Biochem Fun: Exam 1 Review

Front 1

5 Characteristics of Living Organisms

Back 1

1. Complex and dynamic - Biomolecules and biochemical reactions
2. Organized and self-sustaining - Hierarchial order (atoms->organism) and a constant influx of energy and matter. Also has enzyme regulated metabolic pathways.
3. Cellular - cell membranes regulate entrance and exit of crap
4. Information-based - DNA
5. Mutations -> Adaptation and evolution

Front 2

Organic Functional Groups

Back 2

alkene
alcohol
thiol
aldehyde
keton
ester
amine
amide
carboxylic acid

Front 3

Small and Large Biomolecules

Back 3

Amino Acids -> Peptides, Polypeptides and Proteins
Monosaccharides -> Carbs and polyglycans
Fatty Acids (lipids)
Nucleotides -> Nucleic Acids

Front 4

4 Classes of Large Biomolecules

Back 4

Carbohydrates
Lipids
Nucleic Acids
Proteins

Front 5

Structure and bonding of Amino Acids

Back 5

Amino group, Carboxylic Acid group, Side Chain
Peptide/Amide bonds - has double-bond character that impacts overall structure

Front 6

Individual amino acids inside proteins are called

Back 6

residues

Front 7

Polypeptides vs peptides vs proteins

Back 7

Peptides and proteins are TYPES of polypeptides
Peptides have 50 or fewer amino acids
Proteins have more than 50 amino acids

Front 8

Structure and function of sugars/Carbz

Back 8

contain alcohol groups + carbonylz (aldehydres in aldoses and ketones in ketoses)
Functions - energy, structure, communication

Front 9

Structure and function of fatty acids

Back 9

Long hydrocarbon chains with a carboxylic acid group.
They are a component of lipids, so fat soluble but not water soluble
Triglycerols store energy
Phophoglycerides (like phospholipids) function in membrane

Front 10

Structure and function of Nucleotides

Back 10

Five-carbon sugar, 1 or more phosphate groups, and purine/pyrimidine base (2/1 ring nitrogenous base)

Super important in biosynthetic and energy-generating reactions

GA = Pure, 2 rings
UTC = Pyrimidines, 1 ring
CG = 3 bonds
AT = 2 bonds

Front 11

ATP is a type of...

Back 11

Nucleotide??

Front 12

Structure of nucleic acids

Back 12

nucleotides with phosphodiester linkages

Front 13

Big organic functional groups in biomolecules

Back 13

Phosphoester - OPOR
Phosphodiester - ROPOR
Phosphoanhydride - OPOPO
Anhydride - OCOCO

Front 14

Autopoiesis

Back 14

Autonomy, self-organization and self-maintenance

Front 15

Most Common Biochemical Reactions

Back 15

Nucleophilic Substitution (hydrolysis)
Addition
Elimination (hydration)
Isomerization
Redox

Front 16

Anabolism vs catabolism

Back 16

ANA builds biomolecules and the cat claws them apart (biosynth vs degradation)
ANA uses energy and the cat stores it up
Uses electrons vs capturing
Uses oxidation of NADH, FADH2 and NADPH vs reduction of NAD, FAD and NADP+

Front 17

Self-assembly

Back 17

biomolecules in supramolecular structures are able to assemble because of the STERIC INFORMATION they contain

Front 18

Macromolecular crowding

Back 18

cells are densely crowded. Macromolecular crowding is a significant factor in a wide variety of cellular processes

Front 19

Words that are related to signal transduction lol

Back 19

signals
Neurotransmitters
hormones
cytokines
ligands

Front 20

Structure of Prokaryotic cells

Back 20

cell wall and plasma membrane. Has nucleoid

Front 21

Vesicular organelles

Back 21

examples include acid hydrolase-rich lysosome, plant vacuoles, granules, and melanosomes.

Front 22

Peroxisomes

Back 22

generate and break down peroxides - glyoxsomes in plants

Front 23

Plastids

Back 23

plants, algae and some protists - sites of manufacture and storage

Front 24

Hydrophilic vs hydrophobic on structure

Back 24

Hydrophilic molecules readily interact with water molecules via dipole-dipole interactions or h-bonds. Hydrophobic molecules avoid water. Large biomolecules that have hydrophobic and hydrophillic arrange themselves accordingly
Proteins fold so that the hydrophobic sections are tucked inside.

Front 25

Membrane proteins

Back 25

Integral - (embedded) vs peripheral (on surface)
Channel - transport specific ions across the membrane
Carrier - Transport specific molecules across the membrane
Receptors - signal transduction
Anchor - Attach membrane to macromolecules

Front 26

Self assembly occurs because of.....

Back 26

STERIC INFORMATION in the macromolecules: complementary shapes fit together to optimize hydrophilic interactions, hydrophobic interactions, and many weak interactions

Front 27

Molecular machines

Back 27

Examples: ribosomes and sarcomeres
1.Nucleotide binds to motor protein
2.Nucleotide hydrolyzes and releases energy
3.Energy causes changes in shape
4. Change is transmitted to nearby subunits

Front 28

Phases of signal transduction

Back 28

1. Reception - signal molecule (ligand) binds to and activates receptor on membrane surface, causing transduction.
2. Transduction - a change in receptor shape
3. Response - inside the cell, a cascade of events that involves covalent modification of proteins and result in changes such as enzyme activity, gene expression, and motion

Front 29

Common features of prokaryotic cells

Back 29

cell wall
plasma membrane
circular DNA molecules
No internal membrane-enclosed organelles
-Pili and flagella

Front 30

Cell walls of prokaryotic cells (gram +/-)

Back 30

Gram positive - thick peptidoglycan layer outisde plasma membrane
Gram negative - More complex cell walls:
1. glycocalyx - slime layer
2. outer membrane - LPS with porins
3. Periplasmic space - with peptidoglycans and proteins
4. Inner(plasma) membrane

Front 31

DNA of prokaryotic cells

Back 31

Nucleoid - of chromosomes
Also has plasmids - small circles of DNA

Front 32

Eukaryotic plasma membrane structure

Back 32

glycocalyx, receptors, extracellular matrix; cell cortex

Front 33

Eukaryotic ER structure

Back 33

Lumen/cisternal space
Rough - synthesis of membrane proteins and proteins for export
Smooth - lipid synthesis, biotransformation
Sarcoplasmic Reticulus - SER in striated muscle

Front 34

Eukaryotic Golgi Apparatus

Back 34

packages and distributes cell products in compartments
Vesicles
Called dictyosomes in plants

Front 35

Eukaryotic nucleolus

Back 35

synthesis of ribosomal DNA

Front 36

Function of mitochondria

Back 36

aerobic metabolism - oxygen-dependent synthesis of ATP
Regulation of apoptosis

Front 37

Function of peroxisomes

Back 37

break down peroxides (R-O-O-R)

Front 38

Plant-only organelles

Back 38

vacuole - contains acid hydrolases, like lysosomes
microfilaments
cell wall (contains cellulose)
Dictyosomes - like golgi
peroxisomes - one kind is in leaves for photorespiration and GLYOXYSOMES, in germinating seeds convert lips to carbz

Front 39

Plastids are like...

Back 39

MITOCHONDRIA.
Proplastids are plastid precursors:
1. Leucoplasts leukoplasts (storage)
2. Chromoplasts (pigment)
- Chloroplasts - photosynth with grana, thylakoid lumen and membrane
-stroma - like mitochondrial matrix

Front 40

Microtubules (3 types)

Back 40

Structural support for long, thin cells; protein = tubulin
Microfilaments - cytoplasmic streaming and amoeboid movement; protein = actin
Intermediate filaments - maintain cell shape under mechanical stress; various proteins; keratin

Front 41

How can H-bonds form?

Back 41

occur between hydrogen that is attached to an oxygen/nitrogen and a lone pair of electrons (O,N,S)

Front 42

How many hydrogen bonds can form

Back 42

4/molecule

Front 43

What does hydrogen bonding form

Back 43

BP, MP, heat of vaporization, surface tension, heat capacity, and viscosity of water

Front 44

What influences how strong van der Waals forces are?

Back 44

How easily the atom is polarized

Front 45

Types of vdW forces

Back 45

Dipole-dipole
Dipole-induced dipole
Induced-Induced - London dispersion. They are individually the weakest.

Front 46

Influence(s) of solvation spheres

Back 46

1 - charge density. Smaller and more highly charged, larger the solvation sphere
2 - larger solvation spheres make spheres move more slowly

Front 47

What causes sol-gel transitions?

Back 47

temp, matrix architecture, inclusion of solutes

Front 48

Sol-gel transitions

Back 48

gel-like properties of cytoplasm that result from polar surfaces of polymers forming highly structured solvation layers
Contibutes to cell movement and other functions including actin-binding proteins; amoeboid motion

Front 49

What causes hydrophobic interactions?

Back 49

Water molecules maximize hydrogen bonds with other water molecules and minimize interaction with nonpolar moleucles. Attraction of nonpolar molecules contributes, but it's the force of water EXCLUDING nonpolar molecules that drives hydrophobic interactions

Front 50

Cell membrane potential

Back 50

Cytoplasmic side of cell is negatively charged due to amino acid R groups in proteins

Front 51

Buffer formation

Back 51

a weak acid and its conjugate base

Front 52

Buffers are most effective when the pH is...

Back 52

within a range of +/- 1 of the pKa

Front 53

Open vs Closed vs Isolated Systems

Back 53

Front 54

State vs process functions

Back 54

Enthalpy entropy and free energy are state functions
heat and work are process functions

Front 55

How can systems spontaneously decrease entropy?

Back 55

Surroundings become more disordered, overall disorder still has to increase (2nd Law of Thermo)

Front 56

Delta G with a 0 up top

Back 56

Free energy change at standard state: 25 Celsius, 1atm, 1M

Front 57

Delta G with 01 up top

Back 57

Free energy change at BIOCHEMICAL standard state - pH

Front 58

Thermodynamics vs Kinetics

Back 58

Thermo tells whether a reaction will be SPONTANEOUS/EXERGONIC (energy released)

Kinetics tells HOW FAST a reaction will go (involves enzymatic activity)

Front 59

Fibrous vs Globular Proteins

Back 59

Fibrous - Function usually involves structural support
Globular - Function usually involves binding to LIGANDS or other macromolecules (COOPERATIVE BONDING)

Front 60

Biologically Active Amino Acids

Back 60

Chemical Messengers
-Neurotrans - glycine, glutamate, GABA, serotonin, melatonin,
-Hormones - thyroxine, indole acetic acid
Precursors to complex N-molecules
Metabolic intermediates

Front 61

Amino Acid Derivatives

Back 61

formed thru carboxylation, hydroxylation, and phosphorylation
Example - serine, threonine and tyrosine all get phosphorylated (contain hydroxyl groups)

Front 62

Stereochemistry and amino acids

Back 62

All amino acids except glycine contain a chiral carbon
All proteins contain L-Amino acids (Ds are supes rare)

Front 63

Typical pKa that amino acids ionize their COOH and NH2 groups

Back 63

COOH around 2
NH2 around 9

Front 64

Characteristics of Peptide Bonds

Back 64

Partial double bond character - rigid and planar
Alpha carbon NEXT to carbonyl
Psi - rotation around alpha carbon-Nitrogen bond
Phi - rotation around alpha carbon- carbon bond

Front 65

Peptide/Protein sequence using termini

Back 65

N to C terminus. IMPORTANT because order influences bonding which will influence pKa and schtuff

Front 66

Functions of Proteins

Back 66

Catalysis, structure, movement, defense, regulation, transport, storage, stress response

Front 67

Protein shapes

Back 67

Fibrous and Globular

Front 68

Protein compositions

Back 68

Simple vs Conjugated
Conjugated = simple + prosthetic group

HOLOPROTEINS (CONJUGATED) HAVE (prosthetic groups)
BUT
(prosthetic groups are) ABSENT IN APOPROTEINS

Front 69

Characteristics of two types of secondary protein structures

Back 69

Alpha helix - Hydrogen bonds are FOUR residues apart, R groups extend OUTWARD, incompatible with glycine, proline, and sequences with too many charged/bulky R groups
Beta sheet - Parallel or antiparallel, Adjacent chains H-bond, ANTIPARALLEL IS MORE STABLE because bonds are colinear and shorter

Front 70

Stabilizing Factors of Tertiary Protein Structure

Back 70

Hydrophobic Interactions
Electrostatic Interactions
Hydrogen Bonding
Covalent Bonding (disulfide bridges)
Hydration (hydration shells)

Front 71

Features of Tertiary Structure

Back 71

1. Amino acids are far apart in primary structure, but get close and personal once folded.
2. Globular proteins are more compact
3. Large globular proteins contain DOMAINS, compact units with specific function.
4. Modular vs. Mosaic proteins - eukaryotes contain duplicate/imperfect copies of domains that are linked in series

Front 72

What holds quaternary structure in place?

Back 72

noncovalent and
covalent bonds (disulfide bridges, desmosine and lysinoroleucine)
MOST IMPORTANTLY, hydrophobic effect

Front 73

Function of IUPs

Back 73

Intrinsically Unstructured Proteins
Regulation of signal transduction, transcription, translation, cell proliferation.
They're super flexible and search for binding partners (to make them less fugly/disordered)

Front 74

Very basically, what causes denaturation?

Back 74

Disruption of forces that stabilize 3-D structure

Front 75

Denaturing Agents

Back 75

strong acids
strong bases
organic solvents
detergents
reducing agents (disulfide bonds)
salt concentration (salting out)
heavy metal ions
temperature changes
mechanical stress

Front 76

Types of motor proteins

Back 76

1. Classical motors - myosins, kinesins, dyneins
2. Timing devices
3. Microprocessing switching devices
4. Assembly and disassembly factors

Front 77

Traditional Folding Model of Proteins

Back 77

Amino acid side chain interactions force molecule into it's shape
Limitations:
1. Time constraints - seconds, not years
2. Complexity - LOTS of possible rotations

Front 78

Recent Protein Folding Discoveries

Back 78

1. Secondary structure is formed super early
2. Hydrophobic interactions are super important
3. Larger polypeptides have partially folded intermediate structures
4. MOLECULAR CHAPERONES - Bind to unfolded/denatured proteins, protect them from incorrect interactions, assist in folding, and promote degradation when refolding isn't possible

Front 79

Most Molecular Chaperones are...

Back 79

Heat Shock Proteins:
1. Hsp70s - bind to short hydrophobic segments in unfolded PPs to prevent aggregation. ATP hydrolysis releases PP, which is then passed to...
2. Hsp60s (chaparonins or Cpn60) - Mediate protein folding and release the PP upon ATP hydrolysis

Front 80

Fibrous Proteins

Back 80

Structural Function - rodlike/sheetlike (regular secondary structure)
Examples - keratin (hair), collagen (tendons), silk, fibroin (silk)

Front 81

Example of the dynamic function of globular proteins

Back 81

Globular proteins mainly function in binding to ligands or large biomolecules.
Myoglobin (cardiac/muscle) and Hemoglobin (red blood)
Heme decreases affinity for oxygen and protects from irreverible oxidation of Fe2+
Fetal HbF has greater affinity for oxygen than maternal hemoglobin
Myoglobin has greater affinity for oxygen than hemoglobin, will only give up oxygen when the concentration is super low

Front 82

Cooperative binding in hemoglobin is stimulated by...

Back 82

taut state
oxygen binding
High CO2
High BPG
low pH

Front 83

Bohr Effect

Back 83

Dissociation of O2 from hemoglobin is enhanced at low pH.
High CO2 concentration increases H+ concentration by reacting with water to form H+ and bicarbonate ions. H+ stabilizes deoxy form of hemoglobin