TBL Prep carbohydrates and protein structure Flashcards
primary structure of amino acids
chain of amino acids connected via peptide bonds
secondary structure
local structural elements including alpha helices and beta sheets
hydrogen bond
H shared between 2 electronegative atoms
ionic interactions
happens between 2 oppositely charged atoms
van der waals interactions
induced dipole interactions very weak
hydrophobic forces
tendency of hydrophobic molecules to be shielded from aquueous solvent single strongest driving force in protein tertiary conformation
tertiary
structural units that shield a hydrophobic core
quaternary
interactions between multiple polypeptides
myoglobin
hydrophobic forces
collagen
most abundant protein in mammals
collagen tertiary structure
right handed triple helix composed of 3 individuals alpha chains
are alpha chains different from alpha helices
yes
alpha chains
polypeptide strands with left handed helical conformation
alpha helices are right handed
true
collagens primary sequence
gly, pro, 4 hydroxyproline
T or F
crosslinking between alpha chains of different tropocollagen molecules contributes to the strength of collagen fibrils
true
osteogenesis imperfecta or brittle bone disease
can be caused by defects in or reduced type I collagen
Ehlers- Danlos Syndromes
group of diseases caused by hyperextendibility of joints and skin
lathyrism
ingestion of sweet pea seeds, inactivates lysyl oxidase
scurvy
lack of vitaminC, which is required by prolyl and lysyl hydroxylase
what are two types of membrane lipids
glycerophospholipids and sphingolipids
peripheral membran proteins
can be washed away via salt treatment
integral membrane proteins
require something stronger to be removed - detergent
GPI anchors
allow proteins to attach to the outer leaflet
membrane protein fucntions
intercellular joinings
enzymatic activity
transport (active/ passive)
cell-cell recognition
anchorage/ attatchment
signal transduction
lipids can be categorized as either
having fatty acid components or derived from 5 carbon compound , isoprene
what group has a carboxyl group on alpha end and hydrocarbon tail
fatty acids
omega carbon =
final carbon in hydrocarbon tail
most important sterol
cholestrol
nomenclature of carbohydrates and sugar code
aldehyde (aldose) has C=O group “al” (all) the way
at the end
* -ketose (ketone)
* Monosaccharides are named based on the # of carbons
o Triose = 3 C’s, tetrose = 4 C’s, etc.
* Furanose: 5-membered ring
* Pyranose: 6-membered ring
T or F
In the open form, sugars can be reducing agents
true
Benedict’s test
shows if there are reducing sugars present in urine
o Blue = negative (no reducing sugars)
o Red = positive (reducing sugars present)
chirality of carbohydrates
Most monosaccharides have at least 1 chiral carbon à 2 stereoisomers (D and L)
o # stereoisomers = 2^(# of chiral centers)
o Epimers: stereoisomers that differ at 1 chiral
carbon
* Most naturally occurring sugars are D
Anomeric carbon
look for the carbon bound to 2 oxygens!
o 2 configurations
§ Alpha: alpha symbol looks like a fish and fish swim
so -OH group is on the bottom
§ Beta: think of bird and birds fly in the sky so -OH
group is on top
Mutarotation
flipping b/t alpha and beta configuration until
equilibrium is reached b/t the stereoisomers and open chain
§ Glucose, for ex, 65% ß, 35% alpha, and less that
0.1% open chain
Sucrose is unique because
the anomeric carbons react with each other à no
reducing end à thus, sucrose is a non-reducing sugar
Disaccharide
2 monosaccharides linked via O-glycosidic bond
o O-glycosidic bond: formed when hydroxyl of one sugar reacts w/ anomeric carbon of
another sugar
o Non-reducing end: the one donating its anomeric carbon
o Reducing end: retains its open anomeric carbon
§ Remember, look for the C bonded to 2 O’s
Polysaccharides
* Functions
fuel storage (glycogen and starch)
structure (cellulose, chitin and glycosaminoglycans)
information transfer (the sugar code)
how do polysaccharides store fuel
Glycogen structure = main chain of glucoses linked via alpha 1-4 bonds + alpha 1-6
branches every 9-12 sugar residues
o One molecule of glycogen can have many non-reducing ends, but only ONE reducing
end
§ Glucose-1-P molecules are enzymatically released one at a time from the non-
reducing ends à makes glycogen good for energy because numerous non-
reducing ends allows for quick release of glucose when necessary
Glycosaminoglycans
Glycosaminoglycans make up an important part of the extracellular matrix (ECM/ground
substance; gel-like material between cells
Selectins/Lectins:
proteins that use the sugar code to recognize carbohydrate structures to a high
degree of specificity and affinity
o These are NOT enzymes
selectins mediate inflammatory response in
rheumatoid arthritis, asthma,
psoriasis, multiple sclerosis, and transplanted organ rejection à makes selectins a
target of interest for drug research
Tamiflu and Relenza
sugar analogs that inhibit neuraminidase (N)
true or F
The glycans that determine your blood type are complex carbohydrate moieties
that only vary in the terminal sugar residue
True or F Almost all polypeptides undergo proteolytic processing to get rid of the amino terminal
Met residue
T
T or F
Proteins that are trafficked to the endoplasmic reticulum start with a pre- or signal-peptide
T
N-linked glycosylation
sugar is attached to polypeptide at Asn residue
O-linked glycosylation
sugar is attached to polypeptide at Ser or Thr residue
o Happens AFTER the protein is fully folded and has entered the Golgi
o O-linked glycans vary widely
Proteoglycans
Proteoglycans: glycoproteins that have a LOT of carbohydrate
Aggrecan
main proteoglycan of cartilage
How does aggrecan act as a shock absorber?
brushlike structure and
numerous negative charges cause the molecule to be heavily hydrated. As aggrecan is compressed, the water molecules are squeezed out. This continues
until the like charges repel one another. Hence allowing aggrecan’s spring-like
function!
§ Aggrecan gives cartilage its resiliency
what does Ubiquitylation happen in response to?
phosphorylation à ubiquitylation à degradation
Ubiquitin
76 amino acid protein present in all eukaryotic cells
histone code
the idea that modifications (like the ones we’ve talked about: acetylation,
methylation, phosphorylation, ubiquitylation) to histones help determine what parts of DNA will
undergo transcription
each amino acid is composed of
amine group
carboxyl group
hydrogen
side chain (R group)
amino acids are zwitterionic at neutral PH what does that mean
they have both positively and neg charges groups in a single molecule
peptide bonds are formed via
condensation reaction between the amine and carboxyl groups of two amino acids
polypeptides are linear arrays of amino acids linked by peptide bonds
know the functional groups on biomolecules from protein handout dr jones
polar uncharged R groups
serine
threonine
cysteine
asparagine
glutamine
non polar aliphatic r groups
glycine
alanine
proline
valine
leucine
isoleucine
methionine
positively charged R groups
lysine
arginine
histidine
negatively charged r groups
aspartate
glutamate
aromatic r groups
phenylaline
tyrosine
tryptophan
sharing of electrons between two atoms.
Covalent bonds
one atom donates an electron to another, such
as in the formation of sodium chloride
ionic bonds
Hydrogen Bonds
A hydrogen shared between two electronegative atoms, such as O
and N. These are typically depicted by dotted lines on diagrams. Proteins fold so as to
satisfy most of their hydrogen bonding potential.
Attractive forces between opposite charges such as Na+ and Cl-,
including salt bridges and dipole-dipole interactions. Dipoles can be fixed or induced.
Ionic interactions
Induced dipole interactions between atoms that touch.
These interactions are very weak, but there are many of them in the packed interiors
or a proteins. They fall off rapidly in strength as the atoms get farther apart.
Van der vaals
The tendency of hydrophobic molecules to be excluded from
aqueous solvent. This is the single strongest driving force in established the tertiary
fold of a protein
hydrophobic forces
most abundant protein in mammals
collagen
Osteogenesis Imperfecta or “brittle bone disease”
diminished synthesis
or defective type I collagen. In one form of the disease, a point mutation in the collagen
a 2 (I) gene leading to a single Ala substitution at a Gly position is sufficient to
significantly reduce collagen stability and produce an autosomal dominant disease
Ehlers-Danlos Syndromes
constitute a group of at least 10 different diseases all
characterized by hyperextendability of the joints and skin. Some types are associated with
lysyl hydroxylase deficiency, while the genetic defects in others have not been
characterized.
