Monosaccharides

Monosaccharides are aldehydes or ketones that contain two or more hydroxyl groups.

Glyceraldehyde is an aldose because it Dihydroxyacetone is a ketose because

contains an aldehyde group. it contains a ketone group.
 Monosaccharides
Monosaccharides are aldehydes or ketones that contain two or more hydroxyl groups.

Glyceraldehyde is an aldose because it Dihydroxyacetone is a ketose because

contains an aldehyde group. it contains a ketone group.
D-Aldoses
 Chair and Boat Conformations
Carbohydrate rings are drawn as planar structures for clarity, but they adopt chair and
boat forms to accommodate the tetrahedral geometry of the carbons and bulky side
groups. The chair form is the most common due to its conformational stability.
 Polysaccharides - Glycogen
Glycogen is the storage form of glucose in animals. It is a large polysaccharide formed
from a-1,4-glycosidic-linked chains with a-1,6-glycosidic-linked branches every ~10-12
units. It forms soluble granules in all cells, particularly muscle and liver.
 Polysaccharides - Cellulose
Cellulose is a polysaccharide in plants that serves a structural function. It is an
unbranched polymer of b-1,4-glycosidic-linked glucose molecules. Parallel chains form
strong fibrils due to hydrogen bonding interactions. It is among the most abundant
organic compounds on earth.
 Glycoproteins
Carbohydrates can be covalently attached to proteins to form glycoproteins. ~50% of
the proteome consists of glycoproteins. Carbohydrates are attached to the amide
nitrogen of asparagine (N-linkage) or the hydroxyl oxygen of serine or threonine
(O-linkage).
 BIOCH-521A - Exam #3 Review
1. What is glycogen?

Storage form of glucose alpha 1-4 and alpha 1-6

Used for energy storage in cells

2. What is starch?

Used in plants insoluble still alpha 1-4 and alpha 1-6

Digestible

3. What cellulose?

Beta 1-4 linkages structural support, insoluble human can’t break down
 BIOCH-521A - Exam #3 Review
4. What are the different functions of carbohydrates?

Energy storage, modifying proteins, structural support modify lipids, signalling molucles and second messengers

5. What are the chemical characteristics that carbohydrates share? How are they different?

Either an aldehyde or ketone linked to carbons worth hydroxyl groups

Can be aldoses or ketones, different amount of carbons, different chirality

 BIOCH-521A - Exam #3 Review
6. How do carbohydrates form cyclic rings? What’s a furanose? What’s a pyranose?

Aldehyde or ketone can react with alcohol to form hemiacetal (cyclic ring)

Furnaces-5 member ring

Pyranose- 6 membered ring

7. How are glycoproteins formed and what is their importance.

Different enzymes are coming to put carb units on asparagine or serene/ theironine

Allow protein interactions

 Types of Lipids
We will discuss five different types of lipids:
1. Fatty acids - simplest lipid made of a hydrocarbon chain connected to a
carboxylic acid group. Commonly used as energy molecules.

2. Triacylglycerols - the storage form of lipid fatty acids. Generally, three fatty
acid chains connected to a glycerol molecule.

3. Phospholipids - components of membranes. Fatty acid chains attached to a

polar head group containing phosphate. Polar head - nonpolar tail.

4. Glycolipids - components of membranes. Fatty acid chains attached to a

polar head group that contains a carbohydrate.

5. Steroids - unique lipids composed of polycyclic hydrocarbons. Often act as

signaling molecules that control physiological processes. The most
common steroid is cholesterol which is an important membrane lipid.
 Fatty Acids - Chain Length and Double Bonds
Fatty acids are hydrocarbon chains that terminate in a carboxylic acid (carboxylate).
They are the building blocks for other lipids.
Fatty acids vary in the hydrocarbon chain length and the presence of double bonds.

Chain length and presence of double bonds

are going to increase melting temp and
membrane fluidity
Longer the chain the less fluid higher melting
temp
More double bonds the more kinks will push
apart making more fluid and lower melting
temp
 Triacylglycerols are Storage Fatty Acids
Although fatty acids are a principal energy source, they are strong acids so their
presence in the blood/cells is low. Fatty acids are therefore stored as triacylglycerols -
three fatty acids linked to a glycerol backbone by ester linkages.
Fatty acids can be released from triacylglycerols to provide energy. Triacylglycerols are
stored in large amounts in adipose tissues and can provide energy for weeks of fasting.
 Membrane Lipids - Phospholipids
Phospholipids are abundant in biological membranes. They are made of four
components: (1) fatty acid chains, (2) glycerol, (3) a phosphate group, and a variable
alcohol group. Phospholipids are built from a phosphatidate molecule.
 Membrane Lipids - Steroids
Steroids are lipids with a shared cyclical structure (tetracyclic ring). They function as
hormones (estradiol, testosterone), digest lipids (bile acids), and are major components
of membranes (cholesterol). Cholesterol lowers membrane melting temperature.

estradiol testosterone
 Membrane Fluidity - Saturated vs. Unsaturated
The fluidity of the cell membrane is dictated by the composition of the fatty acids chains.
The lower the melting temperature (Tm) of the fatty acids, the more fluid the membrane.
The higher the Tm of fatty acids the more rigid the membrane.
Unsaturated fatty acids and shorter chain lengths will increase membrane fluidity.
Saturated fatty acids and longer chain lengths will increase membrane solidity.
Bacteria regulate membrane fluidity by modifying lipid double bonds and chain lengths.
 Membrane Fluidity - Cholesterol
The steroid lipid cholesterol will insert itself into membranes and increase membrane
fluidity by disrupting the fatty acid chain packing. The hydrophobic chain orients
perpendicularly to the chains and the hydroxyl group hydrogen bonds to head groups.
Animals modulate membrane fluidity using cholesterol.
 Integral, Peripheral, Lipid-Anchored Proteins
There are three different ways proteins associate with membranes:
Integral membrane proteins traverse the membrane with hydrophobic regions.
Peripheral membrane proteins interact with the membrane but do not traverse it.
Lipid-anchor proteins have covalent lipid modifications that embed in the membrane
 Lateral Diffusion - Fluid Mosaic Model
The fluid mosaic model described the lateral movement of lipids and proteins in a
membrane. This is confirmed by fluorescence recovery after photobleaching (FRAP).
Lipids move laterally very quickly - the movement of proteins is more variable.

Voet & Voet, 4th Ed.

 BIOCH-521A - Exam #3 Review
8. What are the 5 major classes of lipids? What are their primary functions?

Fatty acids
Triacelyglycerols-energy storage
Phospholipids-membrane
Glycolipids- membrane
Steroids

9. What different features affect melting temperature/membrane fluidity?

Cholesterol
Chain length
Double bonds
 BIOCH-521A - Exam #3 Review
10. What is the fluid mosaic model?

11. What are the different types of membrane proteins?

 Mediated Transport
Membranes are a barrier to the movement of polar compounds and ions. Transport of
these molecules requires protein transporters in a process called mediated transport.
There are two different types of mediated transport:
1. Passive-Mediated Transport (aka Facilitated Diffusion)
Molecules are transported with the chemical gradient from [High] à [Low].
Does not require an input of external energy.

2. Active Transport
Molecules are transported against the chemical gradient from [Low] à [High].
Requires energy, so it must be coupled to an exergonic process
 Structure Dictates Ion Channel Specificity
The KcsA channel is highly specific for K+ ions compared to Na+ ions, although Na+
ions can fit through the channel. The energetic cost of desolvating K+ ions is
compensated for by carbonyl oxygen interactions, unlike with the smaller Na+ ions.
 Rapid Ion Movement through Transporters
The diagram below outlines the movement of K+ ions through the transporter.
Work very fast and very specific
Uses electrostatic repuldsion can fit a few atoms in the Channel and can use repulsion to push hem through very quickly.
 Active Transport - Na+-K+ ATPase
Active transport uses free energy to transport molecules against their gradient. Most
cells have to control intracellular salt concentrations (particularly nerve cells) and have
high K+ and low Na+ concentrations compared to the extracellular environment.

The Na+-K+ ATPase uses free energy

from ATP hydrolysis to transport 3 Na+
ions out of the cell and 2 K+ ions into the
cell, resulting in an overall negative
intracellular charge.
 BIOCH-521A - Exam #3 Review
12. Why does the KcsA ion channel have a preference for K+ over Na+?

Structure of protein, structure of the protein allows really good binding energy between K and the channel that is overcome the energy needed to
desolate K you don’t get the same binding energy with interactio with Na because it is too small .

13. What are the different types of transporters?

Passive mediated transport-facilitated diffusion with concentration gradient

Active transport- needed energy goes against Concentration gradients
 Signal Transduction - Outline of Events
(1) Release of primary messenger – stimulus in the body triggers release of a primary messenger
(2) Reception by the cell – the primary messenger (ligand) interacts with a cellular receptor
(3) Relay of information by the secondary messenger – transduction/amplification of the signal
(4) Activation of Effectors – production of a cellular/physiological response
(5) Termination of the signal – modulation of the physiological response
 Seven-Transmembrane-Helix (7TM) Receptors
Primary messenger (epinephrine) binds to receptor (b-adrenergic receptor), activating
a G-protein that activates Adenylate cyclase, resulting in secondary messenger
(cAMP) production that activates an effector (PKA) - leading to a cellular response.
Primary Messenger

Receptor

G-protein
Secondary Messenger

Effector

Phosphorylation Cascade
Cellular Response
 Gaq - Other 2nd Messengers and Responses
7TM signaling can also result in other second messengers in addition to the nucleotide
cAMP - carbohydrate (IP3), lipid (DAG), and cation (Ca2+) 2nd messengers can
activate IP3-gated voltage channels and Protein kinase C (PKC) - other responses.

Nucleotide

Cation
Carbohydrate

lipid
 RTKs - Phosphorylation Cascades
Receptor Tyrosine Kinases (like 7TMs, but more so) use phosphorylation of protein and
lipid molecules to amplify signals. Kinases add phosphate groups to molecules.
Phosphatases remove phosphate groups from molecules.
 EGF Signaling Pathway - Ras Activation
EFGR phosphorylation sites act as docking sites for the Grb-2 adaptor.

Grb-2 acts as a docking site for Sos (Son of sevenless).

Sos then activates Ras (a small G-protein) by exchanging GDP for GTP.

Ras then activates downstream kinases that initiate a cellular response.

Downstream
Response
 GEFs and GAPs Modulate Ras Activity
Ras activity is modulated by other proteins.
Guanine Nucleotide Exchange Factors (GEFs) activate Ras: exchange GDP for GTP.
GTPase-Accelerating Proteins (GAPs) inactivate Ras: facilitate GTP hydrolysis.
 Insulin Signaling Pathway
1. Insulin binding causes a structural rearrangement in the kinase domain of the receptor.
2. The structural rearrangement causes cross-phosphorylation of the kinase domain itself.

3. IRS-1 docks to the insulin receptor, binds membrane PIP2, and it also phosphorylated by the insulin receptor.

4. Phosphoinositide 3-kinase (PI3K) docks to IRS-1 and phosphorylates PIP2 to form PIP3 (2nd messenger).

5. PIP3-dependent protein kinase (PDK1) docks to PIP3 and phosphorylates Akt, activating it.

6. Phospho-Akt phosphorylates many downstream targets, resulting in a variety

of cellular responses, including transport of GLUT4 (glucose transporters) to the
cell surface, resulting in glucose uptake by the cell, and glycogen synthesis.

Downstream
Response
(GLUT4 &
Glycogen
Synthesis)
 BIOCH-521A - Exam #3 Review
14. What are the basic steps involved in signal transduction?
Physiological stimulius
Signal in the form on a primary messenger that is received by a receptor
Becomes active and usually leads to a second messenger that leads to
Activate effectors that set off phosphorylation that usually activates cellular response
 BIOCH-521A - Exam #3 Review
18. What do Ras and heterotrimeric G-proteins have in common? What is the difference?

Common
Part of signalling cascades and activated with gdp is exchanged for GTP
Have hydrolytic activity so will eventually go back

Difference
G proteins have 3 subunits with inactive
Ras is a monomeric G protein

19. What is the difference between a GAP and a GEF?

GEF- turn on G proteins
GAP- Turn off G protein
 BIOCH-521A - Exam #3 Review
20. What is a kinase and why are they so important?
Enzyme that adds pohosphate molecule to proteins lipids or carbs

Important because proteins activity is modulated based on presences of phosphate, also changes biophysical characteristics of proteins lipids and carbs
Important

21. How to phosphatases terminate RTK signaling?

Take off the phosphates

22. What are some examples of 2nd messengers?

CAMP calcium pip 3
 Nucleotides: Monomeric Units of Nucleic Acids
Nucleotides are the monomeric unit of nucleic acid polymers.

Their chemical structure consists of the following, linked together:

1) A nitrogenous base

2) A sugar

2) 1 to 3 phosphate groups
 Nitrogenous Bases: Purines and Pyrimidines
Nitrogenous bases (or just bases, or nucleobases) are specific nitrogen-containing
molecules with either a two-membered ring (purines) or a single ring (pyrimidines).

Adenine (A) and Guanine (G) are purines.

Cytosine (C), Thymine (T - DNA only), and Uracil (U - RNA only) are pyrimidines.

A G

C U T
 DNA vs. RNA
DNA (Deoxyribonucleic acid) and RNA (Ribonucleic Acid) are nucleotide polymers.
Major differences are as follows:

DNA RNA
1) Deoxyribose sugars 1) Ribose sugars

2) A, C, G, and T bases 2) A, C, G, and U bases

3) Usually forms double 3) Usually remains single

stranded helix stranded
 DNA Base Pairs Interact by Hydrogen Bonds
DNA base pairs interact by hydrogen bonding interactions. The purine G always
pairs with the pyrimidine C by 3 hydrogen bonds. The purine A always pairs with the
pyrimidine T by 2 hydrogen bonds.
 Single-Stranded RNA forms Complex Structures
Single-stranded RNA (and DNA) can fold back on itself to form complex tertiary
structures. This RNA tertiary structure also allows them to make large complex
structures, such as ribosomes, which are catalytic complexes made of RNA & proteins.
 DNA Replication
DNA is replicated via a semi-conservative mechanism, where one DNA strand serves
as the template for the precise duplication of the genetic information.
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a
possible copying mechanism for the genetic material.” - James Watson and Francis Crick, Nature,
April 25, 1953.
Practice copying the following DNA sequence:
 Transcription - DNA to RNA transcript
The information in DNA is transcribed into an RNA molecule in a process called
transcription. RNA is synthesized from the 5’ to 3’ direction by RNA polymerase.

Practice transcribing the following DNA sequence:

 Translation - RNA transcript to Protein
The information in the RNA transcript is translated into a polypeptide chain to form a
protein in a process called translation. The transcript is read in the 5’ to 3’ direction and
each 3 letters (codon) corresponds to a particular amino acid.

Practice translating the following RNA transcript:

 BIOCH-521A - Exam #3 Review
23. What different parts make up a nucleotide?

24. Why does the DNA helix have a fixed diameter?

25. Which base pairs have a stronger interaction?

 BIOCH-521A - Exam #3 Review
26. What are the major differences between DNA and RNA?

27. How does RNA make higher order structures?

 BIOCH-521A - Exam #3 Review
28. Write out the corresponding DNA strand: 5’-CCTAGGCTGAGGCAG-3’

29. Transcribe this DNA strand into RNA: 5’-TCCAGGACGTTGCCA-3’

30. Translate this RNA strand into a polypeptide chain: 5’-AUGGCGGGGAAUCGAUCG-3’