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Pile Management Card
Biology

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difference between parallel and antiparallel beta pleated sheet
-antiparallel has straight hydrogen bonds
-parallel has skewed hydrogen bonds
how many amino acids per turn in an alpha helix?
3.6
quaternary structure
spatial arrangement of multiple polypeptide chains
tertiary structure
bending path of the polypeptide chain in 3-D space
secondary structure
regular, repeated local spatial patterns
primary structure
linear sequence of amino acids
2 cysteine amino acids bonded together make...
a disulfide bridge
main function of steroids?
cell signaling, regulation, protection!
glucose+fructose
sucrose
glucose+galactose
lactose
aldehydes get oxidized to...
CARBOXYLLIC ACID

C-C-C=O
II
O-H
inside of ER is called?
lumen
Zwitterion
a dipole with both a positive and a negative charge
basically all sugars are _____ isomers
D
basically all amino acids are _____ isomers
L
differences between archaea's phospholipids vs. bacteria?
they have alcohols with branches instead of fatty acids (makes membranes fatter)
these alcohols are linked to glyceride with ETHER BONDS rather than ester bonds.
this makes them more resistant to oxidative damage
what happens if a protein's 3D structure is disrupted?
if amino acid sequence remains, the protein will slowly regain its form because the sequence contains the information which specifies conformation
how does a protein know how to fold?
it behaves with a tendency to retain partly correct intermediates
globular proteins
compact, water soluble, perform most of cell's chemical transactions
lack of vitamin C causes....
scurvy
b/c vitamin C acts as an antioxidant to create hydroxyproline in the formation of collagen fibers
superhelical coil
3 helices wrapped around each other with glycine to fill up spaces

e.g. collagen
coiled coil
2 alpha helices wrapped around each other

e.g. alpha keratin
in which structure are amino acids more spread out, helix or beta sheet?
beta pleated sheet
alpha helixes are usually left handed or right handed?
right handed b/c it minimizes steric clashes
Ramachandran
he made a torsion angle diagram which showed that the only preferable arrangement makes alpha helix or beta pleated sheet
almost all proteins have ______ type of peptide bonds
TRANS
b/c cis can have steric clashes between R groups
3 characteristics of peptide bonds
-planar
-double bond character (strong, short)
-uncharged (not impeded by charge repulsion)
how do plants, animals, and fungi differ from each other?
in how they get food.
plants- photosynthesis
animals- ingestion and internal digestion
fungi- external digestion by secreting digestive enzymes and then absorbtion
How can you detect the presence of phage in a soil sample?
test the ability of the phage to lyse bacterial host cells. place the sample in a culture of E. Coli bacteria. If phages are present, they will create clear zones in the lawn of bacteria
4 types of non-covalent interactions (by decreasing strength)
ionic, H bond, hydrophobic, van der waals
Cellulose
polysaccharide
structural element in plant cell walls
completely unbranched!
lactose intolerance is due to...?
lack of the enzyme lactase, which can break down the beta-1,4 linkage in lactose
saturated fatty acids are solid or liquid at room temperature?
solid!
unsaturated fatty acids are solid or liquid at room tempature?
liquid!
main function of steroids?
cell signaling!
main use of phospholipids?
biological membranes!
function of triglycerides?
energy storage!
glycerols are primary components in which two types of lipids?
triglycerides and phospholipids
glyceraldehydes can be reduced to...
glycerol! (which is a primary alcohol)
glyceraldehyde has how many carbons...?
what's bonded to the top carbon?
3 carbons!
top one is double bonded to an O and single bonded to a H
pKa=
log(1/K)
lactose intolerance is due to...?
lack of the enzyme lactase, which can break down the beta-1,4 linkage in lactose
saturated fatty acids are solid or liquid at room temperature?
solid!
unsaturated fatty acids are solid or liquid at room tempature?
liquid!
main use of phospholipids?
biological membranes!
function of triglycerides?
energy storage!
glycerols are primary components in which two types of lipids?
triglycerides and phospholipids
glyceraldehydes can be reduced to...
glycerol! (which is a primary alcohol)
glyceraldehyde has how many carbons...?
what's bonded to the top carbon?
3 carbons!
top one is double bonded to an O and single bonded to a H
pKa=
log(1/K)
Chirality
asymmetrical, therefore it matters whether something is on the left or right
this is the case for carbons in carbohydrates
components of a phospholipid:
(2 fatty acids+a glycerol)+phosphate+alcohol
hydrophobic hydrophillic
Future biodiesel fuel may come from....
triglycerides from plants or algae,
or extracting fatty acids and converting them to esters with methanol
Omega-3/Omega-6
when there are lots of double bonds in a fatty acid (polyunsaturated), they are counted from the end (the right side). if first double bond is on the 3rd Carbon, it's an Omega-3; if the first one is on the 6th carbon, it's an Omega-6.
These fats are actually very healthy and are found in fish. They assist in brain function, growth and development, and reduce the risk of heart disease
structural diff between saturated and unsaturated fats
saturated have only carbon-carbon single bonds and are therefore straight
unsaturated have one or more carbon-carbon double bonds and are therefore bent
ester linkage is between...
glycerol and fatty acid
components of triglycerides
one glycerol+3 fatty acids
chain lengths usually between 14-24 carbons
3 major types of lipids
steroids
triglycerides
phospholipids
Roles of lipids:
-major component of biological membranes
-energy source and storage
-signaling molecules
-structural/architectural
Lipids (operational definition)
water-insoluble biomolecules that are highly soluble in organic solvents, such as chloroform
ethanol biofuel is obtained through....
fermentation of sugars
Why can't mammals digest wood?
they lack the enzyme which can degrade the beta-1,4 linkage in cellulose
type of linkage in cellulose
beta-1,4
type of linkage that causes straight chain in glycogen and starch
alpha-1,4
type of linkage that causes branches in glycogen and starch
alpha-1,6
Starch
storage form of glucose in PLANTS
branched, but less so compared to glycogen
glycogen
storage form of glucose in ANIMALS
highly branched!
lactose is a disaccharide made up of....
glucose+galactose (with a beta linkage)
bacteria break down lactose using the enzyme ________
Beta-galactosidase
bond between monosaccharides is called....
glycosidic linkage
alpha vs. beta monosaccharides
determined by orientation of aldehyde group
Linear vs. Ring forms of monosaccharide
Ring forms are more stable and predominant under physiological conditions (linear forms are <1%)
Ring formed by reaction between Hydroxyl group and aldehyde group at carbon 5
Hydroxide group on the left of the second to last carbon is a ____ isomer
L isomer
Hydroxide group on the right of the second to last carbon is a ____ isomer
D isomer (most sugars are in this form)
what is a sugar?
a polyhydroxyl aldehyde or a ketone with 3 or more carbons
Typical numbers of carbons in a monosaccharide
3-9
How many monosaccharides in oligosaccharides?
3-20
Uses of carbohydrates
-Energy source, energy stores, metabolic intermediates
-Structural framework of RNA and DNA
-Structural elements in the cell walls of bacteria and plants
-Linked to proteins and lipids
both function and shape of macromolecules are determined by...
sequence and chemical properties of monomers
Hydrolysis reaction
Water is consumed and a dimer breaks apart into two monomers.
Condensation reaction
water is a byproduct and two molecules become connected
Nucleic acid monomer...
nucleotide
Carb monomer...
monosaccharide
Protein monomer...
amino acid
4 types of macromolecules...
proteins, lipids, carbs, nucleic acids
secondary alcohols get oxidized to...
KETONES

O
II
C-C-C
primary alcohols get oxidized to...
ALDEHYDES

C-C-C=O
I
H
Carbon chain with hydroxyl group in the middle...
SECONDARY alcohol
Carbon chain with hydroxyl group on the end...
PRIMARY alcohol
Sulfhydryl
-SH
class of compounds: thiols
Phosphato
O
O P O
O
class of compounds: organic phosphates
Amino
H-N-H
class of compounds: amines
Carboxyl
OH-C=O
class of compounds: carboxyllic acids
Keto
C=O
class of compounds: Ketones
Aldehydes
H-C=0
class of compounds: aldehydes
Hydroxyl
-OH
class of compounds: alchohols
salt bridge
COO- group connected to an NH3 group in proteins
tails of phospholipid bilayer are...
hydrophobic
heads of phospholipid bilayer are...
hydrophillic
Kinesin
motor protein which drives movement down microtubule tracks (walks them)
6 elements most commonly found in biology...
C,H,N,O,P,S
Microtubules
-hollow cylinders made of TUBULIN (alpha and beta)
-causes chromosome movement during mitosis and meiosis
-also causes vesicle movement
Intermediate Filaments
-proteins with coiled-coil domains
-nuclear lamins are one example
Microfilaments
-made of ACTIN, have a positive end (which grows) and negative end (which does not grow)
-drives shape changes and cell movement
-also involved in muscle contractions
3 components of cytoskeleton (by increasing size):
Microfilaments, Intermediate Filaments, Microtubules
final product of photosynthesis is...
starch
Peroxisome
-all eukaryotes
-single membrane
-NOT derived from the secretory pathway
-detox of peroxides (like H2O2)
Reasons for endosymbiont theory of mitochondria/chloroplasts
-size
-DNA/RNA
-double membrane
- in japan, a single cell eukaryote was discovered which had ingested an algae and taken up use of its chloroplast basically
role of thylakoid
transport of electrons during photosynthesis
Glyoxosomes
found ONLY in plants
-performs lipid metabolism (quickly converts fats into useable materials)
Vacuole
-single membrane
-in plants, there is a very large central vacuole which serves as a hydrolytic compartment and as an expandable "space"
Chloroplast
-site of photosynthesis
-double membrane
-inner fluid called stroma
-pancake-like thylakoids make up stacks called grana
Mitochondria
-double membrane
-site of cellular respiration/ energy production
-contains ribosomes/DNA
Where are enzymes in lysosomes synthesized?
first they are made in the RER, then they get sent to the golgi, finally to the lysosome
lysosome
filled with hydrolytic enzymes to lysis foreign particles like viruses
Why can't prokaryotic cells perform post-translational modification?
because they have no golgi/ER which perform this function in eukaryotic cells
exocytosis
export of matter out of the cell
proteins on the surface of vesicles help to direct them to the correct location
endocytosis
import of matter into the cell
phagocytosis=particulate matter
pinocytosis="cellular drinking"
receptor mediated endocytosis (budding off of plasma membrane)
region of golgi closest to plasma membrane
trans
region of golgi closest to nucleus
cis
function of golgi body...
processing and sorting of proteins destined for other cell compartments
Flattened sacs of golgi body are called....
cisternae
Smooth ER
proteins are further processed,
site of synthesis of lipids and steroids
no ribosomes on surface
Rough ER
has ribosomes studded on its surface.
proteins come here for processing (often the addition of sugar groups)
Nuclear Pore Complex
selectively permeable barrier through the nuclear envelope.
if something has the correct nuclear localization sequence (NLS), it can undergo regulated transport via accessory proteins and get in
also, if something is small enough.
Nuclear Lamina
Protein meshwork inside the nucleus which functions like the cytoskeleton
What is the difference between euchromatin and heterochromatin?
Euchromatin: gene rich, decondensed outside of mitosis

Heterochromatin: gene poor, very condensed, often located in nuclear periphery, is used to separate DNA
What are the two types of chromatin?
Euchromatin and Heterochromatin
What is the nuclear plasm filled with?
chromatin
What is the nuclear plasm?
part of the nucleus that is outside the nucleolus
function of ribosomes?
protein synthesis
Places where ribosomes are found?
Rough ER,
in cytosol,
in other organelles, e.g. chloroplast, mitochondria
Nucleolus
located inside nucleus
site of ribosomal biogenesis and assembly
Nuclear Membrane
2 phosphilipid bilayers,
many pores
What differentiates membranes from one another?
the proteins embedded on them
What is it called when a substance has conflicting chemical properties?
Amphipathic
What is the phospholipid bilayer composed of?
Hydrophopic Tails,
Hydropphillic Heads
What is the plasma membrane made of?
Phospholipid Bilayer
Eukaryotic Cells
contains various membrane-bound organelles such as nucleus, vacuole, golgi body
subgroups are plant, animal, fungi
plasma membrane, sometimes with cell wall
Gram Positive
Very thick cell wall
No outer membrane
Gram Negative
layer of cell wall made of peptidoglycan,
layer of porous outer membrane
Prokaryotic Cells
No defined nucleus, subgroups are bacteria and archaea, no membrane-bound organelles, can be gram negative or gram positive
Eukaryotic Cells
contains various membrane-bound organelles such as nucleus, vacuole, golgi body
subgroups are plant, animal, fungi
plasma membrane, sometimes with cell wall
Gram Positive
Very thick cell wall
No outer membrane
Gram Negative
layer of cell wall made of peptidoglycan,
layer of porous outer membrane
Prokaryotic Cells
No defined nucleus, subgroups are bacteria and archaea, no membrane-bound organelles, can be gram negative or gram positive
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