Biochemistry pt 1: THE CELL

Bios

Term which means “life”

Chemistry

Term which means “study of matter”

Biochemistry

• Chemical basis of life

• Study of chemical and chemical reactions occurring inside the body

Cell

Basic unit of life

1. Cell wall

2. Vacuole

3. Chloroplasts

Exclusive parts of the Plant cell

Cell wall

Contributes to the rigidity of the plant cell

Vacuole

Contributes to the turgidity of the plant cell

Chloroplasts

Produce the green pigment called Chlorophyll

Cellulose

Chemical composition of Plants’ cell wall

Peptidoglycan

Chemical composition of Bacteria’s cell wall

Chitin

Chemical composition of Fungi’s cell wall

Cell membrane

• Outermost part of the animal cell

• Forms closed bimolecular sheets that forms barriers to the flow of polar and ionized molecules

• Regulates the entry and exit of substances

Lysis

Too much water enters the cell —> Swell —> Burst

Crenation

Too much water exits the cell —> Shink

1. Phospholipids

2. Cholesterol

3. Glycolipids

4. Glycoproteins

Chemical composition of the Cell membrane

Glycolipids

Conjugates of sugars + lipids

Glycoproteins

Conjugates of sugars + proteins

Sugar

“glyco” means what?

1. Glycolipids

2. Glycoproteins

Sugars found in the cell membrane

Glycoproteins

Proteins found in the cell membrane

1. Phospholipids

2. Cholesterol

3. Glycolipids

Lipids found in the cell membrane

Phospholipids

Major/main type of membrane lipids

1. R = amino alcohol

2. Phosphate group

3. Platform: Glycerol or Sphingosine

4. One or more fatty acids

Chemical composition of Phospholipids

Polar

Are the ff. compounds polar or non-polar?

1. Amino alcohol

2. Phosphate

3. Glycerol

Non-polar

Are the fatty acids found in phospholipids polar or non-polar?

Amphiphilic

Phospholipids are _____________ compound

1. Hydrophilic head (POLAR)

2. Hydrophobic tails (NON-POLAR)

2 Faces of Phospholipids

1. Phosphoglyceride

2. Sphingolipids

2 Types of Phospholipids

1. Lecithin

2. Cephalin

Examples of Phosphoglyceride

Phosphatidylcholine

Other name of Lecithin

Phosphatidylethanolamine

Other name of Cephalin

Sphingomyelin

Example of Spingholipids

Sphingomyelin

• Insulator of Axons

• Chemical composition of Myelin sheets

Cholesterol

Bi-regulator of membrane fluidity

high, fluid

In ______ temperatures, the cell membrane becomes too ______ and cholesterol stabilizes the membrane and raises its melting point

low, rigid

In ______ temperatures, the cell membrane becomes too ______ and cholesterol intercalates between the phospholipids and prevents them from clumping together and stiffening

Glycolipids

Conjugates of sugar + lipids

1. Cerebrosides

2. Globosides

3. Gangliosides

Examples of glycolipids in the cell membrane

Cerebrosides

Simplest glycolipids

1. Glucocerebroside

2. Galactocerebroside

2 kinds of Cerebrosides

Glucose

Sugar portion of glucocerebroside

Galactose

Sugar portion of galactocerebroside

Ceramide

Lipid portion of glucocerebroside and galactocerebroside

1. Sphingosine

2. 1 Fatty acid

Chemical composition of ceramide

Glucocerebroside

Glucose + ceramide

Galactocerebroside

Galactose + ceramide

Globosides

Glycolipids which both of the sugars are present

Ceramide

Lipid portion of globosides

1. Glucose

2. Galactose

3. Ceramide

Chemical composition of Globosides

Gangliosides

Most complex type of Glycolipids

Sialic acid

• Sugar portion of Gangliosides

• Acidic sugar

• Classified as Nonose (9C sugar)

Ceramide

Lipid portion of gangliosides

1. Sialic acid

2. Oligosaccharides

3. Ceramide

Chemical composition of Gangliosides

Blood group antigens

• On the surface of RBC’s

• Determine blood type

Blood type O

Ceramide-Glc - Gal - GalNAc - Gal

l -> a-1,2 glycosidic bond

Fuc

Blood type A

Ceramide-Glc - Gal - GalNAc - Gal - GalNAc

l -> a-1,2 glycosidic bond

Fuc

Blood type B

Ceramide-Glc - Gal - GalNAc - Gal - Gal

l -> a-1,2 glycosidic bond

Fuc

Active transport

Is it Active transport or Passive transport?

• Against a concentration gradient (LOW TO HIGH)

• Uphill direction

Active transport

Is it Active transport or Passive transport?

• Energy requiring

• Harness free energy from hydrolysis of ATP

• Absorption of light

Active transport

Is it Active transport or Passive transport?

Na+-K+ ATPase Pump

Active transport

Is it Active transport or Passive transport?

• Carrier-mediated

• Since the carriers are mostly enzymes, they are: 1. Specific, 2. Saturable, 3. Inhibited by certain compounds

Passive transport

Is it Active transport or Passive transport?

• Along a concentration gradient (LOW TO HIGH)

• Downhill direction

Passive transport

Is it Active transport or Passive transport?

“Not energy requiring”

Passive transport

Is it Active transport or Passive transport?

“Ion-channels”

Passive diffusion

Not carrier-mediated passive transport

Facilitated diffusion

Carried-mediated passive transport

Na+-K+ ATPase Pump

• The transporter protein or PUMP would hydrolyze ATP

• Using the free energy released to drive conformational changes to the enzyme, it expels 3 Na+ from the cell and imports 2 K+ ions

Potassium

Major INTRACELLULAR CATION

Sodium

Major EXTRACELLULAR CATION

GABA

Major inhibitory neurotransmitter in the brain

GABA

• Binds to its receptor

• Conformational changes occur

• Receptor opens, Cl ions enter the cell via passive transport

• Cell becomes hyperpolarized

• Hyperpolarized cell cannot fire an action potential

Organelles

“small organs”; microscopic

Mitochondrion/Mitochondria

• Double membrane structure

• “Power house of the cell”

• Where carbohydrates, fats and amino acids are thoroughly oxidized to drive the synthesis of ATP for the cell

1. Ribose (5C sugar)

2. Adenine (N base)

Chemical composition of Adenosine

Adenosine Tri-Phosphate (ATP)

Contains 3 phosphate groups, Adenosine, and 2 HEPB

Adenosine Di-Phosphate (ADP)

Contains 2 phosphate groups, Adenosine, and 1 HEPB

Adenosine Mono-Phosphate (AMP)

Contains 1 phosphate group, Adenosine, 1 phosphoester bond, and 0 HEPB

High Energy Phosphoanhydride Bond

The acronym HEPB stands for what?

Phosphoanhydride bond

• Bond between 2 phosphate groups

• stores energy

• releases energy (30.5 kj/mol) when hydrolyzed

Phosphoester bond

Bond between adenosine and phosphate group

cAMP

AMP is catalyzed into what?

cAMP

Also known as secondary messenger

Adenylate cyclase

Enzyme that catalyzes AMP to cAMP

Lysosomes

• “Suicide bags of the cell”

• Digestive vesicles containing Hydrolytic enzymes or hydrolases that degrade: Lipids, Nucleic acids, Proteins

• Membrane bound

B-hexosaminidase A

Enzyme that breakdowns excess gangliosides

DNAse, RNAse

Enzymes that breakdowns excess DNA and RNA respectively

Collagenase

Enzyme that breakdowns collagens

Autophagy

• Natural, regulated mechanism of the cell that removes unnecessary or dysfunctional components

• Digest infective organelle inside the cell

Infection control

Pathogens (disease causing microbes and viruses) are “digested” by the enzymes in the lysosomes

Peroxisomes

• Secrete Catalase and Oxidase

• Protects the cell against the harmful effects of Hydrogen peroxidase

Catalase

Enzyme that catalyzes Hydrogen peroxide to Water and Oxygen

Oxidase

Enzyme that neutralizes O2 free radicals

Agua oxigenada

Hydrogen peroxide is also known as?

Ribosomes

• Sites of Protein Synthesis

• 2 Subunits: Small, Large

• not membrane-bound

Small : 30s

Large: 50s

Prokaryotes:

• Small: ____s

• Large: ____s

Small : 40s

Large: 60s

Eukaryotes:

• Small: ____s

• Large: ____s

1. Aminoglycosides

2. Tetracyclines

Antibacterial antibiotics that bind to 30 ribosomal subunits

1. Chloramphenicol

2. Erythromycin (Macrolides)

3. Lincosamides

Antibacterial antibiotics that bind to 50 ribosomal subunits

Endoplasmic reticulum

Continuous network of folded sac-like or tube-like membranes running from the nucleus outward, with many interior channels and vestibules

Rough ER

• ER that has ribosomes

• site of protein synthesis and folding