is in the Aldose group (contains H-C=O)
Term for isomers in which the geometrical positioning of atoms and functional groups in space differs- MIRROR IMAGES
Optic isomers
or
Stereoisomers
Term for isomers in which the atoms and functional groups are joined together in different ways
Structural isomers
Configuration when OH group is on the same side as carbon 6?
Beta Configuration
Configuration when OH group is on the opposite side of carbon 6?
Alpha configuration
define condensation.
A water molecule is released and two monosaccharides become one polysaccharides.
define hydrolysis.
a water molecule is added to a polysaccharide resulting in 2 monosaccharides.
Term for when a water molecule is added to a polysaccharide resulting in 2 monosaccharides.
hydrolysis
what is a sugar derivative?
When a hydroxyl group of a simple Monosaccharide is replaced by a different group.
sugar derivative that is the building block of chitin?
Acetylglucosamine
sugar derivative with a amine group on carbon #2?
glucosamine
sugar derivative with a carboxyl group?
glucuronic acid
disaccharide with 2 glucoses?
Maltose
Disaccharide with 1 glucose and 1 galactose?
lactose
disaccharide with 1 glucose and 1 fructose?
sucrose
saccharide with 30-50 sugars?
oligosaccharide
saccharide with over 50 sugars?
Polysaccharide
polymer of glucose used in energy storage in animals?
glycogen

(starch in plants)
polymer of glucose used in energy storage in plants?
starch

(glycogen in animals)
in the cell walls of plants.
an unbranched polymer of glucose used for structre and other things.
Cellulose
glycogen, starch and cellulose are all examples of what kind of sugars?
POLYSACCHARIDES.
a large molecule (macromolecule) composed of repeating structural units with covalent bonds
polymer
This polymer of glucoronic acid and acytlglucoamine is a structural component of cartilage.
Chondroitin sulfate
(part of proteoglycan)
This polysaccharide of glucose enhances WHITE blood cell function.
Glucan
(the mushrooms!....beta glucan used against tumor cells!)
carbohydrates in the human body are stored in the _____.
liver
a protein "decorated" with oligosaccharide. ?
glycoprotein
function of glycoprotein?
-regulates white blood cell extravasation (leakage)
-cell surface proteins for immune response (ID!)
-cell-cell interactions
structural, etc.
polysaccharides "Decorated" with protein?
Proteoglycans
Function of Proteoglycans?
mostly structural
lipids with a carbohydrate attached?
glycolipids
function of glycolipids?
component of cell membrane
energy
cellular recognition
1 meter ^-9?
nanometer (nm)
1 Liter ^ -6?
microliter (μL)
which is the preferred light microscope for microbiology which shows the image in 3D?
interference contrast microscope
how would you describe the image displayed by a Bright Field Optics microscope?
grey, low contrast, 2D, light microscope (vs electron microscope)
which light microscope shows a highly contrasted 2D image?
Phase Contrast Optics Microscope
what is the maximum resolution for a light microscope?
0.2 μm
What is the maximum resolution for an electron microscope?
0.002 μm
*this is one hundred times more precise than a light microscope!
What are the 2 types of electron microscopes and their corresponding resolutions?
Transmission (TEM): resolution .002 μm in 2D
Scanning (SEM): resolution 0.02 - 0.003 μm in 3D

*These use LASER light!
What is the central dogma of microbiology?
Transcription and translation!
What are the macromolecules in microbiology and their corresponding "building blocks"?
1. Polysaccharides made of sugars.
2. Fats/Lipids/Membranes made of fatty acids.
3. Proteins made of amino acids.
4. Nucleic acids made of nucleotides.
what are the basic shapes of prokaryotic cells?
spherical, rod shaped and spiral.
proteins outside the cell which support the cell and are crucial to it's survival.
Extracellular matrix
Which element has a unique atomic weight and why?
Hydrogen...weight of only 1 because it has no neutron!
the INNER (cytosolic) membrane of the lipid bilayer contains this important phospholipid......
PhosphatidyLINOSITOL
the OUTER membrane of the lipid bilayer contains this important phospholipid......
PhosphatidylCHOLINE
This enzyme helps transfer phospholipids to the other half of bilayer to balance cell membrane...
flippase

*It FLIPS!
chemical property of having a hydrophyllic carboxylic head and a hydrophobic hydrocarbon tail?
amphipathy
(or having both polar and non-polar properties)
the hydrophyllic head of a phospholipid is made of _____.
polar group, such as choline or inositol
and a phosphate
a fat in which all covalent bonds are used up by hydrogens?
saturated
a fat in which there are fewer hydrogens, causing the molecule to kink?
unsaturated
basic structure of a lipid?
fatty acids (hydrocarbon chain)
+
glycerol backbone
Isoprenoid
lipids with multiples of isoprene in the form of (C5H8)n
What are 2 examples of molecules made from isoprene (a lipid) units?
Steroids
&
Terpene (eg. vitamin A)
lipid derivative with a carbohydrate attached?
glycolipids
a fat soluble enzyme which digests, transports and processes stored lipids for use within the body?
lipase
what are the 4 main biological functions of lipids?
1. Structure of membranes
2. energy storage
3. essential vitamins (A, D, E & K)
4. Cell signaling
fats vs carbs: kcal per gram?
carbs: 4 kcal
fats: 9 kcal
where are vitamins A,D,E,& K stored?
liver, fatty tissues
4 fat soluble vitamins that are isoprene based?
A,D,E & K
(stored in liver and fatty tissues)
3 components of a phospholipid?
1. Hydrophyllic head: polar group (like choline on outer or Inositol on inner) + phosphate
2. Linker: glycerol
3. Hydrophobic tail: fatty acids
how thick is the lipid bilayer?
5 nm
Surface of cell membrane is____.
fluid.

lateral diffusion, flexion, rotation, and flip-
Where are phospholipids synthesized?
endoplasmic reticulum

* Then new phospholipids are added to the cytosolic side of cell membrane.
what effect does cholesterol have on a cell membrane?
stiffens it.
what are the 4 main types of membrane proteins?
1. transporters
2. anchors
3. receptors
4. enzymes
function of transporter proteins in membrane?
(example)
Eg: Na+ pump
pumps sodium out and potassium in.
function of anchor proteins in membrane?

(example)
eg. integrins
link intracellular actin filaments to extracellular matrix
function of receptor proteins in membrane?
transmit growth signals
(for example, by binding an extracellular molecule)
function of enzyme proteins in membrane?
eg. use extracellular signal to begin production of intracellular molecules
membrane proteins with oligosaccarides?
glycoproteins
membrane proteins with polysaccharides?
proteoglycans
The meshwork of fibrous proteins attached to the CYTOSOLIC surface of the membrane?
Cell cortex
the major component of the cell cortex.
Long thin flexible rod proteins about 10 nm long.
Spectrin
How are membrane proteins arranged within the cell membrane??
locally confined, forming functionally specialized regions
in what ways do cells create membrane domains (4)
cell cortex
extra-cellular marix
proteins of another cell
diffusion barrier (tight junction)
What do we call the tight junction that cells form?
diffusion barrier
How are intestinal epithelial cells unique?
they forms distinct apical and baso-lateral membrane domains.
what are small amphipathic molecules called?
detergents
what are the two most common detergents we need to know?
SDS (sodium dodecyl sulfate, but call it SDS)
and
Triton X-100 (number indicates strength)
basic structure of an amino acid?
4 parts:
-amino (NH)
-Alpha Carbon attached to side chain (aka R group) (and a hydrogen on the other side)
-Carboxyl (C=O)

R
I
-N-C-C-
I . I . II
H-H-O
what is an R group?
side chain of an amino acid
dehydration forms
___________ to link amino acids.
peptide bonds
what are the types of bonds that give proteins their 3D structure? (5)
1. ionic bonds(between CHARGED amino acids)
2. Hydrogen (with N or O or NH)
3. Van der Waals
4. hydrophobic (attract other hydrophobic)
5. covalent (between sulfurs)
a covalent bond between 2 sulfurs in protein structure?
disulfide bridge
levels of protein structure:
the amino acid sequences.
primary structure
levels of protein structure:
alpha helix or beta sheet
secondary structure
levels of protein structure:
combination of alpha helices and beta sheets (eg. a-b-a)
motif
(a motif of secondary structures)
levels of protein structure:
final folded shape of a polypeptide (protein unit)
tertiary structure
levels of protein structure:
a combination of multiple protein units.
quaternary structure
a segment of a polypeptide chain (protein) which forms a compact stable structure and ysually carries out a function. (usually enzymatic)
Domain
another word for a polypeptide chain?
protein
amino acid represented by
D
Aspartic Acid
Asp
negative side chain
amino acid represented by
E
Glutamic Acid
Glu
negative sidechain
amino acid represented by
R
Arginine
Arg
positive side chain
amino acid represented by
K
Lysine
Lys
positive side chain
amino acid represented by
H
Histidine
His
positive side chain
amino acid represented by
N
Asparagine
Asn
Uncharged polar side chain
amino acid represented by
Q
Glutamine
Gln
Uncharged polar side chain
amino acid represented by
S
Serine
Ser
Uncharged polar side chain
amino acid represented by
T
Threonine
Thr
Uncharged polar side chain
amino acid represented by
Y
Tyrosine
Tyr
Uncharged polar side chain
amino acid represented by
A
Alanine
Ala
nonpolar side chain
amino acid represented by
G
Glycine
Gly
nonpolar side chain
amino acid represented by
V
Valine
Val
nonpolar side chain
amino acid represented by
L
Leucine
L
nonpolar side chain
amino acid represented by
I
Isoleocine
Ile
nonpolar side chain
amino acid represented by
P
Proline
Pro
nonpolar side chain
amino acid represented by
F
Phenylalanine
Phe
nonpolar side chain
amino acid represented by
M
Methionine
Met
nonpolar side chain
amino acid represented by
W
Tryptophan
Trp
nonpolar side chain
amino acid represented by
C
Cysteine
Cys
nonpolar side chain
Amino acids with negative side chains?
Asparitic acid/ asp/ D
Glutamic acid / Glu/ E

DE acids.
Amino acids with positive side chains?
Arginine /Arg /R
Lysine/ Lys/ K
Histidine/ His/ H
amino letters which don't make sense...
Dasp (-)
gluE (-)
Rarg (+)
lysK (+)
asnN
Ytyr
Wtrp
Qgln
differences between negative "acids" and the uncharged polar abbreviations for
aspartic acid vs asparagine
and
glutamic acid vs glutamine
acids: first 3 letters (asp, glu)
uncharged polar: first 2 letters +n.(asn, gln)

*Asn, Gln, Ile (Isoleocine) & Trp (tryptophan) are the ONLY abbreviations that don't start with the first 3 letters!
How many nonpolar side chains?
10...that's half.
how many uncharged polar side chains?
5... a quarter of them.
How many basic and acidic side chains?
3 basic (Arg, Lys & His)

2 acidic (Asp & Glu)
C. elegans:
sexes and ratio of sexes?
most are hermaphroditic
1 in 500 are male
C. elegans:
Life cycle and lifespan?
*important to differentiate!
life cycle: 3 days
life span: 3 weeks
C. elegans vocab:
Dauer
larva goes into a type of stasis and can survive harsh conditions
(can be over 6 months)
C. elegans: reasons they're good for genetic research?
Dauer (stasis) makes it low maintenence.
-genome is sequenced
-short life cycle
- we can manipulate it for lonegevity, cell structure, etc.
Power and benefit of a dissecting microscope?
6.3X to 30X magnification

large working space for dissection.
C. elegans vocab:
oviduct
one of a pair of ducts through which eggs travel from ovary to uterus.
(formerly fallopian tubes)
C. elegans vocab:
oocyte
immature egg of all animals and some protists
C. elegans vocab:
cloaca
chamber or duct in last portion of gut of some animals that serves in excretion, reproduction and sometimes respiration
C. elegans vocab:
spicule
a small hard needle-like piece of bony material, as in the skeleton of a sponge.
C. elegans vocab:
alimentary canal
the passage in the body through which food passes as it's digested. from mouth to anus. aka: digestive tract?
4 functions of extracellular proteins?
1. structure (eg. collagen)
2. enzymes (eg. lysozyme)
3. growth factor (Fibroblast growth factor)
4. immune response (antibodies)
4 functions of membrane proteins?
1. transporters, e.g. __ion channels__
2. anchors, e.g. __integrins___
3. receptors, e.g. growth factor receptors
4. enzymes, e.g. adenylyl cyclase coverts extracellular molecule to an intracellular messenger.
5. recognition, e.g. _glycoproteins___
6 Functions of intracellular proteins?
1. enzymes, e.g. _kinases__
2. structural proteins, e.g. actin filaments, spectrin
3. motor proteins, e.g. myosin
4. receptors, e.g. __hormone receptors__
5. signal transduction
6. special functions, e.g. _DNA bind proteins__ involved in replication, transcription, translation
enzymes are always made of _____.
proteins
Where do enzymes serve functions?
in cell, in membrane and extracellular
what are growth factor proteins?
these are extra cellular proteins like FGF (fibroblast growth factor) that bind with a receptor protein in the cell membrane that in turn alters intracellular molecules creating a response.
How do membrane recognition proteins function?
Recognition proteins are usually glycoproteins with the carbohydrate portion projecting out of the cell and into the extracellular space. These give the cell a biochemical personality (like ID) and are important in cell-to-cell recognition.
How do membrane enzymes function?
they convert extracellular molecules to intracellular messengers.
what is ligase?
a DNA binding protein (special function intracellular protein)
binds 2 strands of DNA together end to end.
It is an enzyme.
chaperones (molecular):
What do they do and where are they found?
molecules that assist in protein folding
ER
Where are motor proteins found?
intracellular!
(move along microtubule substrate)
Where are structural proteins found?
intra & extra cellular
(collagen, actin, etc)
where are receptor proteins found?
membrane and intracellular
signal transduction?
the process by which a cell responds to an extracellular signal
Where are signal transduction proteins found?
intracellular
What connects elastin fibers?
"cross links" = covalent bonds
What are the "Special functions" performed by some intracellular proteins?
transcription, translation, RNA modification, etc
fibrous proteins that are a major component of the extracellular matrix and connective tissues?
collagen & elastin
what are the side effects of protein denaturing?
lose function, cause disease
special mis-folded proteins that cause scapie, mad cow, sickle cell anemia?
Prion
the region where an enzyme interacts with another molecule?
active or binding site
how do protein aggregates form?
a misfolded protein converts normal Prp to abnormal conformation creating aggregates.
PrP?
prion proteins
The place on an enzyme where a molecule that is not a substrate may bind, important for conformation.
allosteric site
allosteric site?
The place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme and influencing its ability to be active. (proper conformation)
Enzymes, receptor and antigens: what does each interact with?
enzyme- substrate
receptor- ligand
antibody- antigen
What is immunuglobulin?
antibodies
shape of antibody/ immunoglobulin?
Y shaped
what gives antibodies their Y shape?
many intra and inter molecular S-S (disulfide) bonds
a domain of an antibody that binds a specific antigen?
variable domain
Why is an antibody called a tetramer?
4 parts: composed of two heavy and two light chains.
technique to separate proteins by charge, size, affinity to other substances or proteins using specific solutions
(matrices)?
Chromoatography
technique to separate proteins by their molecular weight (and net charge)?
electrophoresis ,
including the now obsolete SDS
technique that separates denatured proteins by isoelectric point and then by molecular weight.
Two-dimensional gel electrophoresis
technique which obtains high resolution image of crystal structure of proteins?
X-ray crystallography
basic description of X-ray crystallography
beam of x rays through protein crystals, then they obtain a diffraction pattern which they convert to computer image.
generates a 3-D structure (like x-ray crystallography) but with lower resolution
NMR spectroscopy
extracellular (ECM)
vs
intracellular proteins (cytoskeleton)
extra: collagen and elastin
intra: spectrin and actin
what are integrins?
membrane anchor proteins
where are antibodies located?
extracellular
example of a proteoglycan?
chondroitin sulfate , a structural component of cartilage