MCDB 6 Midterm 1

Smallest to Largest

atom, molecule, macromolecule, organelles, cells

Four Big Elements

H, C, O, N

H, C, O, N make what kind of bonds?

the most stable covalent bonds

Atomic Number

# of protons

Mass Number

protons + neutrons

Atoms with completed valance shells are...

unreactive or inert

Valence electrons...

determine the chemical behavior of atom

Covalent Bonds

sharing a pair of valence electrons

H2, O2, H2O, CH4

some of the strongest bonds

establish the basic structure of macromolecules

Non polar covalent bonds

atoms share electrons equally

Polar covalent bonds

one atom is more electronegative, do not share electrons equally

Ionic Bonds

atoms sometimes strip electrons from their bonding partners

after the transfer, both atoms have chargers and are called ions

What are the weak chemical bonds?

ionic bonds, hydrogen bonds, van der waals interactions

these determine the precise folding pattern

Hydrogen Bonds

forms when hydrogen atom is covalently bonded to one electronegative atom

Van de Waals

electron may be distributed asymmetrically in molecules or atoms

occurs only when molecules or atoms are very close

pretty weak, only strong when there are mannnyyy interactions

What does the molecular shape reveal?

its function

Is water polar or non polar?

polar (and held together by hydrogen bonding)

4 Properties of Water

1. cohesive behavior

2. moderate temperature

3. expansion upon freezing

4. versatility as a solvent

What would happen if we tried to dissolve non-polar compounds in H2O, such as oil?

they'll form two separate layers because it would be hydrophobic

What do all organic compounds include?

carbon

Four Ways Carbon Skeleton can vary

1. length

2. branching

3. double bond position

4. presence of rings

Isomer

same number of atoms, different structure (properties)

Structural Isomers

differ in the covalent arrangements of their atoms

ex: both compounds can be C5H12 but have different structures

Cis-Trans Isomer

differ in their spatial arrangements due to the inflexibility of double bonds

Cis

X's on the same side

Trans

X's on opposite sides

Enantiomers

mirror images of each other and differ in shape due to the presence of an asymmetric carbon

ex: like left hand vs right hand

Adenosine Triphosphate (ATP)

energy currency of the cell attached to a string of 3 phosphate groups

stores the potential to react with water

Macromolecules

polymers built from monomers

Polymer

long molecule consisting of many similar building blocks

Monomer

small building block

Dehydration Reaction

synthesizing a polymer

occurs when 2 monomers bond together through the loss of a H2O molecule

Hydrolysis

breaking down polymers

Carbohydrates

serves as fuel and building material

sugars, monosaccharides, polysaccharides, starch, glycogen, cellulose

Monosaccharides (CH2O)

the simplest carbs

glucose is the most common

Polysaccharides (starch)

composed of many sugar building blocks

Disaccharide

formed when a dehydration reaction joins two monosaccharides

a glycosidic linkage bonds the two monosaccharides

Glycosidic Linkage

a covalent bond that bonds the two monosaccharides

Polysaccharides

the polymers of the sugar (have structural and storage roles)

structure is determined by its sugar monomers and type of glycosidic linkage

Storage Polysaccharides

starch: made in plants, both branched and unbranched

glycogen: made in animals, highly branched

cellulose: unbranched, hydrogen bonding

Structural Polysaccharides

cellulose: major component of tough cell plant wall

chitin: found in exoskeleton of arthropods (spiders, lobsters)

Lipids

energy storage, diverse group of hydrophobic molecules

little to no affinity for water

hydrophobic

consists mostly of hydrocarbons

Phospholipids

makes up most of the cell membrane

the tail is hydrophobic

the head is hydrophilic

when in water they will self-assemble into a bilayer

Amphipathic

when it has two characteristics (like phospholipids)

Lipid Bilayer

thin polar membrane made of 2 layers of lipid molecules

barrier around the cell

Most important Triglycerides

fats, phospholipids, steroids

Triglycerides

fats; constructed from two types of smaller molecules (glycerol and fatty acid)

formed by dehydration reaction

Fatty Acid

consists of a carboxyl group attached to a long carbon skeleton

Saturated Fats

fatty acid chain has maximum number of hydrogen atoms and no double carbon bonds

ex: butter

its straight

Unsaturated Fats

chain has one or more double carbon bonds

cis double bond causes bending

usually liquid at room temp

ex: oil

Hydrogenation of Fatty Acids

used to solidify an oil

formation of trans (more solid at room temperature) fatty acid

Trans Fat

produced artificially from unsaturated fatty acids

it increases risk of heart disease, stroke, etc

worse than saturated fats

Steroids

characterize by a carbon skeleton consisting of four fused rings

Cholesterol

found in animal cell membranes

too much is bad for humans

Proteins

molecules that consists of one or more polypeptide (unbranched polymer built from set of 20 amino acids)

Polypeptide

unbranched polymer built from amino acids

range in length from a few to more than a thousand amino acids

each one has a unique linear sequence of amino acids with an amino end (N-terminus) and a carboxyl end (C-terminus)

Enzymatic proteins

selective acceleration of chemical reactions

ex: digestive enzymes catalyze the hydrolysis of bonds in food molecules

Defensive proteins

function: protection against disease

ex: antibodies inactive and help destroy viruses and bacteria

Storage Proteins

function: storage of amino acids

ex: casein (protein of milk) major source of amino acids for baby mammals

Transport Proteins

function: transport of substance

ex: hemoglobin

Hormonal Proteins

function: Coordination of an organism's activities

ex: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Receptor Proteins

function: Response of cell to chemical stimuli

ex: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Contractile and Motor Proteins

function: Movement

ex: Motor proteins are responsible

for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Structural Proteins

function: support

ex: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Making Proteins

to make a protein thats 10 amino acids long:

there are 20 amino acids in nature

so there are 20 possibilities for the 1st position and the 2nd and so on

20^10 = 200 billion combinations

The protein's structure determines?

its function

The amino acid sequence of each polypeptide determines?

the proteins 3D structure

Which compounds are formed by dehydration reaction?

triglycerides

Which is not a function of proteins?

to carry the information for synthesis from nucleus to ribosome

Four Levels of Protein Structure

primary

secondary

tertiary

quaternary

Primary Structure

unique sequence of amino acids; peptide bonds

change in it causes sickle cell disease

Secondary Structure

found in most proteins, consists of coils and folds in polypeptide chain (hydrogen bonds)

Tertiary Structure

determined by interactions among various side chains (R groups); disulfide bridge

Quaternary Structure

interactions between multiple polypeptide chains

arises when the protein consists of two or more polypeptide chains

Sickle Cell Disease

slight change in primary structure

an inherited blood disorder, from results from a singe amino acid substitution in the protein hemoglobin

What can cause a protein to unravel?

alterations in pH, salt concentration, temperature, etc

Denaturation

loss of a protein's native structure

makes it biologically inactive

X-ray Crystallography

determines 3D protein structure based on diffractions of an x-ray beam by atoms of crystallized molecules

Nucleic Acids

store, transmit, and help express hereditary info

polymers called polynucleotides

Roles of Nucleic Acids

1. deoxyribonucleic acid (DNA)

2. ribonucleic acid (RNA)

gene expression = DNA --> RNA --> protein

Pyrimidines

cytosine, thymine, uracil

way to remember: pyrimidines has a "y" and so does cytosine and thymine

Purines

Adenine, Guanine

Structure of DNA

two polynucleotides (forming a double helix)

antiparallel strands

Structure of RNA

one polypeptide chain

Genomics

approach used to analyze large sets of genes or compare the genomes of different species

Bioinformatics

use of computer software and other tools to analyze the data

The helix is an example of:

a secondary structure stabilized by hydrogen bonds

Watson and Crick Model

first to determine a structure

double stranded helix

later on, the conservative models, etc

2 sugar phosphate backbones on outside

bases on inside

backbone runs antiparallel

1 purine and 1 pyrimidine per base pair

discovered that A only paired with T and G only paired with C

T.H. Morgan

showed that genes are located on chromosomes

the two components of chromosomes—DNA and protein—became candidates for the genetic material

the key factor in determining the genetic material was choosing appropriate experimental organisms

Griffith Experiment

discovery of genetic role of DNA

genetic material survived heating and can be transferred from S cells into R cells, stably converting them into S cells; called transformation

did not say what genetic material was

S is pathogenic, R is non-pathogenic

Avery Experiment

Conclusion:

DNA carries the genetic material, not protein

the transforming substance is DNA

Virus

DNA (or RNA) enclosed by a protective protein coat

must infect cells and take over the cells' metabolic machinery in order to reproduce

ex: phages

Hershey and Martha Experiment

DNA is the genetic material of a phage known as T2

DNA was found in pellet with bacterial cells,

Protein found in supernatant with no cells

DNA but not protein enters cell, DNA must be genetic material

Chargaff's Rules

The base composition of DNA varies between

species

In any species the percentages of A and T bases are equal and the percentages of G and C bases are equal

(these were not understood until the discovery of the double helix)

Wilkins and Franklin

using a technique called X-ray crystallography to study molecular structure

Franklin's X-ray Crystallography

produced an image of the DNA molecule

DNA is helical, like a spiral staircase

DNA is composed of more than one chain, likely 2-3

DNA has a regular structure=long and narrow, constant width

Watson's and Crick's Semiconservative Model of Replication

predicts that when a double helix replicates

each daughter molecule will have one old strand (derived or "conserved" from the parent molecule) and one newly made strand

the "right" model

Three alternative models of DNA replication

the semiconservative is the "right model"

Meselson and Stahl Experiments

main question do the 2 strands of DNA separate from one another during replication??

supported the semiconservative model of DNA replication

N15=heavy DNA, N14=light DNA

used density gradient centrifugation

How many mistakes with every 10 billion nucleotides?

approximately one

Replication begins at sites called?

origins of replication

where the two DNA strands are separated, opening up a "bubble"