BIOCHEMISTRY EXAM 2

Monosaccharides

single unit sugars

General Formula for a carb

(CH₂O)_n

Aldehyde groups make molecules…

More Reactive

Ketose

a sugar with a ketone group

Aldose

a sugar with an aldehyde group

L almost always maps to…

S

D almost always maps to…

R

Can these sigma bonds rotate to interconvert these two molecules?

NO: because vertical sigma bonds are leaning AWAY from you in 3D space, and horizontal sigma bonds are leaning TOWARDS you

Possible stereoisomers =

2ⁿ where n is the number of chiral carbons

Ex. A 6-C aldose w/ 4 chiral carbons = 16 possible molecules

L or D is specified by…

the furthest chiral carbon from the aldehyde or keto group

Enantiomer vs Diastereomer

Enantiomer: differ on ALL chiral carbons

Diastereomer: only differ on one or more chiral carbons

What is an anomer?

a monosaccharide that readily cyclizes into a ring

If these reactions occur in an intramolecular fashion,…

the product is a ring

Glucopyranose

glucose in ring form

Pyranose vs Furanose

Pyranose: any 6 membered ring sugar

Furanose: any 5 membered ring sugar

These anomer reactions are in..

equilibrium (the ring reopens)

What is the equilibrium aqueous mixture of glucose at standard conditions?

33% alpha anomer

66% beta anomer

<1% linear

Is L or D the most common biological stereisomer?

D-stereoisomers

Be able to IDENTIFY all sugars

DRAW and desrcibe the structure of Glucose

good

DRAW and desrcibe the structure of Fructose

good

Glucose and most monosaccharides are…

Reducing Sugars

Tissue Accumulation of Advanced Glycation End-products (AGEs)

may promote disease and aging

What can speed up the advanced glycation end product production?

reactive oxygen species from ETC can speed up process

What reaction causes food browning?

Maillard reaction

What type of glycosidic bond is it when attached to an alcohol?

O-glycosidic

What type of glycosidic bond is it when attached to nitrogen?

N-glycosidic

Linkage to anomeric carbon can happen in…

alpha or beta orientation

Other monosaccharide modifications..

• DO NOT happen at the anomeric carbon

• important for prokaryotes and eukaryotes

What modified monosaccharide is part of the peptidoglycan mesh?

Beta-D-Acetylglucosamine (GlcNAC)

What modified monosaccharide is important for neurodevelopment, cognition, and immune system function?

Sialic acid (Sia)

Modified sugars are used in…

Bacterial peptidoglycan cell wall

Complex Carbohydrates: Disaccharides are..

• complex carbohydrates

• 2 glucoses joined by an 1,4 alpha bond (1 being the anomeric carbon)

Reducing disaccharides can keep forming…

additional glycosidic bonds (formation of a glycosidic bond requires an enzyme)

If there is an H-C-OH on carbon 1 of the sugar to the right..

then the sugar is reducing

Lactose Intolerance

Digestive system needs to break the glycosidic bond between lactose (disacch.); Lactase helps break it down into galactose and glucose

Complex Carbohydrates: Polysaccharides

Glycogen

• the most metabolically important homopolymer of glucose

Where is glycogen stored and what is the function?

in the liver and muscle; can be broken down to rapidly release glucose when repeated muscular activity is necessary

What does branching do?

makes it easier for enzymes to rapidly break into monosaccharide glucose units

What type of linkage does glycogen?

alpha-linkage

Why is it easier to chew bread than wood, even though they are both made up of glucose?

breaking the beta linkage (of cellulose- wood) enzymatically is difficult

Convergent evolution of ruminants and termites

both have bacterial symbionts that secrete cellulases that can break the beta linkage

Your body starts burning more fat after…

stored glycogen starts getting depleted

How do artificial sweeteners work?

transmembrane protein expressed on gustatory cells of the tongue, responsible for intial detection of sugary mono and di-saccharides

Complex Carbohydrates: Polysaccharides

Cellulose

Beta-1,4 linkages (plants); Beta is optimal for structure

Complex Carbohydrates: Polysaccharides

Starch

Alpha-1,4 linkages (plants); Alpha is optimal for storage

Complex Carbohydrates: Polysaccharides

Glycogen

Alpha-1,4 linkages (animals); Alpha is optimal for storage

Complex Carbohydrates: Chitin

Homopolymer of N-acetylglucoseamine (GlcNAc)

• Like glucose but has acetylamine group at C2

• exoskeleton of invertebrate arthropods

What kind of linkage is this?

β-1,4 glycosidic linkage

Complex Carbohydrates: Glycosaminoglycans (GAGs)

• repeating chains of disaccharides

• almost always components of the extracellular matrix

Complex Carbohydrates : Glycosaminoglycans (Hyaluronan)

• Huge number of repeats

• Highly hydroscopic; very viscous and elastic

• Extremely important component of synovial fluid which lubricates joints that are highly impacted (knees, ankles)

Hydroscopic

binds a lot water

Which complex carbohydrate is an extremely important component of synovial fluid which lubricates joints that are highly impacted (knees, ankles)?

Glycosaminoglycans (Hyaluronan)

Complex Carbohydrates: Glycoproteins

1. “Generic” glycoproteins

2. Proteoglycans

3. Mucins

Glycoproteins: “Generic” glycoproteins

mostly protein w/ some sugars covalently attached

In which, organelle are sugars added to glycoproteins

Golgi Apparatus

Glycoproteins: Proteogylcans

glycoproteins covered densely w/ gylcosaminoglycans, mostly carbohydrate

Glycoproteins: Mucins

glycoprotein components of mucus, mostly carbohydrate

Complex Carbohydrates: Generic Glycoproteins

How are sugars added to proteins?

via a glycosidic bond (at the anomeric carbon)

N-linked glycosylation

to an Asparagine (Asn)

O-linked glycosylation

to a Serine (Ser) or Threonine (Thr)

What are the 2 flavors of glycoproteins, and which branching flavor has it?

1. Mannose branching

2. Complex branching

N-linked

Erythropoietin

secreted by kidneys and stimulates production of red blood cells

How does glycosylation affect the kidneys?

helps prevent kidneys from filtering out erythropoietin from the blood

How does glycosylation affect proteins?

• helps proteins fold correctly and may be necessary for enzymatic function

• can extend the conformation of extracellular proteins

Why is the LDL receptor stalk heavily glycosylated?

O-linked sugars keep the long stalk extended/unfolded, positioning the receptor’s working end far from the cell surface so it can interact with LDL

What kind of cell might have an LDL receptor?

Hepatocytes

What is the pathogenesis of Hurler’s Disease?

glycosaminoglycans cannot be degraded; their excess is stored in soft tissue of the face

What complex carbohydrate and Glycoprotein connects hyaluronan scaffold to other GAGs?

Proteoglycans

What are 5 functions of proteoglycans?

1. Protects cells from damage

2. Interacts w/ growth factors

3. Interacts w/ immune system

4. Crucial for function of cartilaginous joints

5. Altered expression in cancer (remodels the tumor microenvironment)

Mucins are components of..

mucus

What are the functions of mucins?

• protection

• lubrication

• immune functions

Complex Carbohydrates: Blood Groups

Different people…

express different glycosyltransferases

Specific glycosylation patterns on erythrocytes are…

recognized by the immune system

Which blood group is a universal donor and which is an universal receiver?

O (Rh-) or O-negative: universal donor

AB (Rh+) or AB-positive: universal reciever

Lectins

proteins that can “read” carbohydrates

Mannan binding lectin

part of the innate immune sensing of fungi snd bcterial glycoproteins

What kind of domain do selectins have and what is their function?

lectin-domain

• help leukocytes (neutrophils) of the inate immune systen ‘roll’ along endothelial (inner blood vessel) cell membrane

What are the 6 key properties of proteins?

1. are linear polymers of amino acids

2. have a variety of functional groups

3. interact w/ one another and other macromolecs.

4. undergo signif. conformational changes

5. some are enzymes

6. can be localized (nuclear, membrane, secreted, etc)

What is the primary determinant of the final FORM and FUNCTION of the protein?

the amino acid sequence

Primary Structure

linear structure of amino acids

Secondary Structure

helices and sheets

Tertiary Structure

final (often globular) form of single polypeptide chain

Quaternary Structure

• dimers, tetramers, etc.

• prosthetic groups, cofactors

The basic structure of an Amino Acid

side chain, carboxylic acid group, amino group, R-group

Proteins only contain the…

L Isomer of Amino Acids

The authors of the Mirror image T7 transcription of chirally inverted ribosomal and functional RNAs generated a D-amino acid based RNA polymerase which makes L-RNA. Which elements have been completed?

Split site 1, Split site 2

Amino acids exist as Dipolar Ions in solution at…

Neutral pH

Sanger Sequencing

method for sequencing DNA

Edman degradation

different method for peptide sequencing

What amino acid do almost all proteins begin with?

Methionine (Met), because translation typically begins at the AUG/ATG start codon

How many amino acids are non-polar (hydrophobic), and what are they? (MINUS CYSTEINE)

9

1. Glycine (Gly)

2. Alanine (Ala)

3. Valine (Val)

4. Leucine (Leu)

5. Isoleucine (Ile)

6. Methionine (Met)

7. Proline (Pro)

8. Tryptophan (Trp)

9. Phenylalanine (Phe)

Aliphatic

open-chain carbon atoms

How amino acids are non-polar (hydrophobic) and aliphatic, and what are they?

5

1. Alanine (Ala)

2. Valine (Val)

3. Leucine (Leu)

4. Isoleucine (Ile)

5. Methionine (Met)

How many amino acids are polar (hydrophilic), and what are they?

6

(Hydroxyl Group)

1. Serine (Ser)

2. Threonine (Thr)

3. Tyrosine (Tyr)

(Carboxamide Group)

4. Asparagine (Asn)

5. Glutamine (Gln)

(Thiol Group)

6. Cysteine (Cys)

How many amino acids are positively charged (hydrophilic), and what are they?

1. Lysine (Lys)

2. Arginine (Arg)

3. Histidine (His)

How many amino acids are negatively charged (hydrophilic), and what are they?

1. Aspartate (Asp)

2. Glutamate (Glu)

Glycine (Gly)

only one H; only non-chiral AA; non-polar (hydrophobic)

Alanine (Ala)

aliphatic; non-polar (hydrophobic); methyl R-group

Valine (Val)

aliphatic; non-polar (hydrophobic)