Biochemistry

Yıldırım Beyazıt Universitesi Tıp Fakültesi
Biyokimya ABD
Prof. Dr. Fatma Meriç Yılmaz

fatmamericyilmaz@hotmail.com
Diyet Proteini
Doku Proteini Amino Asit Havuzu Nonprotein Azot Bileşikleri
transaminasyon
Metabolik ara ürünler
Keton Cisimleri
Asetil CoA
Glutamat amino azotu
deaminasyon
SAS
NH3
CO2
Üre
 Amino asitler üç farklı metabolik durumda oksidatif yıkıma
uğrar.
1. Proteinlerin yıkımıyla açığa çıkan bazı amino asitler eğer yeni
protein sentezi için gereksinim yoksa, oksidatif parçalanmaya
uğrar.
2. Bir diyet proteince zenginse ve alınan amino asitler vücudun
protein sentezi gereksinimini aşıyorsa, fazlası yıkılır; amino
asitler depolanmaz.
3. Karbohidratların ya hiç olmadığı veya uygun yararlanılmadığı ,
açlıkta veya diyabetes mellitusta (DM) yakıt olarak hücresel
proteinler kullanılır.
 Amino asit yapısındaki C ve H
atomlarından son ürün olarak
H2O ve CO2 oluşur
 Amino grubundaki azot
+
atomundan toksik olan
amonyak açığa çıkar
NH3
 Amonyak, enerji gerektiren
bir dizi tepkime ile toksik
olmayan üreye
dönüştürülerek vücuttan atılır.
H2O + CO2
 Katabolizma sırasında amino asitler
amino gruplarını kaybederek, amino
asitlerin “karbon iskeletlerini”
koruyarak α-keto asitleri oluşturur.
 α-keto asitler oksidasyona uğrayarak

CO2 ve H2O’ya dönüşür veya sıklıkla
glukoneogenezle beyin, iskelet kası ve
diğer dokuların yakıtı olan glukoza
çevrilebilen 3 veya 4 C’lu birimleri
sağlar. α-keto asit
1. Glutamat
HÜCRE İÇİNDE:
Aminotransferaz→ α-ketoglutarattan glutamat oluşumu
2. Glutamin
HÜCRELER VE DOKULAR ARASINDA→ 2. amino grubu alır ve
karaciğer ya da böbrekte amonyak şeklinde verir
3. Alanin
KAS-KARACİĞER ARASINDA → Kastan karaciğere amino
grubunu taşır
 Glutamat ve glutamin azot metabolizmasında kritik rol oynar
 Hepatositlerin sitozolünde, çoğu amino asitlerin amino grupları glutamat
oluşturmak için α-ketoglutarata transfer edilir
 Glutamat sonra amino grubunun NH4+ oluşturmak için uzaklaştırıldığı
mitokondri içine taşınır
 Çoğu dokuda oluşan fazla amonyak glutaminin amid azotuna çevrilir,
karaciğere geçerek, karaciğer mitokondrisine girer ya da böbreklerde
amonyum oluşumunu sağlayarak asit-baz regülasyonunda görev alır.
 Kasta fazla amino grupları genellikle piruvata transfer edilerek, karaciğere
amino gruplarının taşınmasındaki diğer önemli molekül, alanin oluşur
Amino Asit Katabolizmasında Glutamin
 Amonyağın organlar arasında taşınması işinde glutamin önemli rol
oynar.
 Beyin dahil birçok dokuda amonyak, glutamin sentetaz etkisiyle
glutamat ile kombine olarak glutamin oluşturur.
Amino Asit Katabolizmasında Glutamin
 Glutamin, amonyağın nontoksik

bir transport şeklidir; normalde
kanda diğer amino asitlerden çok
daha yüksek derişimde bulunur.
 Glutamin biyosentetik
tepkimelerin bir kısmında amino
grubu kaynağı olarak da işlev görür.
 Glutamin kanla karaciğer ve
böbreğe taşınır
 Glutaminaz enzimi glutamini
glutamat ve NH4+’e çevirir.
Amino Asit Katabolizmasında Alanin
 Alanin amino gruplarını,

glukoz-alanin döngüsü olarak
adlandırılan bir yolla, nontoksik
bir yapıda karaciğere taşıyarak
önemli bir rol oynar.
 Kas ve diğer bazı dokularda

yakıt olarak yıkılan amino
asitlerin amino grupları
transaminasyonla glutamat
yapısında toplanır.
GLİKOZ -ALANİN DÖNGÜSÜ
 Glutamat Karaciğere taşınmak

için glutamine çevrilebilir veya α-
amino grubunu alanin amino
transferaz aktivitesiyle, kas
glikolizinin hazır kullanılabilir bir
ürünü olan piruvata transfer
edilebilir.
 Böylece oluşan alanin kana

geçer ve karaciğere ulaşır.
 Hepatositlerin sitozolünde
alanin amino transferaz amino
grubunu alaninden α-
ketoglutarata taşır, piruvat ve
glutamat oluşur.
 Glutamat mitokondriye girebilir, glutamat dehidrogenaz tepkimesi
NH4+ açığa çıkarır veya oksaloasetatla transaminasyona uğrayarak,
üre sentezinin diğer azot vericisi olan aspartat oluşur.
 Kuvvetli kasılan iskelet kasları anaerobik olarak çalışır, glikolizden
piruvat ve laktat ürettiği gibi protein yıkımından amonyak üretir.
 Piruvat ve laktat glukoza dönüşerek kasa geri dönerken, amonyak
atılım için üreye çevrilir
1. Yeniden kullanım
2. Üre döngüsü
Fumarate
Oxaloacetate
 Amino asitlerin katabolizması sırasında amonyak açığa çıkar
 Amonyak, hücreler için son derece toksiktir
 Üre döngüsünde amaç, toksik amonyağın daha az toksik olan
üre dönüştürülmesidir.
 Arginaz enzimi yalnızca karaciğerde bulunduğu için bu döngü
karaciğerde gerçekleşir.
 Ürede 2 azot bulunur ve bunlar oksidatif deaminasyon sonucu
glutamattan oluşan serbest amonyak ve transaminasyon
sonucu oluşan aspartattan sağlanır.
Azotun
mitokondriye
alınması
gerekir
İlk iki reaksiyon mitokondride, Diğer reaksiyonlar sitoplazmada

Azotun Karaciğer Mitokondrisine Taşınması
1. Direkt deaminasyon
2. Transdeaminasyon
 Aminoasidlerin amino gruplarını yok edilmesinde vücutta

temel kullanılan sistem transdeaminasyondur. Direk
deaminasyon yöntemleri çok fazla kullanılan yöntemler
değildir.
 Oksidatif ve nonoksidatif olabilir
 Oksidatif (örnek glisin oksidaz) ve nonoksidatif deaminasyonu
(örnek serin, treonin dehidrataz) içeren direk deaminasyon
reaksiyonları insanda önemsiz olan reaksiyonlardır.
 Aminoasitlerin amino gruplarının uzaklaştırılmasında esas yol
transaminasyondur.
 Transdeaminasyon sistemi iki temel reaksiyondan oluşmaktadır:
 Transaminasyon
 Deaminasyon
 Karaciğerde bu sistem sitozolde gerçekleşen transaminasyon ve

mitokondride gerçekleşen deaminasyonu içerir.
 Karaciğere ulaşan L-aminoasidlerin katabolizmasında 1.
Basamak aminoasidlerden amino grubunun aminotransferaz
veya transaminaz olarak adlandırılan enzimlerle
uzaklaştırılmasıdır.
 Transaminazlar (aminotransferaz) insan organizmasında

yaygın olarak dağılmışlardır ve özellikle kalp kası, karaciğer,
iskelet kası ve böbrekte aktiftirler.
TRANSAMİNASYON:
Amino asit Keto asit
Aminotransferaz Piridoksal fosfat
Amino asit Keto asit

Aminoasit
H -KETOGLUTARAT H
H 3N + C COO- C COO-
R1 R1
AMİNOTRANSFERAZ
PP
H H
C COO- H 3N + C COO-
R1 GLUTAMAT
R2
Ketoasit
 -Ketoglutarat / L-glutamat çifti tüm transaminasyon reaksiyonlarında
amino grup alıcı / verici çiftini oluşturur.
 Bu transaminasyon reaksiyonunda -amino grubu -ketoglutaratın -C
atomuna aktarılır ve -ketoasit ve L-glutamat oluşur.
 Glutamat da biyosentetik reaksiyonlarda amino grubu vericisi olarak rol
oynar.
 Tüm aminoasitlerin amino grupları bu reaksiyon sayesinde -
ketoglutaratta toplanıp glutamat oluşmaktadır.
 -ketoglutaratın aa metabolizmasındaki tek rolü aa’lerden amino grubu
alarak glutamat haline geçmektir.
 Hücreler çeşitli aminotransferaz enzimleri içermektedir
 En önemli aminotransferaz enzimi AST ve ALT’dir.
 Tüm aminotransferazlar prostetik grup olarak piridoksal fosfata (PP)
bağlıdır.
Alanin + -ketoglutarat pirüvat + glutamat
ALT+PP
Glutamat + Oksaloasetat Aspartat + -ketoglutarat

AST+PP
Bu enzimin katalizlediği reaksiyon diğer aminotransferazlardan farklı olarak, glutamat
oluşum yönünde değil, aspartat oluşum yönünde işler.
 Aminotransferazlar normalde hücre içi enzimlerdir
 Kanda artmış düzeyleri bu enzimlerden zengin hücrelerde hasarı
işaret eder
 Örn. Karaciğer hastalıkları: Neredeyse tüm karaciğer
hastalıklarında kan AST, ALT düzeyleri artar
Özellikle yoğun hücre nekrozu olan

viral hepatit, toksik hasar gibi
durumlarda artış çok daha fazladır
 Aminoasitlerin çoğunun -amino grubu -ketoglutarat ile
transaminasyona girerek glutamatta toplanır.
 Hepatositte glutamat sitozolden mitokondriye glutamat taşıyıcıları
ile taşınır ve mitokondride glutamat dehidrogenaz ile oksidatif
deaminasyona uğrar ve -ketoglutarat ve amonyak (amonyum
iyonları) oluşur.
 Aminotransferaz ve glutamat dehidrogenazın etkisi toplu olarak
transdeaminasyon olarak adlandırılır. Çok az bir aminoasit
transdeaminasyonu atlar ve direkt olarak oksidatif deaminasyona
uğrar.
 Glutamatın deaminasyonu ile oluşan -ketoglutarat da TCA’da
glukoz sentezinde kullanılır.
NAD(P) NAD(P)H+H
Glutamat -KG + NH4+
Glutamat dehidrogenaz
 Hem NAD hem de NADP’yi koenzim olarak kullanabilen nadir

enzimlerdendir.
 Allosterik bir enzimdir.
 Reaksiyonun yönü glutamat, -ketoglutarat ve NH3 konsantrasyonuna
ve okside redükte koenzim oranlarına bağlıdır. Örneğin proteinli diyet
sonrası enzim yönü aminoasit yıkımı yönüdür.
 ATP ve GTP enzimin allosterik inhibitörleri iken GDP ve ADP ise
aktivatörleridir.
 Hücre içi alanda GDP ve ADP yüksek yani enerji düzeyi düşük ise
glutamat dehidrogenaz ile aminoasit yıkımı artar ve elde edilen -
ketoglutarat TCA için substrat olarak kullanılır.
Üre Döngüsü
1. Karbamoil fosfat sentaz I
2. Ornitin transkarbamoilaz (Rate-limiting step)
3. Argininosuksinat sentetaz
4. Argininosuksinat liyaz
5. Arginaz
1. Reaksiyon: Karbamoil Fosfat Oluşumu
Amonyak, karbamoil fosfat şeklinde yakalanmış olur.
Enzim: Karbamoil fosfat sentetaz I

Yer: mitokondri
2ATP tüketimi
Karbamoil Fosfatın yapısına giren amonyak, glutamatın oksidatif

deaminasyonundan gelir.
Karbamoil fosfat sentaz
Sentaz I Sentaz II
Mitokondride yer alır Sitozolik
Üre sentezi hız kısıtlayıcı enzimi Pirimidin sentezi hız kısıtlayıcı enzimi
CO2, ATP’nin fosfatı ve NH4 kullanır CO2, ATP’nin fosfatı ve glutaminin amid
azotunu kullanır
Karbamoil fosfatın karbamoil grubu ornitin Karbamoil fosfatın karbamoil grubu

transkarbamoilazla ornitine aktarılır aspartat transkarbamoilazla aspartata
aktarılır
Karbamoil grubu üreye karbon kaynağı Karbamoil grubu primidin halkasının 2.

olarak kullanılır karbonunu yapar
NAG allosterik aktivatördür NAG gerektirmez. PRPP ile allosterik

olarak aktiflenir
Üre Döngüsü
5. Arginaz
2. Reaksiyon: Sitrulin Oluşumu
Enzim: Ornitin transkarbamoilaz

Yer: mitokondri
 Ornitin ve sitrulinbazik amino asitlerdir

 Protein yapısına katılmazlar
 Ornitin her döngüde yeniden oluşur
Açığa çıkan sitrulin sitoplazmaya geçer
Üre Döngüsü
5. Arginaz
3. Reaksiyon: Argininosüksinat Oluşumu
Aspartatın amino grubu

üre molekülünün ikinci
azotunu oluşturur
Enzim: argininosuksinat sentetaz

Yer: Sitozol
1 ATP tüketimi
Üre Döngüsü
5. Arginaz
4. Reaksiyon: Argininosüksinatın Parçalanması
Enzim:Mitokondriye taşınıp Liyaz

Argininosüksinat TCA ya(Argininosüksinaz)
girebilir Malat
Yer: sitozol
Sitoplazmada OAA a çevirilip aspartat ya da glukoz oluşturabilir
Üre Döngüsü
5. Arginaz
5. Reaksiyon: Argininden üre ve ornitin oluşumu
Enzim: Arginaz
Yer: Sitozol
Böbrek gibi diğer organlar bu reaksiyonlarla arginin sentezleyebilir.

Argininden üre oluşumunu yalnızca Karaciğer yapabilir.
Oluşan Üre, Böbrekler yoluyla atılır
ARJİNİN N-ASETİL
GLUTAMAT
KARBOMOİL
FOSFAT SENTAZ-1
NH3
KARBOMOİL
FOSFAT
HCO3
2ATP 2ADP
KARACİĞER-MİTOKONDRİ
Aspartat
ATP AMP
Sitrüllin Sitrüllin Arjininosüksinat

Arjininosüksinat
sentaz
Arjininosüksinat
Karbomoil Ornitin
liyaz
fosfat transkarbamoliaz
Fumarat
Ornitin Ornitin
Arjinin
Arjinaz
3 ATP
4 Yüksek Enerjili Fosfat Üre
2 NH4+ +HCO3- + 3ATP4- + H2O → Urea + 2 ADP3- +4 Pi2- +AMP2- + 5 H+

Aspartat–Arginosuksinat Şantı Üre Döngüsü
ile Krebs Döngüsünü birleştirir
Krebs Bicycle
Üre Döngüsünün Kontrolü
Karbamoil Fosfat Sentaz I Basamağı
hız kısıtlayıcı basamak
NAG KFS I’in aktivatörü
Arginin NAG sentezinin aktivatörü
Arginine
Proteinden Zengin Yemek

NAG konsantrasyonu artar
 Glutamat ve Arginin artar
Üre sentezi hızlanır
KC de sentezlenen üre kan
dolaşımına geçer ve böbreklere
gelerek idrar yolu ile atılır
Sentezlenen ürenin bir kısmı

barsağa geçer
Bakteriyal üreazla CO2ve NH3
parçalanır
Bir kısmı feçesle atılır bir kısmı
kan dolaşımına geçer
 Böbrek yetmezliğinde kan üre düzeyleri yükselir

 Barsağa daha fazla üre gelir
 Barsağa gelen üre bakterilerin üreaz etkisiyle parçalanır ve amonyak
açığa çıkar.
 Böbrek yetmezliği….Hiperamonemi
Glutaminin
oluşturduğu osmotik
etki de nörotoksisiteye
neden olur
Glutamat Glutamin
dehidrogenaz sentaz
NH4 + -ketoglutarat Glutamat + NH4 Glutamin
NAD(P)H NAD(P) ATP ADP
Glutamat beyinde inhibitör etkili

-KG tükenir ve Hücresel
nörotransmitter olan GABA’nın
oksidasyon ve ATP üretimi
öncülüdür. Glutamatın azalması ile
azalır. Özellikle beyin gibi
GABA oluşumu azalır ve eksitasyon
yüksek enerji gereksinimi olan
ortaya çıkar.
dokular zarar görür.
 Aminoasitler: Bir çok dokuda, özellikle de karaciğerde aminotransferaz ve
glutamat dehidrogenaz reaksiyonları ile aminoasitlerden NH3 meydana gelir
 Glutamin: Renal glutaminaz etkisi ile böbreklerde,
İntestinal glutaminaz etkisi ile barsaklarda glutaminden NH3 oluşur
 Barsak bakterileri: Amonyak barsak lümenindeki ürenin bakteriyel yıkımı ile
elde edilir. Portal vene geçen amonyak karaciğerce tutulup üreye çevrilir.
 Aminler: Besinlerden veya hormon ve nörotransmitterler gibi
monoaminlerden elde edilen aminler, MAO ile amonyağa çevrilir.
 Pürin ve pirimidinler: Pürin ve pirimidin katabolizmasında halkalardaki amin
grupları amonyak olarak serbestleşir.
 Hiperamonemi SSS toksisitesi
nedeniyle medikal bir acildir
 2 temel neden:
 1. Karaciğer hastalığı
 2. Üre siklusundaki enzimlerin

genetik eksikliği
 Tremor, konuşmanın peltekleşmesi ve bulanık görme gibi
semptomları vardır.
 Kazanılmış: Alkolizm, hepatit ve bilier obstrüksiyon sonucu
oluşmuş siroz karaciğer çevresinde kollaterallere yol açar.
Portal kan şantlar aracılığı ile karaciğere uğramadan sistemik
dolaşıma katılır ve kan amonyak konsantrasyonları artar.
 Herediter: Üre siklusu enzim eksiklikleri ile oluşur. Yaşamın ilk
haftasında hiperamonyemi oluşur. Mental retardasyon
kaçınılmazdır.
NH3 (μmol/L) KLİNİK VE TANISAL ANLAMI
< 100 *Belirgin klinik bulgu görülmez
* Genel durumu kötü olan YD’larda ayırıcı
tanıya götürmez
* Daha büyük çocuklarda metabolik hastalık ön belirtisi
olabilir, tekrarı gerekir
100-300 * Letarji, konfüzyon, kusma görülebilir
* Metabolik hastalıklara ikincil artmayı
yansıtabilir
300-500 * Belirgin ensefalopati tablosu oluşur

* Öncelikle ÜRE SİKLUS DEFEKTLERİNİ
düşündürür
500-2000 * Koma ve konvulziyonla seyreder

* Yenidoğan başlangıçlı ÜRE SİKLUS
DEFEKTLERİNİ düşündürür
 Üre siklus defekti sıklığı 1/30000 canlı doğum
 Ancak yenidoğan döneminde buna yönelik bir
tarama programı olmadığı için gerçek sıklığı
bilinmiyor
 Progresif hiperamonyemi beyin ödemi, koma
ve ölümle sonuçlanır
 Mortalite daha çok ilk hiperamonyemi
atağında
Tedaviye dirençli hastalarda
İlk atak tanısını geç alan hastalarda
 Hiperamonyemi geri dönüşsüz nörotoksisite
ve SSS’nde hücre nekrozuna neden olabilir
 Tekrarlayan ataklar entellektüel
fonksiyonlarda ilerleyici azalmaya yol açar
En sık Ornitin Transkarbamoilaz Defekti
X e Bağlı Resesif
•NAG Sentaz Defekti

•KFS l Defekti
•Ornitin Transkarbamoilaz Dfk
•ASS Dfk/Sitrulinemi
•AL Dfk/Argininosuksinikasidüri
•Arginaz Dfk /Argininemi
Location Abb. Enzyme Disorder
N-Acetylglutamate synthase
Mitochondria OR N-Acetylglutamate synthetase
deficiency
Carbamoyl phosphate
Mitochondria OR Carbamoyl phosphate synthetase I
synthetase I deficiency
Ornithine transcarbamylase
Mitochondria XR Ornithine transcarbamylase
deficiency
"AS deficiency" or
Cytosol OR Argininosuccinic acid synthetase
citrullinemia
"AL deficiency" or
Cytosol OR Argininosuccinase acid lyase argininosuccinic aciduria
(ASA)
"Arginase deficiency" or
Cytosol OR Arginase
argininemia
 Transaminasyon reaksiyonları: piridoksal fosfat
 Tek Karbon Transferi: biotin
tetrahidrofolat
S-adenosilmetiyonin
 Tetrahidrobiyopterin fenilalanin hidroksilaz reaksiyonunun kofaktörü

Alanin
Sistein
Glikojenik: Piruvat ya da Glisin Lösin
SAS ara ürünlerini oluşturan Serin Lizin
Aa ler Treonin Isolösin Fenilalanin
Triptofan Lösin Triptofan
Triptofan Tirozin
Pirüvat
Asetil KoA Asetoasetil KoA

Aspartat
Asparajin
Ketojenik: Asetil CoA ve
OAA
Aseteoasetil CoA Oluşturan
Aspartat Sitrat AA ler
Fenilalanin Fumarat
tirozin
Arjinin
Izolösin Glutamat
-KG Glutamin
Metionin Süksinil KoA
Treonin Histidin
Valin Prolin
Amino Asitler oluşturdukları son ürüne göre

glikojenik ve ketojenik olarak sınıflandırılırlar
Hem glikojenik hem
Glikojenik Saf ketojenik
ketojenik
Alanin Lösin İzolösin
Arjinin Lizin Fenilalanin
Asparajin Triptofan
Sistein Tirozin
Glutamin
Glisin
Histidin
Hidroksiprolin
Metionin
Prolin
Serin
Treonin
Valin
Oksaloasetat Oluşturan Amino asitler
C4 ailesi: asparagin aspartata dönüşerek, aspartat ise

transaminasyon reaksiyonuyla amino grubunu α-ketoglutarata
vererek oksaloasetata dönüşür.
O
H2O NH 4+ KG Glu
H2C C NH 2 H2C COO – H2C COO –
+
H3N C COO – +
H3N C COO – O C COO –
H Asparaginase H
Glutamate–Aspartate H
Aminotransferase
Asparagine Aspartate Oxaloacetate
α-Ketoglutarat Oluşturan Amino asitler
C5 ailesi bir çok aa glutamat üzerinden -KG’a çevrilir.

 Glutamin glutamata glutaminaz ile
Arginin Prolin
çevrilir.
 Histidinin glutamata çevriminde ara
ürün olarak Figlu (N- Ornitin
formiminoglutamat) oluşur. Figlu
formimino grubunu THF’a aktararak
glutamata çevrilir. Eğer folat eksikliği Glutamat -semialdehit
varsa histidin yıkımında figlu birikimi
ortaya çıkar ve idrarla atılır. Folat
eksikliğinin saptanmasında
kullanılmaktadır. Glutamat
Histidin Figlu Glutamat
THF N5-formimino THF

 C3 ailesi; Alanin, Glisin, Serin, Sistin-sistein ve Treonin, piruvata
çevrilerek metabolize olur
Alanin direkt olarak transaminasyonla pirüvata çevrilir.

ALT+PP
Diğer basit reaksiyon serinin serin dehidratazla pirüvata

çevrimidir.
Serin Pirüvat + NH4

Serin dehidrataz
Glisin N5-N10-metilen
THF dan bir metilen
grubunun eklenmesiyle
serine dönüşebilir
Glisin CO2 ve NH3 e de
dönüşebilir
Serinin çoğu serin hidroksimetil transferazla glisine çevrilir ve bu

reaksiyonda N5-N10-metilen THF oluşur
Ayrıca serin dehidratazla piruvata da direkt dönüşebilir
•Fenilalanin tirozine
dönüşür
•Tirozin ise fumarat ve
asetoasetat oluşturur
•Fenilalanin ve tirozin
hem glikojenik hem
ketojenik aa grubunda
yer alır.
 Metiyonin, Valin ve İzolözin propiyonil CoA oluşturur
 Propiyonil CoA Süksinil CoA dönüşümü tek karbon sayılı yağ
asitlerinin yıkılımında da ortak yol
VitB12
Biotin
Methylmalonyl
Propionyl CoA Coa mutase
caroxylase
 Lözin, izolözin, lizin, triptofan direkt olarak Asetil CoA ya da
asetoasetil CoA oluşturur
 Fenilalanin ve tirozinin katabolizması sırasında da asetoasetat
oluşur (Fumarat+asetoasetat)
 Triptofan (Alanin+asetoasetat)
 İzolözin (Propiyonil CoA+Asetil CoA)
Lösin
Lizin
Isolösin Fenilalanin
Lösin Triptofan
Triptofan Tirozin

Alanin
Sistein
Glisin Lösin
Serin Lizin
Treonin Isolösin Fenilalanin
Triptofan Lösin Triptofan
Triptofan Tirozin
Pirüvat

Aspartat
Asparajin
OAA
Aspartat Sitrat
Fenilalanin Fumarat
tirozin
Arjinin
Izolösin Glutamat
-KG Glutamin
Metionin Süksinil KoA
Treonin Histidin
Valin Prolin
PROTEINS
Structures and Functions of
Fibrous and Globular Proteins
Prof. Dr. Leyla Didem KOZACI

Yıldırım Beyazit University Medical Faculty
Medical Biochemistry Department
Lect. 6-1
• Proteins are long chains of molecules consisting of polymers
assembled from a large number of amino acids like beads on a
necklace.
• The quarternary structure, which is the highest level of structure, is

formed by the noncovalent association of independent tertiary structure
units.
• Knowing the 3D structure of proteins is essential in understanding their

function.
• The primary structure provides little information about the function of

proteins. To carry out their function, proteins must take on a particular
shape, often referred to as an active form, through the folding process.
Lect. 6-2
• Folded proteins, such as egg albumin, can be unfolded by heating.
• Following heating, the albumin, which has undergone an irreversible

folding conformation change, turns white. In this form albumin is said to
be denatured. Denatured albumin cannot be reversed into its natural
state.
• Some proteins can be denatured and renatured repeatedly; that is, they
can be unfolded and refolded back to their natural configuration.
• Diseases such as Alzheimer’s disease, cystic fibrosis, mad cow

disease, an inherited form of emphysema, and even many cancers are
believed to result from protein misfolding.
Lect. 6-3
Fibrous vs. Globular Proteins
Globular Fibrous
1. Compact protein structure Extended protein structure
2. Soluble in water Insoluble in water
3. Secondary structure is complex Secondary structure is simple
with a mixture of α-helix, β-sheet based on one type only
and loop structures
4. Quaternary structure is held Quaternary structure is usually
by noncovalent forces held together by covalent bridges
5. Functions in all aspects of Functions in structure of the body
metabolism (enzymes, transport, or cell (tendons, bones, muscle,
immune protection, hormones, etc). ligaments, hair, skin)
Lect. 6-6
Fibrous Proteins
 Fibrous proteins have high α-helix or β-sheet content.
 Fibrous proteins have polypeptide chains arranged in long

strands or sheets.
 Most are structural proteins.
 Examples include:
Collagen
Elastin
Keratin
Lect. 6-7
Fibrous Proteins
•Much or most of the polypeptide chain is parallel to a single axis
•Fibrous proteins are often mechanically strong & highly cross-
linked
•Fibrous proteins are usually insoluble
•Usually play a structural role
Lect. 6-8
Lect. 6-9
Fibrous Proteins
•Collagen and elastin are the most common fibrous proteins.
•These are basic structural elements.
•These proteins have special mechanical properties.
•They are found as components of skin, connective tissue,
blood vessels, sclera and cornea of eye.
•Each fibrous protein exhibits special mechanical properties,
resulting from its unique structure, which is obtained by
combining specific amino acids into regular, secondary
structural elements.
Dentin
fibrils in tooth
Lect. 6-10
Collagen
Collagen Background
•Collagen is the main component of connective tissue, and is the most
abundant protein in mammals, making up about 25% to 35% of the
whole-body protein content.
• No hydrogen bonds within chains
•A typical collagen molecule is a long, rigid structure in which three
polypeptides ( called as α chains) are wound around one another in a
rope-like triple helix
•The final cooperative quaternary structure is stabilized by numerous

hydrogen bonds.
•It occurs in connective tissues where tensile strength is needed.

Examples: skin, tendons, cartilage, bones. Lect. 6-11
Tensile strength results from the use of:
• The triple helix secondary structure

• The assembly of tropocollagen subunits into a fibre
• Chemical cross linking to strengthen the fibre
Lect. 6-12
Collagen: A Triple Helix
The collagen molecule, also known as the “tropocollagen”, is part of larger

collagen aggregates such as fibrils.
Lect. 6-13
Types of Collagen
•The collagen superfamily of proteins includes more than 25 collagen
types, as well as additional proteins that have collagen-like domains
•The three α chains are held together by hydrogen bonds between the
chains
•Variations in the amino acid sequence of these chains result in
structural components that are about the same size (approximately
1000 aa long) but with slightly different properties
•These α chains are combined to form the various types of collagen
found in the tissues.
•For example, the most common collagen, Type I includes two chains
α1 and one chain α2 (α12α2 ) whereas Type II collagen includes three
α1 chains (α13)
Lect. 6-14
Types of Collagen
• The collagens can be organized into three groups, based on their
location and functions in the body
1. Fibril Forming Collagens. They have rope like structure

2. Network Forming Collagens. They form a three dimensional mesh,
rather than distinct fibrils
3. Fibril-associated Collagens. They bind the surface of collagenfibrils,
linking these fibrils to one another and to other components in the
extracellular matrix.
Lect. 6-15
Fibril Forming Collagens
• Types I,II and III are the fibrillar collagens

• They have the typical rope-like structure described for a collagen
molecule
• Type I collagen fibers are found in supporting elements of high
tensile strength is needed. E.g. Tendon, cornea, skin, bone etc
• Type II collagen molecules are found in cartilageneous tissues like
cartilage, intervertebral disk etc.
• Type III collagen molecules are prevalent in more distensible tissues
like blood vessels.
Lect. 6-16
Network Forming Collagens
• Types IV and VII are the network forming collagens
• They have a mesh like structure
• Type IV molecules are an important part of basement membranes
• Basement membranes are thin, sheet-like structures that provide
mechanical support for neighboring cells
• They function as a semipermeable filtration barrier to
macromolecules in organs such as kidney and the lung
Lect. 6-17
Classification of Collagens
TYPE TISSUE DİSTRIBUTION
FIBRIL FORMING
Type I Skin, bone, tendon, cornea
Type II Cartilage, intervertebral disk, vitreous body
Type III Blood vessels, fetal skin
NETWORK FORMING
Type IV Basement membrane
Type VII Stratified squamous epithelia
FIBRIL ASSOCIATED
Type IX Cartilage
Type XII Tendon, ligaments, other tissues
Lect. 6-18
Collagen Amino Acid Composition
•Nearly one residue out of three is Gly

•Proline content is unusually high
•Many modified amino acids present:
– 4-hydroxyproline
– 3-hydroxyproline
– 5-hydroxylysine
•Pro and HyPro together make 30% of
residues
Lect. 6-19
 Glycine is one - third of total amino acid content of collagen

followed by hydroxyproline and proline account for another one-
third of amino acid content of collagen. It fits into the restricted
spaces where the three chains of the helix come together.
 Proline - facilitate the formation of helical conformation of α-

chain, because its ring structure causes a kink in the peptide
chain.
Lect. 6-20
• Glycine is the part of the repeating

sequence.
Gly- X-Y
• X- is frequently proline
• Y- hydroxy proline or hydroxylysine.
Lect. 6-21
Collagen Amino Acid Sequence
Lect. 6-22
Triple- helix structure
• Amino acids side chains are on the surface of the triple helical
molecule.
• This allows bond formation between the exposed R- groups of

neighboring collagen monomers- This leads to aggregation into
fibrils.
Lect. 6-23
Biosynthesis of hydroxy-Pro and hydroxy-Lys requires O2
and ascorbic acid (vitamin C).
Vit. C deficiency leads to disorders in bone, skin and teeth.
Lect. 6-24
• Biosynthesis of hydroxy-Pro and hydroxy-Lys requires O2
and ascorbic acid (vitamin C).
• Vit. C deficiency leads to disorders in bone, skin and
teeth.
Lect. 6-25
Biosynthesis and assembly of collagen
11 Collagen molecules covalently cross-linked to fibril
OH OH OH OH OH OH
5 6
OH OH S
Tropocollagen with N and
OH OH OH S C terminal peptides removed
10
OH OH OH
4 OH
S S
OH
OH S S
OH OH OH
3 OH OH OH Tropocollagen
OH 9 Extracellular region
Plasma
Exocytosis membrane
2
N terminal C terminal
peptide peptide
7 S
S
1 Signal sequence
8
S Endocytosis
OH OH OH
Collagen S
mRNA
Transport vesicle
1. Synthesis on ribosome. Entry of chains into lumen of endoplasmic

reticulum occurs with the first processing reaction removing signal peptide
2. Collagen precursor with N and C terminal extensions
3. Hydroxylation of selected protein and lysines 26
OH OH OH OH OH OH
5 6
OH OH S
10
OH OH OH
4 OH
S S
OH
OH S S
OH OH OH
Plasma
Exocytosis membrane
2
peptide peptide
7 S
S
1 Signal sequence
8
S Endocytosis
OH OH OH
Collagen S
mRNA
Transport vesicle
4. Addition of Asn-linked oligosaccharides to collagen

5. Initial glycosylation of hydroxylyine residues
6. Alignment of three polypeptide chains and formation of inter-chain 27
disulfide bridges
OH OH OH OH OH OH
5 6
OH OH S
10
OH OH OH
4 OH
S S
OH
OH S S
OH OH OH
Plasma
Exocytosis membrane
2
peptide peptide
7 S
S
1 Signal sequence
8
S Endocytosis
OH OH OH
Collagen S
mRNA
Transport vesicle
7. Formation of triple helical procollagen

8. Exocytosis transfers triple helix to extracellular phase
28
OH OH OH OH OH OH
5 6
OH OH S
10
OH OH OH
4 OH
S S
OH
OH S S
OH OH OH
Plasma
Exocytosis membrane
2
peptide peptide
7 S
S
1 Signal sequence
8
S Endocytosis
OH OH OH
Collagen S
mRNA
Transport vesicle
10. Removal of N and C terminal propeptides by specific peptidase

11. Lateral association of collagen molecules coupled to covalent cross linking
creates fibril
29
Structural Basis of Collagen Triple Helix
•Interchain H-bonds involving HyPro stabilize

helix
•Fibrils are strengthened by intrachain lysine-
lysine and interchain hydroxypyridinium
cross links
In collagen triple helix H-bonds form

between separate chains.
In α-helix H-bonds formed between
residues of the same chain.
Lect. 6-30
Biosynthesis of Aldol Cross-links in Collagen
Lysyl oxidase is a cupper (Cu) containing enzyme and oxidatively

deaminates some of the lysyl and hydroxylysyl residues in collagen
Lect. 6-31
Biosynthesis of Aldol Cross-links in Collagen
Lysine- and hydroxylysine-derived aldehydes can react with corresponding

aldehydes on neighboring polypeptide chains forming aldol condensation
products, or with unmodified lysine and hydroxylysine
Lect. 6-32
Biosynthesis of cross links between
Lys, His, and hydroxy-Lys residues in
collagen.
Lect. 6-33
Degradation of Collagen
•Normal collagens are highly stable molecules, having half lives as long
as several years
•However, connective tissue is dynamic and constantly being remodeled,

often in response to growth or injury of the tissue
•Breakdown of collagen fibers is dependent on the proteolytic action of

collagenases
•For type I collagen, the cleavage site is specific, generating three-

quarter and one-quarter length fragments
•These fragments are further degraded by other matrix proteinases to

their constituent amino acids.
Lect. 6-34
Lect. 6-35
Elastin
Structure of Elastin
• It is a connective tissue protein
• Rubber like properties
• Elastin & glycoprotein microfibrils are
present in lungs, walls of large
arteries, elastic ligaments.
• Can be stretched to several times
their normal length, but recoil back.
Lect. 6-36
Structure of Elastin
• Insoluble protein polymer
• Precursor is Tropoelastin--- it is a linear polypeptide composed

of about 700 amino acids – small and non –polar AA.
• Rich in Proline and Lysine
• Very little hydroxy-proline & hydroxy-lysine.
Lect. 6-37
Elastin
• Tropoelastin is secreted by the cells into the extracellular matrix.
• There it interacts with specific glycoprotein microfibrils – called

fibrillin.
• Fibrillin acts as a scaffold on which tropoelastin is deposited.
Lect. 6-38
Elastin
• Some of the lysyl side chains of the tropoelastin polypeptides

are oxidatively deaminated by lysyl oxidase and forms allysine
residues
Lect. 6-39
Desmosine
Three of the allysine side chains and one lysine residue form a desmosine cross link
CO NH CO NH
CH CH
Allysine
CH2 CH2
CH2 CH2
CH2 CH2
NH NH
NH Allysine CHO Allysine C
NH
CH CH2 CH2 C C CH2 CH2 CH
CH CH2 CH2 CH2 CHO CHO CH2 CH2 CH2 CH
CO C C
CO
NH3+ N+
CO CO
CH2 CH2
CH2 Desmosine CH2
Lysine CH2 CH2
CH2 CH2
CH CH
NH CO NH CO Lect. 6-40
Elastin
• Desmosine cross-links produces elastin- an extensively

interconnected, rubbery network that can strech and bend in any
direction when stressed, giving the connective tissue elasticity
Real aorta vs.

elastin biomaterial
Lect. 6-41
Role of α-1 antitrypsin in elastin
degradation
 Blood and other body fluids contain a protein, α-1
antitrypsin that inhibits a number of proteolytic enzymes
that hydrolyze and destroy proteins.
 α-1 AT comprises more than 90% of the α1 globin fraction
of the normal plasma.
 α-1 AT has the most important physiological role of
inhibiting neutrophil elastase- a powerful protease that is
released into the extracellular space and degrades elastin of
alveolar walls
Lect. 6-42
Role of α-1 antitrypsin in elastin
degradation
 In the normal lung, the alveoli are

chronically exposed to low levels of
neutrophil elastase released from
activated and degenerating
neutrophils
 This proteolytic activity can destroy
the elastin in alveolar walls if is not
protected by the activity of α-1 AT
 Because lung tissue cannot
regenerate, emphysema results from
the destruction of the connective
tissue of alveolar walls
Lect. 6-43
Keratin
• Fibrous (structural) proteins.
• Individual molecules combine to form insoluble structures.
• Keratins are the molecular basis for hair, nails, wool, feathers, claws
and horns.
• Keratin is also found in the cytoskeleton of cells.
• Keratin clusters are found on chromosomes 12 and 17.
• Entire protein is a coiled coil

• Every 7th residue is Leucine (red)
• Packed, 20 degree angles
• “Leucine zippers”
• Hydrophobic sidechains pack
• 11% of the residues are Cysteine
• Stabilization by disulphide
bonds of thiol groups Lect. 6-44
- Keratin
-Keratin is found in hair, nails, outer layer of skin. It forms almost

the entire dry weight of these materials.
The entire secondary structure is a dimer of two - helices.
It is rich in amino acids that favours - helix formation (Phe, Ile, Val,
Met, Ala)
These hydrophobic side chains are on the - helix surface-

explaining its insolubility.
It is also rich in Cysteine residues.

Lect. 6-45
Proposed structure for a- keratin intermediate filaments
• Two monomers (a) pair

form 50- nm-long dimer
(b)
• These then associate to
form 1st protofilament (c)
• These then associate to
form protofibril (d)
• Regular spacing of 25 nm
along the fibers is
accounted for by overlap
Lect. 6-46
- Keratin Structure
Lect. 6-47
Disulphide bridges and toughness in -keratin
Two Cys residues form NH CO NH CO

disulphide bridges in
- keratin, and link the CH Cys CH
- helices together.
CH2 CH2
The more disulphides,
the stronger the - SH S
keratin.
SH S
CH2 CH2
CH CH
Cys
NH CO NH CO
Lect. 6-48
Psoriasis
- a keratin over production disorder-
• In psoriasis, an activated
immune system triggers the
skin to reproduce every three
to four days, building up on
the outer layers (epidermis
and keratin).
• The epidermis thickens, blood

flow increases and reddens
the skin, and silver-gray scales
cover it.
Lect. 6-49
Perming and Relaxing Process in Hair
• When the hair is permed (and

sometimes when straightened) the
disulfide bonds of the hair are
broken through ‘reduction’.
• A reduction reaction involves either
the removal of oxygen or the
addition of hydrogen. In the case of
permanent waving, the reduction is
due to the addition of hydrogen.
Lect. 6-50
• The disulfide bonds join one sulfur

atom on one polypeptide chain to
another sulfur atom on different
polypeptide chain.
• Perms use reducing agents called
thiol compounds, which break the
disulfide bonds by adding a
hydrogen atom to each of the
sulfur atoms in the disulfide bonds.
• With the disulfide bonds broken,
the polypeptide chains are able to
slip into their new shape.
Lect. 6-51
• The broken disulfide bonds are
reformed through the
neutralization process.
• The most common neutralizer is
hydrogen peroxide and the
chemical process that removes
the hydrogen atoms and reforms
the disulfide bonds is called
“oxidation”.
• The removal of the hydrogen
atoms from the sulfur atoms
forces them to reform their
disulfide bonds in the new shape
(around the perm rods).
Lect. 6-52
• The process is the same for

relaxers and straighteners that use
thiol compounds, except that
these are removing curl rather
than creating it.
Lect. 6-53
Fibroin
• Fibroin, is the fibrous protein that

makes up silk cloth and spider webs.
• Made with a -sheet structures
with Gly on one face and Ala/Ser on
the other
• The high glycine (and, to a lesser
extent, alanine) content allows for
tight packing of the sheets, which
contributes to silk's rigid structure
that can't be stretched.
• 80% antiparallel β-sheets
Lect. 6-54
Lect. 6-55
DISORDERS OF COLLAGEN
DEPOSITION
Lect. 6-56
Disorders of Collagen Deposition
• Disorders of collagen deposition
– insufficient collagen content
– presence of chemically and/or morphologically abnormal collagen
– excessive collagen content
– insufficient collagen resorption
– excessive collagen resorption
• Genetic abnormalities of collagen
– mutations that lead to amino acid deletions or additions
– deficient synthesis of a portion
– disorders in post-translational modification (hydroxylation of lysine,
hydroxylation of proline)
– defects in enzymes essential for post-translational modification
• Disorders : Ehlers-Danlos syndrome, Osteogenesis Imperfecta
• Collagen is the building block; thus, its disorders lead to significant
deterioration in the mechanical integrity of tissues Lect. 6-57
Ehlers- Danlos Syndrome
-Cutis hyperelastica-
•Ehlers–Danlos syndrome is a group of

inherited connective tissue disorders,
caused by a defect in the synthesis of
collagen
•EDS can result from a deficiency of

collagen processing enzymes (e.g. Lysyl
hydroxylase or procollagen peptidase) or
from mutations in the amino acid
sequences of collagen types I, III or V
•The most clinically important mutations

are found in the gene for type III collagen
Lect. 6-58
Ehlers- Danlos Syndrome
-Cutis hyperelastica-
•Because type III collagen is an

important component of the arteries,
potentially lethal vascular problems
occur.
•Collagen plays a very significant role

in the skin, joints, muscles, ligaments,
blood vessels and visceral organs;
abnormal collagen leads to increased
elasticity within these structures.
Lect. 6-59
Osteogenesis Imperfecta
• This disease, known as “brittle bone syndrome” is a

heterogeneous group of inherited disorders distinguished
by bones that easily bend and fracture
• The most common mutations cause the replacement of

glycine residues (Gly-X-Y) by amino acids with bulky side
chains.
• The resulting structurally abnormal pro alpha chains prevent

the formation of required triple-helical conformation
Lect. 6-60
Osteogenesis Imperfecta
• Type I. Osteogenesis imperfecta tarda

• Decreased production of α1 and α2
chains.
• Fractures secondary to minor trauma
• Type II. OI congenita

• Most severe form
• Patient die due to pulmonary hypoplasia
in utero or during the neonatal period
Lect. 6-61
DISORDERS OF ELASTIN
Marfan Syndrome
 Mutations in fibrillin are responsible for Marfan’s syndrome.
 Connective tissue supports the tendons, ligaments, blood

vessels, cartilage and heart valves in the body.
 Affects three major organ systems of the body: the heart and
circulatory system, the bones and muscles, and the eyes.
Lect. 6-62
Marfan Syndrome
 Fibrillin is the primary component of the microfibrils that

allow tissues to stretch repeatedly without weakening.
 If fibrillin is abnormal, connective tissues are looser than
usual, which weakens or damages the support structures of
the entire body.
 The most common external signs associated with Marfan
syndrome include excessively long arms and legs.
 Patients with Osteogenesis imperfecta, Ehlers Danlos and

Marfan Syndrome may have blue sclera due to tissue
thinning that allows underlying pigment to show through.
Lect. 6-63
GLOBULAR PROTEINS
Globular proteins have polypeptide chains folded into a

spherical or globular shape.
Lect. 6-64
• In globular proteins, which have a compact
folded structure, nearly one third of the amino
acid residues are in turns or loops where the
polypeptide chain reverses direction.
• These are the connecting elements that link Structure of the

successive runs of a helix or b conformation. enzyme chymotrypsin,
a globular
protein.
• Globular protein structures are compact and varied.
• Human serum albumin (Mr 64,500) has 585 residues in a single
chain.
• The actual size of the protein in its native globular form, the
polypeptide chain must be very compactly
• folded to fit into these dimensions.
Lect. 6-65
Hemoglobin & Myoglobin
•Hemoglobin and myoglobin are oxygen
transport and storage proteins
•Myoglobin is a heme protein present in

heart and skeletal muscle
•Increases the rate of transport of oxygen

within the muscle cells.
•Myoglobin is monomeric; hemoglobin is

tetrameric
• Myoglobin is relatively small (Mr 16,700
• It functions both to store oxygen and to

facilitate oxygen diffusion in rapidly contracting
muscle tissue.
• Myoglobin contains a single polypeptide chain
of 153 amino acid residues and a single iron
protoporphyrin, or heme, group.
• The same heme group is found in hemoglobin,

the oxygen binding protein of erythrocytes, and
is responsible for the deep red-brown color of
both myoglobin and hemoglobin.
Lect. 6-67
Globular Proteins Have a Variety of Tertiary Structures
• Like myoglobin, cytochrome c is a heme

protein.
• It contains a single polypeptide chain of about
100 residues (Mr 12,400) and a single heme
group.
• The protoporphyrin of the heme group is
covalently attached to the polypeptide.
• Only about 40% of the polypeptide is in a-
helical segments, compared with 70% of the
myoglobin chain.
• The rest of the cytochrome c chain contains b
turns and irregularly coiled and extended
segments.
Lect. 6-68
FABP
Fatty acid binding protein
Hydrophobic shielding; hydrophilic outside,
hydrophobic inside
Binds oleic acid
β-meander motif
69
Hemoglobin
 The main function of red blood

cells
Transfer of O2 from lungs to
tissue
Transfer of CO2 from tissue
to lungs
 To accomplish this function red

cells have hemoglobin (Hb)
 Hb, protein constituting 1/3 of

the red blood cells
Globular Hemeproteins
• Specialized proteins that contain heme as a tightly bound
prosthetic group
• The role of heme group differs according to the protein type
• Cytocrome. Electron carrier
• Catalase. Part of the active site that catalysis the breakdown of
hydrogen peroxide
• Hemoglobin. Oxygen transport
• Myoglobin. Oxygen storage
Heme Group
• Heme group includes an iron
atom bound to four nitrogen
atoms and a surrounding
protoporphyrin ring
• Fe+2 can make a 6 bonds in total;

4 of these is coordinated with
nitrogens.
• The other positions are used for

different purposes for different
heme proteins
Hemoglobin Synthesis and
Hemoglobinopathies
Hemoglobin
• Two parts
• Hem
• Globin (α and β chains)
• Haem & globin are produced

at two different sites in the
cells
• Hem in mitochondria
• Globin in polyribosomes
Synthesis of globin
Synthesis of globin
 Various types of globin combines with hem to form different

hemoglobin types
 Eight functional globin chains, arranged in two clusters are

β- gene family (β, γ, δ and ε globin genes) on the short arm
of chromosome 11
α- gene family (α (two genes) and zeta globin genes) on the
short arm of chromosome 16
Hemoglobin structure
heme α β
β α
Hemoglobins in normal adults
What Is Sickle Cell Disease?
• An inherited disease of red blood cells
• Affects hemoglobin
• Polymerization of hemoglobin leads to a
cascade of effects decreasing blood flow
• Tissue hypoxia causes acute and chronic
damage
Why Do Cells Sickle?

• Glutamic acid is substituted
for valine
• Allowing the polymerization
of sickle hemoglobin when
deoxygenated
Normal Vs. Sickle Red Cells
Normal Sickle
• Disc-Shaped • Sickle-Shaped
• Deformable • Rigid
• Life span of 120 days • Lives for 20 days or less
Hemolysis and Vaso-occlusion
Hemolysis: Vaso-occlusion:
The anemia in SCD is caused by Occurs when the rigid sickle
shaped cells fail to move through
red cell destruction, or
the small blood vessels, blocking
hemolysis, and the degree of local blood flow to a microscopic
anemia varies widely between region of tissue. Amplified many
patients. times, these episodes produce
The production of red cells by tissue hypoxia. The result is pain,
the bone marrow increases and often damage to organs.
dramatically, but is unable to
keep pace with the destruction.
Hemolysis and Vaso-occlusion
Acute Manifestations: Chronic Manifestations:
 Bacterial Sepsis or meningitis*  Anemia
 Recurrent vaso-occlusive pain  Jaundice
(dactylitis, muscoskeletal or  Splenomegaly
abdominal pain)
 Functional asplenia
 Splenic Sequestration*
 Cardiomegaly and functional murmurs
 Aplastic Crisis*
 Hyposthenuria and enuresis
 Acute Chest Syndrome*
 Proteinemia
 Stroke*
 Cholelithiasis
 Priapism
 Delayed growth and sexual maturation
 Hematuria, including papillary
necrosis  Restrictive lung disease*
 Pulmonary Hypertension*
 Avascular necrosis
 Proliferative retinopathy
*Potential cause of mortality  Leg ulcers
 Transfusional hemosiderosis*
GENERAL PROPERTIES OF
PROTEİNS
PROF.DR.CEMİLE BİÇER
AYBU , MED. BIOCHEM
OUTLINES
• Classification of proteins
• Protein structure
• Protein turnover in the body, nitrogen
balance
• Protein digestion
• Aminoacid transport and related diseases
• Protein degredation within the cell
Proteins
• The most abundant

macromolecule in organism
• all the major structural and

functional aspects of the body
are carried out by protein
molecules
Abnormality in protein Hemoglobin
structure will lead to

molecular diseases
Insulin
CLASSIFICATION OF PROTEINS
I. On the basis of shape and size

(fibrous proteins, globular proteins)
II. On the basis of functional properties

(defence, contractile, respiratory, structural,
enzymes, hormones)
III. On the basis of solubility and physical properties

(simple, conjugated)
Classification Based on Functions
• 1. Catalytic proteins, e.g. enzymes
• 2. Structural proteins, e.g. collagen, elastin
• 3. Contractile proteins, e.g. myosin, actin
• 4. Transport proteins, e.g. hemoglobin, myoglobin,
albumin, transferrin
• 5. Regulatory proteins or hormones, e.g. insulin, growth
hormone
• 6. Genetic proteins, e.g. histones
• 7. Protective proteins, e.g. immunoglobulins, interferons,
clotting factors
Classification Based on Composition
and Solubility
Simple proteins Conjugated proteins
• Albumin
• Globulins
• Histones
An amino acid structure
Proteins are linear polymers formed by

linking the α-carboxyl group of one
amino acid to the α-amino group of
another amino acid with a peptide
bond
Long polypeptide chains containing
more than 50 amino acids are
called proteins
Condensation and
Hydrolytic Reactions Figure 6.3
Consists of one or more long chains of
amino acid residues (polypeptide
chain ~100-1000aa)
Peptides: fewer than 50 amino acids

Dipeptides: 2 amino acids
Tripeptides: 3 amino acids
Oligopeptides: < 10 aminoacids
(glutathione, oxytocin,bradykinin,
angiotensin,Gastrin,secretin,
ACTH..)
Polypeptide< 50 amino acids
Protein> 50 amino acids

STRUCTURAL ORGANISATION
OF PROTEINS
• Primary Structure
• Secondary Structure
• Tertiary structure
• Quaternary Structure
Organization of a protein molecule
 Primary Structure
 Secondary Structure
 Tertiary Structure
 Quaternary Structure
Protein Folding
The linear sequence of linked amino acids contains the
information necessary to generate a protein molecule
with a unique three-dimensional shape
• The sequence of amino acids in a
protein.
• Amino acids come together and

bind to each other with peptide
bonds to form a protein structure
• The side chains are able to extend

out from the peptide chain and
interact with each other or with
other molecules
• The polypeptide backbone, generally forms regular arrangements of
amino acids which are located near to each other in the primary
structure (folding of short residue 3-30 aa)
• Secondary structure is a regular extended structure stabilized by

hydrogen bonding between peptide bonds.
• Although the side chains are not involved in the hydrogen bonding that
forms the extended structure, they can determine the type of
secondary structure and its stability.
• The two main types of structure; α-helix conformation and the β-

pleated sheet structure
• Stabilized by ; H bonds and disulfide bonds
•α-helix is a right-handed helix with the peptide
bonds located on the inside and the side chains
extending outwards
• It is stabilized by the regular formation of

hydrogen bonds parallel to the axis of the helix;
they are formed between the amino and
carbonyl groups of every fourth peptide bond
•Each turn of an α-Helix contains 3.6 amino-

acids
•With the formation of an α-Helix, amino acid

residues spaced three or four residues apart in
the primary structure come spatially close
together
β-sheet
• A β-sheet can be formed from two or more polypeptide

chains or segments of polypeptide chains
• The orientation of the polypeptide chains can be parallel
or antiparallel to each other.
• All of the peptide bond components are involved in
hydrogen bonding.
• Hydrogen bonds are perpendicular to the backbone
• Nearly half of the residues in a typical globular
proteins are α-helix and β-sheets, half in loops,
turns, bends
• β-bends reverse the direction of a polypeptide
chain
• Helps forming compact, globular shapes
• β-bends name come from β-sheets which they
usually connect
• Generally composed of four amino acids, one of
them usually is proline which causes a “kink” in
the polypeptide chain
• The smallest amino acid, Glycine is also
frequently found in β-bends
• β-bends are stabilized by the formation of
hydrogen and ionic bonds.
Abnormalities in secondary prot
structure and related diseases
• Reason: misfolding of proteins into Beta
sheets, and the presence of these proteins
leading to tissue damage.
• Prion disease (Creutzfeldt-Jakob

disease, spongiform encephalopathies)
• Amyloidosis are two classes of disease

involving changes in the secondary structure
of proteins.
• The term “tertiary structure” refers to the entire three-
dimensional conformation of a polypeptide
• Proteins must fold into a complex three-dimensional structure

in order to function properly
• The primary structure of a polypeptide, determines the

tertiary structure of the protein
• Tertiary structure, defines the final arrangement of the

polypeptide
• Hydrogen Bonds
• Ionic interactions
• Hydrophobic interactions
• Disulfide Bonds
• Van der Waals bonds
• A protein may consist of either a single or two or more
polypeptide chains (each subunit is a seperate polypeptide)
• Quaternary structure of a protein defines the arrangement of

these subunits. Subunits are held together by non covalent
interactions like hydrogen bonds, ionic bonds or hydrophobic
interactions
• These polipeptide chains (subunits) can be identical or totally

unrelated
• Have domains that relate spatially to one another. A domain is a

section of the protein structure sufficient to perform a particular
chemical or physical task such as binding of a substrate or other
ligand
SOURCES AND FATES
OF AMINO ACIDS IN THE BODY
Each day, 1% to 2% of total body
protein turnovers (esp. Muscle prot.).
Amino acids can not be stored in the body
• Aa pool consists of intracellular and extracellular fluid proteins (50-100g

free aa)
• This pool is supplied by three sources:

• 1) amino acids provided by the degradation of body proteins
• 2) amino acids derived from dietary protein
• 3) synthesis of nonessential amino acids from simple intermediates of
metabolism
INTERORGAN EXCHANGE MAINTAINS CIRCULATING
LEVELS OF AMINO ACIDS
Metabolic Fate of Amino Acids
 Body protein in alive cells are continuosly regenerated with protein turnover process
 The term pool used for amino acids contains the sum of the free amino acids within
the intra and extracellular fluid
 An important amount of amino acid is synthesized during tissue metabolism in
addition to the amino acids obtained with the diet Figure 6.7
Protein turnover and Nitrogen Balance
• In normal adults, nitrogen intake matches nitrogen excreted
• Protein content of adult body remains remarkably constant
• Because the rate of protein synthesis is just sufficient to

replace the protein that is degraded
• Hydrolysis and resynthesis of 300–400 g of body protein each

day
Nitrogen Balance
• Nitrogen balance=nitrogen ingested - nitrogen excreted

(primarily as protein) (primarily as urea)
• Nitrogen balance = 0 (nitrogen equilibrium)

protein synthesis = protein degradation
• Positive nitrogen balance

protein synthesis > protein degradation
• Negative nitrogen balance

protein synthesis < protein degradation
Positive Nitrogen Balance
N balance = Nin - Nout

Negative Nitrogen Balance
1. Stress
2. Decreased Intake
3. Lack of an essential AA
Protein Energy Malnutrition
Marasmus: calorie and prot depletion
• kwashiorkor: children experience protein

malnutrition
Protein Degradation
• Digestion of diet protein
• Cell protein turnover

DIET PROTEIN AS A SOURCE FOR
AMINO ACID POOL
Protein Digestion and Amino Acid Absorption
Pepsin initiates protein

breakdown in the stomach
Proteases (proteolytic
enzymes) break down
dietary proteins into peptides
and a.a in the stomach and
intestine
inactive zymogens secreted

from the pancreas are activated
to continue protein digestion
Digestion of Diet Protein
• Proteins are too large to be absorbed through the
intestine
• They have to be broken down to amino acids and di-
tri-peptides before being absorbed
• Protein digestion begins in the stomach
• Acidic pH cause denaturation and makes the protein
more sensitive to the proteases
• Pepsin is the main gastric protease and has an
optimum pH value of 2.0.
• Protein degradation continues in the intestine with
the effect of pancreatic proteases
• Amino acids are then absorbed to the blood and
sent to the tissues
Digestion of Dietary Proteins
A. Digestion of proteins by gastric secretion
• Gastric juice—containing HCl & proenzyme,
pepsinogen
Hydrochloric acid: (pH 2–3), functions to kill
some bacteria and to denature proteins
Pepsin: Acid-stable endopeptidase

 secreted by the serous cells of the stomach as an
inactive zymogen (or proenzyme), pepsinogen
 activated to pepsin, either by HCl, or
autocatalytically by other pepsin molecules
 Pepsin releases peptides and a few free amino
acids from dietary proteins
Pepsin Activation and Effect
Pepsin (Otocatalytic effect)

• B. Digestion by Enzymes from the Pancreas
Activation of zymogens:
by Enteropeptidase w synthesized by
the brush border membrane
mucosal cells of duodenum
Enteropeptidase thus starts a

cascade of proteolytic activity,
because trypsin is the common
activator of all the pancreatic
zymogens
Secretion and activation of pancreatic proteases
Polypeptides Intestinal
Oligopeptides Endocrine
Amino acids Cell
hormones
hormones
Intestinal Mucosal
Pancreatic Epithelial Cell
Acinar
Cell
Enteropeptidase
Trypsinogen Trypsin
Chymotrypsinogen Chymotrypsin
Proelastase Elastase
Procarboxypeptidase Carboxypeptidase
Digestion of Dietary Proteins
C. Digestion of oligopeptides by enzymes of the small intestine
Exopeptidases produced by intestinal

epithelial cells act within the brush border
and also within the cell
The luminal surface of the intestine

contains aminopeptidase
an exopeptidase that repeatedly cleaves

the N-terminal residue from oligopeptides
produce free amino acids and smaller

peptides
Digestion of oligopeptides by
enzymes of the small intestine
Digestion of
proteins
Overview
ABSORPTION OF AMINO ACIDS
 Sodium-aminoacid cotransport
system (secondary active transport)
 γ - Glutamyl cycle
Secondary Active Transport with Na+
gradient
Na+ dependent- AA transporters
• At least 7 different transporters are defined for amino acid

absorption
1- neutral amino acids
2- basic amino acids
3- acidic amino acids
4- prolin and hydroxyprolin
An example of Abnormal Transport of
Amino Acids into Cells
• The small intestine and the proximal tubule of
the kidney have common transport systems
for amino acid uptake
• a defect in transport systems results in an
inability to absorb particular aa into gut &
kidney tubules
CYSTINURIA:
• inherited disorder, defective carrier system
• defective uptake of cystine and the dibasic
amino acids, ornithine, arginine, and lysine
• iall four amino acids appear n the urine
• precipitation of cystine to form kidney stones
(calculi), which can block the urinary tract
A Neutral Amino Acid transporter
Defect: Hartnup Disease
• Hartnup disease is a genetic defect in the Na-coupled
transporter that normally mediates absorption of neutral
amino acid from the lumen of the small intestine and the
proximal tubule
• In the kidney, the inability to reabsorb neutral amino acids

from the ultrafiltrate leads to their excretion in urine (neutral
amino aciduria).
• In the intestine, the defect results in malabsorption of

dietary neutral amino acids.
A Neutral Amino Acid transporter Defect:
Hartnup Disease
• Clinical symptoms are those one would expect for a deficiency of
tryptophan with pellagra-like features, which is an expression of
the decreased availability of tryptophan for conversion to
nicotinamide
Pellagra is clinically
manifested by the 4 D' s:
Photosensitive dermatitis,
Diarrhea
Dementia
Death.
ABSORPTION OF AMINO ACIDS
 Sodium-aminoacid cotransport
system (secondary active transport)
 γ - Glutamyl cycle
BODY PROTEINS AS
SOURCES OF AMINO ACIDS
SOURCES AND FATES
OF AMINO ACIDS IN THE BODY
Each day, 1% to 2% of total body
protein turnovers (esp. Muscle prot.).
Protein degradation
• There are two major enzyme systems
responsible for degrading damaged or
unneeded proteins:
1. the energy-dependent ubiquitin-

proteasome mechanism - mainly
degrade endogenous proteins
2. the non energy-dependent

degradative enzymes (acid hydrolases)
of the lysosomes - primarily
extracellular proteins, such as plasma
proteins, and cell-surface membrane
proteins that are used in receptor-
mediated endocytosis
LYSOSOMAL
DEGRADATION
• Extracellular, membrane-associated,
• long-lived intracellular proteins and blood
glycoproteins are degraded in lysosomes
by ATP-independent processes.
• Degradation of blood glycoproteins
follows loss of a sialic acid moiety from the
nonreducing ends of their oligosaccharide
chains.
• Asialoglycoproteins are then internalized
by liver-cell asialoglycoprotein receptors
and degraded by lysosomal proteases
• Lysosomes degrade
proteins taken up by
endocytosis, or proteins
that traffic within the
endocytic pathway
• Lysosomes contain ~50

hydrolytic enzymes
(proteases). Their pH
optimal is acidic (pH ~5)
ATP & Ubiquitin-Dependent Degradation
Degradation of regulatory
proteins with short half-lives
and
of abnormal or misfolded
proteins occurs in the cytosol,
and requires ATP and
ubiquitin.
polyubiquitinated proteins
enter into the proteasome
and degradated
Diagrammatic representataion of the life cycle of a hypothetical protein
The life cycle begins with the synthesis on a ribosome of a polypeptide chain,
whose primary structure is dictated by an mRNA
Over time, proteins get damaged by chemical attack, deamidation, or

denaturation, and may be “labeled” by the covalent attachment of several
ubiquitin molecules (Ub).
The ubiquitinated protein is subsequently degraded to its component amino acids,

which become available for the synthesis of new proteins
Ubiquitin
CONTROLLED PROTEOLYSIS
The Kiss of Death 1.Ubiquitin is a small (8.5 kDa, 76 residue)

polypeptide that targets many
intracellular proteins for degradation.
2.ubiquitin tags proteins for destruction
3.C-terminal gly attaches to the ε-amino
groups of several lys on a protein destined
for degradation
3.The proteasome digests the ubiquitin
tagged proteins.
UBIQUITIN CONJUGATION
Ubiquitin is activated and attached to proteins using a group of three enzymes
E1=Ubiquitin-Activating Enzyme
E2=Ubiquitin-Conjugating Enzyme
E3=Ubiquitin-Protein Ligase
E1 adenylates ubiquitin, and transfers it to its own cysteine

Ubiquitin is then transferred to a cysteine in E2
Finally E3 catalyzes the final transfer to a lysine residue on the target protein
CLINICAL CORRELATION:
Human papilloma virus (HPV) encodes a

protein that activates a specific E3
enzyme
The enzyme ubiquitinates the tumor
suppressor p53 and other proteins that
control DNA repair which are then
destroyed
The activation of this E3 enzyme is
observed in more than 90% of all cervical
carcinomas
The proteasome digests the ubiquitin
tagged proteins
Ubiquitin-proteasome
proteolytic pathway
PROTEIN DEGRADATION CAN REGULATE
BIOLOGICAL PROCESSES
Dynamically alter the stability of regulatory proteins

Yıldırım Beyazıt University Medical Faculty
Department of Medical Biochemistry
AMINO ACIDS
-Introduction and general properties of amino acids-
Assoc.Prof. Dr. Merve ERGİN TUNÇAY
1
CLASSIFICATION OF MACROMOLECULES
2
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES
LIPIDS
3
4
PROTEINS
5
Amino acids are building blocks of proteins
Others Enzymes
cell signaling, cell Catalyze chemical
adhesion, active reactions
transport , the cell
cycle.
Proteins Hemoglobin
Structural Carries oxygen in the
blood
Functions
Cytoskeleton, hair,
nail, skeletons,
collagen etc Immune System Muscles
Antibodies and Muscle proteins
compleman system enable all muscular
are in protein movements
structure
6
Amino Acid Structure
Side Chain
Amino Group Carboxylic Acid Group

Hydrogen
7
General Properties of Amino Acids
• Proteins contain 20 L-α-amino acids

• These 20 L-α-amino acids come together in different
compositions to form proteins
• All amino acids –except glycine- are chiral
• Amino acids differ from one another by the chemical
composition of their side chains (R groups)
8
Classification of Amino Acids
9
Glycine
H O
+ –
H3N C C O
H
H
Alanine
H O
+ –
H3N C C O
CH3
CH3
10
Amino Acids with Aliphatic Side-Chains
Glycine Alanine
Isoleucine
H CH3
CH CH3
Leucine
Valine CH2
CH2 CH3
CH
CH3 CH3 CH
CH3 CH3
11
aliphatic implies that the amino
acid side chain contains only
carbon or hydrogen atoms in an
What does Aliphatic open chain
mean???
12
Amino Acids Containing –OH Groups
Threonine Tyrosine
Serine
CH2OH CH OH CH2
CH3
Amino Acids Containing –OH
Groups are soluble in water due
to the interaction of –OH group OH
with water by forming H bonds
13
POLARITY DECREASES
Amino Acids Containing –S Groups
Cysteine Methionine
CH2SH CH2
CH2
Forms
disulphide(S-S) S
bond
CH3
14
Acidic Amino Acids and Amides Synthesized from them
Aspartic Glutamic
Asparagine Glutamine
acid acid
CH2 CH2 CH2 CH2

COO– C=O CH2
CH2
NH2 COO–
C=O
NH2
15
Basic Amino Acids
Lysine Arginine Histidine
CH2 CH2 CH2

CH2
CH2
CH2
HN NH+
CH2 NH
+H N=C Imidazole
CH2 2
NH2
NH3+
16
Aromatic Amino Acids
Tyrosine Histidine
Phenylalanine Tryptophan
CH2
CH2 CH2
CH2
HN NH+
N
H Imidazole
OH
17
•The side chain of proline and α-
amino N form a ring structure.
•It contains secondary amino

group instead of primary amino
group and called as an imino-
acid.
•This geometry is unique for

proline and it contributes to the
formation of fibrous structure of
collagen and interrupts the α-
helices found in globular proteins.
18
Amino acids
Non-
Essential
Essential
19
Essential/Non-Essential Amino acids
Obtained Synthesized
from by the
Nutrition Body
Essential
Non-Essential
Amino Acids
Amino Acids
Threonine Leucine
Tryptophan Phenylalanine Alanine Glutamine
Valine Lysine Arginine Glycine
Asparagine Proline
Arginine* Isoleucine Aspratic Acid Serine
Histidine* Methionine Cyteine Tyrosine
Glutamic Acid
20
These ................ Tryptophan
Ten ......... ……… Threonine
Valuable ............Valine
Amino Acids ……Arginine
Have ........ ……….Histidine
Long ........ ……….Lysine
I have to memorize the Preserved .........Phenylalanine
essential amino acids Life ........ …………Leucine
In ...................... Isoleucine
Man ......... ………Methionine
21
Amino acids
Hydrophobic Hydrophilic
22
Hydrophilic/Hydrophobic Amino acids
Glycine Avoid water Associate
with water Acidic Amino Ac
lanine amid
Valine (Aspartate, G
eucine Hydrophobic Asparagine, G
Hydrophilic
soleucine. Amino Acids Basic Amin
Amino Acids
Methionine ( Lysine, Arginin
Glycine Isoleucine
roline Methionine
Aspartic Acid Serine Amino acids with
Alanine Glutamic Acid Threonine (Serine, Threoni
henylalanine Valine Phenylalanine Arginine Tyrosine
Proline Histidine Asparagine Cystei
ryptophan Leucine
Tryptophan Lysine Glutamine
Cysteine
23
Q: What amino acid has the shortest side chain in its R group?
A: Glycine. It has no carbon in its R group.
H O
+ –
H3N C C O
24
Q: What structural feature is common to alanine, serine and cysteine?
A: All three have a single carbon in their R groups.
H O H H
+ + – + –
–
H3N C C O H3N C COO H3N C COO
CH3 CH2OH CH2SH
25
Q: What R group structural feature is common to phenylalanine, tyrosine,
tryptophan, and histidine?
A: All four have rings that are attached to the core with a methylene (–CH2) group
Tyrosine Histidine
CH2
CH2 CH2
CH2
HN NH+
N
H Imidazole
OH
26
AMINO ACIDS-2
-PROPERTIES OF AMINO ACIDS-
27
MODIFIED AMINO ACIDS
• There are more than 300 amino acids which have
been described in nature, however only 20 of them
are commonly found in mammalian proteins.
• These 20 amino acids are called as “standart” amino
acids which means they are coded by DNA with their
original structure.
• An amino acid can also be “modified” after
translation process (protein synthesis); and these
non-standart amino acids are called modified amino
acids. These modified amino acids are quite
important for protein functions.
28
Phosphoserine Hydroxylysine Hydroxyproline GAMA-CARBOXYGLUTAMATE
Synthesis. Addition of Synthesis. Addition of Synthesis. Addition of hydroxyl Synthesis. Addition of carboxylic acid
phosphate group to Serine hydroxyl group to Lysine group to proline group to Glutamate
Functions. component of many Functions. component of Functions. occurs in collagen and Functions. clotting factors and other
proteins, and important in collagen. other connective tissue proteins.
enzymes. proteins of the coagulation cascade. This
modification introduces an affinity for
calcium ions.
29
• Configuration of Amino acids
• Optical Properties of Amino acids
• Acid-Base Behaviour of Amino Acids
• Isoelectric Point
30
Optical Properties of Amino Acids
Chirality. “Chiros” means hand in Greek. The substances which
cannot be superimposed on their mirror image are “chiral”
Chiral means carbon atom is

attached to four different
chemical groups.
Amino Acids contain a chiral

carbon atom (except glycine).
optical activity—the ability to

rotate the plane of
polarization of plane-
polarized light
31
• Simple substances which show optical isomerism
exist as two isomers known as enantiomers.
• The magnitude and direction of the optical
rotation depend on the nature of the amino acid
side chain.
• The temperature, the wavelength of the light used
in the measurement, the ionization state of the
amino acid, and therefore the pH of the solution,
can also affect optical rotation behavior.
32
• The discoveries of optical activity and enantiomeric
structures made it important to develop suitable
nomenclature for chiral molecules.
• Two systems are in common use today: the so-called

D, L system and the (R,S) system. (R,S) system is
more complex than D, L system and for amino acids
it will be sufficient to know D,L nomenclature and
what (+)-(-) means.
33
D, L NOMENCLATURE
Absolute configurations of amino acids are
referenced to D- and L-glyceraldehyde
34
Optical Properties of Amino Acids
• It is found that all of the amino acids derived

from natural proteins are of the L configuration.
• Amino acids of the D configuration are

nonetheless found in nature, especially as
components of certain peptide antibiotics, such
as valinomycin, gramicidin, and actinomycin D,
and in the cell walls of certain microorganisms.
35
OPTICAL PROPERTIES OF AMINO ACIDS
• Some of the Protein-derived amino acids at a

given pH are dextrorotatory and others are
levorotatory, even though all of them are of the L
configuration.
• The direction of optical rotation can be specified

in the name by using a (+) for dextrorotatory
compounds and a (-) for levorotatory compounds,
as in L(+) leucine or L(-) leucine
36
ABSORBANCE OF LIGHT BY AMINO ACIDS
• Amino acids which have an aromatic ring, can absorb

light at 280 nm. This property is used during the
determination of proteins in a solution
37
38
ACID-BASE BEHAVIOR OF AMINO ACIDS
39
Properties of Glycine
• High melting point (>200 C0 )
• Strong interactions.
• Amino group takes up a H+ and has a (+)
charge, while COOH group loses a H+ and has a
(-) charge.
• This form of an amino acid is called a
Zwitterion.
• A zwitterion is a compound with no overall
electrical charge, but which contains separate
parts which are positively and negatively
charged.
40
Properties of Glycine
•The properties of glycine:
high melting point:
(when heated to 233°C it decomposes before it melts)
called a zwitterion or
dipolar ion
41
What happens to an amino acid molecule in different pHs?
l. Acidic Medium (pH<pK1)

Net charge=( +1)
Both carboxyl and amino groups are
protonated (pH < 2.34) pK1=2.34
II. Neutral Medium (pH=pI)

Net Charge=0
Amino group protonated, whereas carboxyl
group is deprotonated (pH=5.97)- Isoelectric
form
III. Basic Medium (pH>pK2)

Net Charge=( -1)
Both carboxyl and amino groups are
deprotonated (pH>9.60) pK2= 9.60
42
Definitions
• Isoelectric point (pI) is the pH at which an amino acid is
electrically neutral (the sum of positive charges is equal
to the sum of negative charges).
• pKa . Each titratable group has a pKa that is numerically

equal to the pH at which exactly one half of the protons
have been removed from that group.
• pK1 , pK2 . The pKa for the most acidic group (COOH) is
pK1 and pKa for the next most acidic group (NH3 if the
amino acid does not contain another ionizable group like
a second COOH) is pK2.
43
Titration curve of Glycine
44
CALCULATION OF ISOELECTRICAL POINT
• In an amino acid that has only two dissociable hydrogens (one for
carboxyl and one for amino group), pI is the average of pK1 and
pK2.
• For glycine
pI = pK1+pK2 = 2.34+9.60 = 5.97

2 2
45
Titration of Glutamic Acid
46
Calculation of Isoelectrical Point
acidic amino acids
• For glutamic acid as an example of acidic amino

acids, pK1 belongs to the α-COOH group, pK2
belongs to the β-COOH group and pK3 belongs
to the α-NH2 group. As you can observe from
the titration curve, the isoelectric point where
the electrical charge of the amino acid is neutral
(Glu0) is between pK1 and pK2.
pI = pK1+pK2
2
47
Titration of Lysine
48
Calculation of Isoelectrical Point
basic amino acids
• For lysine as an example of basic amino acids,

pK1 belongs to the α-COOH group, pK2 belongs
to the α-NH2 group and pK3 belongs to the β-
NH2 group. As you can observe from the
titration curve, the isoelectric point where the
electrical charge of the amino acid is neutral
(Lys0) is between pK2 and pK3.
pI = pK2+pK3
2
49
CALCULATION OF ISOELECTRICAL POINT
• pI is the average of the pKas of the acidic groups

for acidic amino acids like aspartate and
glutamate, whereas it is the average of the pKas
of the basic groups for basic amino acids like
arginine, lysine and histidine.
50
Q. What is the isoelectric point of Alanine? (pK1: 2.34,
pK2: 9.69)
A. 6.01 (pK1+pK2)/2
51
Q. What is the isoelectric point of Histidine? (pK1: 1.82,
pK2: 6.00, pK3: 9.17)
A. 7.59 (pK2+pK3)/2
52
Q. What is the isoelectric point of Aspartate? (pK1:
1.88, pK2: 3.65, pK3: 9.60)
A. 2.77 (pK1+pK2)/2
53
Q: Which amino acids absorb UV light at 280 nm.?
A: Amino acids with aromatic rings.
Tyrosine Histidine
CH2
CH2 CH2
CH2
HN NH+
N
H Imidazole
OH
54
Amino sugars
Proteoglycans
PRO F. D R . L E YL A D İ D EM KOZACI
YILD IRIM B E YA Z IT Ü N İ V E RS İTES İ
TIP FA KÜLTESİ -B İYOKİM YA A D
1
2
Glycoconjugates
- Homoglycans: composed of a single type of monomer (Starch,

cellulose and chitin)
- Heteroglycans: multiple types of monosaccharide units are joined

together
- Glycoconjugates: Polysaccharides (usually heteroglycans) are

covalently linked with other chemical species (proteins, lipids)
- Protein linked glycoconjugates can be organized into three main

types:
a. Proteoglycans (mostly carbohydrate, some protein)
b. Peptidoglycans (short peptides joined to polysaccharide chains)
c. Glycoproteins (proteins with short carbohydrate chains)
3
Proteoglycan locations
They are found in the extracellular matrix and covalently
bind to proteins such as elastin and collagen,
fibronectin, laminin in the matrix.
They exist in the form of integral membrane proteins.
•Since PGs contain sugar and sulfate units, they can attach to the cell
membrane or to areas close to the membrane.
•For example, Syndecan binds to the intracellular cytoskeleton with its
intracellular domain, while interacting with other proteins in the
extracellular matrix - fibronectin.
•Fibronectin also binds to other molecules that regulate cellular
development.
•PGs act as an adhesive that associates the intracellular and extracellular
functions of the cell.
•Many proteins bind proteoglycans via the proteoglycan-binding motif in
the form of BBXB or BBBXXB. (B, basic amino acid).
7
Glycoprotein vs Proteoglycan
Glycoproteins Proteoglycans
Proteins containing a short Proteins containing a long
carbohydrate chain carbohydrate chain
They contain one or more They contain recurrent
saccharides. disaccharide units.
Oligosaccharide units Disaccharide units
glucose, galactose, mannose, Hexosamine and uronic acid
fucose, NANA
The carbohydrate chain is bound
The carbohydrate chain is bound to the protein by O-glycosidic
to the protein by N- and O- bond.
glycosidic bonds.
9
10
11
Monosaccharides Are Joined to Molecules Through Glycosidic Bonds
CHO’s can be attached by glycosidic bonds to non-CHO structures

 like purine and pyrimidine bases (nucleic acids), aromatic rings (such
as those found in steroids and bilirubin), proteins (found in glycoproteins
and glycosaminoglycans), and lipids (found in glycolipids)
O-glycosidic bond : bond formed between
the anomeric carbon atom of a sugar and the
hydroxyl oxygen –OH atom of other molecule
(CHO, alcohol, protein, lipid …)
N-glycosidic bond: between anomeric carbon

atom of a sugar and the nitrogen atom of an
amine -NH2 group on the non-carbohydrate
molecule
12
Amino Sugars
Amino sugars are monosaccharides where one or more of the

hydroxyl groups -OH have been replaced with amino -NH2 groups
◦ Only three amino sugars are common in nature
CHO CHO CHO CHO O

H NH2 H2 N 2 H H NH2 H NHCCH3
HO H HO H HO H HO H
4
H OH H OH HO H H OH
H OH H OH H OH H OH
CH2 OH CH2 OH CH2 OH CH2 OH
D -Glu cosamine D -Mannosamine D -Galactosamine N-Acetyl-D -
glucos amin e
N-Acetyl-D-glucosamine is a derivative of D-glucosamine
13
Amino Sugars
- One simple amino sugar is a-D-glucosamine (GlcN), which

has an amino group on the C2 carbon
- The amino group is often further modified by acylation, as

seen in N-acetyl-a-D-galactosamine (GalNAc)
14
Amino Sugars (Hexosamines) are essential components of ;
Glycosaminoglycans
Glycoproteins
Glycolipids
also found in some antibiotics
The synthetic pathway of amino sugars is

very active in connective tissues, where as
much as 20% of glucose flows through this
pathway erythromycin
Several antibiotics (eg, erythromycin)

contain amino sugars, which are important for
their antibiotic activity
15
Proteoglycans (mostly carbohydrate, some protein)
Peptidoglycans (short peptides joined to polysaccharide chains)
Glycoproteins (proteins with short carbohydrate chains)
16
Extracellular Macromolecules
A major component of
connective tissue
(polysaccarides + proteins)
Glycosaminoglycans
substance
Ground
Proteoglycans
Glycoproteins
Mucins
• Amino sugars are used as components in glycosaminoglycans

• These are composed of repeating disaccharide units, often
further modified with anionic groups, to increase viscosity and
serve as lubricants
17
Extracellular Macromolecules
ground substance + fibers
macromolecule % carb.
glycosaminoglycans* (GAGs) 100
proteoglycans* 90-95
glycoproteins 2-30
fibrous proteins 1-2
Examples of functions:
mechanical support lubrication
cushioning adhesives
cell spacers selective filters
* mucopolysaccharides, mucoproteins, respectively 18

Synthesis of the amino sugars
N-Acetylglucosamine (GlcNAc) & N-acetylgalactosamine (GalNAc):
Fructose 6-phosphate is the precursor of GlcNAc, GalNAc and the
sialic acids, including N-acetylneuraminic acid (NANA, a nine-
carbon, acidic monosaccharide)
19
N-Acetylneuraminic acid (NANA): is a member of the family of sialic acids,
each of which is acylated at a different site
Before NANA can be added to a growing oligosaccharide, it must be
converted into its active form by reacting with cytidine triphosphate (CTP)
This is the only nucleotide sugar in human metabolism in which the carrier
nucleotide is a monophosphate
The carbons and nitrogens in NANA come from N-acetylmannosamine and
phosphoenolpyruvate
20
21
Glycosaminoglycans (GAGs)
exist as:
◦ independent molecules
e.g., hyaluronate & heparin
◦ parts of larger structures
e.g., in proteoglycans
The proteoglycans bind large amounts of water, producing the gel-
like matrix and fill the gaps between the fibrillar components
(collagen…) of the ECM
forms the basis of the body's ground substance
This inhibits the spread of pathogens in the ECM, for example
22
Glycosaminoglycans (GAGs)
•are large complexes of negatively charged
heteropolysaccharide chains
unbranched heteroglycans
repeating disaccharides (AB)n ABABAB… A
sugar
◦ A is usually 1 uronic acid (hexose with C6 as COO– )

(glucuronic acid or its carbon-5 epimer, L-iduronic B
sugar
acid)
◦ B is 1 amino sugar (GlcNac, or GalNac)
• Many of the amino sugars are also be esterified
with sulfuric acid (sulfated) on carbon 4 or 6 or on
a nonacetylated nitrogen also, further increasing
their polarity
23
24
25
Addition of sulfate groups to GAGs
Sulfation of the carbohydrate chain
occurs after the monosaccharide to be
sulfated has been incorporated into the
growing carbohydrate chain
The source of the sulfate is 3'-
phosphoadenosyl-5'-phosphosulfate
(PAPS, a molecule of AMP with a sulfate
group attached to the 5'-phosphate)
Sulfotransferases cause the sulfation of
the carbohydrate chain at specific sites
26
GAGs
1. Hyalurinic acid (hyaluronate)
2. Chondroitin sulfate
3. Dermatan sulfate
4. Heparan sulfate
5. Heparin
6. Keratan sulfate
27
GAG structure: repeating units
GAG A sugar B sugar
hyaluronate glucuronate N-acetyl glucosamine
chondroitin sulfate glucuronate N-Ac galactosamine 4-SO4

dermatan sulfate iduronate "
heparan sulfate glucuronate glucosamine N-SO3, 6-SO4
heparin iduronate 2-SO4 "
keratan sulfate galactose N-Ac glucosamine 6-SO4
*opposite configuration in iduronate
glucuronate/iduronate: epimers at C5 glucose/galactose: epimers at C4
28
29
30
31
32
33
Linkage region of glycosaminoglycans
34
Degradation of Glycosaminoglycans
degraded in lysosomes, which contain hydrolytic enzymes that are

most active at a pH of approximately 5
The low pH optimum is a protective mechanism that prevents the

enzymes from destroying the cell should leakage occur into the
cytosol where the pH is neutral
Relatively short half lifes: 3-10 days (hyaluronic acid, chondroitin

and dermatan sulfate, respectively)
Exception: keratan sulfate, half life more than 120 days
35
Proteoglycans (PGs)
are giant molecule complexes

consisting of CHO (95%) &
proteins (5%)
bottle brush-shaped structure
composed of as many as 200

GAG chains covalently bonded
to a core protein
= protein core + GAGs
36
37
Each
proteoglycan is
covalently linked
to hyaluronic
acid forming
huge
macromolecules
38
aggrecan, the major
Proteoglycans (PGs) proteoglycan of cartilage
macromolecules of the cell surface
or extracellular matrix, connective
tissues
These molecules are often highly
hydrated and occupy a large
volume because their
glycosaminoglycan components
contain polar and ionic groups
This hydration produces elasticity
and resistance to compression,
allowing the cartilage and joints to
absorb and recover from
mechanical shock and vibration
39
Proteoglycans (PGs)
at least 30 members of the proteoglycan superfamily in
mammalian cells
Exp:
Aggrecan (major component of cartilage)
Syndecan (act as transmembrane cell surface receptors
Perlecan (basement membrane)
Neurocan….
40
belongs to the lectican family; a chondroitin sulfate proteoglycan; protein core encoded by the ACAN gene; ACAN found on
Aggrecan chromosome 15q26.1 composed of 19 exons encoding a 2316 amino acid protein; forms a complex with hyaluronan; major
component of articular cartilage
belongs to the lectican family; a chondroitin sulfate proteoglycan; protein core encoded by the BCAN gene; predominantly
Brevican
expressed in the central nervous system; brevican protein devoid of glycosaminoglycan chains is also found within the brain
is a member of the small leucine-rich proteoglycan (SLRP) family; protein core encoded by the DCN gene on chromosome
12q21.33 spanning 38 kb composed of 8 exons; binds to type I collagen fibrils; also interacts with fibronectin,
Decorin
thrombospondin, the epidermal growth factor receptor (EGFR) and transforming growth factor-beta (TGF-β); may play a role
in epithelial/mesenchymal interactions during organ development
a keratan sulfate proteoglycan; protein core encoded by the KERA gene on chromosome 12q21.33 spanning 7.7 kb composed
Keratocan
of 3 exons; is a member of the small leucine-rich proteoglycan (SLRP) family; important to the transparency of the cornea
major keratan sulfate proteoglycan; the protein core encoded by the LUM gene found on chromosome 12q21.33 spanning 7.5
kb composed of 3 exons encoding a 338 amino acid protein; is a member of the small leucine-rich proteoglycan (SLRP) family,
Lumican also referred to as the small interstitial proteoglycan gene (SIPG) family; present in large quantities in the corneal stroma and
in interstitial collagenous matrices of the heart, aorta, skeletal muscle, skin, and intervertebral discs; interacts with collagen
fibrils; may regulate collagen fibril organization, corneal transparency, and epithelial cell migration and tissue repair
belongs to the lectican family; a chondroitin sulfate proteoglycan; a nervous system proteoglycan; protein core encoded by
the NCAN gene; NCAN found on chromosome 19p13.11 spanning 41 kb composed of 14 exons encoding a 1321 amino acid
Neurocan
protein; is a susceptibility factor for bipolar disorder, absence of the NANC gene in mice results in a variety of manic-like
behaviors which can be normalized by administration of lithium
more commonly called heparan sulfate proteoglycan of basement membrane; protein core encoded by the HSPG2 gene on
Perlecan chromosome 1p36.12; possesses angiogenic and growth-promoting properties primarily by acting as a coreceptor for
fibroblast growth factor 2 (FGF2)
a family of cell surface heparan sulfate proteoglycans (HSPGs) that act as transmembrane cell surface receptors; consists of
four members: syndecan-1, -2, -3, and -4; aberrant syndecan regulation plays a critical role postnatal tissue repair,
inflammation and tumour progression; syndecan-1 expression is prevalent in differentiating plasma cells and its expression
can serve as a marker for cells that are secreting immunoglobulin; syndecan-2 (also referred to as the original HSPG) prevalent
Syndecans on endothelial cells; strong expression of syndecan-3 found in many regions of the brain; syndecan-4 prevalently expressed in
epithelial and fibroblastic cells; protein core of syndecan-1 encoded by the SDC1 gene found on chromosome 2p24.1
encoding a 310 amino acid protein; syndecan-2 protein core encoded by the SDC2 gene on chromosome 8q22.1; protein core
of syndecan-3 encoded by the SDC3 gene on chromosome 1p35.2 encoding a 443 amino acid protein; protein core of
syndecan-4 encoded by the SDC4 gene on chromosome 20q13.12
Versican 41
Example PGs: Aggrecan
 1m 
major GAG–PG
in cartilage core protein
link proteins bind
noncovalently
with bound H2O, link proteins
disperses shocks,
hyalur-
compressive force onan
adhesion proteins link to
collagen & cells keratan chondroitin
sulfate sulfate
degraded by aggrecanase,
chondroitin sulfatase, etc
42
Example PGs: Syndecan
cell-surface PG
core protein domains GAG chains
◦ intracellular
◦ transmembrane
outside
◦ extracellular
5 GAGs attached
functions
◦ interactions
◦cell-cell inside
◦cell-matrix core
protein
◦ growth factor receptor
43
44
Functions of Proteoglycans- 1
regulate the extracellular assembly of collagen fibrils
Resist compression and retard the rapid movement of

microorganisms and metastatic cells
 Form molecular filter (in association with basal lamina) of varying

pore sizes and charge distributions that selectively screen and
retard macromolecules as they pass through them
45
Functions of Proteoglycans- 2
Contain binding sites of certain signaling molecules eg. TGF-ß so

mediate the activities of various growth factors
 influence the development of specialized tissues

• Epithelial branching and differentiation
• Eye development
• Limb development
46
Functions of proteoglycans
In the vitreous fluid of the eye,

(in maintaining the transparency of the cornea)
In the synovial fluid of the joints,
(cartilage compressor feature)
On arterial walls,
(in the protection of viscoelasticity)
In skin-tendon-like connective tissues
(ensuring tensile strength)
They act as storage sites for growth factors and
cytokines.
Proteoglycans (mostly carbohydrate, some
protein)
Glycoproteins (proteins with short carbohydrate
chains)
Peptidoglycans (short peptides joined to
polysaccharide chains)
48
Peptidoglycans
• heteroglycan chains linked to
peptides
• Major component of bacterial cell
walls
• Heteroglycan composed of
alternating N-acetylglucosamine
(GlcNAc) and N-acetylmuramic acid
(MurNAc)
• b-(1-4) linkages connect the units
• The antibiotic penicillin works by

interfering with the structure
49
Mucopolysaccharidoses
Hereditary disorders (1:25,000 births), clinically progressive
Characterized by accumulation of GAGs in various tissues
Causing varied symptoms, such as skeletal and extracellular matrix
deformities, and mental retardation
Mucopolysaccharidoses are caused by a deficiency of any one of the
lysosomal hydrolases normally involved in the degradation of
heparan sulfate and/or dermatan sulfate
This results in the presence of oligosaccharides in the urine, because
of incomplete lysosomal degradation of glycosaminoglycans
These fragments can be used to diagnose
50
Children who are homozygous for one of these diseases are
apparently normal at birth, then gradually deteriorate
In severe cases, death occurs in childhood
All of the deficiencies are autosomal and recessively inherited

except Hunter syndrome, which is X-linked
Bone marrow and cord blood transplants have been used to

treat Hunter syndrome
51
Hurler Synd
Hunter Synd
Mucopoly-saccharidoses
52
53
54
55
Biyokimya ABD
CONVERTION OF AMINO ACIDS TO

SPECIALISED PRODUCTS

Diet Protein
Tissue Protein Amino acid Pool Nonprotein Nitrogen

Compounds
transamination
Metabolic intermediates
Ketone Bodies
Acetyl CoA
Glutamate amino nitrogen
deamination
TCA
NH3
CO2
Üre
α-nitrogen atom of amino acids is a primary source for many
nitrogenous compounds
Porphyrines
Amino Acids Heme
Purines
Pyrimidines
Hormones
Neurotransmitters
Biologically active
peptides
Creatine
Histamine
Melatonine
Polyamines
Glutamine and aspartate,
are used in pyrimidine
synthesis
Glycine, glutamine and aspartate,

are used in purine synthesis
Glycine, is used in porphirine synthesis
Glutathione, is a tripeptide
composed of glutamate,
cysteine and glycine
It is responsible from
absorbtion of amino acids
Has an important role in
detoxification of free radicals
-
glutamilAminoacid
Aminoacid
5-oxoprolin
transferase
-glutamyl
Cysteinilglycine
Aminoacid Glutamate
Cystein -glutamylcystein
syntetase
Glycine
GSH -glutamylcystein
GSH
syntetase
ADP ATP
-Glutamil cycle
Creatin, is synthesized from glycine and arginine amino acids;
also takes a methyl group from S-adenosyl methionine (SAM)
Creatin, is synthesized in most
tissues and stored as creatine
phosphate. It is used for ATP
synthesis when needed.
When energy is required, creatine

phosphate will donate a phosphate
to ADP, to regenerate ATP for
muscle contraction
Creatine phosphate is an unstable compound. It spontaneously cyclizes, forming
creatinine
Creatinine cannot be further metabolized and is excreted in the urine.
Nitric oxide (NO.), is synthesized from arginine with the effect
of nitric oxide synthase (NOS)
AMINES
Amines are derivatives of aa’s ammonia,
NH3, where one or more hydrogen atoms
have been replaced by an organic (R)
group
AMINE NEUROTRANSMITTERS
-Catecholamines
(tyrosine derivatives)
•norepinephrine
•epinephrine
•Dopamine
-serotonin
(from tryptophan)
-histamine
-(from histidine)
Neurotransmitters found in the nervous
system
Neurotransmitter
a chemical bridge
between nerve cells
EXCITATORY
• Acetylcholine
• Aspartate
• Dopamine
• Histamine
• Norepinephrine
• Epinephrine
• Glutamate
• Serotonin
INHIBITORY
• GABA
• Glycine
neurotransmitters
adrenalin
noradrenalin
dopamin
TYROSINE
skin pigments
melanins thyroid hormones
T3&T4
Catecholamine Synthesis
from Amino Acids
Adrenalin (epinephrine), noradrenalin

(norepinephrine) and their intermediate product
dopamine, are known as catecholamines
Adrenalin and noradrenalin,

are hormones of adrenal
medulla
BIOLOGICALLY IMPORTANT AMINES
 Epinephrine (adrenaline) – more important as a hormone than a

neurotransmitter
 Fight-or-flight hormone, released in response from storage vesicles in

the adrenal medulla to pain, anger, or fear, exercise, cold, and low
levels of blood glucose and increases blood glucose level for energy
 Outside the nervous system, norepinephrine and its methylated

derivative, epinephrine act as regulators of carbohydrate and lipid
metabolism.
 They increase the degradation of glycogen and triacylglycerol, as well

as increase blood pressure and the output of the heart.
 These effects are part of a coordinated response to prepare the

individual for emergencies, and are often called the Fight-or-flight
reactions
Used as a drug: Adrenalin
• Treatment for cardiac arrest and anaphylactic reactions
• Bronchodilator properties used in asthma
• Agonists and antagonists to adrenergic receptors are also used as

drugs
GABA Synthesis
NH3 +
Glutamate
-
decarboxylase NH3+
O 2 CCH 2 CH 2 CHCO 2 - -
O 2 CCH 2 CH2 CH2
Glutamate Gamma-aminobutyrate
CO2 (GABA)
GABA is the major inhibitory neurotransmitter in the brain

Produced by the decarboxylation of glutamate
•Directly regulates muscle tone

•Its lack leads to convulsions, epilepsia
•Involved in mechanism of memory
Drugs (e.g., benzodiazepines) that enhance the effects of GABA are useful in
treating epilepsy
Catecholamine Degradation
•One released, catecholamines have a half-life of
ca. 1 min due to subsequent inactivation
•Epinephrine and norepinephrine are catabolized
to inactive compounds through the sequential
actions of catecholamine-O-methyltransferase
(COMT) and monoamine oxidase (MAO)
•The metabolic products of these reactions are
excreted in the urine as;
METANEPHRİNE,
NORMETANEPHRİNE,
VANILYLMANDELIC ACID (VMA)
HOMOVANILIC ACID (HVA)
Catecholamine Degradation
•Decreased levels of noradrenalin in the brain are associated

with some forms of clinical depression
•MAO inhibitors and methamphetamine block catecholamine
degradation, allowing their accumulation in the presynaptic
neuron and subsequent leakage into circulation, providing an
antidepressant action
Tyramine "cheese effect"
OH
OH
MAO
CH2 CH2 NH2 Tyramine-Rich Foods:

CH2 CHO Do They Trigger Migraines?
Tiramin
( blood pressure)
a naturally occurring monoamine compound

acts as a catecholamine releasing agent
Tyramine found naturally in several types of cheese; also beer,red wine
 Tyramine intake can cause hypertensive crisis in persons taking a MAO
inhibitor ( norepi release)
 cause uterus contractions
Parkinson Disease
 Parkinson's disease occurs due to the damage of dopaminergic

neurons
 It most commonly occurs between the ages of 55 and 65 and

leads to progressive neuropathy
 Walking, speaking, writing difficulty
 They are treated with L-dopa (levadopa)
 Psychotic symptoms in schizophrenia are

associated with dopamine levels
L-DOPA Tx in Parkinsonism
Although it is dopamine that is deficient it cannot cross the blood brain barrier
L-dopa crosses the barrier (on amino acid transporters), where it is decarboxylated
to produce dopamine
Blood Brain
L-DOPA L-DOPA Dopamine

HO
CH3 Blocks
HO CH2 -C-CO2 H
Carbidopa NHNH 2 Parkinsonism associated with

dopamine in brain through loss of
Dopamine neurons in basal ganglia
Tx: Carbidopa + L-DOPA
Blood Brain Barrier

DRUGS OF ABUSE
OTHER EXAMPLES FOR IMPORTANT AMINES
– Amphetamines – nervous system stimulants, similar in structure to

epinephrine
– Abuse of amphetamines has severe detrimental effects on the
body and the mind
IMPORTANT HARD DRUGS ARE AMINES!!!
Alkaloids – a class of nitrogen-containing organic compounds

obtained from plants
Examples include:
– Nicotine – found in tobacco
– Caffeine – found in coffee and cola drinks
– Quinine – used to treat malaria
– Opium – used to make codeine (in cough medicines), morphine (pain killer),
and heroin
adrenalin
noradrenalin
dopamin
TYROSINE
skin pigments
T3&T4
Thyroid Hormones
• Thyroid hormones are

synthesized from tyrosine
amino acid with the addition of
iodine groups
• Synthesis takes place on
thyroglobulin which is a
compound build up by a long
peptide chain with tyrosine
units and a carbohydrate unit
Hypothyroidism:
• Thyroid hormones are

synthesized from tyrosine aa
• Thyroxin levels (T4) too low;

individuals present with lethargy,
cold skin and often overweight
• low iodine in the diet often the

result of low iodine in the
soil….leads to a goiter
Cretinism
• Thyroxine (T4) is essential for

normal growth and development
• A deficiency in the fetus

(congenital hypothyroidism)will
result in cretinism, a condition
defined by mental retardation,
stunted growth
adrenalin
noradrenalin
dopamin
TYROSINE
skin pigments
T3&T4
Melanin
• Melanin is a pigment that occurs in

several tissues in the body,
particularly in the eye, hair, and
skin.
• is synthesized in the epidermis by
pigment-forming cells called
melanocytes
• function is to protect underlying
cells from the harmful effects of
sunlight
Melanin
• The first step in melanin formation

from tyrosine is a hydroxylation to
form dopa, catalyzed by the copper-
containing enzyme tyrosine
hydroxylase (tyrosinase)
• Subsequent reactions leading to the

formation of brown and black
pigments are also thought to be
catalyzed by tyrosine hydroxylase or to
occur spontaneously.
AGING WITH GRAY HAIR
Natural loss of hair color occurs as a result of aging when

melanin production shuts down in human melanocytes
located near the base of hair follicles and these defective cells
are not replaced as they normally are in younger individuals
Type 1 albinism is an autosomal recessive
genetic mutation in the tyrosinase gene
Albinism: genetic deficiency

of tyrosinase
Interestingly, individuals with

phenylketonuria can have light skin
and hair at birth because of low
levels of tyrosine
Tryptophan-Derived Neurotransmitters
Tryptophan serves as the precursor for the synthesis of

• serotonin (5-hydroxytryptamine, 5-HT)
• melatonin
Serotonin Synthesis
A derivative synthesized by the decarboxylation of
tryptophan
 two reactions:
1) Hydroxylation:
Enzyme: Tryptophan Hydroxylase, rate limiting step
Cofactor: Tetrahydrobiopterin
2) Decarboxylation:
Enzyme: hydroxytryptophan decarboxylase
Serotonin is synthesized in CNS, & enterochromaffin

cells of the GI
present at highest concentrations in platelets and in

the gastrointestinal tract, lesser in brain
Inactivated by MAO
Serotonin
• Serotonin has multiple physiologic roles,
including pain perception, affective disorders ,
regulation of sleep, temperature, and blood
pressure
• low levels of serotonin have also been linked

to depression
• SSRI Drugs (Eg.Prozac) acts to inhibit the

degradation of serotonin
• A number of psychoactive drugs (psilocybin,

amphetamine, cocaine, LSD, and Ecstacy)
modulate serotonin levels
Serotonin Metabolism: 5-HIAA
CH2 CH2NH2 CH2 CHO

HO MAO HO
N N
H H
Serotonin Dehydrogenase
CH2CO2H
Carcinoid tumors: HO
• Malignant GI tumor type
• Excretion of large amounts of 5-HIAA N
H
5-Hydroxyindole acetic
acid (5-HIAA) (Urine)
Tryptopan serves as the precursor for the synthesis
of serotonin and melatonin
• Acetylation of seratonin (serotonin N-acetylase)

• Conversion to melatonin (hydroxyindole-O-methyltransferase)
Synthesis and secretion of melatonin increases during the

dark period of the day
Serotonin Metabolism: Melatonin
CH2 CH2NH2 CH2CH2NHCOCH3

HO H3CO
2 Steps
N N
H H
Serotonin Melatonin
Melatonin:
• Formed principally in pineal gland
• Synthesis controlled by light (synthesized in dark)
•Important in circadian rhythms
•Possible use in sleep disorders
Histamine Synthesis
 secreted by mast cells
 histamine is formed by decarboxylation of histidine
 Synthesized by histidine decarboxylase, a pyridoxal-5’-
phosphate-dependent enzyme
 Histamine is an extracellular chemical messenger
mediating a range of cellular responses including
allergic and inflammatory reactions, gastric acid
secretion, and possibly neurotransmission in parts of
the brain
 At least 2 type histamine receptors: H1 and H2
•H1 blockers (Benedryl™) blocks allergic reactions,

hives and itching, and causes drowsiness
•H2 blockers (Tagamet™) blocks acid secretion from

parietal cells of stomach
POLYAMINES
 The polyamines are organic compounds
having two or more primary amino
groups - such as putrescine, cadaverine,
spermidine, and spermine - that are
essential molecules for cell growth.
 Putrescine is synthesized biologically via

two different pathways, both starting
from arginine
 Cadaverine is synthesized from lysine in a

one-step reaction with lysine
decarboxylase (LDC)
Carnosine
 Carnosine is the dipeptide of the amino acids
β-alanine and histidine
 Carnosine is highly concentrated in muscle and

brain tissues.
 Scavenger of ROS (radical oxygen species).
 Protection of the peroxidation of cell

Carnosine
 Membrane fatty acids during oxidative stress.
 Possibly improving Alzheimer´s disease through

inhibition of growing an aggregates of b-amiloid
proteins in the brain.
IMPORTANT FUNCTIONS OF
AMINO ACIDS
Glycine
• Part of various body proteins, hormones and enzymes
• An important component of collagen and elastine
• Provides C-4, C-5 and N-7 atoms of purines
• Precursor for porphirines and heme
• Involves in detoxification process
• Is used in bile acid congugation
• Is a part of glutathione
• Involves in creatin and creatin phosphate formation
Alanine
Transport of amino group from muscle to liver
Branched Chain Amino Acids
(valine, leucine, isoleucine)
Branched Chain Amino Acids are used as energy sources

especially in muscles, adipose tissue, kidney and brain
Maple Syrup Urine Disease: Autosomal ressesive

Branched-chain -ketoacid dehydrogenase complex (BCKAD)
deficiency
Elevated levels of branched-chain ketoacids, their amino acid
precursors, and alloisoleucine
Serine
• Serine, is commonly found in phosphoproteins
• Some enzymes called serine proteases include serine residues in the active
side
• Is used in phospholipid synthesis
• Begins the sphingosine synthesis with Palmitoil-CoA which then forms
sphingomyelin
Cysteine
• Is found abundantly in keratine
• Forms disulphide bridges and stabilizes the proteins
• Is a part of glutathione
• Involves in Coenzim A structure
• Taurine which is used in conjugation of bile acids is synthesized from
cysteine
Methionine
• The most important methyl donor within the organism

• The active form for methyl transfer is S-adenosylmethionine
(SAM)
• SAM gives the methyl group and forms homocysteine
high levels of homocysteine is associated
with atherosclerosis, heart disease, stroke,
and kidney disease
Homocysteine can be converted back to methionine but this
convertion is dependent on Vitamin B12 and folic acid
It can be used in cysteine synthesis and this process is dependent
on Vitamin B6
B12 and B6 vitamin

deficiencies cause
homocystein elevation
Aspartic Acid
• Gives amino group in urea and purine synthesis

• Begins the pyrimidine synthesis
Glutamate
• Takes the amino groups of the amino acids and carries to mitochondria
in the hepatocyte
• Precursor of -aminobutiric acid (GABA)
• Is a part of Glutathione (-glutamil-cysteinil-glycine)
• Is a part of folic acid (pteroilglutamic acid)
Glutamine
• Toxic ammonnia is used to

synthesize glutamine and
carried in blood in
glutamine
Gives the amine in its side chain to

purine and pyrimidine,
glucosamine and urea
Arginine
• Involves in creatin synthesis

• Is found in protamines. Sperm nucleoproteins are rich in arginine
• Nitric oxide (NO) and citrulline is synthesized from L-arginine
NO·, makes a hormone like action

using cGMP as a second
messenger. Makes vasodilation.
Lysine
Hydroxylysine in collagen is synthesized from lysine
Desmosine in elastine is
formed from four lysil
residues
Proline and hydroxyproline, are important components
of collagen
INTEGRATION OF
METABOLISM
OUTLINES
• Anabolic and catabolic reactions
• Regulatory mechanisms of metabolic
pathways
• Hormonal regulation of fasting and
absorptive phases
• Regulation of metabolism in different tissues
METABOLİSM
1. Catabolism
2. Anabolism
3. Macromoleculer
synthesis and
growth
Anabolism:
• The biosynthetic reactions Catabolism:
• The chemistry of anabolism is more
❖Foods are oxidized to CO2 and H2O
complex
• Metabolic intermediates in ❖The formation of ATP
catabolism are the precursor for ❖Reduce NADP+ to NADPH
anabolism ❖The intermediates serve as
• NADPH supplies reducing power substrates for anabolism
• ATP is the coupling energy
Interconnected
Pathways
ATP is generated by oxidation of

glucose, fatty acids, and amino
acids ; common intermediate ->
acetyl CoA ; electron carrier ->
NADH and FADH2
Regulatory mechanisms of metabolic pathways
1. Availability of substrates (min)

2. Allosteric regulation of enzymes (min)
3. Covalent modification of enzymes (min-hr)
4. Control of enzyme synthesis, primarily through
transcription (hr-days)
5. Compartmentalization
6. Specialization of organs
INTEGRATION OF METABOLISM
REGULATION OF METABOLISM
BY INSULIN
Production in beta-cells
• 1. Glucose
import
• 2. K+ channels
close
• 3. Ca+2 influx
• 4. High Ca+2
activates insulin
release
Metabolic effects of
insulin
FED STATE
FASTING STATE METABOLISM
Maintainance of Blood-Glucose
REGULATION OF METABOLISM BY
GLUCAGON
Glucagon secretion and action on cells
Glucagon action on metabolism
Glucagon effect on F2-6BP
Early Fasting State -> During the Night
Glucagon:
-> signals starved state
-> mobilizes glycogen stores (break
down)
-> inhibits glycogen synthesis
-> main target organ is liver
-> inhibits fatty acid synthesis
-> stimulates gluconeogenesis in liver
-> large amount of glucose in liver
released to blood stream -> maintain
blood-glucose level
Muscle + Liver use fatty acids as

fuel when blood-glucose level drops
21
FASTING STATE
• The usual order of preference for use of major
fuel depots is glycogen, triacylglycerol and
protein
The tissues of the body work together to maintain
energy homeostasis
• 4 Major tissues play a dominant role in
metabolism:
– Liver
– Adipose tissue
– Muscle
– Brain
Metabolic
relationships
among the major
human organs
Organs differ in the metabolic fuels they prefer as substrates
for energy production
Liver metabolism at absorptive phase
Carbohydrate metabolism of liver
Liver
It supplies the fuel to the the
brain, muscles, and other
organs.
The liver removes by insulin
independent manner about
two-thirds of the glucose
absorbed by the intestine and
converts it to glucose-6-
phosphate
1. Increased phosphorylation of
glucose
2. Increased glycogenesis
3. Increased activity of PPP
4. Increased glycolysis
Lipid metabolism in liver
In the well fed state dietary
fatty acids are converted to
triacylglycerols (fat) and
secreted into the blood as
VLDL.
In the fasted state the liver
converts fatty acids into
ketone bodies.
At feeding state;
1. Increased de-nova fatty
acid synthesis
2. Increased triacylglycerol
synthesis
Metabolism of
Aminoacids in liver
The liver removes
most of the aa
absorbed by the
intestine
The priority use is
protein synthesis
Excess amino
- the liver secretes acids are
about 30 g of urea/day deaminated and
converted into
- the a-ketoacids are common
used as fuels or for metabolic
gluconeogenesis. intermediates for
energy or fa synt
- a-ketoacids are the
major fuel for the liver
itself.
Brain
Brain has two remarkable
metabolic features
1. very high respiratory metabolism
20 % of oxygen consumed is used by
the brain at resting
2. A little glycogen reserve for

emergency
require a steady supply of glucose
from the blood.(120g-140 g/day)
• Glucose enter via GLUT1
&GLUT3)
• Generate ATP to maintain the
membrane potentials (to
power the Na+,K+-ATPase)
essential for transmission of
nerve impulses
• Fat metabolism: The brain has

no significant stores of TAG,
circulating FFA do not
efficiently cross the blood-
brain barrier
In long fasting glucose

consumption drop to 40 mg to
serve glucose for other tissues
In fasting conditions, brain
can use -hydroxybutyrate
(from fatty acids in liver),
converting it to acetyl-CoA
for the energy production
via TCA cycle
Ketone bodies such as

βOH-butyrate provide the
brain with a source of
acetyl-CoA when glucose is
unavailable
Skeletal Muscle
Muscle
• Skeletal muscles is responsible for about 30% of the O2
consumed by the human body at rest, although during
intense exercise it may use 90%
- ATP is needed for muscle contraction and relaxation
- Resting muscle uses fatty acids (predominantly), glucose
(during well-fed state), and ketone bodies for fuel and
makes ATP via oxidative phosphorylation
• Rest muscle contains about 2% glycogen and 0.08%
phosphocreatine (capable of providing enough ATP to
power about 4 seconds of exertion)
Carbohydrate metabolism in resting
muscle:
1- Increased glucose transport:
GLUT-4 of skeletal muscles cells are
insulin-sensitive.
2- Increased glycogen
synthesis:During absorptive period,
glucose is stored in the form of
glycogen in skeletal muscles
Amino acid metabolism in resting muscle:
1. Increased protein synthesis
Increase in amino acid uptake and protein synthesis
occurs in the absorptive period after ingestion of a meal
containing protein
This synthesis replaces protein degraded since the
previous meal.
2. Increased uptake of branched-chain amino acids
Muscle is the principal site for degradation of branched-
chain amino acids (leucine, isoleucine, and valine) (it
contains the required transaminase)
Muscle tissue and exercise
Glycolysis rapidly lowers pH

(lactate accumulation),
causing muscle fatigue
Sprint: (intence muscle contraction for 5-6 sec) powered
by ATP, creatine phosphate, and with more seconds,
anaerobic glycolysis of muscle glycogen -> lactate (cause a
drop in blood pH)
Medium length sprint: complete

oxidation of muscle glycogen ->
CO2 (production slower) ->
velocity lower
Marathon: complete oxid. of muscle and liver glycogen -> CO2

plus complete oxidation of fatty acids from adipose tissues ->
CO2 (ATP is generated even at slower rate)
Low blood-glucose level -> high glucagon/insulin ratio ->
mobilization of fatty acids
Cori cycle Cori cycle:
In actively contracting skeletal muscle, the
rate of glycolysis far exceeds that of the citric
acid cycle, and much of the pyruvate formed
is reduced to lactate, some of which flows to
the liver, where it is converted into glucose
Alanine cycle:
A large amount of alanine is formed in active
muscle by the transamination of pyruvate.
The glucose– alanine cycle

Muscle Protein Degradation
During fasting or excessive activity, amino
acids are degraded to pyruvate, which can
be transaminated to alanine
• Alanine circulates to liver,
where it is converted back to
pyruvate – a substrate for
gluconeogenesis
• This is a fuel of last resort for
the fasting or exhausted
organism
Heart Mucle
• The activity of heart muscle is constant and rhythmic
• The heart functions as a completely aerobic organ and is
very rich in mitochondria
• the normal fuel is fatty acids (at resting) which are
converted to acetyl-CoA and oxidized in the citric acid
cycle and ATP is produced by oxidative phosphorylation
• Continually nourished with oxygen and free fatty acid,
glucose, lactate, or ketone bodies (acetoacetate) as fuel
• heart muscle consumes acetoacetate in preference to
glucose.
• The heart contains negligible energy stores, such as
glycogen or lipid.
Adipose tissue
• people usually store enough fat to sustain energy
production for ~3 months.
• ~65% of the weight of adipose tissue is triacylglycerol
• Adipocytes have a high rate of metabolic activity -
triacylglycerol molecules turn over every few days, with
breakdown controlled largely via the activation of
hormone-sensitive lipase
Adipose tissue
1. Increased glucose transport
2. Increased glycolysis, PPP
• Increase glucose uptake by
insulin dependent GLUT-4
• Increase glycolysis serves a
synthetic function by supplying
glycerol phosphate for TAG
synthesis
• Increase HMP, NADPH
production for lipid synthesis.
• F.a synt in adipose tissue is low
in human
- normally, free fatty acids are
obtained from the liver for fat
synthesis.
- because adipocytes have low
activity for glycerol kinase they
cannot recycle the glycerol from
fat breakdown enough but must
obtain glycerol-3-phosphate by
reducing the DHAP produced by
glycolysis.
- adipocytes also need glucose to
feed the pentose phosphate
pathway for NADPH production.
Adipose Cell
Adipocytes of white and brown adipose
tissue
Brown fat
• A specialized type of adipose tissue, found in all
mammals, is abundant in newborn and
hibernating animals
• Rich in mitochondria
• Thermogenin, uncoupling protein-1, permitting
the H+ ions to reenter the mitochondria matrix
without generating ATP
• Is specialized to oxidize fatty acids for heat
production rather than ATP synthesis
Kidneys
Major function: urine production in order to excrete waste
products and maintain osmolarity.
Blood plasma is filtered about 60 times a day.
Most of the material filtered out of the blood is reabsorbed. This
reabsorption requires a lot of energy.
Kidneys are only 0.5% of body mass but consume 10% of the
oxygen.
During starvation the kidneys become an important site of
gluconeogenesis and may contribute as much as half of the blood
sugar.
• The kidney also provides
compensation for the acidosis
that accompanies the increased
production of ketone bodies
(organic acids)
• glutamine from BCAA catabolism
in muscle is used to generate
ammonia (NH3) used for the
SUMMARY
Integration of metabolism at different feeding
periods
Metabolism at well-fed period
Metabolism at fasting period
Fasting –Prolonged fasting response
Fasting: control of fuel use
short-term
• most cells mainly use fatty acids & ketone bodies
– source
lipolysis in adipocytes
stimulated by glucagon & epinephrine
• brain major exception; requires glucose
– sources
liver glycogen (~60 g/day)
protein (~75 g/day)
stimulated by glucagon (liver) & cortisol (muscle)
8
fasting or uncontrolled diabetes
Fuel sources in prolonged fasting
• After many days, brain adapts to using
ketone bodies
eventually supply ~½ brain's energy needs
result: protein
consumption decreases
from ~75 g/day to
~20 g/day
Prolonged fasting metabolism
4-5 days later

starvation starts
Adipose tissue
has significant
role in this
period
Prolonged Starvation
First priority -> provide sufficient glucose to brain and other tissues that
are dependent on it
Second priority -> preserve protein -> shift from utilization of glucose to
utilization of fatty acids + ketone bodies
-> mobilization of TAG in adipose tissues + gluconeogenesis by liver -> muscle
shift from glucose to fatty acids as fuel
After 3 days of starvation -> liver forms large amounts of ketone bodies
(shortage of oxaloacetate) -> released into blood -> brain and heart start to
use ketone bodies as fuel
After several weeks of starvation -> ketone bodies major fuel of brain
After depletion of TAG stores -> proteins degradation accelerates -> death
due to loss of heart, liver, and kidney function
61
-Protein and amino acids
Assoc. Prof. Dr. Merve Ergin Tunçay
Ankara Yıldırım Beyazıt University Faculty of Medicine
Department of Biochemistry
• A nutrient is a substance used by an organism to survive,
grow, and reproduce.
• Nutrients are broadly classified as
• Macronutrients
― carbohydrates,
― proteins, and
― lipids;
• Micronutrients
― minerals (e.g., sodium and chloride), trace minerals (e.g., iodine
and copper),
― vitamins (e.g., carotenoids and sterols), and
― organic acids (e.g., citric acid).
• Essential nutrients are defined as those that cannot be
synthesized, or are inadequately synthesized de novo by
animals to meet their physiological demands
– some amino acids (e.g., leucine and valine) and
– fatty acids (e.g., polyunsaturated fatty acids [PUFAs])
Macronutrients
Proteins
• Protein is the basic structural material of all cells.
• Biologically active proteins include enzymes,
immunoglobulins, hormones,
neurotransmitters, nutrient transport and
storage compounds, and cell membrane
receptors.
• Involved in the maintenance of osmotic pressure,
clotting of blood, muscle contraction.
Proteins as Energy Source
• Body proteins is not a preferred energy source.
• During starvation, proteins (amino acids) serve
as the major suppliers of energy.
Proteins
• Food Sources:
– Meat, fish, eggs, poultry, dairy products,
legumes, nuts and seeds. (Breads, cereals and vegetables also contain
small amounts of protein.)
• Function in the Body:
– Provides energy.
– Help to build, maintain, and repair body tissues.
• Proteins are made up of chemical compounds called amino
acids. There are 20 amino acids.
6
Digestion and absorption
• Through the process of digestion, animals break down ingested protein into free amino
acids that can be used for protein synthesis.
• The digestion of protein begins in the stomach by the action of the enzyme pepsin.
• Pepsin is particularly effective in the highly acid stomach medium (hydrochloric acid) in
breaking down the collagenous connective tissue fibers in meat.
• The hydrochloric acid:
– activates pepsin,
– helps to keep stomach free from bacteria,
– improves absorption of the mineral iron and calcium,
– inactivates plant and animal hormones.
• Stomach enzymes and acids attack the long, complex protein. They are degraded to smaler
units called polypeptides and peptides.
• The peptide fragments are dismantled in the small intestine by alkaline enzymes released
from the pancreas.
• The smaller protein fragments are then absorbed and transported to the liver for further
assimilation.
• When amino acids reach the liver, one of three things
happens. They are:
1. converted to glucose,
2. converted to fats, or
3. released directly into bloodstream as plasma protein such as
albumin, or as free amino acids to serve the anabolic
requirements of various tissues.
• Dietary protein consumed in excess of requirements is not
stored, but is deaminated, or its storage as glycogen or fat,
depending upon the specific amino acid and the energy
balance at the time. The nitrogen waste generated is excreted
in the urine as either urea or ammonia.
• High protein intakes can increase urinary calcium excretion.
Amino Acids
Of the 20 amino acids, the human body is capable of producing 11 of them.
The other 9 called, “Essential Amino Acids” must be supplied by food sources.
• Two types of Protein:

– Complete Proteins:
• Contain all 9 essential amino acids.
• They are found in animal sources.
– Incomplete Proteins:
• Lack one or more of the essential amino acids.
• They are found in plant sources.
The best way to give the body complete proteins is to eat a wide variety of foods throughout the day.
9
Classification of Amino Acids
Essential Amino Acids Nonessential Amino Acids
Isoleucine Alanine
Leucine Arginine*
Valine Aspartic acid
Lysine Cysteine*
Methionine Cystine
Phenylalanine Glutamic acid
Threonine Glutamine*
Tryptophan Glycine
Proline
Serine
Tyrosine
*These amino acids, along with taurine, may be considered conditionally
essential in that their requirements are increased during periods of catabolic
stress.
• Amino acids are joined together by peptide bonds,
– the joining of two amino acids produces a dipeptide (three a tripeptide)
– configuration of up to as many as 11-100 amino acids is known as a
polypeptide
– more than 100 amino acids produces proteins
The condensation of two amino acids to form a peptide bond:

• Proteins differ chemically from carbohydrates and lipids in
that they contain nitrogen in addition to other elements
such a sulfur, phosphorus, and iron.
• Many proteins are enzymes that catalyze biochemical reactions, and are
vital to metabolism.
• Biological value of a dietary protein is determined by the amount and
proportion of essential amino acids it provides.
• If any one of the essential amino acids is not available in sufficient
amounts or is present in excessive amounts relative to other essential
amino acids, protein synthesis will not be supported!
• Animal proteins, found in such food as eggs, milk, meat, fish, and poultry,
are considered complete proteins because they contain all of the
essential amino acids our bodies need.
• Plant proteins, found in vegetables, grains, and beans, lack one or more of
the essential amino acids.
• Egg protein has been found to have the highest known biological value of
any protein in humans.
Evaluation of proteins
The parameters used for net protein
evaluation are:
– Biological value
– Digestibility coefficient
– Protein efficiency ratio
– Net protein utilization (NPU)
14
• Protein from animal sources (meat, fish, dairy products, egg
white) is considered high biological value protein or a
"complete" protein because all essential amino acids are present
in these proteins.
• Plant sources of protein (grains, legumes, nuts, and seeds)
generally do not contain sufficient amounts of one or more of
the essential amino acids.
• Plants that are entirely lacking in essential amino acids are
considered incomplete proteins or sources of low biological
value protein.
The recommended dietary/daily
allowances (RDA) for protein
• The recommended dietary/daily allowances (RDA) represents
the quantities of the nutrients to be provided in the diet daily
for maintaining good health & physical efficiency of the body.
• Sex:
– The RDA for men is about 20% higher than that of women.
– Additional requirements (20-30% above normal) are needed for
pregnant & lactating women.
• Age:
– In general, the nutrient requirement is much higher in the growing
age.
– For instance, the protein requirement for a growing child is about 2
g/kg body wt/day compared to 1 g/kg body wt/day for adults.
The Recommended Dietary Allowance
• The RDA of protein intake for adults is 0.8-1 g per kilogram of

body mass.
• The protein requirements tends to decrease somewhat with
age;
• conversely, stress, disease, injury, and prolonged heat
exposure increase the protein requirement
Vegetarian approach
• Grains and legumes are excellent proteins sources, but neither
provides the full complement of essential amino acids (AA).
• Grains lack the essential AA lysine, while legumes contain lysine
but lack of the sulfur-containing essential AA methionine for
which grains are rich sources.
• However, because large quantities of those foods must be eaten
to obtain the requirement quantity of essential AA, most
people eat some animal food.
• Evidence from a few large cohort studies suggests that
vegetarians have lower overall mortality ratios than the
general population, but this is not the case when vegetarians
are compared with similar non-vegetarian groups who follow
a health-conscious lifestyle.
• Vegetarianism has been associated with a reduction in several

of the established risk factors for coronary heart disease
(CHD), including more favourable blood lipid profile, lower
body mass index and lower blood pressure.
There are four major types of lifestyles and eating habits that vegetarians may include in a diet:
Type Prohibited Foods Typical Health Practices

Lacto vegetarian Meat, fish, poultry, These will include dairy products as part of their
eggs meals. Some use vitamin and mineral
products; others do not.
Lacto-ovo- Meat, fish, poultry This is the major form of vegetarian lifestyle that
vegetarian many take part in. These include eggs as well
as dairy products. More likely than omnivores
to be physically active and not smoke or
use alcohol.
Semivegetarian Meat, but may Links to conventional health care system tend to be
include small stronger than those of vegans.
amounts of fish
and poultry in
the diet
Vegan Meat, fish, poultry,
eggs, dairy, Vegans tend to be physically active, avoid drugs
honey and tobacco products, and rely on
unconventional rather than conventional health
care.
Possible benefits of vegetarian eating:
Characteristic Comments/Possible Mechanisms
Leanness Vegetarians tend to be more physically active than nonvegetarians.
Higher intakes of dietary fiber may decrease absorption of food by
2-3 % and contribute to a feeling of fullness.
Lower blood Vegans, who consume a diet very low in fat, tend to have blood
pressure pressures 10 to15 mm Hg lower than nonvegetarians of similar age
and gender. Much of this effect appears to be related to body weight
rather than other dietary variables.
Lower serum Total blood cholesterol levels are lower in vegans than in lactovegetarians
cholesterol or nonvegetarians. Whole-fat milk products and eggs tend to raise
serum blood lipids due to their saturated fat and cholesterol content.
Vegetarians often use non- or lowfat milk, and vegans use no milk or
eggs at all
Less colon Diets high in meat may increase the incidence of colon cancer by
cancer increasing the fecal concentration of various carcinogens. A high
intake of animal fat also may increase the risk of colon cancer. It is
also possible that carcinogens are produced by cooking meat at very
high temperatures.
Possible risks of vegetarian eating:
The major source that may be lacking in this type of lifestyle is protein. Because of this, it is
important to make sure that protein is eaten through grains, beans, tofu, nuts, eggs or peas.
The second nutrient that is needed in a vegetarian diet is calcium. If you eat dairy, this will be
easier to consume. However, if not, calcium is found in darker greens. Vitamin D, Iron and
Vitamin B 12 are the other three nutrients that may be lacking in this diet.
Risk Comments
Osteoporosis There is little evidence that a vegetarian diet causes
osteoporosis.
Iron-deficiency Low serum ferritin levels (a sensitive measure of iron storage
anemia status) were found in 5% of male and 27% of female lacto-
ovo-vegetarians
Anemia Signs of vitamin B12 deficiency have been observed in some

breast-fed infants of women who are strict vegetarians.
Slowed growth Excessive leanness and/or slow growth are have been noted
among vegan and vegetarian infants.
Meat in the Diet
• Meat makes an important contribution to intake of a number of nutrients, in

particular micronutrients such as iron and zinc.
• Iron deficiency anaemia is one of the most common nutritional deficiencies in
the westernized society, particularly in young children and women of
childbearing age.
• If meat is eliminated from the diet, a small increase in oil-rich fish such as
mackerel, salmon, sardines or trout, would compensate for any deficit in
intake of long chain fatty acids and vitamins D and B12.
• Care should be taken, however, to ensure adequate intakes of iron and
zinc. Inclusion of legumes, nuts and fortified cereals will help contribute to
intake of these minerals for those who choose to avoid animal products.
Meat, poultry and fish are rich sources of high biological value protein.
Plant sources of protein (legumes, nuts, and seeds) contribute additional amounts of protein.
• Biological value measures protein quality by calculating the
nitrogen used for tissue formation divided by the nitrogen
absorbed from food. This product is multiplied by 100 and
expressed as a percentage of nitrogen utilized. The
biological value provides a measurement of how efficient
the body utilizes protein consumed in the diet. A food with
a high value correlates to a high supply of the essential
amino acids.
• Animal sources typically possess a higher biological value
than vegetable sources due to the vegetable source’s lack
of one or more of the essential amino acids.
• Experts recommend that protein intake make up only 10-20
% of our daily calorie intake.
Protein Balance
• Protein intake is usually about 15% of dietary energy and
the protein in the body represent about one-third of the
total stored energy in a 70 kg man.
• The daily protein intake amounts to a little over 1% of the
total protein stores.
• The protein stores increase in size only in response to
growth stimuli, such as growth hormone, androgens,
physical training and weight gain, but not simply from
increased dietary protein.
• Protein stores are, therefore, tightly controlled and, on a
day-to-day basis, protein balance is achieved.
The mass of nutrients given in the figure is the amount consumed in a 24 hour period.
Starvation
• During prolonged starvation, the primary source of glucose
is gluconeogenesis from amino acids arising from muscle
proteolysis. To spare glucose use (and thus spare
muscle protein) most tissues of the body utilise fat‐derived
fuels (fatty acid and ketone bodies).
• Urea concentrations decrease with increased starvation:
• Muscle protein breakdown is ‘spared’ as tissues use ketone
bodies & fatty acids instead of glucose
• Death by starvation: when loss of ~ 40% body weight (30-
50% body protein, 70 to 98% fat stores)
• ~ BMI 13 men, 11 women
Assessment of Protein nutrition status
• Protein nutrition status is measured by
Serum Albumin Concentration.
– It should be more than 3.5 g/dl.
– Less than 3.5 g/dl shows mild malnutrition.
– Less than 3.0 g/dl shows severe malnutrition.

31
The "nitrogen or amino acid pool" is a grand mixture of amino acids available in
the cell derived from dietary sources or the degradation of protein. Since proteins
and amino acids are not stored in the body, there is a constant turnover of
protein.
NITROGEN EXCRETION
• Amino acid breakdown yields an amino
group (containing nitrogen)
• This molecule is unstable and is
converted to ammonia
• Ammonia is toxic, so it is excreted from
the cells and sent to the liver, where it is
converted to urea and water
• The urea is transported to the kidney,
where it is filtered from the blood and
finally sent to the bladder for excretion
in the urine
• Nitrogen is also lost through hair, skin,
GI cells mucus, nails, and body fluids
like sweat.
Positive nitrogen balance:
• This is a state in which the nitrogen intake is
higher than the output.
• Some amount of nitrogen is retained in the
body causing a net increase in body protein.
• Positive nitrogen balance is observed in
growing children, pregnant women or during
recovery after serious illness.
Negative nitrogen balance:
• In this, the nitrogen output is higher than the input.
• Some amount of nitrogen is lost from the body depleting the body
protein.
• Prolonged negative nitrogen balance may even lead to death.
• Observed in children suffering from kwashiorkor or marasmus.
• Negative nitrogen balance may occur due to inadequate dietary
intake of protein (deficiency of a single essential amino acid) or
destruction of tissues or serious illness.
• Growth hormone & insulin promote positive nitrogen balance while
corticosteroids result in negative nitrogen balance.
• Cancer & uncontrolled diabetes cause negative nitrogen balance.
The requirement of protein
• The requirement of protein is dependent on its nutritive value,
caloric intake & physiological states (growth, pregnancy lactation)
of individual.
• For an adult, 0.8-1.0 g protein/kg body weight/day is adequate.
• The requirement is nearly double for growing children, pregnant
& lactating women.
• The protein content of foods is variable, Cereals have 6-12%;
pulses 18-22%; meat 18-25%, egg 10-14%; milk 3-4% and leafy
vegetables 1-2%.
• In general, the animal proteins are superior than vegetable
proteins as the dietary source.
Protein-energy malnutrition (PEM)
• Protein-energy malnutrition (PEM)-sometimes called
protein-calorie malnutrition (PCM)- is the most common
nutritional disorder of the developing countries.
• It is prevalent in infants & pre-school children.
• Kwashiorkor & marasmus are the two extreme forms of
protein-energy malnutrition
• The majority of world’s children live in developing countries
• Lack of food & clean water, poor sanitation, infection &
social unrest lead to PEM.
CLASSIFICATION
– A. CLINICAL
– Parameter: weight for age +
oedema
– Reference standard (50th
percentile)
– Grades:
• 80-60 % without oedema is under
weight
• 80-60% with oedema is Kwashiorkor
• < 60 % with oedema is Marasmus-
Kwash
• < 60 % without oedema is
Marasmus
Protein Diets
• Over the past few years high protein diets have become a method used by the general
population to enhance weight reduction.
• A popular premise of high-protein diets is that excess carbohydrate results in elevated
insulin levels, which in turn promotes storage of body fat and other metabolic
consequences.
• To induce weight loss, the high ratio of protein and fat to carbohydrate purportedly
promotes metabolic changes that reduce serum insulin levels. However, in fact, protein
intake also stimulates insulin secretion.
Protein Intake and Metabolic Disease Risk
• In 2001, the American Heart
Association published a
statement on dietary protein
and weight reduction and
suggested that individuals
following such a diet may be
at potential risk for
metabolic, cardiac, renal,
bone and liver diseases.
• High-protein diets may also
be associated with increased
risk for coronary heart
disease due to intakes of
saturated fat, cholesterol,
and other associated dietary
factors.
One of the major concerns for individuals on high protein, low carbohydrate diets is the
potential for the development of metabolic ketosis.
As carbohydrate stores are reduced the body relies more upon fat as its primary energy
source.
The greater amount of free fatty acids that are utilized by the liver for energy will result in
a greater production and release of ketone bodies in the circulation.
A recent multi-site clinical study (Foster et al., 2003) examined the effects of low-
carbohydrate, high protein diets and reported significant elevation in ketone bodies
during the first three months of the study. However, as the study duration continued the
percentage of subjects with positive urinary ketone concentrations became reduced, and
by six months urinary ketones were not present in any of the subjects.
• One of the major concerns for individuals on high protein, low carbohydrate
diets is the potential for the development of metabolic ketosis.
• As carbohydrate stores are reduced the body relies more upon fat as its
primary energy source.
• The greater amount of free fatty acids that are utilized by the liver for
energy will result in a greater production and release of ketone bodies in the
circulation.
• It does appear that protein from animal
sources is an important source of protein for
humans from infancy until mature adulthood.
• With a proper combination of sources,

vegetable proteins may provide similar
benefits as protein from animal sources.
Thank you...
PLASMA PROTEINS
Outlines
• Functions and characteristics of plasma proteins
• Types of plasma proteins
• Detection of plasma proteins (Electrophoresis)
• Acute phase proteins

The human body is made up of water, protein, fat, minerals,
carbohydrates, and other substances.
Over half the body consists of water.

• Plasma contains >300 different proteins
PLASMA PROTEİNS
• Total protein content of normal plasma is 6 to 8 g/dl

(~7g/dl, which in total makes 7% of total blood
volume)
• The plasma proteins consist of:

 Albumin (3.5 - 5 g/dl)
 Globulins (2.5 – 3.5 g/dl)
 Fibrinogen (200 – 400 mg/dl)
• The albumin : globulin ratio is usually between

1.2:1.0 to 1.5:1.0 (T.prot –Alb = Globulin)
General characteristics of plasma proteins
• All the plasma proteins are synthesized in liver except

immunglobulins which are synthesized by plasma cells
• Synthesized in ribosomes on GER as pre-proteins
• Almost all the plasma proteins are glycoproteins(also

some simple proteins, conjugated proteins like lipoproteins)
• Some of the plasma proteins exhibit polymorphism(exist in

different phenotypes)(e.g α1 antitrypsin, transferrin and
haptoglobulin, ceruloplasmin, VitDBP, Ig..)
• Each plasma protein has a characteristic half life

Functions of plasma proteins
1. Coagulation of blood – Fibrinogen to fibrin
2. Defense mechanism of blood – Immunoglobulins, complement
3. Transport mechanism (transport hormones, gases, drugs, metals,

lipids,vit., metabolites etc)– Albumin, Ceruloplasmin, Haptoglobin,
Retinol Binding Protein, Sex Hormone Binding Globulin, Thyroid
Hormone Binding Protein, Transferrin
4. Maintenance of osmotic pressure in blood (albumin)
5. Acid-base balance (buffering)
6. Provides viscosity to blood (thickness of bld- esp large size &

asymmetry of globulins)
7. Reserve proteins: source of aa for tissues in starvation

The relative dimensions
and molecular masses of
some of the most important
plasma proteins
• Plasma proteins can be grouped according to
specific functions
 transport proteins
 proteins of immune system
 system of proteases and antiproteases
 proteins of hemocoagulation system
 signal proteins
 enzymes, hormones
 cellular proteins
Seperation techniques of plasma proteins
• Precipitation by salts
• Sedimentation by ultracentrifugation
• Chromatography
• Electrophoresis (a screening test)
– •Identify
abnormalities in immunoglobulin fraction by
serum immunofixation
– •Follow specific protein abnormalities by quantitative

analysis of the protein by immunoassay
ANALYTICAL APPROACH
• In clinical laboratory most common method for

seperation of serum proteins; electrophoresis
• Electrophoresis: the movement of charged

particles through an electrolyte when subjected
to an electric field
Electrophoresis/instrumentation
• Apparatus: tank and its parts (electrodes, buffer

reservoirs, support medium area..)
• Power suply: constant-current supply
• Buffer: Carry applied current, fix PH, determine
electrical charge…
• Support medium: cellulose acetate, agorose
gel, polyacrylamide gel…
Agorose gel is most common used: large pore size allows Ag and Ab
migration through the gel
Buffer Solution
Proteins are amphoteric, they will carry negative charges in alkaline

medium.
Using a pipette, samples are loaded into the wells of the gel.
A gel box is a buffer-filled container configured with a cathode at one end, an

anode at the opposite end.
External power source is turned on, an electrical field is applied to the buffer
causing charged molecules to move through the gel towards the opposite terminal
The rate of protein migration depends on:
a) the amount of charges carried by each protein.
The positively charged particles (cations) move to
cathode and negatively charged ones (anions) to anode
b)The molecular weight and size of proteins

Smaller molecules will migrate through the gel matrix
faster than larger ones
http://www.sebia-usa.com/products/reagents.html (Feb 2007)
Classification of plasma proteins
• by electrophoretic
mobility
 prealbumins
 albumin
 alpha, beta and
gama-globulins
 fibrinogen
Albumin has the maximum and gamma

globulin has the minimum mobility in
the electrical field
Normal Pattern of Plasma Protein Electrophoresis
Principal proteins of each fraction
2-macroglobulin immunoglobulins:
IgG, IgA, IgM
haptoglobin
1-antitrypsin transferrin
orosomucoid C3-complement
Electrophoresis is used to study protein
abnormalities
• Serum protein electrophoresis: a screening test which

can be followed by quantitative assay of specific
proteins; independent measurement of total protein is
required for conversion to absolute amounts
Prealbumin (Transthyretin)
(Thyroxin binding pre-albumin)
• Migrates faster than albumin in electrophoresis

• Separated by immunoelectrophoresis
• A transport protein for thyroid hormones
• Makes a complex with retinol (vitA) binding protein, together carry VitA
• It can bind loosely with all substances which are carried by albumin
• Useful indicator for protein-malnutrition
• Lower levels found in:
– liver disease, nephrotic syndrome, acute phase inflammatory response,
malnutrition
• Normal range: 20-40 mg/dl
• Short half-life (2 days)

Albumin (69 kDa)
• Most abundant plasma protein (~4 g/dL) in normal adult
• Constitutes about 60% of plasma proteins
• Synthesized in the liver as preproalbumin and secreted as

albumin
• Half-life in plasma: 20 days
• Decreases rapidly in liver injury, infection and surgery
• therapeutically useful to treat burns, hemorrhage and shock

Functions of Albumin
• 1. Maintains oncotic pressure:
– The osmotic pressure exerted by
plasma proteins that pulls water
into the circulatory system
– Maintains fluid distribution in and
outside cells and plasma volume
– Edema may occur when plasma
Albumin level falls very low
• 80% of plasma oncotic pressure is

maintained by albumin
• Hypoalbuminemia = Edema
• 2. Buffering function
Functions of Albumin
• 3. major transport of various hydrophobic substances

in plasma
• A non-specific carrier of
– Bilirubin, steroid hormones, free fatty acids, drugs,
metals-zinc, calcium,copper, heavy metals etc.
• 4. Nutritional function for cells

• Tissue cells can take up albumin by pinocytosis where it
is hydrolyzed to amino acids
• So albumin may be considered as the transport form of
essential amino acids from liver to extrahepatic cells
Abnormal albumin levels:
Hypoalbuminemia:
1. Decreased synthesis:
• May be due to malnutrition or malabsorption
• May be a feature of advanced liver disease
2. Abnormal distribution or dilution:

• May be induced by overhydration
• May be caused by increased capillary permeability as
occurs in septicemia (escape of alb)
3. Abnormal excretion or degradation:

• • May be causes by: Nephritic Syndrome, Protein losing
Enteropathies, Burns, Hemorrhage, Catabolic states
Hypoalbuminemia
Effects
• Edema due to low oncotic pressure
– Albumin level drops in liver disease causing low oncotic
pressure
– Fluid moves into the interstitial spaces causing edema
• Reduced transport of drugs and other substances in

plasma
• Reduced protein-bound calcium

– Total plasma calcium level drops
– In hypoalbuminemia, there will be a compensatory

increase in globulins which are synthesized by the
reticuloendothelial system
Abnormal albumin levels:
Hyperalbuminemia
• No clinical conditions are known that cause
the liver to produce large amounts of
albumin
• The only cause of hyperalbuminemia is

dehydration
GLOBULINS
1 antitripsin
1 acid
1 glycoprotein
(orosomucoid)
1 lipoprotein
(HDL)
1 fetoprotein
1-Antitrypsin (AAT-protease inhibitor )
• Makes 90% of 1 band in electrophoresis
• Synthesized by the liver and macrophages (over 30 types are known)
• An acute-phase protein that inhibits serine proteases such as

plasmin, thrombin, trypsin, chymotrypsin, elastase
• about 95% of the anti-protease activity in plasma is due to AAT
• Proteases are produced endogenously and from leukocytes and

bacteria
– Digestive enzymes (trypsin, chymotrypsin)
– Other proteases (elastase, thrombin)
• Infection leads to protease release from bacteria and from leukocytes

Genetic deficiency of 1-Antitrypsin
Smoking significantly decreases AAT !!!!!!!

Genetic deficiency of 1-
Antitrypsin
Laboratory Diagnosis
1. Lack of 1-globulin
band in protein
electrophoresis
2. Quantitative
measurement of 1-
Antitrypsin
GLOBULINS
1 antitripsin
1 acid
1 glycoprotein
(orosomucoid)
1 lipoprotein
(HDL)
1
fetoprotein
-Fetoprotein (AFP)
• Synthesized in the developing embryo in yolk sac and by

the fetal liver
• AFP levels decrease gradually during intra-uterine life
and reach adult levels at 1st year
• Function is unknown but it may function as
immunregulator
-Fetoprotein (AFP)
• Elevated
maternal AFP
levels are
associated with:
– Fetal defects,
Neural tube
defect,
anencephaly
• Decreased
maternal AFP
levels are İncreased AFP is a tumor marker for:
associated with: Hepatoma and cancer in testes,
– Increased risk of ovaries, stomach, pancreas, biliary
Down’s syndrome
tract
GLOBULINS
1 antitripsin
1 acid
1 glycoprotein-
orosomucoid
1 lipoprotein
(HDL)
1 fetoprotein
1 acid glycoprotein AAG-
(orosomucoid)
• synthesized primarily in hepatocytes
• A glycoprotein with high carbohydrate content
• act as a carrier of basic and neutrally charged

lipophilic compounds (esp basic drugs-positively
charged)
• A positive acute phase protein

GLOBULINS
Haptoglobin
2 2 macroglobulin
Ceruloplasmin
Ceruloplasmin
• Synthesized by the liver
• Contains 6 to 8 copper atoms per molecule (>90% of

serum copper, 10% binds albumin)
• An oxidoreductase enzyme that inactivates ROS
causing tissue damage in acute phase response
• Important for iron absorption from the intestine
• Also called as Ferroxidase, an enzyme which helps in
the incorporation of iron into transferrin (oxidation of Fe2+
(ferrous iron) into Fe3+ (ferric iron)
Ceruloplasmin (Alpha 2 globulins)
• To be absorbed iron
should be in the ferrous
form (Fe+2)
• Ferroportin: iron
exporter
• Hephaestin: like
cerulolplasmin
a ferroxidase that can
oxidize Fe2+ to Fe3+
Cu Transporter
protein genetically
• Wilson’s disease: affected
– A protein that links copper to ceruloplasmin is inheritedly

affected
– Copper is accumulated in the liver and brain
– low plasma levels of copper and ceruloplasmin
GLOBULINS
Haptoglobin
Ceruloplasmin
Haptoglobin
• Alpha 2 globulin
• Synthesized by the liver
Binds to free hemoglobin to form complexes that are

metabolized in the RES
Limits iron losses by preventing Hb loss from kidneys
Plasma free haptoglobin level decreases during hemolysis, so

used to screen for intravascular hemolytic anemia
GLOBULINS
Haptoglobin
Ceruloplasmin
2-macroglobulin
• largest major nonimmunoglobulin protein in

plasma
• acts as an antiprotease (functions as an

inhibitor of coagulation, fibrinolysis)
• Also act as a carrier protein because it also

binds to numerous growth factors and cytokines
• Carry zinc %10 (%90 carried by albumin)

Transferrin
Hemopexin
1
-lipoprotein
(apoprotein B)
C4
Transferrin
 A major iron-transport protein in plasma

 30% saturated with iron
 Protects the body against the toxic effects of free iron
 Tf delivers iron to cells using an endocytotic pathway

involving the transferrin receptor (TfR)

Transferrin
• Plasma level drops in:

– Malnutrition, liver disease, inflammation,
malignancy
• Iron deficiency results in increased hepatic synthesis
• A negative acute phase protein

Fibrinogen (between
 and  bands)
C3
2
2 microglobulin
2–Microglobulin
• A component of human leukocyte antigen (HLA)
• Present on the surface of lymphocytes and most

nucleated cells
• Filtered by the renal glomeruli due to its small size (11.800 dalton)
but most (>99%) is reabsorbed
• High urine levels: renal tubular diseases

• Elevated serum levels are found in malignancies, especially hematologic
malignancies and several benign conditions such as chronic inflammation,
liver disease, renal dysfunction, some acute viral infections
– May be a tumor marker for: Leukemia, lymphomas, multiple myeloma
(increased cell turnover)
CRP
IgG
IgA
IgM
C-Reactive Protein (CRP)
• Synthesized by the liver, most sensitive acute phase
reactant
• Important for phagocytosis, activates complement
• High plasma levels are found in many inflammatory

conditions such as rheumatoid arthritis
• can be used to follow progression of disease
• “high sensitivity” CRP is used as a prognostic indicator

of future adverse cardiac events
Immunoglobulins
• Immunoglobulins are a group of structurally related
proteins that function as Antibodies
• Y-shaped protein produced mainly by plasma cells ( B-

lymphocytes) that is used by the immune system to
identify and neutralize pathogens such as bacteria and
viruses
• Contains light and heavy chains

Polyclonal gammopathy
• Inflammation, infection or antigenic stimulation of any
cause (e.g. chronic liver, respiratory , gastrointestinal, or
dermatologic disease) can induce the secretion of mixed
immunoglobulins.
If more than one type Ig

synthesis is increased,
found as “polyclonal
band ” where stimulation
of many clones of B cells
produce a wide range of
antibodies
Immunoglobulins migrate in
the γ and β regions
Monoclonal gammopathy
• Immunoglobulins produced by a single clone of B
lymphocytes or plasma cells typically forms a tall narrow peak
in the β- to γ-region (depending on the involved Ig). This is
called a monoclonal gammopathy.
•
A monoclonal gammopathy
is usually due to :
Immunoglobulin-secreting
B-cell neoplasms, e.g.
chronic lymphocytic
leukemia or lymphoma of B
cells.
Plasma cell tumors, e.g.

multiple myeloma.
If increase biosynthesis of one
type Ig, on electrophoresis it is
observed as a single discrete
band “Monoclonal band
Monoclonal
Gammopathy
If additional study with immunofixation

were performed, with antibodies to
specific immunoglobulins, the the
abnormal globulin could be further
characterized, as follows (in this
example IgG, kappa):
Bence-Jones Protein
• When increased in amount, because of small

size light chains pass to the urine
• Monoclonal free light chains in the urine are

called Bence Jones proteins (22-24 kDa)
•
Acute phase proteins
• The varied reactions of the host to infection, inflammation,
or trauma are collectively known as the acute-phase
response (APR)
• Acute Phase Protein response leads to greatly increased

biosynthesis (mainly in Liver) of some plasma proteins
along with decrease in levels of other proteins in plasma
•Acute-phase proteins are a class of proteins

whose plasma concentrations increase
(positive acute-phase proteins) or decrease
(negative acute-phase proteins) in acute-
phase reaction
Synthesized due to body’s response to injury
Response is stimulated by release of

Cytokines: Interleukin-1, Interleukin-6 and
Tumor necrosis factor (TNF)
Acute Phase Protein response is an adaptive
response to diseases;
Example:
• • Increases in plasma levels of CRP and Complement will contain
and eliminate infection,
• • Increased Coagulation Factors will aid and prevent excess blood

loss,
• • Protease Inhibitors will prevent the spread of tissues necrosis

when damaged cells at the site of injury release Lysosomal
enzymes,
• • Clinically some Acute Phase proteins are used to monitor progress

of some disease condition or its response to treatment
Positive acute phase Negative acute
reactants: phase reactants:
• CRP • Transferrin
• 1 antitrypsin • Albumin
• Haptoglobin • Prealbumin
• 1 acid glycoprotein • Retinol binding
• Fibrinogen protein
• Ceruloplasmin Synthesis of these proteins
decrease to save amino
• Complements C3, C4 acids for positive acute
phase proteins
• IgG, IgM, IgA

• 2-microglobulin
Biyokimya ABD

Diet Protein
Tissue Protein Amino acid Pool Nonprotein Nitrogen

Compounds
transamination
Metabolic intermediates
Ketone Bodies
Acetyl CoA
Glutamate amino nitrogen
deamination
TCA
NH3
CO2
Üre
 Amino acids undergo oxidative degradation in three different
metabolic conditions:
1. Amino acids coming from protein degradation if there is no
need for new protein synthesis.
2. If a diet is rich in protein and the amino acids taken exceed the
body's need for protein synthesis, the excess is destroyed; amino
acids are not stored.
3. Cellular proteins are used as fuel in starvation or diabetes
mellitus (DM), where the carbohydrates are either not at all or
not properly utilized.
 The C and H atoms of the
amino acid structure form
H2O and CO2 as final products
 The nitrogen atom in the
amino group is released as +
Ammonia (toxic) NH3
 Ammonia is removed from the
body by converting it into a
non-toxic urea by a series of
reactions that require energy.
H2O + CO2
 During catabolism, amino acids lose
their amino groups, forming α-keto
acids, protecting the "carbon
skeletons" of amino acids.
 α-keto acids are converted to CO2 and

H2O by oxidation, or by
gluconeogenesis, they provide units
of 3 or 4 C that can be converted to
glucose, which is the fuel of the brain,
skeletal muscle and other tissues. α-keto asit
1. Glutamate
IN THE CELL:
Aminotransferase →glutamate formation from α-ketoglutarate
2. Glutamine
BETWEEN THE CELLS AND THE TISSUES → takes the 2nd amino
group and gives it as ammonia in the liver or kidney
3. Alanine
BETWEEN MUSCLE-LIVER → Carries the amino group from muscle
to the liver
 Glutamate and glutamine play a critical role in nitrogen metabolism
 In the cytosol of hepatocytes, the amino groups of most amino acids are
transferred to α-ketoglutarate to form glutamate
 Glutamate is then transported into mitochondria where the amino group
is removed to form NH4 +
 In most tissues, excess ammonia is converted to amide nitrogen of
glutamine, passes through the liver, enters the liver mitochondria, or acts
in acid-base regulation by providing ammonia formation in the kidneys.
 The intramuscular excess amino groups are usually transferred to the
pyruvate to form alanine which transports amino groups to the liver
 Glutamine plays an important role in the transport of ammonia
between organs.
 In many tissues, including the brain, ammonia combines with
glutamate to form glutamine
 Glutamine is a non-toxic transport
form of ammonia; it is found at a
much higher concentration than
the other amino acids in the blood.
 Glutamine also functions as a
source of amino group in some of
the biosynthetic reactions
 Glutamine is transported to the
liver and kidney by blood
 The glutaminase enzyme converts
glutamine to glutamate and NH4 +
 Alanine plays an important
role by transporting the amino
groups to the liver in a nontoxic
structure, in a way called the
glucose-alanine cycle.
 Amino groups of amino acids

broken down as fuels in muscle
and some tissues are transferred
to the glutamate structure by
transamination.
Glucose-Alanine Cycle
 Glutamate can be either
converted to Glutamine or
Alanine to be transported to the
liver
The formed alanine passes to

the blood and reaches the liver.
 In the cytosol of hepatocytes,

the amino group of the alanine is
carried to α-ketoglutarate to form
pyruvate and glutamate (enzyme:
alanine aminotransferase)
 Glutamate enters to the mitochondria
 NH4 + is released with glutamate dehydrogenase reaction or it is
transaminated with oxaloacetate to form the other nitrogen donor
of the urea synthesis: Aspartate.
1. Re-use
2. Urea Cycle
Fumarate
Oxaloacetate
 During the catabolism of amino acids, ammonia is released
 Ammonia is extremely toxic to cells
 The purpose of the urea cycle is to convert toxic ammonia to
urea, which is less toxic
 Because the arginase enzyme is found only in the liver, this
cycle occurs in the liver.
 Urea contains 2 nitrogens and they come from aspartate and
free ammonia, which is the result of oxidative deamination of
glutamate.
Nitrogen is
needed to be
taken to the
mitochondria
First two reactions take place in mitochondria, the others in the cytoplasm
Transport of Nitrogen to Liver Mitochondria
1. Direct deamination
2. Transdeamination
The basic system for the removal of nitrogen groups used in the
body is transdeamination. Direct deamination methods are not
widely used.
 May be oxidative and nonoxidative
 Direct deamination reactions involving oxidative (eg glycine
oxidase) and nonoxidative deamination (eg serine, threonine
dehydratase) are insignificant reactions in man.
 Transamination is the primary pathway for the removal of
amino groups of amino acids.
 The transdeamination system consists of two basic reactions:
 transamination
 deamination
 In the liver, this system involves transamination and

mitochondrial deamination that takes place in the cytosol.
 In the catabolism of L-aminoacids reaching the liver, the 1st
step is the removal of the amino group with enzymes called
aminotransferase or transaminase.
 Transaminases (aminotransferases) are widely distributed in

the human organism and are especially active in the heart,
liver, skeletal muscle and kidney.
TRANSAMINATION
Amino acid Keto acid
Aminotransferase Pyridoxal phosphate
Amino acid Keto acid

Aminoacid
H -KETOGLUTARATE H
H3N+ C COO- C COO-
R1 R1
AMİNOTRANSFERASE
PP
H H
C COO- H3N+ C COO-
R1 GLUTAMATE
R2
Ketoacid
 The α-ketoglutarate / L-glutamate pair forms the amino group acceptor /
donor pair in all transamination reactions.
 In the transamination reaction, the -amino group is transferred to -C
atom of -ketoglutarate and -ketoacid and L-glutamate are formed.
 Glutamate also acts as an amino group transmitter in biosynthetic
reactions.
 Amino groups of all amino acids are collected in -ketoglutarate by this
reaction and glutamate is formed.
 The only role of α-ketoglutarate in aa metabolism is to take the amino
group from AA and convert it to glutamate.
 Cells contain various aminotransferase enzymes
 The most important aminotransferase enzymes are AST and ALT.
 All aminotransferases are bound to pyridoxal phosphate (PP) as a
prosthetic group.
Alanine + -ketoglutarate pyruvate + glutamate
ALT+PP
Glutamate + Oxaloacetate Aspartate + -ketoglutarate

AST+PP
Unlike other aminotransferases, this enzyme catalyzes the reaction in the direction of
aspartate formation, not in the direction of glutamate formation.
 Aminotransferases are intracellular enzymes
 Increased levels indicate damage of the cells which are rich in
these enzymes
 Eg. Liver Diseases: In almost all liver diseases, blood AST, ALT
levels increase
The increase is much more

pronounced in viral hepatitis,
especially the intense cellular
necrosis and in cases such as toxic
damage
 In the majority of amino acids, the α-amino group enters the
transaminase reaction and is accumulated in glutamate.
 Hepatocyte glutamate is transported through mitochondria from
cytosol and is oxidized by glutamate dehydrogenase with oxidative
deamination, and α-ketoglutarate and ammonia (ammonium ions)
are formed.
 The effect of aminotransferase and glutamate dehydrogenase is
collectively referred to as transdeamination. Very little amino acid
bypasses transdemination and directly undergoes oxidative
deamination.
 α-ketoglutarate, formed by the deamination of glutamate, is also
used in glucose synthesis.
NAD(P) NAD(P)H+H
Glutamate -KG + NH4+
Glutamate dehidrogenase
 It is a rare enzyme which can use both NAD and NADP

 It is an allosteric enzyme.
 The direction of the reaction is dependent on the concentration of glutamate,
α-ketoglutarate and NH3 and on the ratio of the oxidation-reduction
coenzyme. For example, after protein diet, the direction of the enzyme is the
direction of amino acid degradation.
 ATP and GTP are allosteric inhibitors of the enzyme, whereas GDP and ADP are
activators.
 If the GDP and ADP are high in the intracellular area, which means the energy
level is low, glutamate dehydrogenase increases amino acid degradation and is
used as a substrate for the obtained α-ketoglutarate in TCA.
Urea Cycle
1. Carbamoyl phosphate synthase
2. Ornitine transcarbamoylase
(Rate-limiting step)
3. Argininosuccinate synthetase
4. Argininosuccinate lyase
5. Arginase
1. Reaction: Carbamoyl Phosphate Formation
Ammonia is caught in the form of carbamoyl phosphate.
Enzyme: Carbamoyl phosphate synthetase I

Location: mitochondria
2ATP consumption
Ammonia entering into the structure of carbamoyl phosphate comes from the
oxidative deamination of glutamate.
Carbamoyl phosphate synthase
Synthetase I Synthetase I
Mitochondria Cytosol
Rate limiting enzyme in urea synthesis Rate limiting enzyme in pyrimidine synthesis
Uses CO2, ATP and NH4 Uses CO2, ATP and amide nitrogen of
glutamine
The carbamoyl group of carbamoyl The carbamoyl group of carbamoyl

phosphate is transferred to the phosphate is transfared to aspartate with
ornithine with the ornithine aspartate transcarbamoylase
transcarbamoylase
Carbamoyl group is used as carbon The carbamoyl group makes the 2nd carbon
source for urea of the pyrimidine ring
NAG is the allosteric activator is activated by PRPP

Urea Cycle
5. Arginase
2. Reaction: Citrulline Formation
Enzim: Ornithine transcarbamoylase

mitochondria
 Ornithine and citrulline are basic amino acids

 They do not enter in protein structure
 Ornithine re-occurs in each cycle
The released citrulline undergoes cytoplasm
Urea Cycle
5. Arginase
3. Reaction: Argininosuccinate Formation
Amino group of
aspartate gives the
second ammonia group
of urea
Enzyme: argininosuccinate synthetase

Location: Cytosol
1 ATP consumption
Urea Cycle
5. Arginase
4. Reaction: Cleavage of argininosuccinate
Enzyme: Argininosuccinate Liyase (Argininosuccinase)

Can be transported to mitochondria Malate
Location: cytosol
and enter TCA
Can be converted to OAA in cytoplasm to form aspartate or glucose
Urea Cycle
5. Arginase
5. Reaction: Formation of urea and ornithine from arginine
Enzyme: Arginase
Location: Cytosol
Other organs, such as the kidney, can synthesize arginine through these
reactions.
Only the liver can make urea formation from arginine.
Urea is eliminated via the kidneys
ARGININE N-ACETYL
GLUTAMATE
CARBOMOYL
PHOSPHATE
NH3 SYNTHETASE-1
CARBOMOYL
PHOSPHATE
HCO3
2ATP 2ADP
LIVER-MİTOCHONDRIA
Aspartate
ATP AMP
Citrulline Citrulline Argininosuccinate

Arjininosüksinat
sentaz
Arjininosüksinat
Carbomoyl Ornitine
liyaz
phosphate transcarbamoylase
Fumarat
Ornitine Ornitine
Arginine
Arginase
3 ATP
4 High Energy Phosphate Urea
2 NH4+ +HCO3- + 3ATP4- + H2O → Urea + 2 ADP3- +4 Pi2- +AMP2- + 5 H+

Aspartate-Arginosuccinate Shunt Combines
Krebs Cycle with Urea Cycle
Krebs Bicycle
Regulation of Urea Cycle
Carbamoyl Phosphate Synthase I
Rate limiting step
NAG: Activator of CPS I
Arginine: Activator of NAG synthesis
Arginine
Protein Rich Meal

 NAG concentration increases
 Glutamate and arginine
increase
 Urea synthesis is accelerated
The urea synthesized in liver,
passes into the bloodstream and is
removed from the kidneys by
urine
A part of the synthesized urea

passes through the intestine
Bacterial urease cleaves urea to
CO2 and NH3
Some are excreted by feces and
some go into circulation
 Blood urea levels increase in renal failure

 More urea comes to the intestine
 The urea in the intestine is broken down by the urease action of the
bacteria and ammonia is released.
 Kidney failure ... Hyperammonemia
The osmotic effect of
glutamine also causes
neurotoxicity
Glutamate Glutamin
dehydrogenase synthetase
NH4 + -ketoglutarat Glutamate + NH4 Glutamine
NAD(P)H NAD(P) ATP ADP
Glutamate is the precursor of GABA,

-KG is exhausted and cellular
an inhibitory neurotransmitter in the
oxidation and ATP production is
brain. Decreased glutamate reduces
reduced. Especially the tissues
GABA formation and excitation
with high energy requirements
occurs.
such as the brain are damaged.
Aminoacids: Amino acids and aminotransferases in many tissues, especially the
liver, react with NH3 from amino acids through dehydrogenase reactions
Glutamine: Renal glutaminase effect in the kidneys,
Intestinal glutaminase effect causes glutamine to form NH3 in the gut
Bowel bacteria: Amonia is obtained by the bacterial destruction of the urine in the
intestinal lumen. Ammonia passing through the portal vane is caught in the liver
and turned into urea.
Amines: Amines derived from foods or monoamines, such as hormones and
neurotransmitters, are converted to ammonia with MAO.
Purines and pyrimidines: In the purine and pyrimidine catabolism, the amine
groups in the rings are liberated as ammonia.
 Hyperammonemia is a medical
emergency because of CNS toxicity
 2 main reasons:
 1. Liver disease
 2. Genetic deficiency of enzymes in

the urea cycle
 Symptoms such as Tremor, effected speech and blurred
vision.
 Acquired: Alcoholism, hepatitis and bilirubin-induced
cirrhosis lead to collaterals around the liver. Through portal
blood shunts, systemic circulation is absorbed through the
liver and blood ammonia concentrations are increased.
 Hereditary: The urea cycle occurs with enzyme deficiencies.
Hyperammonia occurs in the first week of life. Mental
retardation is inevitable.
 Urea cycle defect frequency is 1/30000 live
births
 However, since there is no screening program
during the newborn period, the actual
prevalence is unknown
 Progressive hyperammonia results in brain
edema, coma and death
 Mortality is mostly associated with
◦ the first hyperammonia attack
◦ Treatment-resistant patients
◦ Patients with late onset of first episode
 Hyperammonia can cause irreversible
neurotoxicity and cell necrosis in the CNS
 Recurrent episodes lead to progressive
reduction in intellectual function
Most common Ornithine Transcarbamoylase Defect
X-linked Recessive
Location Abb. Enzyme Disorder
N-Acetylglutamate synthase
Mitochondria OR N-Acetylglutamate synthetase
deficiency
Carbamoyl phosphate
Mitochondria OR Carbamoyl phosphate synthetase I
synthetase I deficiency
Ornithine transcarbamylase
Mitochondria XR Ornithine transcarbamylase
deficiency
"AS deficiency" or
Cytosol OR Argininosuccinic acid synthetase
citrullinemia
"AL deficiency" or
Cytosol OR Argininosuccinase acid lyase argininosuccinic aciduria
(ASA)
"Arginase deficiency" or
Cytosol OR Arginase
argininemia
 Transamination reactions: pyridoxal phosphate
 Single Carbon Transfer: biotin
tetrahydrofolate
S-adenosylmethionine
 Tetrahydrobiopterin: The cofactor of the phenylalanine hydroxylase

reaction:

alanine
cysteine
Glycogenic: Aa s which form glycine
pyruvate or SAS Leucine
serine Lysine
intermediates threonine Isoleucine Phenilalanin
tryptophan Leucine Tryptophan
Tryptophan Tyrosine
Piruvate
Acetyl CoA Acetoacetyl CoA

Aspartate
Asparagine
Ketogenic: Aa s which form
OAA
Acetyl CoA and Aseoacetyl
Aspartate Citrate CoA AA
Phenilalanine Fumarate
Tyrosine
Arginine
Isoleucine Glutamate
-KG
Methionine Succinyl CoA Glutamine
Threonine Histidine
Valine Proline
Amino Acids are classified as glycogenic or

ketogenic according to the final product they form
Both glycogenic and
Glycogenic Pure ketogenic
ketogenic
Alanine Leucine Isoleucine
Arginine Lysine Phenylalanine
Asparagine Tryptophan
Cysteine Tyrosine
Glutamine
Glycine
Histidine
Hydroxyproline
Methionine
Proline
Serine
Threonine
Valine
Amino acids which form Oxaloacetate
C4 family: asparagine is transformed into aspartate, while

aspartate is transformed into oxaloacetate by transamination to
give the amino group α-ketoglutarate.
O
H2O NH 4+ KG Glu
H2C C NH 2 H2C COO – H2C COO –
+
H3N C COO – +
H3N C COO – O C COO –
H Asparaginase H
Glutamate–Aspartate H
Aminotransferase
Asparagine Aspartate Oxaloacetate
Amino acids which form α-Ketoglutarate
C5 family: Many aa s is converted to -KG from glutamate

 Glutamine is converted to glutamate by
Arginin Prolin
glutaminase.
 N-formiminoglutamate is formed as an
intermediate product during the
Ornitin
convertion of glutamate into histidine. If
there is folate deficiency, histidine
Glutamat -semialdehit
deposition breaks down, Figlu levels
increase and they are excreted with
urineIt is used for the detection of
folate deficiency. Glutamat
Histidin Figlu Glutamat
THF N5-formimino THF

 C3 family; Alanine, Glycine, Serine, Cystine-cysteine and Threonine,
are metabolised through pyruvate
Alanine is converted to pyruvate with direct transamination

ALT+PP
Another simple reaction is the convertion of serine to pyruvate

with serine dehydratase
Serin Pirüvat + NH4

Serin dehidrataz
Glycine can be
converted to serine by
adding a methylene
group from N5-N10-
methylene THF
Glycine can also convert
to CO2 and NH3
Most of the serine is converted to glycine by serine hydroxymethyl

transferase and N5-N10-methylene THF is formed in this reaction
In addition, serine dehydratase can also be convert serine directly into the
pyruvate
 Phenylalanine is
converted to tyrosine
 Tyrosine forms fumarate
and acetoacetate
 Phenylalanine and
tyrosine are involved in
both the glycogenic and
the ketogenic group aa.
 Methionine, Valine and Isoleucine form propionyl CoA
 Propionyl CoA succinyl CoA conversion also is a common
pathway in the degradation of single-carbon fatty acids
VitB12
Biotin
Methylmalonyl
Propionyl CoA Coa mutase
caroxylase
 Lysine, isoleucine, lysine, tryptophan directly form Acetyl CoA or
acetoacetyl CoA
 Phenylalanine and acetoacetate are formed during the catabolism of
tyrosine (Fumarate + acetoacetate)
 Tryptophan (Alanine + acetoacetate)
 Isolözin (Propionyl CoA + Acetyl CoA)
leucine
Lysine
isoleucine phenylalanine
leucine tryptophan
tryptophan tyrosine

alanine
cysteine
glycine Leucine
serine Lysine
threonine Isoleucine Phenilalanin
tryptophan Leucine Tryptophan
Tryptophan Tyrosine
Piruvate

Aspartate
Asparagine
OAA
Aspartate Citrate
Phenilalanine Fumarate
Tyrosine
Arginine
Isoleucine Glutamate
-KG
Methionine Succinyl CoA Glutamine
Threonine Histidine
Valine Proline
Ankara Yıldırım Beyazıt University Medical Faculty
Medical Biochemistry Department
Glucuronic Acid Pathway &

Glycoproteins
Prof. Dr. Gülsen YILMAZ
gyilmaz@ybu.edu.tr
MARCH 2022
Glucuronic acid
• Glucuronic acid (from Ancient Greek"sweet" + "urine") is a carboxylic

acid.
• Its structure is similar to that of glucose.
• However, glucuronic acid's sixth carbon is oxidized to a carboxylic

acid. Its formula is C6H10O7.
Glucuronic acid PTW = Uronic Acid Pathway
• minor route of glucose metabolism

• occurs in liver cytoplasm, mainly
• like the pentose phosphate pathway, it provides biosynthetic precursors
• and interconverts some less common sugars to ones that can be
metabolized
• does not lead to generation of ATP
Synthesis of
glucuronic acid
Synthesis of glucronic acid
1. formation of glucose-6-phosphate
2. its isomerization to glucose-1-P
3. activation of glucose-1-P to form uridine diphosphate glucose
(UDP-glucose)
• UDP-glucose is then oxidized at carbon 6 to UDP-glucuronic
acid by NAD + and UDP-glucose dehydrogenase
2 3
1 3
4
3
1 2
2 3
1
Uronic Acid Pathway is needed in:
Conjugation to less polar compounds as bilirubin, steroids and some

drugs making them more water soluble (detoxicated) .
Synthesis of glycosaminoglycans (mucopolysaccharide) as heparin,

hyaluronic acid.
In plants and some animals (not Human) glucuronic acid serves as a
precursor of L-ascorbic acid.
The uronic acid pathway also provides a mechanism by which dietary D-

xylulose enter the central pathway.
Additional pathway for pentoses synthesis

UDP-glucuronic acid is
utilized in biosynthetic
reactions
• In liver used for conjugation &

detoxification of steroids, bilirubin, some
drugs, etc.
• condensation of glucuronic acid with a variety

of molecules to form an ether (glycoside), an
ester, or an amide, depending on the nature of
the acceptor molecule
DETOXIFICATION
Biotransformation that eliminates an ultimate toxicant

or prevents its formation is called detoxification.
Importance of Detoxification
• Increasing exposure to foreign chemicals
• Increasing Stress
• Use of processed and nutrient poor foods
• Increasing access to and use of pharmaceutical drugs

The basis of
Detoxification
• To convert lipid-soluble, non-polar, non excretable

forms of chemicals to water-soluble, polar forms that
are excretable in bile and urine
Lipophilic
Xenobiotic
Phase I - Activation
(non-polar)
Reactive intermediate
Phase II - Conjugation
Conjugate
Water soluble
Excretion (polar)
The conjugation of xenobiotic molecules (substances foreign to

our body) with hydrophilic molecular species such as glucuronic
acid is known as phase II metabolism
Conjugation to less polar compounds
• Glucuronidation is the addition of glucuronic acid to a substrate by UDP-

glucuronosyltransferase enzymes
• The substances resulting from glucuronidation are known as glucuronides

Conjugation to less polar compounds
• Because glucuronic acid is highly polar, its conjugation with less polar
compounds, such as steroids, bilirubin, and some drugs, can reduce their
activity and make them more water-soluble, thus facilitating renal
excretion


hyaluronic acid.


UDP-glucuronic acid is
utilized in biosynthetic
reactions
• In Connective tissue used for
proteoglycans synthesis
• Glucuronic acid is a component of the

structural polysaccharides called
glycosaminoglycans
Proteoglycans
• It is part of mucous animal

secretions (such as saliva),
cell glycocalyx and intercellular
matrix (for instance hyaluronan)


hyaluronic acid.


L-gulonolactone
oxidase
Synthesis of glucronic acid


hyaluronic acid.


NADPH dependent
Xylulose reductase
• L-xylitol (alcohol) which loses H+ to NAD to become NADH and D-
Xylulose results by a reductase enzyme
• if this enzyme is deficient then L-Xylulose accumulates in the

blood,causing “Essential Pentosuria”, a clinically benign inborn
error of metabolism
• This is a common, clinically asymptomatic genetic trait in

Ashkenazi Jews.


hyaluronic acid.


HMP
Glycogenolysis DIET Gluconeogenesis
GLUCOSE
GLUCOSE 1P GLUCOSE 6P
PENTOSE P PTW
GLYCOGENESIS
URONIC ACID PTW GLYCOLYSIS
UDP-GLUCOSE
TCA NADPH
URONIC ACID PTW RIBOSE
NADH
UDP-GLUCURONIC ACID
ATP FA
SYNTHESIS NA
PROTEOGLYCAN
SYNTHESIS
SYNTHESIS
DETOXIFICATION
Glycoconjugates
• Glycoconjugates is the
general classification for
carbohydrates covalently
linked with other
chemical species such
as proteins, peptides,
lipids and saccharides.
• Glycoconjugates are
formed in processes
termed glycosylation.
GLYCOPROTEINS
• A glycoprotein is a type of
protein molecule that has
had a
carbohydrate attached to it.
CH chain length is 2-10
sugar residues and
branched.
• The process either occurs

during protein translation or
as a posttranslational
modification in a process
called glycosylation.
GLYCOPROTEINS
Protein >> carbohydrate
The carbohydrate is a short molecule,

often branched, and may consist of
(primarily D-hexoses):
• simple sugars (e.g., glucose,

galactose, mannose, xylose)
• amino sugars (sugars that have an
amino group, such as N-
acetylglucosamine or N-
acetylgalactosamine)
• acidic sugars (sugars that have a
carboxyl group, such as sialic acid
or N-acetylneuraminic acid)
may or may not be negatively
charged
Glycoproteins are categorized according to the
attachment site of the carbohydrate to an amino
acid in the protein.
• In N-linked
glycosylation the
sugar is attached
through a nitrogen
(NH) within the a
asparigine or arginine
side group on the
protein
• In O-linked glycosylation
the sugar is attached
through a oxygen on a
hydroxyl group (OH) to a
serine, threonine, or
tyrosine
Three Main Types of Glycoprotein
Structures
Glycosylphosphatidylinositol
GPI-linked
O-linked
GPI =
N-linked
Serin Three main types according to glycosylation to proteins
Treonin
Amid bağı
Tirozin Asparajin
 Fosfatidil
etanolamin
OH N
Glukoz
Glukoz Glukoz
Galaktoz
Galaktoz Galaktoz
O-bağlı N-bağlı Glikozilfosfatidil

glikoproteinler glikoproteinler inozitol (GPI)

GPI’nin yağ asitleri ile
membrana tutunur
GLYCOPROTEINS
Man3GlcNH2
All N-linked oligosaccharides have in common a pentasaccharide core consisting of

three mannose and two N-acetylglucosamine residues. Additional sugars are
attached to this core to form the great variety of oligosaccharide patterns found in
glycoproteins
Saccaharide core consisting of
Man3GlcNH2, a bridge
between the phospholipid in
the membrane and the protein
This type of glycoproteins are bound to plasma membrane with fatty acids.
For example: Acetylcholinesterase to erythrocyte membrane, ALP to
intestine and placenta, 5’-nucleotidase to cells.
N-linked Glycoproteins
N-linked glycosylation :
Asn
• N-glycans predominates
in serum glycoproteins
• almost all of the globular
proteins present in
human plasma are
glycoproteins
O-linked glycosylation : Ser, Thr
• membrane bound or ECM
glycoprot, mucins
• ABO Blood Group determinants
ABO Blood Group determinants
O-linked oligosaccharides on the surface of RBCs help provide the

ABO blood group determinants
Types of glycoproteins
• Membrane proteins
• Secreted proteins
Antibody
hormones
milk proteins (lactalbumin)
proteins released by the pancreas
lysosomal proteins
Outer face of plasma membrane, ECM, blood
Inside cells; golgi, secretory granules, lysosomes
Advantages of oligosaccharide
attachment
• Hydrophilicity (polarity & solubility)

• Destination label
• Label for protein quality control
• Protein folding
• Protection from proteolytic attacks
• Informational roles (recognition & communication)
• Targeting signal for removal of damaged or mis-folded
proteins from the cell
A glycoprotein may contain only one type of glycosidic linkage (N- or

O-linked), or may have both O- and N-linked oligosacchs within same
molecule
Functions of Glycoproteins
• Membrane-bound glycoproteins
• Specific sites for recognition

by other cells, hormones, viruses…
(information-rich oligosaccharide)
• Cell surface antigenicity (such as the

blood group antigens)
FUNCTIONS OF GLYCOPROTEINS
GLYCOPROTEIN FUNCTION
COLLAGENS Structural molecule

MUCINS Lubricant and protective agent
TRANSFERRIN, Transport molecule for iron and copper
CERULOPLASMIN
IMMUNOGLOBINS, Immunologic molecule
HISTOCOMPATIBILITY ANTIGENS (HLA)
HUMAN CHORIONIC Hormone
GONADOTROPIN(hCG),
TYROID STIMILATING HORMONE (TSH),
ERYTHROPOIETIN (EPO)
VARIOUS, E.G., ALKALINE PHOSPHATASE Enzyme
Biosynthesis of the N-linked core oligosaccharide
Synthesis starts on the cytosolic surface of
the ER membrane by the addition of
sugars, one by one, to dolichylphosphate.
After the last of the three glucoses have

When two N-acetylglucosamines and five been added, the oligosaccharyltransferase
mannoses have been added, the enzyme complex catalyzes the transfer of the
oligosaccharide is flipped to the lumenal side core oligosaccharide to the asparagine
of the membrane, and seven further sugars residues of nascent, growing polypeptide
are added from lipid precursors chains
• O-linked glycosylation occurs through the stepwise addition of
monosaccharides in either the ER or Golgi complex.
• Most O-linked oligosaccharides are short, containing only four
sugars.
The Golgi Apparatus has two major
functions:
• Modifies the N-linked

oligosaccharides and adds O-
linked oligosaccharides
• Sorts proteins so that when

they exit the trans Golgi network,
they are delivered to the correct
destination
Targeting of Lysosomal Enzymes to Lysosomes
The phosphate is
added in the Golgi
N-linked glycoproteins being

processed through Golgi can be
phosphorylated at one or or
more specific mannosyl residues This was first
attached in
the ER.
Addition of mannose 6-phosphate M6P as chemical marker

to lysosomal enzymes
Targeting of Lysosomal Enzymes to Lysosomes
Mannose 6-P receptors in Golgi by binding Mannose 6P residues of

these enzymes provides the translocation to lysosomes.
Acidic pH causes the

release of hydrolase
from its receptor.
Lysosomal degradation of glycoproteins
• Glycoproteins are degraded in lysosomes by

acid hydrolases similar to that of GAGs.
• “last on, first off”
• A deficiency of one of these enz’s results in
a glycoprotein storage disease
(oligosaccharidosis), resulting in
accumulation of partially degraded
structures in the lysosome
• After cell death, the oligosacch fragments
appear in the urine
• Disorders are very often directly associated
with the same enzyme deficiencies involved
in mucopolysaccharidoses & the inability to
degrade glycolipids
Mechanism for transport of N-linked glycoproteins to the lysosomes
Inclusion-cell disease
(I-CELL DISEASE)
• a rare syndrome in which the acid hydrolase enz’s normally

found in lysosomes are absent, resulting in an accumulation of
substrates normally degraded by lysosomal enz’s within these
vesicles
• individuals with I-cell disease are lacking the enzymic ability to

phosphorylate the mannose residues of potential lysosomal enz’s
• causing an incorrect targeting of these proteins to extracellular

sites (high amounts in plasma), rather than lysosomal vesicles
• I-cell disease is so-named because of the large inclusion bodies

seen in cells of patients with this disease
I-CELL DISEASE
• I-cell disease is characterized by;

• skeletal abnormalities,
• restricted joint movement,
• coarse facial features
• severe psychomotor
impairment
• Death (usually by age 8 yrs)
I-Cell Disease Summary
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Yıldırım Beyazıt Universitesi Tıp Fakültesi

Prof. Dr. Fatma Meriç Yılmaz

Doku Proteini Amino Asit Havuzu Nonprotein Azot Bileşikleri

 α-keto asitler oksidasyona uğrayarak

 Glutamin, amonyağın nontoksik

 Alanin amino gruplarını,

 Kas ve diğer bazı dokularda

 Glutamat Karaciğere taşınmak

 Böylece oluşan alanin kana

İlk iki reaksiyon mitokondride, Diğer reaksiyonlar sitoplazmada

 Aminoasidlerin amino gruplarını yok edilmesinde vücutta

 Karaciğerde bu sistem sitozolde gerçekleşen transaminasyon ve

 Transaminazlar (aminotransferaz) insan organizmasında

Aminotransferaz Piridoksal fosfat

Amino asit Keto asit

Glutamat + Oksaloasetat Aspartat + -ketoglutarat

Özellikle yoğun hücre nekrozu olan

 Hem NAD hem de NADP’yi koenzim olarak kullanabilen nadir

2. Ornitin transkarbamoilaz (Rate-limiting step)

Amonyak, karbamoil fosfat şeklinde yakalanmış olur.

Enzim: Karbamoil fosfat sentetaz I

Karbamoil Fosfatın yapısına giren amonyak, glutamatın oksidatif

Mitokondride yer alır Sitozolik

Karbamoil fosfatın karbamoil grubu ornitin Karbamoil fosfatın karbamoil grubu

Karbamoil grubu üreye karbon kaynağı Karbamoil grubu primidin halkasının 2.

NAG allosterik aktivatördür NAG gerektirmez. PRPP ile allosterik

2. Ornitin transkarbamoilaz (Rate-limiting step)

Enzim: Ornitin transkarbamoilaz

 Ornitin ve sitrulinbazik amino asitlerdir

2. Ornitin transkarbamoilaz (Rate-limiting step)

Aspartatın amino grubu

Enzim: argininosuksinat sentetaz

2. Ornitin transkarbamoilaz (Rate-limiting step)

Enzim:Mitokondriye taşınıp Liyaz

2. Ornitin transkarbamoilaz (Rate-limiting step)

Böbrek gibi diğer organlar bu reaksiyonlarla arginin sentezleyebilir.

Sitrüllin Sitrüllin Arjininosüksinat

2 NH4+ +HCO3- + 3ATP4- + H2O → Urea + 2 ADP3- +4 Pi2- +AMP2- + 5 H+

Proteinden Zengin Yemek

Sentezlenen ürenin bir kısmı

 Böbrek yetmezliğinde kan üre düzeyleri yükselir

NAD(P)H NAD(P) ATP ADP

Glutamat beyinde inhibitör etkili

 2. Üre siklusundaki enzimlerin

300-500 * Belirgin ensefalopati tablosu oluşur

500-2000 * Koma ve konvulziyonla seyreder

•NAG Sentaz Defekti

 Tek Karbon Transferi: biotin

 Tetrahidrobiyopterin fenilalanin hidroksilaz reaksiyonunun kofaktörü

Asetil KoA Asetoasetil KoA

Amino Asitler oluşturdukları son ürüne göre

C4 ailesi: asparagin aspartata dönüşerek, aspartat ise

C5 ailesi bir çok aa glutamat üzerinden -KG’a çevrilir.

Histidin Figlu Glutamat

THF N5-formimino THF

Alanin + -ketoglutarat pirüvat + glutamat

Diğer basit reaksiyon serinin serin dehidratazla pirüvata

Serin Pirüvat + NH4

Serinin çoğu serin hidroksimetil transferazla glisine çevrilir ve bu

Asetil KoA Asetoasetil KoA

Asetil KoA Asetoasetil KoA

Prof. Dr. Leyla Didem KOZACI

• The quarternary structure, which is the highest level of structure, is

• Knowing the 3D structure of proteins is essential in understanding their