Biochemistry 2 -Block 4; Aminoacids, Peptides, Proteins

Front 1

List the enzymes of the urea cycle
Which part of the cell do they work in?

Which reactions requires nitrogen?

Back 1

mitochondria
- carbamoyl phosphate synthetase*
- Ornithine transcarbamolase

Cytosol
- argininosuccinate syntethase*
- argininosuccinase
- arginase

* requires nitrogen

Front 2

How does Malate dh reaction affect the urea cycle?

Back 2

- It is the reaction binding CAC to the urea cycle.
- It produces NADH (=2,5 ATP) thereby reducing the energy cost of the urea cycle

Front 3

Which AA are converted to alfa-ketoglutarate

Back 3

- Glutamate
- Glutamine
- proline
- arginine
- Histidine

Front 4

which AA are degraded to acetyl-CoA

Back 4

- Tryptophan
- phenylalanine
- lysine
- Leucine
- isoleucine
- tyrosine

Front 5

which AA are degraded to pyruvate

Back 5

- Tryptophan
- Phenylalanine
- lysine
- Leucine
- isoleucine
-glycine

Front 6

Which pathways has PRPP as an intermediate?

Back 6

- Biosynthesis of Histidine
- Biosynthesis of Tryptophan
- nucleotide synthesis (both pathways)

Front 7

Long term regulation of urea cycle

Back 7

Transcriptional regulation of
- the four urea cycle Enzymes
- carbamoyl P syntethase 1

Front 8

Which AA are converted into oxaloaceteate?

Back 8

- Aspartate
- Aspargine

Front 9

Which AA are converted into succinyl CoA

Back 9

- Methionine
- isoleusine
- Valine
- Threonine

*sussen er Mett (på) Is (og) Threnger Vaselin)

Front 10

Short term regulation of urea cycle

Back 10

- Allosteric activation of Carbamoyl P synthetase by N-acetyl glutamate
- the rest of the urea cycle enzymes activity is controlled by the [ ] of their substrates

Front 11

Sources of AA

Back 11

- Dietary Protein
- intracellular turnover

Front 12

On which organ and organelle(s) does ira cycle occur?

Back 12

- Organ; Liver
- Organelles; mitochondria and cytosol

Front 13

How is ammonia transported from Extrahepatic tissues to the liver or kidneys?

Back 13

It is transported as glutamine or Alanine

Front 14

What is transdeamination?

Back 14

The combined action of Aminoacid transferase and glutamate dh

Front 15

Which enzyme can use both NADH and NADP?

Back 15

Glutamate dh

Front 16

What are the sources of ammonia?

Back 16

- AA degradation
- Nucleotide (pyrimidine) degradation
- intestinal bacteria - from AA and urea

Front 17

What does hyperammonia lead to?

Back 17

- Cerebral edema
- increased cranial pressure

Front 18

Which enzyme is responsible for elongation during protein synthesis?

Back 18

Peptidyl tranferase

Front 19

How is the termination of protein translation in bacteria and Eukaryots?

Back 19

- Bacteria: RF1 &2 recognizes stop codons and causes release of peptide transcript. RF3 (GTP binding protein) causes dissociation of RF1 & 2

- Eukaryots: e RF1 recognizes the stop codons while eRF 3 causes dissociation of eRF1 after completed polypeptide synthesis. (eRF3 is a ribosome dependent PTPase)

Front 20

Name the ubiquination enzymes and their function

Back 20

- E1; Ubiquitin activating enzyme, catalyzes the first step which targets a protein for degradation
- E2; Ubiquitin conjugating enzyme
- E3; unbiquitin- protein ligase

Front 21

What is the second genetic code?

Back 21

The second genetic code is the proof reading by aminoacyl tRNA syntethase which makes sure that the amino asid added to the growing peptide chain is the right one.
This requires a specific interaction btw tRNA and the aminoascyl tRNA syntethase

Front 22

What are the respiratory chain proteins?
Where are they encoded?

Back 22

In humans they are encoded in the mtDNA
- Complex I; NADH dh
- Complex II; succinate dh
- Complex III; ubiquinon : cytochrome C
oxidoreductase
- Complex IV; Cytochrome oxidase
- Complex V; ATP synthase

Front 23

What is the start and stop codons in mitochondria and cytosol?

Back 23

Cytosol
- Start; AUG
- Stop; UGA

Mitochondria
- Start; AUA
- Stop; AGA

Front 24

What is the differences btw prokaryotic and prokaryotic protein synthesis?

Back 24

- The size and composition of the Ribosome
-Eu; 80s (60s + 40s)

-Pro; 70s (50s + 30s)
- in procaryotes the translation begins before the trancription finishes and there are several ribosomes translating the same mRNA at the same time. This is not the case in eucaryots

Front 25

WHat are the three sites on the ribosome?

Back 25

A: Aminoacyl
P: Peptidyl
E: Exit

Front 26

what are the different ways of post-translational protein modification?

Back 26

- Methylation
- Phosphorylation
- Carboxylation
- hydroxylation
- sulfation
- glycosylation
- prostetic groups
- disulfide cross link formation

Front 27

What ensures accuracy of protein synthesis?

Back 27

- Wobble in the condon-anticodon pairing
- proofreding by Aminoacyl tRNA syntethase
- Codon-anticodon check at the ribosome

Front 28

How are proteins moved into the ER?

Back 28

Signal recognition particles (SRP) binds to GTP, this halts the translation and directs the ribosome to the SRP receptor. SRP then binds to the peptide translocase complex in the ER membrane which moves the protein into the ER

Front 29

Properties of Mitochondrial DNA replication

Back 29

- individual mtDNA replicate randomly
- Not limited to S Phase

Front 30

What is PLP and which reactions uses it?

Back 30

- PLP a prostetic group and the co enzyme form of vit B6

- aminotransferases
- glycogen phosphorylase
- Glutamate decarboxylase
- histidine decarboxylase

Front 31

Part of the mitochondrial transcription

Back 31

- PolRMT = mitochondrial RNA polymerase
- TFAM = transcription factor activator mitochondria
- TFB1M

-TFB2M

Front 32

Degradation of proteins in bacteria

Back 32

- Lon, an ATP dependent protease
- other proteases

Front 33

What is microautophagy?

Back 33

when small cytoplasmic vesicles are formed and endocytosed into the lysosome

Front 34

What is macroautophagy?

Back 34

entire organelles or other largecytoplasmic entieties are engulfed and then fused with the lysosome

Front 35

which molecules plays a role in protein transport into mitochondria?

Back 35

- Tom -receptor (outer memb)
- Tim - receptor (inner memb)

Front 36

What may be caused by defect degradation of proteins?

Back 36

- Cancer
- Kidney failure
- Liddle syndrome
- autoimmune diseases
- cystic fibroses
- asthma
- neurodegenerative diseases

Front 37

How are proteins transported into the nucleus?

Back 37

Nuclear localization sequence (NLS) on the protein binds to importin alfa and beta thsi leads to translocation of the protein into the nucleus through a nuclear pore complex
- this process requires Ras related nuclear proteins (RAN)

Front 38

degradation of proteins in eucaryotes

Back 38

occurs through ATP-dependent proteolysis factor1 (APF-1 =ubiquitin) this occurs in two steps

1. ubiqunation
2. proeasomes

Front 39

What is the N-end rule?

Back 39

Average protein halg lifes correlates with the N-terminal residue

- Met, gly, ser >20h
- Arg ~ 2min

Front 40

Chaperone families with function

Back 40

-Hsp25 prevents aggregation in the lens (catararact) and protects against cellular stress'
- Hsp60: protein transportation from cytoplasm to mitochondria, folding and refolding
-Hsp 70: stabilizes newly synthesized poly peptides. and transport across mambranes

Front 41

function of proteosome

Back 41

- endopeptidase activity (breaks peptide bonds)
- Proteins are degraded into short peptides
- Proteasomes recognizes unfolded and ubiquinated proteins and translocate them into the core particle

Front 42

Which polymerase synthesized Eucaryotic RNA

Back 42

RNA polymerase II

Front 43

What are the true ketogenic AA?

Back 43

Leucine and lycine

Front 44

Whstis is the sequence of E.coli promoters?

Back 44

TTGACA

Front 45

Waht is the repressor binding site called?

Back 45

Operator

Front 46

What is the activator binding site called

Back 46

promotor

Front 47

What is an operon?

Back 47

an operon is a genecluster under regulation of a single promoter

Front 48

What does most antibiotics work on?

Back 48

they act against protein synthesis, usually on the ribosomre

Front 49

How can phosphorylation of initiation factors affect them?

Back 49

makes them less active

Front 50

How can hormones regulate transcription?

Back 50

- Hormonereceptor compexes binds the specific DNA sequences called hormone response elements (HRE) like dimers
- zink fingers recognizes the binding to HRE

- can enhance or suppress transcription

Front 51

What is needed to initiate eucaryotic RNA synthesis

Back 51

- TBP -> TATA binding protein
- PIC -> preinitiation Complex, induces TFIIA, -B,
-E, -F, -H and pol II
-transcription activator

Front 52

How does the antibioticum Tetracycline work?

Back 52

they bind to the small subunit of the ribosome

Front 53

How does the antibioticum erythromyocin work

Back 53

Blocks the polypeptide exit tunnel on the large subunit

Front 54

How does the antibioticum puromyocin work?

Back 54

it disrupts peptide bond formation by working as a aminocyl tRNA analog

Front 55

Which aminoacid is the only one who do not contain a chiral carbon

Back 55

Glycine

Front 56

mention some non polar (hydrophobic) uncharged Amino acids

Back 56

- phenylalanine
- tryptophan
- leucine
- isoleucine

Front 57

mention some polar (hydrophilic and uncharged AA

Back 57

- glycine
- serine

- glutamine
- tyrosine

Front 58

Mention the acidic and charged AA
(Polar)

Back 58

Aspartate and glutamate

Front 59

Mention the basic and charged AA (Polar)

Back 59

- Histidine
- arginine
- lysine

Front 60

What are the properties of the peptide bond?

Back 60

- flat structure
- stabilized by resonnance
- covalent amide bond
- made by condensation
- broken by hydrolysis (by peptidases or proteases)

Front 61

Peptide hormones

Back 61

- ACTH
- Beta-MSH
- Gastrin
- glucagon
- secretin
- ADH
- oxyostin

Front 62

Name some antibiotics

Back 62

antibiotics are peptides
- pencilin
- polymyxins
- tyrocidine
- gramicidins

Front 63

Mention some neuromodulators

Back 63

neuromodulates are peptides
- endorphins
- enkephalins

Front 64

mention 2 toxic peptides

Back 64

- microcystin
- nodularin

Front 65

wht are izozymes

Back 65

enzymes that differ in sequence but catalyze the same rxn

Front 66

what are zymogens?

Back 66

inactive procursors of enzymes

Front 67

what are the 3 steps of protein synthesis

Back 67

1. folding
2. post- translational modifications
3. targeting

Front 68

autosomal lysosomal degradation

Back 68

- non-selective
- proteases

- micro and macro autophagy

Front 69

Mention some inhibitors of translation

Back 69

- Puromyocin (both)
- tetracyclin (pro)
- streptomyocin (pro)
- cycloheximide (eu)

Front 70

short term positive regulators of protein synthesis

Back 70

- IGF-1
- increase insulin
- sex steroids

Front 71

Short term positive regulators of protein degradation

Back 71

- thyroid hormone excess
- Glucagon
- glucocortiocoids
- adrenalin

Front 72

Cadherin
where can we find it?
function
function in disease

Back 72

- Only in eukaryotes
- calcium mediated
- the main adhesive molecule
- loss of E-cadherin --> Cancer

Front 73

Integrins

Back 73

- activates signal transduction pathways
- requires ca
- found in all animals

Front 74

Pathways activating HIF-1alfa

Back 74

1. RTK -> PI3K/AKT -> mTOR ->HIF-1alfa
2. RTK -> MAPK -> ERK1/2 or p 38 -> HIF-1 alfa
3. TLR -> NF-kB -> HIF-1 alfa
4. ROS -> HIF-1 alfa

Front 75

Which enzyme is defect in marple syrup disease?

Back 75

branched chain alfa-ketoacid dh complex

Front 76

Which enzyme is defect in argininemia?

Back 76

Arginase

Front 77

Which enzyme is defect in Phenylketuria?

Back 77

Phenylalanine hydroxylase

Front 78

Which enzyme is defect inTyrosinemia II

Back 78

Tyrosine aminotransferase

Front 79

Which enzyme is defect in tyrosinemia III

Back 79

p-hydroxyphenylpyruvate dioxygenase

Front 80

Which enzyme is defect in Tyrosinemia 1

Back 80

Fumarylacetoacetase

Front 81

Which enzyme is defect in Alkaptonuria

Back 81

homogentisate dioxygenase

Front 82

Which enzyme is defect in Albinism

Back 82

Tyroine monoxygenase / tyrosinase