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BIOCHEMISTRY • Introduction – Defn = chemistry of living organisms – 98% is C, H, O (99% is CHNOPS) – Organic chemistry deals mainly with ________. – Why is carbon so versatile? Draw its Lewis Dot structure. “All life is chemistry.” Jan Baptist van Helmont (1648)

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Page 1: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

BIOCHEMISTRY

• Introduction – Defn = chemistry of living organisms– 98% is C, H, O (99% is CHNOPS)– Organic chemistry deals mainly with ________.– Why is carbon so versatile? Draw its Lewis Dot

structure.

“All life is chemistry.” Jan Baptist van Helmont (1648)

Page 2: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

How many atoms of each element a human baby has.

Page 3: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

KEY for Model Building

• Black = ?

• White = ?

• Blue = ?

• Red = ?

• What do the white tubes represent?

Page 4: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Try making methane = CH4

It’s 3-D shape is what you built.

Is it polar or Nonpolar?

Page 5: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Try building carbon dioxide=CO2

Is it polar or nonpolar?

Page 6: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Functional group, -COOH(aka, carboxylic acid)

Why is it called an “acid?”

Page 7: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Organic Polymers that Life Requires

The BIG 4 Biomolecules1. Carbohydrates

2. Lipids/Fats

3. Proteins

4. Nucleic Acids (DNA & RNA)

All made up of C,H, O, N

Page 8: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

1. Carbohydrates

• Include mono- & polysaccharides

• Examples: glucose, fructose, sucrose, deoxyribose, amylose

• Named “carbo” “hydrates” b/c …

each carbon is hydrated w/ H- and –OH.

• Formula = Cn(H2O)n where n = whole number so carbs have 1C:2H:1O ratio.

Page 9: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

A. Monosaccharides

• Building blocks of polysaccharides

• Means “single sugars”

• Examples include glucose, fructose, galactose (all C6H12O6)>>isomers=same chemical make-up, different arrangement

Page 10: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Glucose

Page 11: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Why is glucose so important?

It is the energy molecule made by photosynthesis!

Page 12: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

B. Disaccharides

• “double sugars”• 2 monosacs joined together via dehydration

synthesis reaction

+ H20

• examples: glucose + glucose = maltose + water (see above) glucose + fructose = sucrose (table sugar) + H20 galactose + glucose = lactose (milk sugar) + H20

Page 13: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

C. Polysaccharides

• “many sugar” polymer made up of 200+ monosacs (“bricks”) to make a macromolecule “house”

• Usually long chains of glucoses joined together via dehydration synthesis

Page 14: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Examples of Polysaccharides

• I’ll provide 1 structural & 1 energy store for both plants & animals

• Made out of the same “brick”=glucose

• How those glucoses are arranged is what makes them different (structurally and functionally)

• Can you see how in the following 4 examples?

Page 15: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

#1=

-What monomer is repeated in this chain?-What do you notice about how they are positioned in the long chain?-What kind of reaction occurred to join all of them together?

Page 16: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Cellulose=structural polysac made up of α-glucoses joined 14 alternating orientation found in plant cell walls (tough& fibrous).

Page 17: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Can we humans digest it? • Humans cannot digest cellulose (but it is a source of

good fiber)• Neither can cows nor termites but their microbial

partners in their guts can

Page 18: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

#2=STARCH (aka, Amyloseose) made up of chains of glucoses w/ 14 right-

side up linkages How are these glucoses joined differently than those in

cellulose?

Page 19: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Can we animals digest starch?

Page 20: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

YES! With Amylase =enzyme found in saliva that digests amylose by breaking bonds betw. glucoses

Page 21: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Starch granules in plant cells

Photo by David Webb

How do animals store carbohydrates?

Page 22: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

#3=Glycogen (animals’ complex storage carb)

Page 23: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Glycogen(use it all & you’ll hit the wall)

Page 24: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

#4=Chitin (animal structural polysac). What does it resemble?

Page 25: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Chitin (continued)

• Monomer=glucosamine (amine group at the #2 carbon in the glucose ring)

• Found in the exoskeleton cuticle of insects and crustaceans

Page 26: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Chitin--found in the exoskeleton of the cicada

Page 27: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Chitin is sometimes purified &used in surgical wire

Page 28: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Indicator Tests for Carbs1. Reducing (simple) sugars: Benedict’s Solution made up of a Cupric ion (Cu 2+) which is blue reacts with reducing sugars that donate electrons resulting in Cuprous Oxide (Cu 1+) which is reddish in color.

Page 29: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

• Lugol’s Iodine solution is yellow-orangish in color but changes to bluish-black in the presence of the complex carb, starch.

2. Starch Test

Page 30: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

2. Lipids• Include fats, oils, waxes, & steroids

• Chemically different group classified together b/c they are insoluable in water (NONPOLAR).

A. Triglycerides = 3 fatty acids + glycerol

Page 31: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is
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Saturated vs. Unsaturated Fats

• So named b/c each carbon is “saturated with hydrogens”

• Found mainly in animals vs. plants

• Contain only single covalent bonds in long hydrocarbon chain vs. double bonds present in unsat. that lead to “kinks” in the long chain.

• Solid vs. liquid at room temp.

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Importance of Fats

• Great source of long-term energy storage (each gram of fat produces 2X as much energy as carbs/protein)

• Insulation (esp. needed in first 3 years of brain development of humans to insulate your brain nerve cells)

• Lubrication (keeps organs from tearing each other apart)

Page 38: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

B. Phospholipids=make up the bilayer of the cell membrane

OUTSIDE

INSIDES of a CELL

Inside of Cell Membrane

Page 39: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is
Page 40: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

C. Steroids->all made from cholesterol = a set of 4 hydrocarbon rings

Page 41: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

1.) Sex Steroids are hormones that use cholesterol as backbone

Figure 2: Estradiol

Page 42: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

2.) Fat-soluble vitaminslike Vitamin D

Formed from cholesterol.Important in maintaining strong bones and boosting immune system.

Page 43: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Lipid Indicator test: Sudan stain.Sudan IV is not soluble in water; it is, however, soluble in lipids. Red Sudan IV is added to a solution along with ethanol to dissolve any possible lipids. If lipids are present the Sudan IV will stain them reddish-orange, giving a positive test, usu. Forming a layer on top.

Page 44: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Sleep-Fat Study

• ttp://www.npr.org/blogs/health/2012/10/17/163018568/poor-sleep-may-lead-to-too-much-stored-fat-and-disease

Page 45: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

3. PROTEINS• Means “first place”

• Monomer = amino acids: central carbon w/ 1. Amino group

2. Carboxylic acid grp.

3. A Hydrogen

4. R group

Page 46: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

What is an R group?

• R = Replacement Group

• Could be anything but only 20 that life uses (see p. 367 for a list of them).

• Build yours and attach (see index cards).• Gives each amino acid its uniqueness &

specificity (dictates how the amino acid interacts w/ others)

• Either nonpolar, polar, or charged

Page 47: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is
Page 48: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

AA1 + AA2 Dipeptide + H20Left=remove –OH from carboxyl / Right =remove H

from amine. Connect 2 aa with peptide bond

+ H2O

Page 49: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Polypeptide= many amino acids joined together to create

long amino acids chain.

Smallest human one = gastric peptide (10aa)

Largest human protein = TITAN (>27,000 aa)

•For each peptide bond formed, a water molecule is lost thru dehydration synthesis.

•How that polypeptide folds and takes on a 3-D shape is determined by its R groups and how they interact w/ each other.

Page 50: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Roles that Proteins Play

1.) Speed up chemical reactions (catalysts) = ENZYMES

Ex: amylase: starts breaking down starch

Pepsin: starts breaking down proteins

ATP Synthase: helps make ATP

Page 51: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

2.) Structural / supportiveEx: collagen in tendons

Does this look like anything we’ve seen before?

Page 52: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

3.) Transport Ex: hemoglobin in red blood cells moves O2 throughout the body

Page 53: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

4.) Communication Hormones = messenger molecules that are secreted one place but have their effect elsewhere (Ex: insulin : secreted from pancreas & tells body cells to remove glucose from bloodstream)

Honors + Neurotransmitters (serotonin)

Page 54: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

insulin

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5.) Energy storage—egg whites contain albumin

Page 57: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

6.) Defense—antibodies that help immune system destroy invaders

Page 58: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

7.) Movement—actin & myosin in muscle fibers

Page 59: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

4. Nucleic Acids

• Named so because they are found mainly in the nucleusnucleus of cells.

• Include DNA & RNA.

• Monomer = nucleotide

Page 60: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

A. Structure– the nucleotide is made up of 3 parts

1.) 5-carbon sugar = Deoxyribose or Ribose

Page 61: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

2.) Nitrogen-Carbon Ringed Base

• DNA has 4 = A, C, G, or T

• RNA has 4 = A, C, G, or U

Page 62: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

3.) Phosphate Group

Page 63: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

NUCLEOTIDE: all 3 parts together

• See p. 48, Fig 2-16• See class model

-Red pentagon = sugar

-Purple = phosphate

-Middle colored “stairs” = adenine, thymine, cytosine, guanine

Page 64: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

B. Function of NAs

• The “code of life”

• Specifically they code for proteins• Each NA’s role:

DNA—stores the info (w/in chromosomes) for all of life’s processes (growth, metabolism, reproduction, etc.)

RNA—messenger that carries the info out

Page 65: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

Nucleic Acid Polymer Structure

A. DNA = double helix wound w/in large chromosomes

Page 66: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

`

B. RNA = single stranded, much shorter nucleotide sequences, comes in many different forms to perform different jobs in the decoding process

Page 67: BIOCHEMISTRY Introduction –Defn = chemistry of living organisms –98% is C, H, O (99% is CHNOPS) –Organic chemistry deals mainly with ________. –Why is

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