TBL Prep carbohydrates and protein structure Flashcards
1
Q
primary structure of amino acids
A
chain of amino acids connected via peptide bonds
2
Q
secondary structure
A
local structural elements including alpha helices and beta sheets
3
Q
hydrogen bond
A
H shared between 2 electronegative atoms
4
Q
ionic interactions
A
happens between 2 oppositely charged atoms
5
Q
van der waals interactions
A
induced dipole interactions very weak
6
Q
hydrophobic forces
A
tendency of hydrophobic molecules to be shielded from aquueous solvent single strongest driving force in protein tertiary conformation
7
Q
tertiary
A
structural units that shield a hydrophobic core
8
Q
quaternary
A
interactions between multiple polypeptides
9
Q
myoglobin
A
hydrophobic forces
10
Q
collagen
A
most abundant protein in mammals
11
Q
collagen tertiary structure
A
right handed triple helix composed of 3 individuals alpha chains
12
Q
are alpha chains different from alpha helices
A
yes
13
Q
alpha chains
A
polypeptide strands with left handed helical conformation
14
Q
alpha helices are right handed
A
true
15
Q
collagens primary sequence
A
gly, pro, 4 hydroxyproline
16
Q
T or F
crosslinking between alpha chains of different tropocollagen molecules contributes to the strength of collagen fibrils
A
true
17
Q
osteogenesis imperfecta or brittle bone disease
A
can be caused by defects in or reduced type I collagen
18
Q
Ehlers- Danlos Syndromes
A
group of diseases caused by hyperextendibility of joints and skin
19
Q
lathyrism
A
ingestion of sweet pea seeds, inactivates lysyl oxidase
20
Q
scurvy
A
lack of vitaminC, which is required by prolyl and lysyl hydroxylase
21
Q
what are two types of membrane lipids
A
glycerophospholipids and sphingolipids
22
Q
peripheral membran proteins
A
can be washed away via salt treatment
23
Q
integral membrane proteins
A
require something stronger to be removed - detergent
24
Q
GPI anchors
A
allow proteins to attach to the outer leaflet
25
membrane protein fucntions
intercellular joinings
enzymatic activity
transport (active/ passive)
cell-cell recognition
anchorage/ attatchment
signal transduction
26
lipids can be categorized as either
having fatty acid components or derived from 5 carbon compound , isoprene
27
what group has a carboxyl group on alpha end and hydrocarbon tail
fatty acids
28
omega carbon =
final carbon in hydrocarbon tail
29
most important sterol
cholestrol
30
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
31
T or F
In the open form, sugars can be reducing agents
true
32
Benedict’s test
shows if there are reducing sugars present in urine
o Blue = negative (no reducing sugars)
o Red = positive (reducing sugars present)
33
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
34
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
35
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
36
Sucrose is unique because
the anomeric carbons react with each other à no
reducing end à thus, sucrose is a non-reducing sugar
37
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
38
Polysaccharides
* Functions
fuel storage (glycogen and starch)
structure (cellulose, chitin and glycosaminoglycans)
information transfer (the sugar code)
39
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
40
Glycosaminoglycans
Glycosaminoglycans make up an important part of the extracellular matrix (ECM/ground
substance; gel-like material between cells
41
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
42
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
43
Tamiflu and Relenza
sugar analogs that inhibit neuraminidase (N)
44
true or F
The glycans that determine your blood type are complex carbohydrate moieties
that only vary in the terminal sugar residue
45
True or F Almost all polypeptides undergo proteolytic processing to get rid of the amino terminal
Met residue
T
46
T or F
Proteins that are trafficked to the endoplasmic reticulum start with a pre- or signal-peptide
T
47
N-linked glycosylation
sugar is attached to polypeptide at Asn residue
48
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
49
Proteoglycans
Proteoglycans: glycoproteins that have a LOT of carbohydrate
50
Aggrecan
main proteoglycan of cartilage
51
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
52
what does Ubiquitylation happen in response to?
phosphorylation à ubiquitylation à degradation
53
Ubiquitin
76 amino acid protein present in all eukaryotic cells
54
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
55
each amino acid is composed of
amine group
carboxyl group
hydrogen
side chain (R group)
56
amino acids are zwitterionic at neutral PH what does that mean
they have both positively and neg charges groups in a single molecule
57
peptide bonds are formed via
condensation reaction between the amine and carboxyl groups of two amino acids
58
polypeptides are linear arrays of amino acids linked by peptide bonds
59
know the functional groups on biomolecules from protein handout dr jones
60
polar uncharged R groups
serine
threonine
cysteine
asparagine
glutamine
61
non polar aliphatic r groups
glycine
alanine
proline
valine
leucine
isoleucine
methionine
62
positively charged R groups
lysine
arginine
histidine
63
negatively charged r groups
aspartate
glutamate
64
aromatic r groups
phenylaline
tyrosine
tryptophan
65
sharing of electrons between two atoms.
Covalent bonds
66
one atom donates an electron to another, such
as in the formation of sodium chloride
ionic bonds
67
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.
68
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
69
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
70
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
71
most abundant protein in mammals
collagen
72
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
73
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.
