Biology 20A - Midterm 1 - John Tamkun UCSC

Most Common Elements in Cells

CHONPS

Strength of Bonds (Weakest to Strongest)

Hydrogen bonding < Ionic Bonding < Covalent Bonding (Non-polar < Polar

When pH decreases (becomes more acidic

Concentration of H+ goes up

5 Special Properties of Water

Cohesive, High Heat Capacity, High Heat of Vaporization, denser as a liquid, good solvent for polar molecules

1 m

10^-6 µm, 10^-9 nm, 10^-12 pm

How does perspiration keep our bodies cool?

Water has high heat of vaporization due to H-bonding, thus sweating (evaporation of water) has cooling effect on human body.

What is a buffer?

prevents changes in pH, usually weak acid with corresponding base. Can accept/release protons to maintain constant pH

Cells are mainly composed of...

Water and carbon-based molecules

Hydrocarbons

Molecules that contain only C and H

Linked by nonpolar covalent bonds

hydrophobic (not soluble in water)

Importance of Carbon chemistry

Unique in ability to form long chains, branched molecules, rings

Versatile building block for wide variety of complex molecules

Diversity of Hydrocarbon Skeletons

Vary in length

can be linear or branched

may contain one or more multiple bonds/rings

Common functional groups

Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydral, Phosphate

Hydroxyl Group

founds in alcohols, sugars, and other organic molecules

Carbonyl Group (Ketone)

middle of carbon chain=keytone

Carbonyl Group (Aldehyde)

end of carbon chain=aldehyde

Carboxyl Group

organic acid, exists in non ionized and non-ionized for(means O loses a H)

Amino Group

basic group, accepts protons

Sulfhydral Group

found on thials (??)

Phosphate Group

-Po4 (-2). Acidic group found on the 5' carbon in deoxyribose and ribose [DRAW THIS!]

4 Major Groups of Macromolecules

Carbohydrates

Proteins

Nucleic Acids

Lipids

Bonds are often made/broken by...

Dehydration reactions/Hydrolysis Reactions

Proteins (monomer/polymer)

Monomer: Amino Acids

Polymer: Polypeptide

Functions of Proteins

Structure, Regulation, Signaling, Movement, Metabolism, Transport

Amino Acid

[DRAW THIS!] Label amino group, alpha carbon, r-group, and carboxyl group!

How do R groups affect amino acids

It affects their structure/shape. Determines how they fold.

Alanine

A, Ala Nonpolar

Phenylalanine

F, Phe, Nonpolar

Glycine

G, Gly, Nonpolar

Isoleucine

I, Ile, Nonpolar

Leucine

L, Leu, Nonpolar

Methionine

M, Met, Nonpolar

Proline

P, Pro, Nonpolar

Valine

V, Val, Nonpolar

Tryptophan

W, Trp, Nonpolar

Cysteine

C, Cys, Polar

Asparagine

N, Asn, Polar

Glutamine

Q, Gin, Polar

Serine

S, Ser, Polar

Threonine

T, Thr, Polar

Tyrosine

Y, Tyr, Polar

Aspartate

D, Asp, Charged (Acidic)

Glutamate

E, Glu, Charged (Acidic)

Histidine

H, His, Charged (Basic)

Lysine

K, Lys, Charged (Basic)

Arginine

R, Arg, Charged (Basic)

All NON-POLAR Amino acid R-Groups

Mnemonic: GLAM VIP, WF (Glam vip, winner forever)

G (Gly) glycine

L (Leu) Leucine

A (Ala) Alanine

M (Met) Methionine

V (Val) Valine

I (Ile) Isoleucine

P (Pro) Proline

W (Trp) Tryptophan

F (Phe) Phenylalanine

All POLAR Amino acid R Groups

Mnemonic: QSCNTY ( Queen, So, CuNTY)

Q (Gln) glutamine

S (Ser) serine

N (Asn) asparaine

T (Thr) threonine

Y (tyr) tyrosine

All CHARGED ACIDIC Amino acid R-Groups

Mnemonic: DE (Diva, Endorser)

D (Asp) Aspartate

E (Glu) Glutamate

All CHARED BASIC Amino acid R-Groups

Mnemonic: HKR (Hawkeye Kissed Roy)

H (His) Histidine

K (Lys) Lysine

R (Arg) Arginine

Deoxyribose Structure

[DRAW THIS!] Mark where the nitrogenous base goes and where the phosphate group goes. Number the carbons and show ALL bonds

Ribose Structure

[DRAW THIS!] Mark where the nitrogenous base goes and where the phosphate group goes. Number the carbons and show ALL bonds

How do amino acids join together?

Peptide Bonds to form proteins

Written from N -> C Terminus

4 Levels of Protein Structure

Primary - sequence of amino acids

Secondary - short regions of folding on polypeptide backbone (due to polarity)

Tertiary - 3D structure of entire polypeptide

Quarternary - Structure of protein complexes

Proteins can be denatured by...

heat temperature, pH changes, salt concentration or solvent polarity

Carbohydrates (monomer/polymer)

Monosaccharides: Single sugars, eg glucose, fructose

(-ose ending)

General Formula: CnH2nOn

How are carbohydrates formed?

Two monosaccharides are joined via dehydration reaction

Oligosaccharides

Few monosaccharides bonded together (>3)

Carbohydrates (Polysaccharides)

Store chemical energy

Structural roles

Cellulose/plant starch are glucose polymers

arranged differently, animals can only digest one not the other

Lipids

hydrophobic

energy storage (fats and oils)

Major component of cell membranes

steroid hormones and signalling molecules

3 major classes of lipids

fats

phospholipids

steroids

Fats

Triglycerides

Glycerol + 3 fatty acids

fatty acid (pictured)long hydrocarbon with carboxyl group at end

added through dehydration

Phospholipids

glycerol + 2 fatty acids + phosphate-containing head group

hydrophillic head

hydrophobic tails

Amphipathic

form bilayers

structural basis for membranes

Saturated fatty acids vs Unsaturated fatty acids

Saturated contain no double bonds (more viscous)

unsaturated contain one or more double bonds (more fluid)

Saturation can influence the fluidity of...

...fats, oils and phospholipid bilayers

Nucleic Acids

Monomer: Nucleotides

Polymers: Nucleic Acids (eg DNA, RNA)

Dehydration builds polymers, hydrolysis breaks them down

DNA

Deoxyribonucleic acid

RNA

ribonucleic acid

Central Dogma of Molecular Bio

DNA (gene) encodes RNA (which encodes protein)

-->DNA contains genetic blueprint of cell

-->Transcription of DNA yields RNA

-->Translation of mRNA yields protein

-->tRNA and rRNAs involved in translation

Nucleotides

Composed of Nitrogenous Base, Sugar, Phosphate

Purines

Adenine, Guanine

Have double ring structure

Pyrimidines

Thymine, Uracil, Cytosine

Have single rings

Nucleoside

base + sugar

How are the nucleotides added to each other

Dehydration reaction of the 5' phosphate to the 3' OH of another

DNA (coupling of nucleotides)

A ----- T

G ----- C

RNA (coupling of nucleotides)

A ---- U

G ---- C

Two Major Classes of Metabolic Pathways

Catabolic

Anabolic

Catabolic

breakdown of molecules,

releases energy stored in chemical bonds

does not require energy

Anabolic

biosynthetic

creation of molecules

require energy

1st Law of Thermodynamics

energy neither created nor destroyed, only converted from one form to another

2nd Law of Thermodynamics

Every energy transfer increases the entropy (randomness) of the universe

if free energy is negative...

...reaction is exergonic, energy released can be used for work, spontaneous

if free energy is positive...

...reaction is endergonic, energy absorbed

ATP

Adenosine Tri Phosphate. Universal "currency" of the cell. Stores energy.

ATP to ADP reversible reaction

ATP hydrolysis releases energy by breaking the high-energy phosphate bonds. The reverse reaction combines ADP + Pi to regenerate ATP from ADP

Important Facts about Enzymes

Enzymes reduce activation energy, do not affect free energy

cant force reactions to occur

enzymes are specific

Cells contain thousand of different enzymes

How do cells regulate metabolic pathways?

By regulating activity of enzymes

What factors regulate enzyme activity?

Amount of enzymes in cell

phosphorylation of STY residues

Binding of small molecules

competitive inhibitors bind active site

compete with substrates

noncompetitive inhibitors/activators

aka allosteric effectors

alter structure and activity by

binding away from active site

How does changing a single amino acid in beta globin cause sickle cell disease?

changes secondary and tertiary structure leading to defective quarternary structures

What ends do the 5' and 3' ends have in nucleic acids?

5' end has a phosphate group. 3' end has a hydroxyl group. (next nucleotide monomer added to 3' end of polymer)

Bond that connect nucleotides

Phosphodiester bonds.

2 Major cell types

prokaryotes (ex. bacteria, archaebacteria) and eukaryotes (ex. protists, fungi, plants, animals)

Prokaryotic cell structure

Very simple. "Sack of enzymes plus DNA". Diameter about 1 micrometer

Eukaryotic Cell Structure

Highly organized and complex. Has a nucleus, cytoplasm, plasma membrane, and organelles. Complicated reproduction cycle. Diameter of typically 10 to 100 micrometers

Eukaryotic cell organelles:

Mitochondria: "powerhouse: of the cell, site of ATP synthesis

Chloroplasts: unique to plant cells, site of photosynthesis

Lysosomes: "trash can" of cell, has enzymes that digest macromolecules

Vacuoles: store nutrients and wastes

Endoplasmic reticulum and Golgi Apparatus: lipid synthesis, processing and sorting of membrane, secreted and lysosomal proteins (?)

Plasma membrane

seperate cells from external walls

internal membrane

subdivide eukaryotic cells into separate "compartments"

Microtubules

Made of tubulin, hollow tubes, and "straw-like. Promote cell movement, vesicle transport, and chromosome segregation

Microfilaments

Made of actin, are like filaments. Support cell shape and movement, muscle contraction, and cell division,

Intermediate filaments

Made of intermediate filaments, are "rope-like" cables . Promote structural integrity of cells and tissues.

Organization of microtubules

Have polarity (- and + ends), grow out of "microtubule organizing center" (ex. centrosome). Microtubules used like "rail-road" tracks to support vesicle transport along spinal cord.