Biochem - S Flashcards
(125 cards)
1
Q
What type of bonds stabilize 1° protein structures
A
Peptide Bonds
2
Q
What type of bonds stabilize 2° protein structures (alpha helix vs. Beta sheets)
A
Hydrogen Bonds
3
Q
What type of bonds stabilize 3° protein structures (4)
A
Ionic /Hydrophobic /Hydrogen /Disulfide Bonds
Tertiary = overall shape after compact folding of secondary structure
4
Q
Describe Disulfide Bonds
A
Strong Covalent bonds between 2 cysteine residues within the same polypeptide chain –> prevents denaturation
5
Q
After 12-18 hours of fasting, ____ becomes the main source for blood glucose. Recall the reaction that ends with Glucose vs. energy.
A
Gluconeogenesis;
Pyruvate —(pyruvate carboxylase)–> Oxaloacetate —(PEP carboxykinase) —> PEP
ActetylCoA upregulates pyruvate carboxylase
6
Q
What are [Transmembrane Domains] made of and what is their function?
A
[Alpha helices made with Hydrophobic Amino Acids]; anchors Integral proteins to phospholipid bilayer
7
Q
[Methylmalonic Acidemia] MOD
A
Organic acidemia due to deficiency of methylmalonyl-CoA mutase
8
Q
[Methylmalonic Acidemia] Labs (3)
A
- HyperAmmonemia
- Ketotic hypOglycemia
- INC Urine Proprionic Acid - metabolic acidosis
9
Q
[Familial Dysbetalipoproteinemia Type 3] Mode of inheritance
A
auto recessive
10
Q
[Familial Dysbetalipoproteinemia Type 3] MOD
A
Defects in [ApoE3 and E4]–> DEC clearance of chylomicrons & VLDL remnants
11
Q
[Familial Dysbetalipoproteinemia Type 3] Clinical Presentation (3)
A
- Xanthomas
- Atherosclerosis
- INC Cholesterol & Triglyceride
12
Q
Which Vitamin deficiency is [Egg White Avidin] associated with and how does this present (3)?
A
Having No Bio makes me MAD!
[Biotin B7]; [Myalgia(lactic acidosis)] + Anorexia + Dermatitis
(Egg White Avidin Avidly Binds [Biotin B7])
13
Q
1 gram protein = ___ calories
A
[1 gram protein] = [4 calories]
14
Q
1 gram fat = ___ calories
A
[1 gram protein] = [9 calories]
15
Q
Spliceosomes require ____ to Function. What is their function and what are they made by?
A
snRNPs (small nc. ribonucleaic acid - made by RNA Pol 2 in nucleus)
Remove introns containing [GU at 5’] and [AG at 3’] from pre-mRNA –> Forms [Mature mRNA Exons]
snRNPs are targeted by SLE Smith Ab
16
Q
How is Ca+ associated with Glycogen Degradation in Skeletal m.
A
Sarcoplasmic Retic. releases Ca+ –> Activates [Phosphorylase kinase] –> Stimulates Glycogen phosphorylase —> Glycogenolysis
17
Q
Where does Vitamin __ hydroxylation of proline and lysine of collagen occur?
A
Vitamin C; Rough ER
Vitamin C deficiency –> Scurvy
18
Q
Xeroderma Pigmentosum defect
A
defect in DNA excisional repair; exacerbated with UVB radiation
19
Q
Xeroderma Pigmentosum Clinical Presenatation at:
A: 1 yo (4)
B: Later in life
A
Dry Pigmented Skin
- 1 yo: Scaling + Erythema + [Lentigo on face] + Hyperpigmentation
- Later in life: Skin Atrophy + Telangiectasia + CA
20
Q
Xeroderma Pigmentosum Mode of inheritance
A
auto recessive
21
Q
What 2 mechanisms regulate the Lac Operon
A
- Repressor binding to operator locus = negative regulation
- cAMP-CAP binding upstream of promoter = positive regulation
22
Q
What happens when mutations impair binding of repressor to the operator locus?
A
Constitutive Expression of Lac Operon
23
Q
Describe Alternative Splicing
A
Exons of a gene are reconnected during post-tx processing – > different mRNA –> different proteins
24
Q
Is Alternative Splicing a normal function of Eukaryotes? Why or why not?
A
Yes; INC biodiversity of proteins
25
What is HgbC caused by and how does it manifest?
Missense mutation resulting in Glutamate being replaced by Lysine (*less negative charge*) in beta globin chain --\> milder form of sickle cell
26
[Spinal Muscular Atrophy] MOD
SMN1 mutation --\> impaired assembly of snRNPs in LMN --\> Flaccid paralysis
27
Transamination occurs between ____ and \_\_\_\_. Which molecule serves as a cofactor for transamination and decarboxylation
Transamination occurs between [**amino acids**] and [**a-keto acid**]. [**Pyridoxine B6**] = transamination cofactor
28
What is the the Wobble Hypothesis
First 2 nucleotide positions on mRNA codon require traditional base pairing, but the [third wobble nucleotide] may undergo nontraditional base pairing --\> more than 1 codon can code for an AA
29
How does [Pyruvate Kinase] deficiency cause Hemolytic anemia and Splenomegaly
Failure of Glycolysis --\> insufficient ATP to maintain RBC structure --\> [splenic **red pulp** hyperplasia] to remove these deformed RBC
30
[Tetrahydrobiopterin BH4] is a cofactor for the synthesis of what compounds? (3)
Tyrosine
Dopapmine
Serotonin
31
What Dz occurs from [Tetrahydrobiopterin BH4] deficiency? MOD
(PKU) Phenylketonuria; Dihydropteridine Reductase becomes deficient w/out cofactor --\> Inability to convert Phenylalanine --\> Tyrosine
32
Phenylketonuria tx (2)
1. low phenylalanine diet
2. BH4 supplementation
33
Which DNA Polymerase has exonuclease activity and what is the exonuclease function (2)
[DNA Pol **1** and **3**] has [3 ---\> 5 exonuclease activity] + [5--\>3 Polymerase] activity
Exonuclease removes RNA primer and repairs DNA sequences
34
What type of relationship does TNFa have with Insulin receptors?
TNFa Phosphorylates [serine & threonine AA of insulin receptors and their subtrates] --\> Insulin Resistance
## Footnote
*Catecholamines/Glucocorticoids/Glucagon also do this*
35
HyperHomocysteinemia is due to mutations in ____ (3)
*6 / 9 / 12*
[Pyridoxine B**6**] vs. [Folate B**9**] vs. [B**12**]
36
HyperHomocysteinemia Manifestations (3). INC risk for what?
1. Marfanoid Habitus
2. Ectopia Lentis
3. Developmental Delay
INC RISK FOR THROMBOEMBOLISM
37
Describes Homocysteine metabolism
38
[Pyruvate Dehydrogenase Deficiency] causes ____ and ____ clinically. MOD
**Lactic Acidosis** ; **Neuro defects**
Inability to convert Pyruvate --\> AcetylCoA --\> shunting of Pyruvate to Lactic Acid during oxidative phosphorylation
39
[Pyruvate Dehydrogenase Deficiency] Tx
[Exclusive _Ketogenic_ Amino Acids (Lysine vs. Leucine)]
since these will provide AcetylCoA w/out INC lactate
40
Describe the path for Pyruvate --\> Energy
41
Describe the path for Pyruvate --\> Glucose
*AcetylCoA upregulates [Pyruvate Carboxylase]*
42
Glycolysis, Fatty Acid Synthesis and Pentose phosphate all occur in what part of the cell?
Cytosol
43
B-oxidation, TCA and Pyruvate Decarboxylation all occur in what part of the cell?
Mitochondria
44
What is Transketolase
**[Pentose Phosphate pathway] enzyme** that uses [Thiamine VitB1] to shuttle 2-carbon fragment between sugar molecules & to convert [Fructose6phosphate] w/the help of TransAldolase
45
[Aldolase B Deficiency] MOD.
Hereditary **Fructose** intolerancE
## Footnote
* THIS CAN BE LIFE THREATENING*
* Surcose --\> Fructose & Glucose*
46
[Fructokinase Deficiency] MOD
Fructose from diet is absorbed & secreted into urine due to impairment of Fructose ---(*Fructokinase*)---\> Fructose1P
**\*Detected via Positive Copper Reduction Test\***
47
What is the function of [AcylCoA Dehydrogenase] and how is it related to fasting?
Catalyzes first step in B-oxidation of Fatty acids and ironically, **the most commonly deficient**.
Without it --\> hypOglycemia with fasting
48
NAD+ is required to convert _____ into ____ during glycolysis. What occurs under ANaerobic conditions?
NAD+ converts [Glyceradehyde3Phosphate] --\> [1-3 Bisphosphoglycerate] during glycolysis
ANAerobic conditions: NADH transfers electrons to pyruvate --\> Lactate and More NAD+
49
[Acute Intermittent Porphyria] tx (2)
Glucose vs. Hemin (Both inhibit ALA synthase activity)
50
Identify
51
How does [Short non-coding RNA sequences] such as ___ and ___ work?
microRNA & [small interfering RNA] both induce posttx gene silencing by base-pairing with complementary sequences on target mRNA molecules
52
Where is [Hormone sensitive Lipase] found and what is its function
Adipose; Breaks down Stored TAG --\> Fatty Acids & Glycerol during starvation. *Needed for Hepatic Gluconeogenesis & ketone body formation*
53
Galactose is converted to Galactitol by _____ and can cause ___ eye damage if in excess --\> \_\_\_\_\_.
This ultimately occurs from a _____ deficiency which should convert Galactose ---\> \_\_\_\_. How does Lactose play a role in this?
Galactose is converted to Galactitol by **Aldose Reductase** and can cause **Osmotic** eye damage if in excess---\> **Cataracts**. This ultimately is from **Galactokinase** deficiency which should convert Galactose --\> Galactose1P.
Lactose is converted --\> Galactose by [BGalactoSidase]
54
[Ribo**F**lavin B2] is a precursor for ___ and \_\_\_. Which of these participates in the TCA cycle?
****_F_**MN** and ****_F_**AD**.
**FAD** acts as electron acceptor for [Succinate Dehydrogenase Complex 2] in ETC and converts succinate --\> Fumarate in TCA
55
Explain how the [Phospholipase C] 2nd messenger system causes Ca+ release and smooth m. contraction?
56
Why is [Total T**3** levels] normal in early hypOthyroidism?
T**3** is converted from T4 in peripheral tissues and so only T4 (made from thyroid) may be initially low
57
What are [P Bodies]
Cytoplasmic important molecules for mRNA translation and degradation
58
When is the RAS oncogene normally active?
ONLY when bound to G**T**P
59
Proteins destined for Lysosomes require ______ to ensure proper transit through \_\_\_\_\_\_
Proteins destined for Lysosomes require [**phosphorylation of mannose residues**] to ensure proper transit through **Golgi**
60
[Ehlers Danlos] MOD
Heritable Abnormal Collagen formation from [Procollagen Peptidase deficiency (impaired cleavage of N-terminal propeptides)] --\>abnormal collagen
61
\_\_\_\_ is the most common NON-nuclear DNA in Eukaryotic cells. It codes for what 3 major things?
**Mitchondria DNA**
* [Oxidative metabolic pathway] proteins
* rRNA - for mitochondrial proteins
* tRNA - for mitochondrial proteins
62
Which parameter of O2 does **not** change with Methemoglobinemia?
O2 Partial Pressure (free floating)
## Footnote
*Dissolved O2 in plasma is unrelated to HgB function*
63
Why is Dysphagia a problem in Demented Elderly?
It's a RF for Aspiration PNA --\> Requires Hospitlization
64
Hyperammonemia is common in cirrhotic pts, from inability to metabolize _____ . How does this affect CNS?
[**Nitrogenous Waste**]; Crosses BBB --\> Excess Glutamine accumulation within astrocytes--\> DEC Glutamine needed for Glutamate neuroexcitatory actions
65
What's the most abundant amino acid in collagen? How does it play a role in Collagen shape?
**Glycine**; Triple helical conformation of collagen is from reptitive amino acid sequence within each alpha chain. Glycine occupies every 3rd position on that chain (Gly - X - Y)
66
How does 2,3 BPG facilitate O2 release
Forms ionic bonds with beta-subunits of DeOxygenated HgBA and facilitates O2 release --\> peripheral tissue
67
How is 2,3 BPG related to Fetal HgB
When 2,3 BPG is mutated --\> [HgB A] starts to resemble [HgB F] since its O2 affinity will be much HIGHER
68
Which enzyme partially compensates for [Fructokinase deficiency: fructosuria]
Hexokinase converts excess dietary fructose --\> [fructose6Phosphate] but this isn't sufficient
69
Which Dz are snRNPs attacked in
SLE (by Smith Ab)
70
Alkaptonuria MOD
Not having [Homogentisic acid Dioxygenase] blocks Tyrosine metabolism --\> accumulation of homogentisic acid
71
Alkaptonuria Clinical Presentation (3)
1. **Black Urine** when exposed to air
2. **Blue** connective tissue (sclerae & ear)
3. Arthropathy
72
Alkaptonuria Mode of Inheritance
auto recessive
73
Which hormones utilize [Protein Kinase A] GPCR second messenger? (3)
TSH
Glucagon
PTH
74
[Marfan Syndrome MOD].
Where is this protein found normally (3)
[Fibrillin1 defect (an extracellular scaffold for elastin)]
1. Lens
2. Periosteum
3. Aortic Media --\> Aortic Root Dilation --\> Dissection
75
What does Polycistronic mean with Bacterial mRNA
1 mRNA codes for several proteins at same time
## Footnote
*Regulated by single promoter/operator and regulatory elements*
76
Why does Fructose have a more rapid rate of metabolism than Glucose?
Dietary fructose --(Liver phosphorylated)--\> F1P --\> **rapidly** metabolized because it bypasses PFK1
PFK1 = major rate-limiting enzyme in glycoslysis
77
[Niemann Pick] MOD
Sphingomyelinase Deficiency --\> accumulation of Sphingomyelin
78
[Niemann Pick] Clinical Presentation (3)
1. Cherry Red Macular Spot
2. Neuro Regression
3. **Hepatosplenomegaly (*differentiates from Tay-Sachs)***
79
Tay-Sachs Clinical Presentation (2)
1. Cherry Red Macular Spot
2. Neuro Regression
80
Tay-Sachs MOD
[B-Hexosaminidase A Deficiency] --\> GM2 accumulation in neurons
81
How is [Malonyl-CoA] significant in Fatty acid synthesis
[Malonyl-CoA] inhibits [mitochondrial carinitine acyltransferase] --\> inhibits Beta-oxidation
## Footnote
*Malonyl-CoA is formed from acetyl-CoA*
82
Name the genetic predisposition to Gout
[PRPP synthetase activating mutations] --\> INC Risk for Gout due to abnormal purine regulation
## Footnote
*Neutrophils are indicated in Gout pathology*
83
How does Insulin stimulate glycogen synthesis once it activates Tyrosine Kinase signaling
Tyrosine Kinase activates **Protein Phosphatase** --\> Dephosphorylates Glycogen Synthase --\> Glycogenesis
84
How do Kidneys excrete Acid in Chronic acidemic states
Tubular epithelium metabolize Glutamine --\> GlutamATe, generating NH4+ --\> excreted in urine while HCO3 is ReAbsorbed
85
What is Southwestern blotting used to detect (3)
DNA-binding proteins (transcription factors vs. nucleases vs. histones)
86
[Alpha Glucosidase Acid Maltase] deficiency presents _____ with lysosomal ___ accumulation. Clinical manifestations (3)?
early infancy with lysosomal glycogen(*PAS+*) accumulation;
"Big Heart, Big Tongue, No Muscle"
- Cardiomegaly
- Macroglossia
- Muscular hypOtonia
87
What is the rate-limiting enzyme in the [Pentose Phosphate Pathway] and what does it produce
[Glucose - 6 - Phosphate Dehydrogenase] = Major source of Cellular NADPH
## Footnote
*If deficient, will resemble [Glutathione Reductase deficiency] = [Hemolytic anemia from oxidative stress]*
88
NADPH function (2)
Reduces Glutathione (preventing oxidative damage) and [Biosynthesis of Cholesterol/Fatty Acids/Steroids]
## Footnote
*[Glutathione Reductase deficiency] may cause similar pathology*
89
How is Cortisol related to Epi and NorEpi
Cortisol INC conversion of [Epi and NorEpi] in adrenal Medulla by INC expression of [phenylethanolamine methyltransferase]
90
What is Glucokinase and what Dz develops from its mutation?
[Pancreatic beta cell: Glucose Sensor] that controls rate of glucose entry into TCA cycle; [Maturity onset Diabetes of the young]
91
[McArdle Glycogen Storage Dz 5] MOD
Myophosphorylase Deficiency--\> DEC Muscle Glycogenolysis
92
[McArdle Glycogen Storage Dz 5] presentation (3)
Myoglobinuria with Exercise
93
Why does HgB-**S** cause worst sx than HgB-**C**
HgB**S** has a valine substituted for glutamic acid @ 6th position of B-globin chain --\> **Hydrophobic** **interactions** between different HgBs--\> RBC Sickling
94
Explain the biochemistry for why INC [Fructose 2,6 Bisphosphate] Aids in the treatment of DM
95
Lead (poisoning) directly inhibits __ and \_\_\_\_
Lead (poisoning) directly inhibits [**ALA Dehydratase**] and Ferrochelatase
96
Intracellular Receptors that contain [**Zinc** finger binding domains] interact with which hormones? (3)
1. Steroids
2. Thyroid Hormone
3. ADEK Vitamins
97
[Cori Debranching Glycogen Storage Dz 3] presentation (3)
1. Short stature
2. hypOglycemia
3. Muscle weakness & hypOtonia
98
[Cori Debranching Glycogen Storage Dz 3] MOD
Debranching enzyme deficiency --\> accumulation of glycogen with abnormal short outer chains (inability to degrade at alpha1-6 branch points)
99
Base excision repair corrects \_\_base DNA. Describe the process starting with removing defective base (4)
**Single**;
1. Glycosylases remove defective base
2. Sugar-phosphate site is cleaved and removed by endonuclease & lyase
3. DNA Pol replaces missing nucleotide
4. Ligase seals remaining nick
100
PKU-Phenylketonuria Clinical Manifestation (4)
1. Musty Odor
2. Seizures (look for upward eye deviation)
3. Eczema
4. Retard
101
Orotic Aciduria MOD
Defective [5-UMP synthase]--\> INC Urinary Orotic Acid --\> DEC pyrimidine synthesis. Improved with Uridine supplement
102
What are Amatoxins and what do they inhibit
Toxin from Poisonous Mushrooms that inhibit [RNA Pol 2] --\> NO mRNA synthesis
103
Which enzyme is impaired in Galactosemia and what do you expect to see in the urine?
GALT; [Reducing Substance Unmetabolized Sugar]
104
[Ehlers Danlos] Clinical Presentation (3)
Hypermobile Joints
Hyperelastic Skin
Easy Bruising & Hemarhtrosis
105
Glycerol, made from ____ in Fat can be used by ____ in the ____ to make Glucose
Glycerol, made from **Triglycerides** in Fat, can be used by **Glycerol Kinase** in the **Liver& Kidney** to make Glucose
## Footnote
*This is often the case in DKA pts*
106
Ab to Citrullinated proteins are highly associated with what Dz
Rheumatoid Arthritis
107
[Beta Glucuronidase] is implicated in what condition
Pigment Gallstones
## Footnote
*It's released from injured liver cells and bacteria bilirubin glucuronides --\> unconjugated bilirubin*
108
What is the recognition sequence for tRNA at its __ end
**3** end recognition sequence = CCA
109
Homocystin**uria** is most commonly caused by what
Defect in Cystathionine Synthase --\> inability to convert Homocysteine to Cysteine. The Homocysteine then accumulates --\> Elevated Methionine
## Footnote
*Homocysteine is Thrombotic!*
110
Carinitine Deficiency MOD
Defective Fatty acid transport from cytoplasm into mitochondria --\> prevents Beta-oxidation during fasting (No Acetoacetate)
111
All 3 [Prokaryotic DNA Pol] have the abiliy to do what?
ALL can remove mismatched nucleotides via [3--\>5 exonuclease activity]
## Footnote
*Only DNA Pol 1 has [5--\>3 exonuclease activity]*
112
Which intracellular pathway does GH use
JAK-STAT
## Footnote
*Cytokines also use this pathway*
113
\_\_\_\_ converts glucose --\>Sorbitol, which is then ---\> Fructose by \_\_\_\_\_. Where is this pathway most common? (2)
**Aldose Reductase** converts glucose --\>Sorbitol, which is then --\> Fructose by **Sorbitol Dehydrogenase**.
Lens & [Seminal Vesicles]
114
HgB molecules are structurally similar to \_\_\_\_. What does this mean?
**myoglobin**; if separated into alpha & beta monomers, the O2 disassociation curve would resembles myoglobins
115
[Mccune Albright] MOD
G Protein activating mutation
116
What is Heteroplasmy
Presence of both normal and mutated
mtDNA --\> in variable expression in
mitochondrial dz
117
How does Carnitine deficiency affect the body?
Carnitine deficiency impairs fatty acid transport from cytplasm --\>mitochondria --\> Inhibits B-oxidation (formation of Acetoacetate) --\> [Myocyte injury from lack of TCA ATP] + [DEC Hepatic ketone production]
## Footnote
*Carnitine is a [Mitochondrial acyltransferase]*
118
Which compound inhibits Carnitine
Malonyl-CoA
119
Arginase is a ____ cycle enzyme that makes \_\_(2)\_\_\_ from arginine. What's clinical manifestation of Arginase deficiency? (2)
Arginase is an **U****rea** cycle enzyme that makes [Urea & Ornithine] from arginine.
## Footnote
Deficiency = Progressive Spastic Diplegia + growth delay
120
[Biotin B7] is a cofactor for what type of enzymes? (3)
Any CARBOXYLATION enzymes!
1. Pyruvate --\> Oxaloacetate
2. AcetylCoA ---\> MalonylCoA
3. PropionylCoA --\> MethylMalonylCoA
121
Function of Primase
RNA polymerase that incorporates short RNA primers into replicating DNA
122
Where are [**Very** Long chain fatty acids] & [Fatty acids with branch points at odd # carbons] oxidized?
Peroxisomes
123
Function of Lactate Dehydrogenase
Pyruvate --\> Lactate ; **ANEROBIC**
124
\_\_\_\_\_ is the AA that transfers nitrogen to Liver for disposal. How is Nitrogen eliminated? (2)
Alanine;
1. Amino groups are transfered to a-ketoglutarate --\> Glutamate --\> [Forms Urea in Liver] --\> Urinated out
2. _Free_ Amonia also urinated out
*Alanine must transfer Amino group before conversion to Glucose*
125
In which parts of the TCA cycle do you get \_\_\_(x)\_\_\_ and how many ATP do they give
A: NADH
B: GTP
C: FADH2
*Can I Keep Selling Sex For Money, Officer?*
## Footnote
A: NADH = 2.5 ATP each = (I-Keep) (Keep-Selling) (Money-Officer)
B: GTP = 1 ATP = (Selling - Sex) - **used in Gluconeogenesis by PEP Carboxykinase to convert Oxaloacetate--\>PEP**
C: FADH2 = 1.5 ATP each = (Sex - For)
