Biochemistry Final

Front 1

What is the hierarchy of atoms to organisms?

Back 1

1. Atoms
2. Molecules
3. Macromolecules
4. Macromolecular Assemblies
5. [Organelles]
6. Cells
7. [Tissues]
8. Organisms

Front 2

What are the 2 major types of cells?

Back 2

Prokaryotes & Eukaryotes

Front 3

Eukaryotes: 4 characteristics & Example

Back 3

1. No nucleus
2. No organelles
3. Single-Circular Chromosomes
4. Divide Quickly

Ex.) Bacteria

Front 4

Prokaryotes: 4 characteristics & Example

Back 4

1. Has Nucleus
2. Has Organelles
3. Multiple-Linear Chromosomes
4. Longer to Divide

Front 5

Organelles

Back 5

- Discrete, membrane bound compartment within a cell with a discrete function

- Not all cells have organelles in equal amounts: the type and # reflect function

Front 6

Nucleus

Back 6

DNA replication & transcription

Front 7

Nucleolus

Back 7

Not an organelle; makes ribosomes

Front 8

Mitochondria

Back 8

Citric acid cycle, beta oxidation, oxidative phosphorylation, generate ATP

Front 9

Rough Endoplasmic Reticulum (RER)

Back 9

Directs proteins (secreted or membrane) to location

Front 10

Golgi Body

Back 10

Carbohydrates are attached to proteins (only secreted/membrane)

Ex) Blood proteins - A carb, B carb, both, or none

Front 11

Smooth Endoplasmic Reticulum (SER)

Back 11

Fat metabolism

Front 12

Lysosome

Back 12

Breaks down macromolecules

Front 13

Macromolecular Assemblies

Back 13

Made of macromolecules not held by a covalent bond

Ex) Protein & DNA

Front 14

What are the most common atoms in organisms?

Back 14

C, H, O, N

Front 15

Functional Groups: Carbon-Carbon

Back 15

1. Alkane
2. Alkene (trans or cis)

Front 16

Functional Groups: Carbon-Oxygen

Back 16

1. Alcohol
2. Ketone
3. Aldehyde
4. Carboxylic Acid
5. Ester
6. Ether

Front 17

Functional Groups: Carbon-Nitrogen

Back 17

1. Amide
2. Amine

Front 18

Amino Acids

Back 18

Macromolecule: protein
How Big: hundreds of a.a.
Bond: peptide
Function: enzymes, communication (ex. Insulin), transport (ex. Hemoglobin), structure (ex. Collagen), defense (ex. Antibody), other

Front 19

Draw Amino Acids & Protein

Back 19

Front 20

Sugars

Back 20

3 common 6 carbon sugars: glucose, fructose, galactose
Macromolecule: glycogen, starch (animal); cellulose (plant)
Bond: alpha 1-4 ether bond (glucose)

Front 21

Draw Glucose & Starch

Back 21

Front 22

Nucleotide

Back 22

- Nitrogenous base (A,G,C,T,U) + 5 carbon sugar (Ribose or Deoxyribose)
Macromolecule: DNA (Deoxyribose) & RNA (Ribose)

DNA + Phosphate + A/C/T/G
RNA + Phosphate + A/C/U/G

- DNA Function: stores genetic info (3 nucleotides encode 1 a.a.)
- RNA Function: intermediate in flow of genetic info

Front 23

Draw a Nucleotide & DNA

Back 23

To form macromolecule, phosphate of incoming nucleotide attaches to 3' OH of sugar

Front 24

Simple Fats

Back 24

Fatty Acids: Saturated or Unsaturated (Double Bonded Carbons)

Bonds: Ester, phosphoester, amide, ether
Macromolecules:
1.TAG (energy storage)
2. PL (membrane)
3. Sphingolipid (membrane)
4. Cholesterol (stiffens membrane, starting point for synthesis of steroid hormones)

Front 25

Draw Saturated & Unsaturated Fatty Acids

Back 25

Front 26

What is the problem with trans fat?

Back 26

1. Can be catabolized
2. Tend to raise LDL (bad cholesterol) and lower HDL (good cholesterol)

Front 27

Difference b/w Cis & Trans

Back 27

- All naturally occurring fats are cis
- Trans fats are made by hydrogenation of naturally occurring fats

Front 28

What are omega fats?

Back 28

Omega number is number of carbons in 1st double bond from non-carboxylic acid end

Front 29

Triacylglycerol (TAG)

Back 29

Glycerol + 3 fatty acids

[Ester Bond]

Front 30

Phospholipid (PL)

Back 30

Glycerol + 2 fatty acids + phosphate + "x"

[Ester (fatty acids) & Phosphoester Bonds (phosphate)]

Front 31

Sphingolipid

Back 31

Sphingosine + fatty acid + sugar

[Amide (Fatty acid) & Ether (Sugar) Bonds]

Front 32

Cholesterol

Back 32

Front 33

What is metabolomics & how is it done?

Back 33

Separate & ID all molecules in any given cell

How?
1. High powered NMR
2. Gas Chromoatography-Mass Spectrometry (GC)

Front 34

Process of Metabolomics

Back 34

Front 35

Acid & Base: Ka

Back 35

Front 36

Acid & Base: pKa

Back 36

- Log of Ka
- Meaning: pH at which 50% HA and 50% A-

Front 37

Henderson-Hasselbach

Back 37

Calculates ratio of acid to base

Use to find % acid & % base to calculate overall charge

Front 38

How to calculate charge

Back 38

1. Find % acid and % base
2. Draw acid form & base form to find individual charges (0, +1, -1)
3. Multiply charges by percentages & add

Charge = %A(charge) + %HA(charge)

Front 39

% HA and % A- when pH is ______ than pKa. (3 less, 2 less, 1 less, equal, 1 more, 2 more, 3 more)

Back 39

3 < : 99.9% HA, 0.1% A-
2 < : 99% HA, 1% A-
1 <: 90% HA, 10% A-
equal: 50% HA, 50% A-
1 >: 10% HA, 90% A-
2 >: 1% HA, 99% A-
3 >: 0.1% HA, 99.9% A-

Front 40

Rule of thumb w/ pKa & pH

Back 40

pH < pKa: acid

pH +1 or -1 from pKa: mixture

pH > pKa: base

Front 41

Titration Curve

Back 41

Flat = buffer regions
Steep = equivalence points

Titrant: NaOH

Front 42

Draw Amino Acid Backbone at pH 2, 7, 11

Back 42

Amine group: pKa=9
Carboxylic Acid group: pKa=2
R group: variable

Front 43

Are amino acids good physiological buffers?

Back 43

Physiological pH is 7.

Unless R group has a pKa around 7, a.a. are not good buffers.

Front 44

What are physiological buffers in the cells & in the blood?

Back 44

Cells: phosphoric acid (H2PO4)

Blood: carbonic acid (H2CO3)

Note: CO2 + H2O can dissociate like carbonic acid, so increased or decreased levels of CO2 (depends on breathing) can effect blood pH

Front 45

Respiratory Alkalosis

Back 45

Blood pH > 7.45

Front 46

Respiratory Acidosis

Back 46

Blood pH < 7.45

Front 47

Zwitterion

Back 47

Formal charges on molecules, but overall charge

Ex) amino acids

Front 48

(1) What enantiomer form are most amino acids found in nature? (2) Where is the other form found?

Back 48

1. L form
2. D form found in bacterial cell wall

Front 49

What are the 2 categories of nonstandard a.a.?

Back 49

Modified: covalent modification of standard a.a.

Specialized: not related to standard a.a. (ex. Ornithine from urea cycle)

Front 50

Why only 20 standard amino acids?

Back 50

Only ones found in genetic code (sequence of nucleotides: 3 nucleotides = codon)

3 stop codons - 61 codons that create a.a.

64 codons for 20 a.a.

Front 51

Why is the genetic code considered to be degenerate?

Back 51

There can be more than 1 codon for a.a.

Front 52

Nonessential Amino Acids

Back 52

Can be made in the body so don't have to come from the diet

Front 53

Essential Amino Acids

Back 53

Can't be made in the body must come from diet

Front 54

Are the standard amino acids the only ones found in proteins?

Back 54

No standard amino acids can be modified post-translationally

Front 55

What are the covalent modifications to the std a.a. ?

Back 55

1. Phosphorylation: requires alcohol (Ser, Thr, Tyr)

2. Glycosylation: occurs in Golgi body; N-linked requires amide (ASN, GLN), O-linked requires alcohol (Ser, Thr, Tyr)

3. Alkylation: variety of a.a.