Proteins Lipids and Carbohydrates Flashcards
1
Q
building blocks of the cell
A
sugars, fatty acids, amion acids, nucleotides
2
Q
larger units of the cell
A
polysacharides, lipids, proteins, nucleic acids (macromolecules)
3
Q
water cell
A
cell is 70% water; water has polarity and can therefore hydrogen bond; hydrophilic structures are polar and attracted to water hydrophobic structures are non polar and are repelled by water (non polar surfaces attract to each other to decrease contact with water)
4
Q
hydrogen bond
A
partial sharing of hydrogen, weak bond
5
Q
covalent bond
A
STRONG bond; sharing an electron; not broken by water
6
Q
ionic bond
A
transfer of electron; stronger than hydrogen bond but can be broken by water
7
Q
vänder wals forces
A
these are weak and dependent on atomic radii
8
Q
DNA ->mRNA
A
transcription
9
Q
mRNA-> protein
A
translation
10
Q
protein functions
A
- structural proteins
- Enzymes
- Adaptors
- Activators and Inhibitors
11
Q
Structural proteins
A
controlling elasticity, stiffness, morphology, and transport
12
Q
enzymes
A
Proteolysis, signal transduction (kinases, phosphates, G-proteins), Metabolism
13
Q
Adaptation
A
linking signaling reactions and pathways; controlling spacial distribution of proteins
14
Q
Activator and inhibiotrs
A
growth factors, hormones, antibodies
15
Q
sickle cell anemia
A
prime example of protein structure not functioning properly and disease occurring from it
16
Q
proteins made of
A
one or more distinct domains made up of helices and sheets; information determining protein structure encoded in amino acid sequence
17
Q
signaling proteins and cancer
A
deregulated growth factor receptors are associated with genesis and severity of cancer
18
Q
amino acid
A
building blocks of proteins; there are 20; made of backbone and side chain; backbone = carboxyl group, amino group, alpha carbon; side chain is R group
19
Q
gleevec
A
drug targeting aberrant (diverging from normal) signaling molecules; cancer therapy
20
Q
amino acids and protein diversity
A
different chemical qualities among AA lead to diff chemical properties
- AA can be charged (negative or positive)
- Glycine only has H as side chain
- proline loops and is bonded to backbone nitrogen
- two cycsine side chains can form a disulfide bond (covalent bond)
21
Q
protein structure
A
- Primary
- Secondary
- Tertiray
- Quaternary
22
Q
primary structure
A
sequence of amino acids
23
Q
peptide bones
A
rigid, movement allowed around other 2 bonds on amino acid; these bonds have favored rotational angles depending on 3-d structure; bond between 2 amino acids; occur at ribosome joined by amide linkage
24
Q
secondary structure
A
alpha helices and beta sheets and loops, can be parallel (all running in same direction with amino terminals at one end and carboxyl terminals on other end) or antiparallel running every other one); this structure is way to form hydrophobic core and hydrophilic exterior; driven by hydrogen bonding
25
tertiary structure
protein domain; stably folded units consisting of secondary structural elements and motifs; can constitute entire protein or one domain of a protein; interior or protein hydrophobic held together by vanderwals interactions, hydrophobic interactions, salt bridges, and hydrogen bonding
26
quaternary structure
folded protein; can be functional unit where one long polypeptide chain is folded into multiple domains or domains that fold separately are are held together by flexible linkers; protein subunits can be subunits encoded by different polypeptide chains (multisubunit or oligomeric proteins)
27
allosteric control
activation of one protein subunit in oligomeric protein can change property of another
28
Src homology domain
exists as single subunit protein or as multi domain protein
29
N terminus
always written toward the left
30
amino acids can be
uncharged (polar and non polar) or charged negative (acid) or positive (base); acids interact with water salt and basic side chains ; basic side chains can engage in ionic bonds
31
birth of a protein
polypeptide chain given one distinct fold which gives protein its structure which dictates its function
32
anfinsen's dogma
structure of protein determined by AA sequence
33
Levinthal's paradox
there are too many possible conformations to try to sample all possible conformations when a protein is folding
34
protein domains and complexity
proteins made up of domains which are mixed and matched domains can stand alone as isolated proteins or as part of soluble or membrane bound proteins
*study if time*
35
SH2 domain
binds to sequences that are phosphorylated on tyrosine; if receptor tyrosine kinase phosphorylates a substrate SH2 domain in protein can then bind to the substrate as linker molecule to bring another protein into signaling complex or to activate directly a downstream process
*study if time*
36
SH2 domain medically
can bind to GRB proteins (growth factor receptor binding proteins) through their SH2 domains these are related to metastasis in breast cancer
*Study if time*
37
SH3 domain
first described in Src; found in signaling, membrane bound, and cytoskeletal proteins; function as adaptor binding proline rich sequences
*study if time*
38
protein kinase
terminal phosphate of ATP transferred to hydroxyl group of serine, threonine, and tyrosine by protein kinase; protein kinases can be soluble or membrane bound proteins
39
what dictates protein structure
driven by forces between chemical groups (vander waals attractions, ionic bonds (electrostatic), hydrogen bonds); additionally non-polar side chains cluster to middle polar to outside
40
alpha helix
n terminus to c terminus; corkscrew turns; 3.6 residues per turn; oxygen interacts with hydrogen attached to nitrogen every 4th amino acid giving stability
41
beta sheet
hydrogen bonding engages through peptide bones; side chains point up or down
42
mixed folding
have alpha helices surrounding beta sheets
43
Src kinase
SH3, SH2, kinase= domains all off 1 polypeptide chain
44
homotetramer
protein complex made of 4 identical subunits
45
heterotetramer
protein complex where 1 or more subunits differ
46
molecular chaperones
prevent aggregation and help proteins fold
47
why proteins fold efficently
1. nature of peptide bond introduces constraints
2. interaction of amino acids with compatible properties
3. formation of secondary structure motifs reduces complexity
4. chaperones assist in folding
48
mutations
```
changes in genetic code
1. silent'
2.missense
3. nonsense
4.frameshift
Can alter activity and/ or folding of protein by preventing interactions or producing aberrant interactions
```
49
silent mutation
change in genetic code but does not alter AA in sequence and does not alter protein sequence
50
missence mutation
change in nature of residue leading to change in AA sequence
51
nonsense mutation
codes for stop codon
52
frameshift mutation
insertion or deletion of nucleotides shifts reading frame or can insert stop codon
53
amyloidosis
protein folding diseases; bovine spongiform encephalopathy (mad cow) and scrapie (sheep and goats), Alzheimers, Huntington's
54
alzheimers
proteolytic cleavage amyloid peptide ->amyloid fibril formation -> dementia
55
Huntintton's
trinucleotide repeats expansion in Huntington ->aggregation prone poly-Q stretch -> neurological disorders
56
protein misfolding in cell
can try to refold it or can get rid of amyloyoid state
57
Proteasomes
cell's trash can; central cylinder is protease; tag protein you want to get rid of with polyubiquitin chain proteasome chops it up and recycles it
58
Regulation of protein function
proteins are dynamic, regulated, capable of adopting distinct conformations, can switch between active and inactive state
59
Posttranslational modifictions
1. Proteolytic processing
2. Lipid attachment and glycosylation
3. Phosphorylation
4. Other types post translational processing
60
proteolytic processing
use for cleavage of signal sequence and for processing hormones and proteolytic enzymes and viral proteins
61
proinsulin
proteolytic processing; proinsulin translated as one peptide that is cleaved into two disulfide bonded peptides A and B chains of active form of insulin
62
mamalian digestive enzymes
proteolytic processing; prezymogens with signal for secretion in pancerease, signal sequence cleaved at secretion to form zymogen; makes enzyme active only when needed (ex trypsin and chymotrypsin)
63
viral processing
proteolytic processing; all RNA including proteases can be translated to make polyprotein so inhibition of proteolytic enzyme can inhibit viral replicatoin
64
lipid attachment and glycosylation
lipid attachment in intracellular signaling proteins
glycosilation (attachment of sugar chains) important for membrane bound proteins sugars found on part of protein exposed to extracelluar solvent/ water
65
Phosphorylation
placing phosphate on specific amino acid side chain in a protein; most commonly on hydroxyl groups of serine, threonine, and tyrosine; leads to change in charge to neg; phosphorylated sites can be docking sites for other protein facilitating complex formations
66
level of phosphorylation controlled by
kinases which add phosphate group and phosphatases which remove them; this makes it reversible so it can be used to turn intracellular signaling on/off
67
other post translational modifications
may be reversible or not add to diversity of protein function and control mechanisms available to cell
- nucleotide binding
- hydroxylation of proline
- carboxylation of glutamine
- ADP-ribosylation
- Ubiquitination/ sumoylation
68
G protein switch
protein controlled by small G protein exchange GDP for GTP turn it on in case of Ras works bc create small conformational change in certain region of protein; in cancer protein locked in on position regardless of GTP present or not
69
Lipids
water insoluble molecule; soluble in organic solvents; building blocks of cell membrane and some secondary messengers and hormones (steroids and eiocosanoids)
70
fat
solid at room temp
71
oil
liquid at room temp
72
role of lipids and membrane
building blocks of biological membranes, organelle identity and shape, barrier, signaling platform, secondary messenger and hormones, energy storage; forms physical barrier for polar substances, establishes electrochemical gradient
73
medical relevance of lipids and membrane
metabolic disease, cancer, neurological disorders, heart disease
74
fatty acids
fats like triglycerides and phospholipids (also eicoanoids, glycolipids, sphingolipids); hydrophilic carboxylic acid head group and hydrophobic hydrocarbon tail; tail can be unsaturated (no 2x bonds) or saturated (with cis 2x bonds)
75
fatty acid chain
long tail hydrocarbon make it very hydrophobic; can have straight tail (saturated) no double bonds present or kinked tail (unsaturated) double bonds present, they reduce melting point
76
phospholipid
glycerolphospholipids have two fatty acids and a polar phosphate head group; these are building blocks of cell membrane; polar head groups play a role in cell signaling
77
isoprene derived
non-glycerides; steroids (cholesterol- metabolite; testosterone- hormone)
78
triacylglycerols
fatty acids stored as energy reserve through ester linkage to glycero; glycerol linked to 3 fatty acids via ester bonds; energy reserve for cell; these = neutral fats
79
glycerophospholipids
building blocks of biomembranes; polar head group non polar tail can be straight or kinked
80
driving forces of membrane assembly
hydrophilic head groups surround themselves with water via hydrogen bonds hydrophobic tails move to inside to avoid water
81
fatty acids in water
can form micel (circle with heads outside and tails inside) or surface film
82
triacylglycerols
can form large spherical fat droplets in cell cytoplasm
83
phospholipids and glycolipids
form lipid bilayers
84
head groups in bilayer
head groups hydrophilic can change head groups to give different properties (phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, phosphitidylinositol, phosphatidic acid)
85
organelles with bilayer
Golgi apparatus, endosome, viral buddying
86
single platform receptors
membranes can work as single platform receptors activated by extracellular ligand and do work on phospholipids to signal
87
phosphatidylinositols
inositol has 7 positions that can all be modified and can lead to different protein interactions
88
roles of PIP2
importnat to cellular processes at cell membrane including:
endocytosis, exocytosis, phagocytosis, macropinocytosis, signal transduction, second messenger, cell adhesion, microtubules, cell motility, ion channels, transporters
89
Lipids as secondary messengers and hormone producers
1. enzymatic hydrolysis of head groups
2. arachidonic acid
3. phosphate modification of PI
90
Enzymatic hydrolysis of head groups
via phospholipiases, ex. PIP2 -> IP3 + diacylglycerol (DAG)
IP3->Ca2+ release from ER
DAG -> stimulation protein kinase C; source for prostaglandins
91
arachidonic acid
polyunsaturated fatty acid generated from PI, PC, PE;precursor for other molecules involved w signaling
92
phosphate modifications of PI
via kinases and phoshatases
93
cholesterole
isoprene derived lipid; has polar head group and bulky non polar tail; small compared to phospholipids; part of membrane in hydrophobic part dictates its flexibility(stiffens it); precursor for steroid hormone, clinical relevance: atherosclerosis, inflamation, heart attack, and stroke
94
sphingolipids
lipids derided from sphingosine (AA); linked to fatty acid, enriched in neutral tissue, mechanical and chemical stability of plasma membrane
95
glycolipids
carbohydrate attached lipids; extracellular surface of plasma membrane, energy providers, cellular recognition; GPI anchors on proteins (glycosylphosphatidylinosoitols); cerebrosides (gaucher disease, lysosomal storage disease), gangliosides (glycosphingolipids, influenza virus recognition, receptor for cholera toxin)
96
polar head group of phospholipid
dictates size charge and function of phospholipid
97
eicosanioid
short range hormones produced from fatty acids in the cell and nuclear membrane; ex. prostanoids involved in inflammation and pain Leukotrines also involved in inflammation
98
glycolipids
composed of two long hydrophobic hydrocarbon chains and polar head groups containing one or more sugars (NO phosphate); provide energy and play a role in cell recognition, located on extraceullar surface of plasma membrane
99
sphingolipids
lipids derived from sphingosine found in neutral tissue, play a role in signal transmission, cell recognition, and metabolites; contrinbute to mechanical and chemical stability of plasma membrane
100
isoprene derived lipids
(non-glycerides); polyisoprenes and steroids made from isoprene units; steroids have ring structure
101
signal transduction
enzymatic cleavage of head groups via phospholipase produces second messengers and precursors for biosynthesis of hormones; phosphorylation of phosphatidyl inositol head groups of cell membrane phospholipids trigger signaling events and control membrane/ organelle identity and membrane trafficking ; polar lipid head groups also serve as specific docking sites for proteins
102
determining shape and identity of cell membranes
lipid and protein composition of cell membranes contribute to this
103
cholesterole clincial relevance
has been linked to atherosclerosis and coronary heart disease
104
cholesterole transport
transported in the blood by low and high density lipoproteins
105
membrane microdomains
aka lipid rafts; membrane domains enriched in cholesterole, glycolipids, and sphingolipids; some viruses require lipid rafts to infect cell, blood clotting via tissue factor proteins requires these; signaling reactions are believed to be modulatable by partitioning of proteins into or away from membrane micro domains
106
carbohydrates
sugars (monomers), polysaccharides (polymers)
107
building blocks of simple sugars
(CH2O)n
108
carbohydrate energy storate
degradation of glucose (glycogen) essential for ATP production
109
glycosominaglycans
animal connective tissue
110
glycol-lipids-and-proteins
receptors, cell signaling
111
antigens
blood group determinants
112
monosacharides
aldose (double bond on tail) and ketoses (double bond internal)
113
3 carbon sugar
triose
114
5 carbon sugar
pentose
115
6 carbon sugar
hexose
116
sugar ring formation
in adquous solution aldehyde or ketone group of sugar molecule tends to react with hydroxyl group of same molecule closing molecule into a ring
117
functions of carbs
can be energy reserve or for structural role or for recognition motif
118
sugar derivatives
replace hydroxyl group of simple monosaccharide and get amino-sugar such as glucosamine, glucuronic acid, and N-acetylglucosamine, GlcNAc found in bacterial cell wall, chitin, and keratan sulfate
119
disacharide
2 monosaccharides bonded together
120
protein modification with sugars
occurs in ER lumen
121
protein glycosylation
can modify proteins with sugars in ER Lumen; surface carbohydrates on cell serves as point of attachment for other cells, infection bacteria, viruses, toxins, hormones, and many other molecules
122
sugar funcitons
can be structural, lubricants, and many other things such as transport function, enzymatic reaction, ect.
123
glycolysis
breakdown of glucose; main source for ATP production of cell
124
polymerization of monosacharids
to disaccharide, oligosacharides, or polysaccharides
125
hydrolysis
convertes polymerized monosaccharides back into smaller units
126
sugar linked to lipid
glycolipid; synthesized in Golgi apparatus
127
sugar linked to protein
glycoprotein which play a role in cell signaling, as receptors, and as antigens; modified in ER and golig apparatus
