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Cell Biology > Chapter 4 - Protein Structure And Function > Flashcards

Chapter 4 - Protein Structure And Function Flashcards

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1
Q

What are the kind of transport proteins

A

Hemoglobin and myoglobin

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2
Q

What are the function of specific transport proteins like hemoglobin and myoglobin

A

Carry O2 and CO2 in blood and muscles

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3
Q

What are the kind of structural proteins

A

Collagen and keratin

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4
Q

What is the function of structural proteins like collagen and keratin

A

Form cartilage, hair, and nails

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5
Q

What are the motor proteins

A

Actin and myosin

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6
Q

What is the function of motor proteins like actin and myosin

A

Allow muscles to contract

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7
Q

What are the defense proteins

A

Immunoglobulins

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8
Q

What are immunoglobulins

A

Antibodies produce by WBCs

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9
Q

What are the functions of defense proteins

A

Recognize foreign organisms and cancer cells

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10
Q

Enzymes

A

Are proteins that catalyze chemical reactions

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11
Q

Pepsin

A

Enzyme that breaks down proteins in stomach

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12
Q

What is an example of storage protein

A

Ferritin

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13
Q

What is the function of a storage protein, ferritin

A

stores iron in the liver

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14
Q

What is a signal protein that controls blood glucose levels

A

Insulin

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15
Q

What cells produce insulin

A

Beta cells of pancreas

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16
Q

How does insulin control blood glucose levels

A

By decreasing blood glucose levels

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17
Q

Receptors

A

Are proteins that detect signals and transmit them to the cell’s response machinery`

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18
Q

What is a type of regulatory protein

A

Transcription factors

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19
Q

Transcription factors

A

Regulatory proteins that regulate gene expression

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20
Q

GFP, green fluorescent protein

A

Is special purpose protein from jelly fish that emits green light

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21
Q

Proteins are made up of many what, and what is that called

A

Monomers, polymers

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22
Q

Polymers of proteins

A

Amino acids building block of protein

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23
Q

Example Protein that is made of up one polypeptide or polypeptide chain

A

Myoglobin

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24
Q

Example of proteins that are made up of two or more polypeptide

A

Hemoglobin

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25
Q

What groups make up a protein

A

Side chain (R group)
Amino group
Carboxyl group

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26
Q

Carboxyl group behaves as a what, what charge

A

Acids, donating H ions to solution, negative charge

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27
Q

Amino group behaves as what, what charge

A

Base by accepting h ions, positively charged

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28
Q

Who are amino acids joined together and forms what kind of bond

A

Dehydration synthesis to form peptide bonds

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29
Q

How are covalent bonds formed for amino acids

A

Carboxyl group of one amino acids shares electrons with the nitrogen atom from the amino group of second amino acid

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30
Q

Polar covalent bonds

A

Bond between atoms that don’t share their electrons equally because they have different electro negativities

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31
Q

Electronegativity

A

Atom’s attraction (pull) for shared electrons

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32
Q

Examples of polar covalent bonds

A

C-N
O-H
S-H

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33
Q

No polar covalent bonds

A

Bond between atoms that equally share their electrons because they have the same or similar electronegatives

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34
Q

Example of nonpolar covalent bonds

A

C-C
C-H
O=O
S=C

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35
Q

Peptide bonds are what kind of bonds

A

Polar covalent

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36
Q

Amino acids are linked together into

A

Polypeptide chain

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37
Q

What are unique to proteins

A

N and C terminus

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38
Q

Which way does amino acids link

A

N to C direction

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39
Q

N terminus

A

Amino terminus, positively charged

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40
Q

C terminus

A

Carboxyl terminus, negatively charged

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41
Q

Side chains aka

A

R groups

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42
Q

Why are side chain important

A

Determine chemical properties of amino acids

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43
Q

Side chain or r groups can be classified into what

A

Polar (hydrophilic) or non polar (hydrophobic)

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44
Q

How many amino acids are there

A

20

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45
Q

GeorgiA

What charge

Basic or acidic

Polar or nonpolar

A

Aspartic acid
Glutamic acid

Negative

Acidic

Polar, hydrophilic

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46
Q

Home in ALabama

What charge

Basic or acidic

Polar or nonpolar

A

Histidine
Lysine
Arginine

Positive charged
basic
Polar hydrophilic

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47
Q

Calls Sally and George by AT&T

What charge

Basic or acidic

Polar or nonpolar

A 
Cysteine
Serine
Glutamine
Asparagine
Threonine
Tyrosine

Uncharged
Neither basic or acidic
Polar

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48
Q

What is unique to polar amino acids in their side chains

A

They have oxygen or hydroxyl groups (OH-)

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49
Q

LT GAV PIMP

What charge

Basic or acidic

Polar or nonpolar

A

Leucine, tryptophan, glycine, alanine, valine, proline, isoleucine, methionine, phenylalanine

No charge

Not basic or acidic

Non polar, hydrophobic

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50
Q

What is unique to nonpolar amino acids side chains

A

Have CH2, or methyl CH3 group in their side chains

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51
Q

What is the pneumonic to remember all 20 amino acids

A

LT GAV PIMP Calls Sally and George by AT&T from GeorgiA to their Home in ALabama

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52
Q

What determines the proteins function and with the help of what

A

The shape, with the help of three types of non covalent bonds

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53
Q

What are the three types of non-covalent bonds for proteins

A

Ionic bonds
Hydrogen
Van Dre Waals attraction

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54
Q

What happens when they are many of van der waals attraction

A

Causes bond to be strong

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55
Q

Ionic bonds

A

Bonds form between opposite charges

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56
Q

Van der waals

A

Weak attraction that form between atoms at very short differences due to their fluctuating electrical charges

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57
Q

Why are hydrogen bonds important for hydrogen bonds

A

Help stabilize proteins folded shape

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58
Q

What are the three types of hydrogen bonds

A

Backbone to backbone
Backbone to side chain
Side chain to side chain

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59
Q

Interactions that contribute to protein shape

A

Hydrophobic forces

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60
Q

What are so unique to hydrophobic forces to proteins

A

Help proteins fold into compact conformations (final folded structures)

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61
Q

In biology what bond is the strongest

A

Covalent

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62
Q

In chemistry was bonds are the strongest

A

Ionic

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63
Q

List the bonds to strongest to weakest

A

Covalent > Ionic > H bonds > hydrophobic forces > Van der waals attractions

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64
Q

What type of bond can be found in a single protein

A

H bonds

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65
Q

Denatured

A

Unfolded

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66
Q

How can proteins become denatured

A

Through exposure to heat, wrong pH or chemicals

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67
Q

How does desaturation works

A

It disrupts the noncovalent interactions holding the folded chain

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68
Q

Denatured proteins have only what bond

A

Peptide covalent bonds

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69
Q

Renaturation

A

Some proteins can be regenerated upon removal of denature good agent

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70
Q

What agent can causes denaturation to proteins

A

Urea

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71
Q

How can urea causes denaturation

A

Squeezes between H bonds

Diminishes hydrophobic forces

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72
Q

Can denaturation be undone

A

In some cases, but mostly no

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73
Q

Protein aggregation

A

Occur when misfolded proteins aggregate

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74
Q

Protein aggregation causes underlying number of neurodegenerative disorders which are

A

Alzheimer’s disease and Huntington’s disease

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75
Q

Prion diseases causes what in sheep, cattle, and humans

A

Scrapie
Mad cow
CJD creutzfeld jacob disease

Protein aggregate

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76
Q

What disrupt brain function that can result in death due to aggregates

A

Amyloid fibril

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77
Q

How can abnormal prion proteins be transferred to normal individuals

A

Blood, food or surgical instruments

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78
Q

Chaperons

A

Proteins that help incorrectly folded and newly synthesized proteins fold correctly

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79
Q

Heat shock proteins HSP

A

Produce when cells are exposed to elevated temperatures and other stresses

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80
Q

What organelle has many chaperons

A

Rough ER

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81
Q

What does the alpha helix looks like and what bonds are formed

A

Spiral, which the N-H of every peptide bond is hydrogen bonded to the C=O neighboring peptide bond

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82
Q

How does alpha helixes form

A

Backbone to backbone h bonds

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83
Q

The b sheet resembles what

A

Picket fence

84
Q

The b sheets are connected by

A

Which individual polypeptide chains strands in the sheet are held together by hydrogen bonding between peptide bonds in different strands

85
Q

Hydrophobic side chains of the amino acids formin the alpha helix contact what

A

They hydrophobic hydrocarbon tails of the phospholipids

86
Q

Hydrophilic parts of the polypeptide backbone form what

A

Hydrogen bonds with another interior of the helix

87
Q

Two alpha helixes can wrap around each other with …

A

Hydrophobic side chains

88
Q

What is left exposed to the aqueous environment for intertwined alpha helices

A

Hydrophobic side chains

89
Q

What are the proteins levels or organization

A

Primary, secondary, tertiary, quaternary structure

90
Q

What are two types of protein secondary structures

A

Beta sheets and alpha helix

91
Q

Primary structure

A

Sequence of amino acids, this is not functional

92
Q

What types of bonds does primary structures have

A

Only peptide bonds, covalent

93
Q

Secondary structures functional or non functional

A

Non functional

94
Q

What kind of bonds does secondary structure protein has

A

Backbone to backbone, h bonds and peptide bonds

95
Q

Tertiary structure

A

Final 3D shape of protein consisting of a single polypeptide chain

96
Q

Quaternary structure

A

Arrangement of 2 or more polypeptide chains in space

97
Q

What kind of bonds does quaternary structure

A

Back bone to backbone, h bonds, peptide bonds, and any other bonds

98
Q

If a protein is made up of one polypeptide chain, how does it become functional

A

By reaching its tertiary structure

99
Q

What is an example of a protein that is made of one polypeptide chain

A

Myoglobin

100
Q

Denatured myoglobin loses what structures

A

Secondary and tertiary structures

101
Q

How does a proteins that is made out of 2 or more polypeptides becomes functional

A

By reaching its quaternary structure

102
Q

Example of a protein made out of 2 or more polypeptides

A

Hemoglobin

103
Q

Hemoglobin is made out of how many polypeptides

A

4

104
Q

Denatured hemoglobin loses what structures

A

Secondary, tertiary, and quaternary structures

105
Q

Protein dissociation and how can this happen

A

2 or more polypeptides that makes up a protein come apart; loses quaternary structures, this happens by exposure to salts

106
Q

How is protein dissociation related to denaturation

A

Easier to fix than denaturation

107
Q

Protein is made up of only 1 polypeptide undergoes what…

Denaturation or dissociation

A

Denaturation only

108
Q

Protein made 2 or more polypeptides undergoes what

Denaturation and dissociation

A

Both

109
Q

Protein domain

A

Any segment of polypeptide chain that can fold independently into compact, stable structure

110
Q

Unstructured regions in proteins

A

Separate proteins domains from each other

111
Q

Protein family

A

Each family member has amino acids sequences and 3D conformation that closely resembles that of the other family members

112
Q

Active site

A

Region of enzyme where peptide bond of its protein substrate is bound and cleaved by hydrolysis

113
Q

Binding site

A

Any region on proteins surface that interacts with another molecule through sets of noncovalent bonds

114
Q

What are the different subunits of hemoglobin

A

2 alpha globin subunits and 2 beta globin subunits

115
Q

Each subunits contains what for hemoglobin

A

Heme group with iron atom for O2 binding

116
Q

Dimer

A

A molecule consisting of two identical molecules linked together

117
Q

Protein with just one binding site can form what

A

Dimer with another identical protien

118
Q

Identical proteins with two different binding sites will often form what

A

Helical filament

119
Q

How can proteins form a ring

A

Two binding sites of identical proteins are disposed appropriately to each other

120
Q

Actin filament is what kind of structure

A

Helical structure

121
Q

How is actin filaments formed

A

Many identical protein subunits

122
Q

Single protein subunits can pack to form

A

Filaments, tube or spherical shell

123
Q

Types of proteins that has elongated fibrous shapes

A

Collagen and elastin

124
Q

Fibrous proteins

A

Relatively simple, elongated 3D shaped

125
Q

Collagen

A

Triple helix formed by three polypeptide chains

126
Q

Elastin

A

Cross linked together by covalent bonds to form rubberlike elastic fibers

127
Q

Disulfide bonds are stronger or weaker than peptide bonds

A

Weaker

128
Q

Are disulfide bonds polar or nonpolar

A

Non polar

129
Q

Disulfide bonds

A

Covalent bonds that form between the sulfur atoms of adjacent cysteine side chains

130
Q

What is important about the disulfide bonds

A

Help stabilize the tertiary and quarternary conformations

131
Q

The activity of proteins depends on

A

Their ability to bind specifically to other molecules, allowing them to act as catalyst, structural supports, signal receptors and tiny motors

132
Q

What is needed to enable protein to bind tightly to ligand

A

Many noncovalent bonds are needed

133
Q

Binding sites allow protein to interact with …

A

Specific ligand by forming noncovalent bonds

134
Q

What is unique to the binding sites of antibodies

A

They are versatile

135
Q

Antibodies

A

Immunoglobulins proteins that are produced by white blood cells called B sites

136
Q

What are antibodies used for

A

Immune system to recognize foreign molecules found on the surface of cancer cells invade microorganisms

137
Q

Antigen

A

Foreign molecules

138
Q

Antibodies are composed of what

A

2 identical heavy chains and 2 identical light chains held together by disulfide bonds

139
Q

How does antigen bonding site forms

A

When Vh and Vl domains come close together

140
Q

What domain is closely involved in binding to antigen

A

Vl domain

141
Q

Enzymes convert substrates to what

A

Products

142
Q

Catalyst does what to activation energy

A

Lowers it

143
Q

Each enzyme has its own _______ which binds to the __________

A

Substrate; active site

144
Q

Hydrolase

A

General term for enzymes that catalyze a hydrolytic cleavage reaction

145
Q

Nuclease

A

Breaks down nucleic acids by hydrolyzing bonds between nucleotides

146
Q

Protease

A

Breaks down proteins by hydrolyzing peptide bonds between amino acids

147
Q

Ligase

A

Joins two molecules together; DNA Ligase joins the two DNA strands together end to end

148
Q

Isomerase

A

Catalyze the rearrangement of bonds within a single molecule

149
Q

Polymerase

A

Catalyze polmerization reactions such as the synthesis of DNA and RNA

150
Q

Kinase

A

Catalyze the addition of phosphate groups to molecules. Protein kinases are an important group of kinases that attach phosphate groups to proteins

151
Q

Phosphatase

A

Catalyzes the hydrolytic removal of a phosphate group from a molecule

152
Q

Oxide-reductase

A

General name for enzymes that catalyzes reactions in which one molecule is oxidized while the other is reduced.

153
Q

ATPase

A

Hydrolyzes ATP. Many proteins have an energy harnessing ATPase activity as part of their function, including motor proteins such as myosin

154
Q

DNase and RNase

A

Nucleases that break down DNA and RNA by hydrolyzing phosphodiester bonds

155
Q

Ribozymes

A

Enzymes that RNA molecules in nature

156
Q

Peptidyltranserase

A

rNA of the large ribosomal subunit that catalyzes the formation of peptide bonds between amino acids

157
Q

Lysozyme

A

Enzyme which cleaves the polysaccharide chains that form the cell wall of the bacteria, act as a natural antibiotics

158
Q

Polysaccharides are made up of what

A

Glycosidic links

159
Q

What is true about enzymes and reactions,can it be consumed?

A

No, It can be reused in rxns

160
Q

What happens of the active site of lysozymes

A

Bonds are bent and brokenness

161
Q

Proteins are controlled by what

A

Inhibitors and activators

162
Q

Allosteric enzymes has how many binding sites that influences one another

A

Two or more

163
Q

Phosphorylation can control activity by causing

A

Conformational change

164
Q

Regulatory GTP binding proteins are switched on and off by

A

The gain and loss of phosphate group become when GPD binds to them they become active.

165
Q

Allosteric site

A

Region of enzyme where molecule other than substrate binds

166
Q

Biochemical pathway

A

Consist of multiple chemical reaction that occur at the same area and the product of one enzyme becomes the substrate of the next

167
Q

Where glycolysis occurs

A

Cytoplasm

168
Q

Feedback inhibition (negative regulation)

A

Process in which late product of the pathway inhibits enzynme acting early in the pathway by binding to allosteric site, it will make site inactive

169
Q

How does feedback inhibition triggers conformational change

A

By altering the enzymes active site

170
Q

Competition inhibition

A

Competes with substrate for the enzymes active site while noncompeptitor inhibition does not, it binds to allosteric site.

171
Q

Non competition inhibition or allosteric inhibitor

A

Allosteric activations help enzymes work better. They invade cofactors; some are inorganic copper zinc and iron

172
Q

Positive feedback or positive regulation

A

Process in which the enzyme activity is stimulated by regulatory molecule

173
Q

Production of what is an example of positive feedback

A

Oxytocin

174
Q

Oxytocin

A

Hormone causes contractions of uterus

175
Q

What is true about ATP levels

A

When they are low, ADP levels are high and ADP activates the enzyme that catalyzes the conversion of sugar to produce more ATP

176
Q

The transfer of phosphate group from ATP to the hydroxyl group on serine, threonine, or tyrosine side chain of what target protein

A

Protein kinase

177
Q

Protein phosphatases does what

A

Dephosphorylate phosphorylated proteins

178
Q

Why is phosphorylation of a protein by protein kinase

A

Can either increase or decrease the protein’s activity depending on the site of phosphorylation and the structure of the protein

179
Q

If protein is activated by phosphorylation, it is _________ by dephosphorylation

A

Inactivated

180
Q

When GTP is bound to proteins, they are what

A

Active

181
Q

What is GTP

A

Guanosine triphosphate

182
Q

GTP is made up of what

A

5 c sugar, ribose
Guanine
3 phosphate groups

183
Q

When does GTP becomes inactive

A

When GTP is hydrolyzed into GDP, releasing Pi (inorganic phosphate)

184
Q

What 3 main things are motor proteins responsible for

A

Muscle contractions, separation of chromosomes during mitosis, and movement of materials and organelles within the cell.

185
Q

What allows motor proteins to move continuously in one direction along the cytoskeletal filament

A

Three conformational changes

186
Q

What covalent modification control the activity and degradation of the tumor suppressor protein p53

A

Phosphorylation, ubiquitylation, acetylation

187
Q

Acetylation

A

Acetyl groups (COCH3) are added to protein

188
Q

P53 regulates what

A

Cells response to DNA damage

189
Q

What kind of gene is p53

A

A tumor suppressor gene

190
Q

What makes p53 function

A

Acetylation and phosphorylation

191
Q

What degrades p53

A

Ubiquitylation

192
Q

When do we want p53 active and when do we not want it active

A

We want it active when there is DNA damage

When there is no damage, we don’t need p53

193
Q

Will all the modifications for p53 be present

A

No

194
Q

What is the most mutated gene

A

P53

195
Q

What is the function of normal p53

A

Stops cell division when DNA is damaged

Triggers the production of the DNA repair enzymes

If DNA is fixed, the cell divides

If DNA is not fixed, p 53 proteins causes the cell to commit suicide or apoptosis

196
Q

Ubiquitylation

A

Marks protein for degradation binds with another protein

197
Q

Proteasome

A

Cylindrical complexes found in cytoplasm and nucleus of eukaryotes and are made of proteases

198
Q

How are proteins studied

A

Centrifuge
Chromatography
Gel electrophoresis
Isoelectric focusing

199
Q

Centrifugation

A

Separates cells components on the basis of size and density.

200
Q

What are the three kinds of chromatography

A

Ion exchange chromatography
Gel filtration chromatography
Affinity Chromatography

201
Q

What is the importance of affinity chromatography

A

Isolated the binding partner of protein of interest.

202
Q

How is protein x related to insulin

A

Receptor protein

203
Q

Where does glucagon made from

A

Alpha cells of pancreas

204
Q

Adrenaline is made

A

Cells of adrenal glands

205
Q

Insulin is made where

A

Beta cells of pancreas

206
Q

What does SDS causes polypeptides to do

A

To unfold and makes them negatively charged

Cell Biology (9 decks)

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