Biochem Test 1

Front 1

Polypeptides are linear _______.

Back 1

heteropolymers

Front 2

Proteins are folded into specific shapes based on 1°, 2°,3°,and 4°. These shapes are called the ______ of the protein.

Back 2

native conformation

Front 3

Molecular weight of proteins is highly variable and is expressed in ______.

Back 3

kilodalton (kDa)

Front 4

Proteins function as...

Back 4

1. Enzymes
2. Regulators of gene expression
3. Hormones, growth factors, receptors, signal transducers
4. Structural elements
5. Antibodies and other elements of the immune system

Front 5

In the case of starvation, proteins can function as _______.

Back 5

an energy source

Front 6

Proteins can be infectious particles in the form of _____.

Back 6

prions

Front 7

A simple protein contains only ______. A conjugated protein contains ______.

Back 7

amino acids; non-protein components, including lipids, carbohydrates, nucleic acids, metals, and organic prosthetic groups.

Front 8

Proteins are polymers of ____.

Back 8

Alpha amino acids.

Front 9

Alpha amino acids can have two isomeric structures (enantiomers), named _____.

Back 9

L and D

Front 10

Are proteins made of L or D amino acids?

Back 10

L

Front 11

D amino acids are rare and can be found in bacteria ______, toxins from ______, or as ________ in mammals.

Back 11

peptidoglycans, cone snails and platypuses, neurotransmitters

Front 12

As pH changes, so does the ________ of the amino acid.

Back 12

ionization state

Front 13

When the amino acid has both a positive and negative charge, and has no net charge, it is referred to as a _______.

Back 13

Zwitterion

Front 14

When pH=pK, that particular site is ____ ionized. When pH is near the pK of a weak acid or base, the weak acid or base can act as a _____.

Back 14

50%, buffer

Front 15

The pH where the aa has no net charge is referred to as the ______.

Back 15

isoelectric point or pI. This will happen in between the pK of the amino group and the pK of the carboxyl group unless the R chain has an ionizable group.

Front 16

How many L-alpha-amino acids are found in proteins?

Back 16

20

Front 17

Name the amino acids with positively charged side chains.

Back 17

Lysine(K), Arginine(R), Hystidine(H, also aromatic)

Front 18

Name the amino acids with polar, uncharged side chains.

Back 18

Serine(S), Threonine(T), Cysteine(C), Asparagine(N), Glutamine(Q)

Front 19

Name the amino acids with nonpolar aliphatic side chains.

Back 19

Glycine(G), Alanine(A), Valine(V), Leucine(L), Isoleucine(I), Proline(P), Methionine(M)

Front 20

Name the amino acids with negatively charged side chains.

Back 20

Aspartate(D), Glutamate(E)

Front 21

Name the amino acids with aromatic side chains.

Back 21

Histidine(H, also can be positively charged), Phenylalanine(F), Tryosine(Y), Tryptophan(W)

Front 22

A mutation of an amino acid to an amino acid with similar properties is called a ______ and is more likely to be tolerated in a protein.

Back 22

conservative mutation

Front 23

______ amino acids can form salt bridges.

Back 23

charged

Front 24

During the titration of aspartic acid, you will see three ______. The pI is midway between the pKs of _____ and _____.

Back 24

buffer zones; the carboxyl group; the side chain

Front 25

During the titration of lysine, there will be three ______. The pI will be midway between the pKs of____ and _____.

Back 25

buffer zones; the side chain; the amino group

Front 26

At physiological pH, glutamic acid will be ______. At physiological pH, asparagine will be ______.

Back 26

negatively charged; positively charged

Front 27

____, ____, and ____ will absorb light at ______. This gives them all a unique __________.

Back 27

Tryptophan; tyrosine; phenylalanine; extinction coefficient.

Front 28

______ has only one _____, and is the least frequent, and largest of the amino acids.

Back 28

Tryptophan; codon

Front 29

______ is the only nonchiral amino acid.

Back 29

Glycine

Front 30

The polar, noncharged amino acids contain _____, _____, and _____ groups.

Back 30

hyrdoxyl; sulfhydryl; primary amide

Front 31

______ is involved in disulfide bond formation.

Back 31

Cysteine

Front 32

L-DOPA and 5-HTP are both examples of proteins functioning as ______. Briefly describe what L-DOPA and 5-HTP do.

Back 32

neurotransmitters; L-DOPA is the precursor of dopamine, epinephrine, and norepinephrine and is used to treat Parkinson's. 5-HTP is the precursor of serotonin.

Front 33

9 of the amino acids are essential. Name them. What is the mnemonic device we were given in class?

Back 33

1. Ingesting (Isoleucine)
2. These (Threonine)
3. Little (Leucine)
4. Molecules (Methionine)
5. Has (Histidine)
6. Value (Valine)
7. When (Tryptophan)
8. Knowledge (Lysine)
9. Fails (Phenylalanine)

Front 34

Animal proteins are termed "complete" because they contain ______.

Back 34

all the essential amino acids

Front 35

Name two diseases that belong to the class known as Protein-Energy Malnutrition (PEM).

Back 35

marasmus and kwashiorkor

Front 36

_________ happens when the body is unable to convert ______ into tyrosine. ______ and its breakdown products build up in the blood, causing _________.

Back 36

Phenylketonuria (PKU), phenylalanine, phenylalanine, mental retardation

Front 37

Individuals with phenylketonuria (PKU) must avoid the sweetener ________, which is an ester of the ________ dipeptide.

Back 37

aspartame; Asp-Phe

Front 38

The position of the peptide bond can be described using two rotation angles _____ and _____. The angles are relative to the ______ plane.

Back 38

phi; psi; H-Calpha-Rgroup

Front 39

_____ is the N-Calpha angle. _____is the Calpha-C angle

Back 39

Phi; psi

Front 40

In some cases, protein folding is aided by helper proteins called _______.

Back 40

chaperones

Front 41

Name some secondary structures of proteins.

Back 41

Alpha helix, beta sheet, beta strand, beta turn, random coil.

Front 42

What is the Ramachandran plot?

Back 42

It shows the favored angles of psi and phi. The graph shows that there are two places where most of the combinations will fall. One represents the angles of the alpha helix (smaller area on the bottom), the other represents the angles of the beta sheet (larger area on the top).

Front 43

The alpha helix is a ____ handed coil with _____ residues per turn and a pitch of ____ angstroms. The helix is held together by ________ between the ______ atoms.

Back 43

right; 3.6; 5.4; hydrogen bonds; backbone

Front 44

What is an amphipathic helix? Where might you find one?

Back 44

This is when all the hydrophic aas line up on one side of an alpha helix, with all the hydrophilic aas on the other side of the helix. You might find this in a membrane protein

Front 45

Alpha helices in transmembrane proteins will usually be one of these two types.

Back 45

1. A single hydrophobic helix
2. a barrel of amphipathic helices (often 7), with their hyrophilic sides on the inside

Front 46

What is a leucine zipper?

Back 46

Two alpha helices that are "zipped" together by leucine that is repeated every 7 residues (roughly two turns) of each helix.

Front 47

Which secondary structure is most common? Second most common?

Back 47

1. alpha helix
2. beta sheet

Front 48

In beta sheets, the backbones are almost ______. The sheet is held together by ________ between the backones.

Back 48

fully extended; hydrogen bonds

Front 49

Porins are _______ proteins that are made entirely of _______. They are much less common than ______.

Back 49

transmembrane; beta sheets; alpha helices

Front 50

What protein structure is represented? Which two amino acids are often found in this kind of turn?

Back 50

Beta turn. Proline and glycine.

Front 51

Beta turns often promote the formation of ________.

Back 51

antiparallel beta sheets

Front 52

What is supersecondary structure? Name three examples.

Back 52

The aggregate of adjacent secondary structures to form familiar motifs, such as the beta-alpha-beta, the beta-meander, and the Greek key.

Front 53

Supersecondary structures: The _____ is common in DNA binding proteins. The ____ is common in calcium binding proteins.

Back 53

helix-loop-helix, E-F hand

Front 54

Protein disulfide isomerase...

Back 54

helps proteins find the correct disulfide bond.

Front 55

Prosthetic groups are...

Back 55

non polypeptide structure or inorganic ion tightly bound to a protein and essential for its function.
e.g. heme in hemoglobin

Front 56

snRNP stands for....

Back 56

small nuclear ribonucleoproteins

Front 57

______ are RNA-protein complexes that combine with unmodified pre-mRNA to form a _____.

Back 57

snRNPs; spliceosome

Front 58

The splicing of pre-mRNA into mRNA occurs only in _______ of eukaryotic cells. It occurs on the ________.

Back 58

the nucleus; spliceosome

Front 59

A spliceosome is a complex of _____ and ______ that removes ______ from pre-mRNA in the nucleus.

Back 59

snRNA; protein subunits; introns

Front 60

Name five things that can cause denaturation.

Back 60

1. Heat
2. changes in pH
3. changes in salt content
4. detergents
5. oxidants/reductants

Front 61

PRPsc is the abnormal prion protein. How/why does it replicate?

Back 61

It can be genetic or ingested. The abnormally folded protein can get next to a normal protein and induce the formation of a homodimer. This process continues until an amyloid plaque of abnormal proteins develops.

Front 62

Which residues typically undergo post-translational glycosylation? Is it permanent?

Back 62

This covalent addition is relatively permanent. Ser/Thr are likely to undergo O-linked glycosylation, which Asn will undergo N-linked glycosylation.

Front 63

What kind of permanent post-translational modification did we learn about? What examples were given?

Back 63

Partial proteolysis. Zymogens. Insulin.

Front 64

What effect do oligosaccharides have when added to proteins?

Back 64

They are hydrophilic and thus increase protein solubility.

Front 65

Glycoproteins created in the cell are destined to be....

Back 65

either secreted or exposed on the cell surface.

Front 66

Where does N-glycosylation occur? What sequence must be present?

Back 66

In the lumen of the RER. The sequence must be Asn-X-Ser/Thr where X is not Pro or Asp.

Front 67

Where does O-linked glycosylation occur? What sequence must be present?

Back 67

In the Golgi. No sequence is necessary. Ser and Thr undergo O-glycosylation, as does an already hydroxylated Lys in collagen.

Front 68

Lipids added post-translationally often serve as anchors in _____. What residues did we see examples of?

Back 68

the cell membrane. C-terminal or internal Cys. N-terminal Gly.

Front 69

What is a GPI anchor? Where would you be likely to find one? What purpose does it serve?

Back 69

A GPI is glycosyl-phosphatidyl inositol, which is a lipid that is added to proteins as a post-translational modification near the C-terminus. The GPI/proteins are likely to be found in membrane raft areas. They allow proteins to be more mobile on the cell surface.

Front 70

_______ occurs on the three amino acids containing a hydroxyl group (which are...). This is a reversible process.

Back 70

Phosphorylation. Serine, threonine, and tyrosine.

Front 71

Post-translational phosphorylation is catalyzed by_____. Dephosphorylation is catalyzed by ________.

Back 71

kinases; protein phosphatases

Front 72

EPO is....

Back 72

erythropoietin, a performance enhancer than carries more red blood cells to muscles. It is a naturally occurring protein that is also available as a recombinant protein for the treatment of anemia.

Front 73

How can we tell if the EPO is natural, or if athletes are doping?

Back 73

Although the primary structure of EPO and rEPO is the same, the post-translational modifications are not. These modifications change the pI, so the two forms can be distinguished by isoelectric focusing.

Front 74

In isoelectric focusing, proteins move across a ____ and a _____ until they reach their pI.

Back 74

pH gradient (high to low); electric field (negative to positive)

Front 75

Protein structures are obtained by using _____ or _____.

Back 75

X-ray crystallography; NMR

Front 76

Proteins work according to these two fundamental principles, which are often intimately linked.

Back 76

Binding and conformational change.

Front 77

The molecule bound to the protein is called the ____.

Back 77

ligand

Front 78

The affinity of a protein for a ligand is expressed as ______. It has units of _____.

Back 78

The dissociation constant Kd; unit of concentration of ligand

Front 79

Kd=

(two formulas)

Back 79

Kd = [Ligand(free)] * [binding sites(free)] / [protein-ligand]

Kd = kd/ka

Front 80

Kd is.....
A high Kd corresponds to _____.

Back 80

The concentration of ligand at which 50% of ligand will be bound.

High Kd = low affinity

Front 81

Two important things to remember about the Scatchard plot.

Back 81

1. Bmax is the X-axis intercept.
2. slope = -Kd

Front 82

kd represents the ______ of a protein/ligand compound. A high kd corresponds to _____. (NB: kd /=Kd)

Back 82

stability; a rapid rate of dissociation

Front 83

What is the oxidation state of the heme iron? What residue does it form a bond with?

Back 83

The iron is ferrous (reduced iron, Fe2+).

It bonds with histidine.

Front 84

The increased affinity of hemoglobin for oxygen after one O2 has bound is an example of _____.

Back 84

allosteric (or cooperative) binding

Front 85

What are the shapes of the myoglobin and hemoglobin oxygen affinity curves?

Back 85

Myoglobin: hyperbolic
Hemoglobin: sigmoid

Front 86

What is the Bohr effect?

Back 86

Describes how hemoglobin affinity for O2 decreases as:
1. pH decreases
2. CO2 increases
3. temperature increases
4. 2,3-BPG increases

This means more will be released to myoglobin.

Front 87

In sickle cell, a normal _____ residue is replaced with a _____ residue.

Back 87

glutamate; valine

Front 88

The ELISA test is used to...

Back 88

determine the presence of an antigen or antibody. (Used for HIV)

Front 89

The Ompg porin is a channel that will be _____ at biological pH and will be _____ at lower pH.

Back 89

open; closed

Front 90

SNAREs are...

Back 90

proteins involved in vesicle transport (exocytosis).

Front 91

If A+B <----> C +D, then Keq=

Back 91

Keq= [C][D]/[A][B]

Front 92

DeltaG=

Back 92

deltaG = -RTln(Keq)

Front 93

If Keq > 1, the reaction is said to be...

Back 93

favorable (exergonic)

Front 94

If Keq < 1, the reaction is said to be...

Back 94

unfavorable (endergonic)

Front 95

The same catalyst molecule can catalyze many reactions. This is called ______.

Back 95

turnover

Front 96

This rxn is catalyzed by ______:
ATP+glucose ---> ADP + glucose-6-phosphate

Back 96

hexokinase

Front 97

In gluconeogenesis, pyruvate + CO2 ----> _______. What must happen to make this rxn energetically favorable?

Back 97

oxaloacetate; It must be couple to the hydrolysis of ATP. The enzyme pyruvate carboxylase makes this coupling possible.

Front 98

This rxn is catalyzed by _____:
ATP + sulfate -----> adenosyl phosphosulfate +PPi

Back 98

pyrophosphatase

Front 99

_____ as well as proteins can be enzymes. They are called ____. They are the part of the ribsome responsible for _______.

Back 99

RNA; ribozymes; translation of RNA

Front 100

Name the six major groups of enzymes.

Back 100

Type 1: oxidoreductases

Type 2: transferases

Type 3: hydrolases

Type 4: lyases

Type 5: isomerases

Type 6: ligases

Front 101

Glyceraldehyde-3-phosphate dehydrogenase is know to be an enzyme that "moonlights," meaning....

Back 101

it is know to have other functions than it's well-known role in glycolysis. In this case, it has many.

Front 102

In the enzyme binding site, there are two kinds of residues: _____ and _____. There may also be _____ or metal ions.

Back 102

binding; catalytic; cofactors

Front 103

Regulatory sites where inhibitors or activators bind to an enzyme are called ______.

Back 103

allosteric sites

Front 104

What is a morpheein? What example were we given in class?

Back 104

PGBS regulated by Mg2+. The morpheeins are the two different kinds of quaternary structure. PGBS w/o Mg2+ will exist as an inactive hexamer. W/ Mg2+, it will be an active octamer.

Front 105

An enzyme without its cofactor is called a/an ______. An enzyme with its bound cofactor is called a/an ________.

Back 105

apoenzyme; holoenzyme

Front 106

In enzyme kinetics, k1 is...? k2? k3?

Back 106

k1 is the rate of formation of ES from E+S

k2 is the rate of dissociation of ES to E+S

k3 is the rate of formation of E+P from ES

Front 107

If there is much more substrate than enzyme, the the velocity of the formation of product is what?

Back 107

v = k3 x [ES]

Front 108

What is the formula for v for all substrate concentrations?

Back 108

v = (Vmax[S])/(Km +[S])

Front 109

What is the Lineweaver-Burk plot? What useful values does it provide?

Back 109

It is the double reciprocal plot. (Reciprocal of Michaelis-Menton) The y-intercept = 1/Vmax. The x-intercept = 1/-Km.

Front 110

In the conversion of threonine to isoleucine, _____ acts as an allosteric inhibitor early in the pathway. This is an example of _______.

Back 110

isoleucine; feedback inhibition

Front 111

Chymotrypsinogen is an inactive _____. It is activated by __________.

Back 111

zymogen; proteolytic cleavage

Front 112

Pyruvate carboxylase uses the cofactors ___ and ____, and has _____ as an allosteric activator. These molecules can modulate the ____ structure of pyruvate carboxylase.

Back 112

biotin; Mg; acetylCoA; quaternary

Front 113

How fast is the fastest enzyme?

Back 113

Turnover is about 10^10/sec

Front 114

Antibiotics:
Vancomycin and beta-lactam inhibit _____.

Back 114

formation of cell wall

Front 115

Antibiotics:
Erythromycin and tetracyclin disrupt ____.

Back 115

ribosomes

Front 116

Antibiotics:
Quinoline and sulfonamide inhibit _____.

Back 116

DNA synthesis/replication.

Front 117

Penicillin type drugs are _______ antibiotics. They work by _________.

Back 117

beta-lactam; inhibiting crosslinking of bacterial cell wall.

Front 118

What is beta-lactamase? What can be used to combat beta-lactamase?

Back 118

It breaks down beta-lactam antibiotics, giving bacteria immunity to penicillin. In this case, augmentin, a combination drug should be used. It contains both beta-lactam and an irreversible beta-lactamase inhibitor.

Front 119

Define isoenzyme.

Back 119

Isoenzymes are enzymes that differ in their primary sequence, but catalyze the same reaction. These enzymes usually display different kinetic parameters (e.g. Km values).

Front 120

What is epigenetics?

Back 120

The study of how factors other than DNA can change gene expression. In our case, I believe we are concerned with the packaging of DNA into chromatin.

Front 121

About how many base pairs in the human genome?

Back 121

~3.2 billion bp in a HAPLOID human genome.

Front 122

What percentage of DNA codes for proteins? How many protein coding genes are there in a human?

Back 122

<1.5%. There are around 25,000.

Front 123

There are around 25,000 genes that code for protein in a human, but there are around 100,000 proteins. Explain.

Back 123

The mRNA can be spliced in different ways to create different proteins. Also, the proteins can be post-translationally modified.

Front 124

About how many base pairs will be different from human to human?

Back 124

1/1000 bp

Front 125

Name three disease susceptibility genes identified through the Human Genome Project.

Back 125

Risk factors for:
1. Atrial fibrillation and stroke
2. Crohn's
3. myocardial infarction

Front 126

What are housekeeping genes?

Back 126

They are expressed in most cells.

Front 127

Name some genes that might be expressed in only a certain type of cell.

Back 127

1. Hb in red blood cells
2. insulin in beta cells of pancreas

Front 128

How far would the human genome stretch if DNA was not coiled?

Back 128

About 1 meter, meaning each chromosome would be about 4.3inches long.

Front 129

DNA wrapped around a histone is called a _____.

Back 129

nucleosome

Front 130

Nucleosomes are coiled to form the _____ form. It is about ___ nm high.

Back 130

solenoid; 30

Front 131

The solenoid strand is bound to a protein ______.

Back 131

scaffold

Front 132

The width of naked DNA is about __ nm. The histones are __ nm. The solenoid form is __ nm. The solenoid on the scaffold is __ nm.

One chromatid is __ nm wide. Therefore, the chromosome is ___ nm wide.

Back 132

2,11,30,300,700,1400

Front 133

What is condensin?

Back 133

It is a multiprotein complex that plays a role in compacting DNA.

Front 134

Are histone proteins basic or acidic? Why? How many protein subunits in a histone?

Back 134

Histones are basic so they can interact with the acidic/negative backbone of the DNA. Histones are octamers (4 different subunits).

Front 135

What does histone H1 do?

Back 135

It promotes the coiling of nucleosomes into the solenoid form.

Front 136

What kind of tails extend from a histone?

Back 136

They are N-terminal tails. They may promote condensation.

Front 137

Where will you find heterochromatn?

Back 137

At the centromere and the telomeres. It is permanently condensed.

Front 138

What is euchromatin?

Back 138

During interphase, it is the portion of DNA that will have some uncoiled, actively-transcribed portions.

Front 139

What do chromatin remodeling complexes do?

Back 139

They loosen the coil to make some portions of DNA more open and therefore, more accessible to transcription factors.

Front 140

Chromatin remodeling complex require ___ to function.

Back 140

ATP

Front 141

What kind of modifications can occur to Lys in chromatin?

Back 141

N-terminal Lys can be methylated or acetylated. Looks like arginine can also be methylated

Front 142

What kind of modifications can be made to Ser in chromatin?

Back 142

Phosphorylation

Front 143

What covalent chromatin modification creates a more open DNA structure, leading to more transcription?

Back 143

acetylation

Front 144

What proteins regulate acetylation of chromatin?

Back 144

Histone DeACetylase (HDAC): removes acetyl group, coils histones more tightly.

Histone AcetylTransferase (HAT): adds acetyl groups, uncoils histones.

Front 145

What is a Barr body?

Back 145

It is the inactive X chromosome in a female. Some cells express the maternal X, while some cells express the paternal X. This leads to mosaicism.

Front 146

What causes the coiling/inactivation of the Barr body?

Back 146

XIST RNA

Front 147

Describe how Duchenne muscular dystrophy is expressed differently in males and females.

Back 147

This is an X-linked recessive disorder. The male has only one X chromosome. All cells will have the mutant DNA and will express the disease.

The female is likely to be heterozygous, with only some cells expressing the mutant gene.

Front 148

What is a transcription unit?

Back 148

The part of the gene that is transcribed into RNA (exons and introns included).

Front 149

The gene that codes for this protein has 178 exons.

Back 149

Titin

Front 150

Where is a promoter? How big is it?

Back 150

It is upstream (towards 5' end) from exon 1. It is 200-400 bp.

Front 151

What types of RNA are the following polymerases associated with? Pol I, Pol II, Pol III

Back 151

Pol I: rRNA
Pol II: mRNA
Pol III: tRNA

Front 152

RNA is composed on the ______ strand (aka the template strand), meaning that but for the substitution of uracil, its sequence is the same as the ____ strand.

Back 152

antisense; sense

Front 153

What are these things:
TATA box
TBP
TFIID

Back 153

The TATA box is where transcription starts.

TATA box Binding Protein (TBP) binds to the TATA box.

TBP is part of the larger Transcription factor II-D.

Front 154

Two things I'd like to remember that TFII's do.

Back 154

1. Find the TATA box.
2. Attract Pol II

Front 155

What is an enhancer?

Back 155

It promotes the transcription of a certain gene. It is the binding site of the activator, which can be quite far upstream from the site of transcription. Remember the DNA curves around so the activator can interact with the transcription factors. This contact sets Pol II flying.

Front 156

What do regulatory transcription factors do?

Back 156

They control the rate of transcription. They can be activators or repressors and are often tissue specific.

Front 157

Describe the three important regions of most tx factors.

Back 157

1. Activation domain: Where the factor interacts with other tx factors
2. DNA binding domain: Where is connects to the DNA. Usually an alpha-helix. Usually has basic amino acids.
3. Dimerization domain: I don't know what happens here, but it is hydrophobic and usually functions as a dimer.

Front 158

Describe the structure of TBP.

Back 158

It is a single subunit. Unusually, it is a beta strand that lies in the minor groove. There are helical parts, but they interact with other tx factors.

Front 159

What are the two tx factor DNA binding motifs we learned about?

Back 159

the basic-zipper (bZip), and the basic helix-loop-helix (bHLH)

Front 160

Describe the bHLH.

Back 160

It looks like the bZip... but with loops.

Alpha helices contact DNA in the major groove.

It is made of amphipathic helices that dimerize into a coiled coil by hydrophic interactions.

Front 161

Describe the bZip. One example of bZip motif.

Back 161

Two straight alpha helices.

N terminus regulates binding to major groove.

C terminus regulates dimerization.

The Leucine Zipper is a bZip. So is AP1.

Front 162

Zinc finger as DNA binding motif.

Back 162

Folds into a-helices and b-strands. The a-helix sits in the major groove.

Front 163

How does the nuclear receptor family of transcription factors differ from the other dimer transcription factors?

Back 163

They require a ligand.The ligands are small lipid-soluble hormones and vitamins.

Front 164

What kind of tx factors will often moderate a gene's response to a hormone?

Back 164

nuclear receptor transcription factors. The hormone can act as a ligand.

Front 165

What are some hormones that activate nuclear receptor transcription factors? Where do they bind?

Back 165

They bind to INTRACELLULAR receptors. The hormone-receptor complex enters the nucleus. Some examples: cortisol, aldosterone, testosterone, estradiol, etc.

Front 166

What does MyoD do?

Back 166

It controls skeletal muscle differentiation. (Myf5 and myogenin are also needed for myogenesis from somites.) bHLH motif. transcription factor.

Front 167

What does Runx2 do?

Back 167

It controls osteoblast differentiation. It is a Runt domain tx factor. It clamps the DNA with its C-terminal "tail" in the major groove, and its "wing" in the minor groove.

Front 168

Cleidocranial dysplasia is due to mutations in _____.

Back 168

Runx2

Front 169

What is a basal complex?

Back 169

Looks like a whole mess of tx factors that bind at the TATA box and around it. It interacts with many far upstream transcription regulators.

Front 170

What is the structure of the mRNA cap?

Back 170

It is 7-methyl-guanosine attached to the 5' end of the mRNA through a 5'-5' triphosphate bond.

Front 171

How does the spliceosome know where the introns are?

Back 171

Consensus sequences

Front 172

Describe how the intron detaches.

Back 172

A 2'OH somewhere in the intron attacks the 5' end of the intron, forming a little lasso attached to the 3' splice site. The upstream exon then attacks the still attached end of the intron and the intron is released.

Front 173

Where do you find snRNPs? How do they relate to the consensus sequence of the intron?

Back 173

They are in spliceosomes. They are complementary to consensus sequences.

Front 174

What enzyme regulates the removal of introns.

Back 174

It is actually the snRNA of the spliceosome that catalyzes this rxn. RNA acts as an enzyme.

Front 175

Where is the polyA tail attached?

Back 175

At the 3' end of mRNA after the consensus sequence AAUAAA

Front 176

What enzyme links the amino acid to the 2' or 3' OH of the tRNA?

Back 176

aminoacyl tRNA synthetase

Front 177

AMP-aa +tRNA --> AMP + aa-tRNA

What reaction is this coupled to?

Back 177

ATP ---> AMP + PPi
PPi ---> 2Pi

Front 178

What are the three bonding sites of aminoacyl tRNA synthetases?

Back 178

Amino acid, tRNA, and ATP

Front 179

How many aminoacyl tRNA synthetases are there?

Back 179

20. One for each amino acid.

Front 180

How many subunits in a ribosome? What are the constituents of the subunits? Which subunit is the ribozyme?

Back 180

There are two subunits, the large and the small. Each subunit has proteins and RNA molecules. The large subunit is the ribozyme, catalyzing peptide bond formation.

Front 181

What type of proteins carry tRNA to the ribosome?

Back 181

G proteins

Front 182

The hydrolysis of _____ provides some of the energy for protein synthesis.

Back 182

GTP

Front 183

What are the three tRNA binding sites on a ribosome?

Back 183

A. aminoacyl tRNA
P. peptidyl tRNA
E. exit

Front 184

GTP binds to G proteins (tRNA carriers) to activate them. Describe this. There is one thing you should know.

Back 184

The inactive G protein is coupled with GDP. Then, GDP is COMPLETELY REMOVED, and GTP is added. However, to deactivate the protein, GTP is simply dephosphorylated.

Front 185

At which binding site do aminoacyl tRNAs enter the ribosome?

Back 185

They enter at the A site, except the initiator tRNA, which codes for Met, which will enter at the P site.

Front 186

What do G proteins do (relative to RNA translation)?

Back 186

They bring tRNA to the ribosome.

Front 187

What does a release factor do?

Back 187

It enters the ribosome when it comes to a stop codon.

Front 188

eIF, eEf, and termination factors. What do these do?

Back 188

Eukaryotic initiation factors are involved in translation initiation. Eukaryotic elongation factor are involved in growing the polypeptide chain. Termination factors are involved in the release of the protein from tRNA.

Front 189

What are two things that might cause a bit of mRNA to be translated less efficiently?

Back 189

A suboptimal AUG consensus sequence.

Secondary structure in the 5' untranslated region.

Front 190

Eukaryotic mRNA forms circular structures due to the interactions between _____ and _____.

Back 190

the 5' cap; the poly A tail

Front 191

What is a benefit of the mRNA forming a circular structure?

Back 191

It promotes reinitiation, meaning that after the protein is translated, it's 5' end will be positioned to bind the ribosome again.

Front 192

How many high energy molecules are used during protein synthesis?

Back 192

At least three for each amino acid (1 ATP, 2 GTP)

Front 193

Name two viruses that modify eukaryotic translational machinery.

Back 193

Diptheria and polio.

Front 194

Streptomycin, tetracycline, erythromycin, and chloramphenicol all inhibit bacterial translational machinery by binding where?

Back 194

At the interface of the two ribosomal subunits.

Front 195

In which direction are proteins synthesized? Relate this to the reason some ribosomes are attached to RER.

Back 195

N-terminus to C-terminus. The N-terminus has a sequence on it that will tell the ribosome to attach to the ER.

Front 196

Describe the signal sequence on the N-terminus of proteins destined for the secretory pathway.

Back 196

There will be one or two basic residues (R or K) followed by 15-25 mostly hydrophobic residues). It will be removed by signal peptidase.

Front 197

What is ubiquitin?

Back 197

It tags proteins for destruction. It's a protein that attaches to lysine. The tagged protein gets degraded by proteasomes and the ubiquitin is recycled.

Front 198

Where does ubiquitinylation/proteasome degradation take place?

Back 198

In the cytoplasm.

Front 199

What two essential fatty acids are used as a starting point for the the others?

Back 199

alpha-linolenic acid and linoleic acid

Front 200

Describe the omega naming convention for fatty acids.

Back 200

Omega is the last carbon on the fatty tail. If a FA is "omega-3" that means that there is a double bond at the third carbon from omega.

Front 201

What are triacylglycerides?

Back 201

TAGs are the storage form of fatty acids. They have been esterified by addition of glycerol. There is no hydrophilic portion.

Front 202

List the components of a phospholipid.

Back 202

Glycerol backbone attached to two FA tails and one phosphate group. A hydrophilic group is attached to the phosphate.

Front 203

How do sphingolipids differ from phospholipids?

Back 203

Instead of a glyerol backbone, they have a sphingosine backbone. Also, the FA on the second bond is linked through a CO-NH bond.

Front 204

What is the head group of sphingomyelin? Where might you find it?

Back 204

Phosphocholine. Essential component of myelin sheaths. Associated with membrane rafts.

Front 205

What are anchored membrane proteins?

Back 205

They are proteins with a lipid tail that connects them to the membrane. They are more mobile than transmembrane proteins.

Front 206

What is a GPI anchor? How is it attached? Where does the attaching take place?

Back 206

It is a lipid tail that anchors a protein in a cell membrane. It is attached in the lumen of the ER by cleaving a couple of residues on the C-terminal and attaching there.

Front 207

Where do GPI anchored proteins often accumulate?

Back 207

Cholesterol rich microdomains (membrane rafts)

Front 208

Name some things you will probably see in membrane rafts.

Back 208

Lipids with saturated tails, GPI-anchored proteins, cholesterol, sphingolipids

Front 209

Name some functions of a lipid raft.

Back 209

Signaling platforms, exocytosis, targets for pathogens

Front 210

What are flippases, floppases and scrambleases? Which is ATP-independent?

Back 210

They facilitate transverse diffusion across the phospholipid membrane. Scrambleases are dependent on calcium, not ATP.

Front 211

Where would you find a phosphoinositide?

Back 211

Anchored on the INSIDE of a cell in the cell membrane.

Front 212

What does a phosphoinositide do?

Back 212

When it is cleaved from the cell membrane in the form of inositol 3-phosphate (IP3), it activates the release of Ca2+.

Front 213

Which human organelles have a double membrane?

Back 213

mitochondria and nucleus

Front 214

What do dynamin and ESCRT have in common?

Back 214

Both enzymes for membrane fission.

Front 215

When just the outer leaflets of two membranes have fused, this is referred to as ______.

Back 215

hemifusion

Front 216

What are SNAREs?

Back 216

They are intracellular enzymes that facillitate membrane fusion. There is a SNARE in both membranes to be fused.

Front 217

What are liposomes?

Back 217

Artificial vesicles made from phospholipids and cholesterol. Used to deliver drugs.

Front 218

Why are liposomes well-suited for drug delivery?

Back 218

They are biocompatible, non-immunogenic, non-toxic, and have a long half life when injected.

Front 219

What are the 4 kinds of cell signaling?

Back 219

1. endocrine
2. paracrine (incl. autoparacrine)
3. neuronal
4. contact-dependent

Front 220

What effect does acetylcholine have on heart muscle? Salivary glands? Smooth muscle?

Back 220

1. decreased contraction
2. secretion
3. contraction

(The heart muscle and salivary glands have the same receptor.)

Front 221

Extracellular signals can change cell function slowly or rapidly. Which kinds of signals produce a rapid change?

Back 221

If a signal alters protein function, it will alter cell behavior rapidly. If a signal induces the transcription of DNA to make new proteins, change will be slower.

Front 222

Cortisol, etradiol, testosterone, thyroxine. What do these have in common?

Back 222

They are cell signalers that act on intracellular receptors.

Front 223

What are GPCRs?

Back 223

G-protein coupled receptors in the cell membrane. They have 7 transmembrane domains.

Front 224

What happens when a GPCR binds to its extracellular ligand?

Back 224

It will activate the G-protein, which will then activate a number of membrane proteins, including adenylyl cyclase and phospholipase C.

Front 225

Which enzyme sythesizes cAMP? What degrades cAMP? What is cyclic AMP?

Back 225

Adenylyl cyclase. Phosphodiesterase. cAMP is a second messenger.

Front 226

What are some hormones that use cAMP as their second messenger?

Back 226

Adrenaline, ACTH, glucagon

Front 227

Describe how adrenaline stimulates glycogen breakdown.

Back 227

Adrenaline > GPCR > G-protein > adenylyl cyclase > cAMP > PKA > phosphroylase kinase > glycogen phosphorylase > glycogen breakdown

Front 228

What are enzyme coupled receptors?

Back 228

When an extracellular ligand binds to them, their separate parts are brought together and activated.

Front 229

Which enzyme couple receptor did we learn about?

Back 229

Receptor tyrosine kinase (RTK). When the ligand binds, multiple phosphoryl groups attach to the tyrosine. Signaling proteins then bind to the phosphotyrosines.

Front 230

When receptor tyrosine kinase is activated, what do the signals that is sends do? (There are many answers, but which one did we learn about?)

Back 230

They can activate the G protein, Ras. They are the receptor for insulin.

Front 231

What cascade will the G protein Ras activate?

Back 231

It will activate a MAP kinase cascade that will both change protein activity and gene expression.

Front 232

Which type of receptors is responsible for transmission of signals across synapses?

Back 232

Ion-channel coupled receptors, like the one for acetylcholine.

Front 233

What structure can hold inactive signaling proteins in closer proximity to the receptor protein?

Back 233

A molecular scaffold.

Front 234

What does an integrator protein do?

Back 234

It incorporates signals from multiple pathways before passing the signal onward.

Front 235

All mammalian steroid hormones are formed from cholesterol
through a common intermediate
________.

Back 235

pregnenolone

Front 236

Tri-iodothryronine (T3), thyroxine (T4), epinenphrine, and norepinephrine are all derivatives of _______.

Back 236

tyrosine

Front 237

How is insulin activated from its prohormone state?

Back 237

A middle swath is cleaved and the two ends form disulfide bonds with one another.

Front 238

What kind of receptor is the insulin receptor?

Back 238

It is a receptor tyrosine kinase (RTK).

Front 239

What kind of receptor is the receptor for glucagon?

Back 239

A GPCR

Front 240

What are integrins?

Back 240

They are receptors that mediate a cell's attachment to other cells or to the ECM.