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biochem > TBL Prep carbohydrates and protein structure > Flashcards

TBL Prep carbohydrates and protein structure Flashcards

1
Q

primary structure of amino acids

A

chain of amino acids connected via peptide bonds

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2
Q

secondary structure

A

local structural elements including alpha helices and beta sheets

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3
Q

hydrogen bond

A

H shared between 2 electronegative atoms

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4
Q

ionic interactions

A

happens between 2 oppositely charged atoms

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5
Q

van der waals interactions

A

induced dipole interactions very weak

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6
Q

hydrophobic forces

A

tendency of hydrophobic molecules to be shielded from aquueous solvent single strongest driving force in protein tertiary conformation

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7
Q

tertiary

A

structural units that shield a hydrophobic core

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8
Q

quaternary

A

interactions between multiple polypeptides

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9
Q

myoglobin

A

hydrophobic forces

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10
Q

collagen

A

most abundant protein in mammals

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11
Q

collagen tertiary structure

A

right handed triple helix composed of 3 individuals alpha chains

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12
Q

are alpha chains different from alpha helices

A

yes

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13
Q

alpha chains

A

polypeptide strands with left handed helical conformation

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14
Q

alpha helices are right handed

A

true

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15
Q

collagens primary sequence

A

gly, pro, 4 hydroxyproline

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16
Q

T or F
crosslinking between alpha chains of different tropocollagen molecules contributes to the strength of collagen fibrils

A

true

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17
Q

osteogenesis imperfecta or brittle bone disease

A

can be caused by defects in or reduced type I collagen

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18
Q

Ehlers- Danlos Syndromes

A

group of diseases caused by hyperextendibility of joints and skin

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19
Q

lathyrism

A

ingestion of sweet pea seeds, inactivates lysyl oxidase

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20
Q

scurvy

A

lack of vitaminC, which is required by prolyl and lysyl hydroxylase

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21
Q

what are two types of membrane lipids

A

glycerophospholipids and sphingolipids

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22
Q

peripheral membran proteins

A

can be washed away via salt treatment

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23
Q

integral membrane proteins

A

require something stronger to be removed - detergent

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24
Q

GPI anchors

A

allow proteins to attach to the outer leaflet

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25
Q

membrane protein fucntions

A

intercellular joinings
enzymatic activity
transport (active/ passive)
cell-cell recognition
anchorage/ attatchment
signal transduction

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26
Q

lipids can be categorized as either

A

having fatty acid components or derived from 5 carbon compound , isoprene

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27
Q

what group has a carboxyl group on alpha end and hydrocarbon tail

A

fatty acids

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28
Q

omega carbon =

A

final carbon in hydrocarbon tail

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29
Q

most important sterol

A

cholestrol

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30
Q

nomenclature of carbohydrates and sugar code

A

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
Q

T or F
In the open form, sugars can be reducing agents

A

true

32
Q

Benedict’s test

A

shows if there are reducing sugars present in urine
o Blue = negative (no reducing sugars)
o Red = positive (reducing sugars present)

33
Q

chirality of carbohydrates

A

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
Q

Anomeric carbon

A

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
Q

Mutarotation

A

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
Q

Sucrose is unique because

A

the anomeric carbons react with each other à no
reducing end à thus, sucrose is a non-reducing sugar

37
Q

Disaccharide

A

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
Q

Polysaccharides
* Functions

A

fuel storage (glycogen and starch)
structure (cellulose, chitin and glycosaminoglycans)
information transfer (the sugar code)

39
Q

how do polysaccharides store fuel

A

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
Q

Glycosaminoglycans

A

Glycosaminoglycans make up an important part of the extracellular matrix (ECM/ground
substance; gel-like material between cells

41
Q

Selectins/Lectins:

A

proteins that use the sugar code to recognize carbohydrate structures to a high
degree of specificity and affinity
o These are NOT enzymes

42
Q

selectins mediate inflammatory response in

A

rheumatoid arthritis, asthma,
psoriasis, multiple sclerosis, and transplanted organ rejection à makes selectins a
target of interest for drug research

43
Q

Tamiflu and Relenza

A

sugar analogs that inhibit neuraminidase (N)

44
Q

true or F

A

The glycans that determine your blood type are complex carbohydrate moieties
that only vary in the terminal sugar residue

45
Q

True or F Almost all polypeptides undergo proteolytic processing to get rid of the amino terminal
Met residue

A

T

46
Q

T or F
Proteins that are trafficked to the endoplasmic reticulum start with a pre- or signal-peptide

A

T

47
Q

N-linked glycosylation

A

sugar is attached to polypeptide at Asn residue

48
Q

O-linked glycosylation

A

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
Q

Proteoglycans

A

Proteoglycans: glycoproteins that have a LOT of carbohydrate

50
Q

Aggrecan

A

main proteoglycan of cartilage

51
Q

How does aggrecan act as a shock absorber?

A

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
Q

what does Ubiquitylation happen in response to?

A

phosphorylation à ubiquitylation à degradation

53
Q

Ubiquitin

A

76 amino acid protein present in all eukaryotic cells

54
Q

histone code

A

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
Q

each amino acid is composed of

A

amine group
carboxyl group
hydrogen
side chain (R group)

56
Q

amino acids are zwitterionic at neutral PH what does that mean

A

they have both positively and neg charges groups in a single molecule

57
Q

peptide bonds are formed via

A

condensation reaction between the amine and carboxyl groups of two amino acids

58
Q

polypeptides are linear arrays of amino acids linked by peptide bonds

A
59
Q

know the functional groups on biomolecules from protein handout dr jones

A
60
Q

polar uncharged R groups

A

serine
threonine
cysteine
asparagine
glutamine

61
Q

non polar aliphatic r groups

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine

62
Q

positively charged R groups

A

lysine
arginine
histidine

63
Q

negatively charged r groups

A

aspartate
glutamate

64
Q

aromatic r groups

A

phenylaline
tyrosine
tryptophan

65
Q

sharing of electrons between two atoms.

A

Covalent bonds

66
Q

one atom donates an electron to another, such
as in the formation of sodium chloride

A

ionic bonds

67
Q

Hydrogen Bonds

A

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
Q

Attractive forces between opposite charges such as Na+ and Cl-,
including salt bridges and dipole-dipole interactions. Dipoles can be fixed or induced.

A

Ionic interactions

69
Q

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.

A

Van der vaals

70
Q

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

A

hydrophobic forces

71
Q

most abundant protein in mammals

A

collagen

72
Q

Osteogenesis Imperfecta or “brittle bone disease”

A

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
Q

Ehlers-Danlos Syndromes

A

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.

biochem (10 decks)

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