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Block Two Cell Bio > Proteins Lipids and Carbohydrates > Flashcards

Proteins Lipids and Carbohydrates Flashcards

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Biology 101 flashcards
1
Q

building blocks of the cell

A

sugars, fatty acids, amion acids, nucleotides

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2
Q

larger units of the cell

A

polysacharides, lipids, proteins, nucleic acids (macromolecules)

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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)

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4
Q

hydrogen bond

A

partial sharing of hydrogen, weak bond

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5
Q

covalent bond

A

STRONG bond; sharing an electron; not broken by water

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6
Q

ionic bond

A

transfer of electron; stronger than hydrogen bond but can be broken by water

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7
Q

vänder wals forces

A

these are weak and dependent on atomic radii

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8
Q

DNA ->mRNA

A

transcription

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9
Q

mRNA-> protein

A

translation

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10
Q

protein functions

A
  1. structural proteins
  2. Enzymes
  3. Adaptors
  4. Activators and Inhibitors
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11
Q

Structural proteins

A

controlling elasticity, stiffness, morphology, and transport

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12
Q

enzymes

A

Proteolysis, signal transduction (kinases, phosphates, G-proteins), Metabolism

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13
Q

Adaptation

A

linking signaling reactions and pathways; controlling spacial distribution of proteins

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14
Q

Activator and inhibiotrs

A

growth factors, hormones, antibodies

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15
Q

sickle cell anemia

A

prime example of protein structure not functioning properly and disease occurring from it

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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

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17
Q

signaling proteins and cancer

A

deregulated growth factor receptors are associated with genesis and severity of cancer

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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

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19
Q

gleevec

A

drug targeting aberrant (diverging from normal) signaling molecules; cancer therapy

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20
Q

amino acids and protein diversity

A

different chemical qualities among AA lead to diff chemical properties

  1. AA can be charged (negative or positive)
  2. Glycine only has H as side chain
  3. proline loops and is bonded to backbone nitrogen
  4. two cycsine side chains can form a disulfide bond (covalent bond)
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21
Q

protein structure

A
  1. Primary
  2. Secondary
  3. Tertiray
  4. Quaternary
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22
Q

primary structure

A

sequence of amino acids

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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

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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

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25
Q

tertiary structure

A

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

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26
Q

quaternary structure

A

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)

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27
Q

allosteric control

A

activation of one protein subunit in oligomeric protein can change property of another

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28
Q

Src homology domain

A

exists as single subunit protein or as multi domain protein

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29
Q

N terminus

A

always written toward the left

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30
Q

amino acids can be

A

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

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31
Q

birth of a protein

A

polypeptide chain given one distinct fold which gives protein its structure which dictates its function

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32
Q

anfinsen’s dogma

A

structure of protein determined by AA sequence

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33
Q

Levinthal’s paradox

A

there are too many possible conformations to try to sample all possible conformations when a protein is folding

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34
Q

protein domains and complexity

A

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

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35
Q

SH2 domain

A

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

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36
Q

SH2 domain medically

A

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

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37
Q

SH3 domain

A

first described in Src; found in signaling, membrane bound, and cytoskeletal proteins; function as adaptor binding proline rich sequences
study if time

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38
Q

protein kinase

A

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

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39
Q

what dictates protein structure

A

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

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40
Q

alpha helix

A

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

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41
Q

beta sheet

A

hydrogen bonding engages through peptide bones; side chains point up or down

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42
Q

mixed folding

A

have alpha helices surrounding beta sheets

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43
Q

Src kinase

A

SH3, SH2, kinase= domains all off 1 polypeptide chain

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44
Q

homotetramer

A

protein complex made of 4 identical subunits

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45
Q

heterotetramer

A

protein complex where 1 or more subunits differ

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46
Q

molecular chaperones

A

prevent aggregation and help proteins fold

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47
Q

why proteins fold efficently

A
  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
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48
Q

mutations

A 
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
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49
Q

silent mutation

A

change in genetic code but does not alter AA in sequence and does not alter protein sequence

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50
Q

missence mutation

A

change in nature of residue leading to change in AA sequence

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51
Q

nonsense mutation

A

codes for stop codon

52
Q

frameshift mutation

A

insertion or deletion of nucleotides shifts reading frame or can insert stop codon

53
Q

amyloidosis

A

protein folding diseases; bovine spongiform encephalopathy (mad cow) and scrapie (sheep and goats), Alzheimers, Huntington’s

54
Q

alzheimers

A

proteolytic cleavage amyloid peptide ->amyloid fibril formation -> dementia

55
Q

Huntintton’s

A

trinucleotide repeats expansion in Huntington ->aggregation prone poly-Q stretch -> neurological disorders

56
Q

protein misfolding in cell

A

can try to refold it or can get rid of amyloyoid state

57
Q

Proteasomes

A

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
Q

Regulation of protein function

A

proteins are dynamic, regulated, capable of adopting distinct conformations, can switch between active and inactive state

59
Q

Posttranslational modifictions

A
  1. Proteolytic processing
  2. Lipid attachment and glycosylation
  3. Phosphorylation
  4. Other types post translational processing
60
Q

proteolytic processing

A

use for cleavage of signal sequence and for processing hormones and proteolytic enzymes and viral proteins

61
Q

proinsulin

A

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
Q

mamalian digestive enzymes

A

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
Q

viral processing

A

proteolytic processing; all RNA including proteases can be translated to make polyprotein so inhibition of proteolytic enzyme can inhibit viral replicatoin

64
Q

lipid attachment and glycosylation

A

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
Q

Phosphorylation

A

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
Q

level of phosphorylation controlled by

A

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
Q

other post translational modifications

A

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
Q

G protein switch

A

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
Q

Lipids

A

water insoluble molecule; soluble in organic solvents; building blocks of cell membrane and some secondary messengers and hormones (steroids and eiocosanoids)

70
Q

fat

A

solid at room temp

71
Q

oil

A

liquid at room temp

72
Q

role of lipids and membrane

A

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
Q

medical relevance of lipids and membrane

A

metabolic disease, cancer, neurological disorders, heart disease

74
Q

fatty acids

A

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
Q

fatty acid chain

A

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
Q

phospholipid

A

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
Q

isoprene derived

A

non-glycerides; steroids (cholesterol- metabolite; testosterone- hormone)

78
Q

triacylglycerols

A

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
Q

glycerophospholipids

A

building blocks of biomembranes; polar head group non polar tail can be straight or kinked

80
Q

driving forces of membrane assembly

A

hydrophilic head groups surround themselves with water via hydrogen bonds hydrophobic tails move to inside to avoid water

81
Q

fatty acids in water

A

can form micel (circle with heads outside and tails inside) or surface film

82
Q

triacylglycerols

A

can form large spherical fat droplets in cell cytoplasm

83
Q

phospholipids and glycolipids

A

form lipid bilayers

84
Q

head groups in bilayer

A

head groups hydrophilic can change head groups to give different properties (phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, phosphitidylinositol, phosphatidic acid)

85
Q

organelles with bilayer

A

Golgi apparatus, endosome, viral buddying

86
Q

single platform receptors

A

membranes can work as single platform receptors activated by extracellular ligand and do work on phospholipids to signal

87
Q

phosphatidylinositols

A

inositol has 7 positions that can all be modified and can lead to different protein interactions

88
Q

roles of PIP2

A

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
Q

Lipids as secondary messengers and hormone producers

A
  1. enzymatic hydrolysis of head groups
  2. arachidonic acid
  3. phosphate modification of PI
90
Q

Enzymatic hydrolysis of head groups

A

via phospholipiases, ex. PIP2 -> IP3 + diacylglycerol (DAG)
IP3->Ca2+ release from ER
DAG -> stimulation protein kinase C; source for prostaglandins

91
Q

arachidonic acid

A

polyunsaturated fatty acid generated from PI, PC, PE;precursor for other molecules involved w signaling

92
Q

phosphate modifications of PI

A

via kinases and phoshatases

93
Q

cholesterole

A

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
Q

sphingolipids

A

lipids derided from sphingosine (AA); linked to fatty acid, enriched in neutral tissue, mechanical and chemical stability of plasma membrane

95
Q

glycolipids

A

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
Q

polar head group of phospholipid

A

dictates size charge and function of phospholipid

97
Q

eicosanioid

A

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
Q

glycolipids

A

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
Q

sphingolipids

A

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
Q

isoprene derived lipids

A

(non-glycerides); polyisoprenes and steroids made from isoprene units; steroids have ring structure

101
Q

signal transduction

A

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
Q

determining shape and identity of cell membranes

A

lipid and protein composition of cell membranes contribute to this

103
Q

cholesterole clincial relevance

A

has been linked to atherosclerosis and coronary heart disease

104
Q

cholesterole transport

A

transported in the blood by low and high density lipoproteins

105
Q

membrane microdomains

A

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
Q

carbohydrates

A

sugars (monomers), polysaccharides (polymers)

107
Q

building blocks of simple sugars

A

(CH2O)n

108
Q

carbohydrate energy storate

A

degradation of glucose (glycogen) essential for ATP production

109
Q

glycosominaglycans

A

animal connective tissue

110
Q

glycol-lipids-and-proteins

A

receptors, cell signaling

111
Q

antigens

A

blood group determinants

112
Q

monosacharides

A

aldose (double bond on tail) and ketoses (double bond internal)

113
Q

3 carbon sugar

A

triose

114
Q

5 carbon sugar

A

pentose

115
Q

6 carbon sugar

A

hexose

116
Q

sugar ring formation

A

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
Q

functions of carbs

A

can be energy reserve or for structural role or for recognition motif

118
Q

sugar derivatives

A

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
Q

disacharide

A

2 monosaccharides bonded together

120
Q

protein modification with sugars

A

occurs in ER lumen

121
Q

protein glycosylation

A

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
Q

sugar funcitons

A

can be structural, lubricants, and many other things such as transport function, enzymatic reaction, ect.

123
Q

glycolysis

A

breakdown of glucose; main source for ATP production of cell

124
Q

polymerization of monosacharids

A

to disaccharide, oligosacharides, or polysaccharides

125
Q

hydrolysis

A

convertes polymerized monosaccharides back into smaller units

126
Q

sugar linked to lipid

A

glycolipid; synthesized in Golgi apparatus

127
Q

sugar linked to protein

A

glycoprotein which play a role in cell signaling, as receptors, and as antigens; modified in ER and golig apparatus

Block Two Cell Bio (9 decks)

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