Biology 1113 Exam 1

Ch1-6

Amino Group

Carboxyl Group

Carbonyl Group (Aldehyde)

Carbonyl Group (Ketone)

Hydroxyl Group

Phosphate Group

Sulfhydryl

Amino Group

Amines. Acts as a base - tends to gain a proton in solution and form NH3+

Carboxyl Group

Carboxylic Acids. Acts as an acid, tends to lose a proton in solution

Carbonyl Group

Aldehydes and Ketones. Can react with other compounds to form larger molecules

Hydroxyl Group

Alcohols. Highly polar, makes compounds more soluble through H interactions w/ water, can act as a weak acid and drop a proton

Phosphate Group

Organic Phosphates. Molecules with more than 1 phosphate linked together store large amounts of chemical energy.

Sulfhydryl Group

Thiols. In proteins, form disulfide bonds (S-S) that contribute to protein structure.

Question

Typically based on an observation

Hypothesis

Proposed, testable explanation for an observation

Null Hypothesis

The counterpart to a hypothesis, predicting no effect

Prediction

Specefic, testable outcomes. If-then statement

The Cell Theory

Robert Hooke and Anton van Leeuwenhoek. All organisms are made of cells, all cells come from preexisting cells

Robert Hooke

Coined the term Cell, cell theory

Anton van Leeuwenhoek

better microscope, animalcules, cell theory

Chromosomal Theory of Inheritance

Hereditary info is encoded in units called genes located on chromosomes. DNA is the hereditary material, genes are sections of DNA that code for cell products

Theory of Evolution by Natural Selection

Species are related by common ancestry. Characteristics of species can be modified from generation to generation.

evolution

a change in allele frequency in a population over time

Natural Selection

Individuals with specific heritable traits produce more surviving offspring, so those traits become more common

Fitness

An individual’s ability to produce surviving, fertile offspring relative to others in the population

Adaptation

A heritable trait that increases an individual’s fitness in a particular environment relative to individuals lacking that trait

Prokaryotes

Bacteria and Archaea, no nucleus or membrane bound organelles

Eukaryotes

contain a nucleus and membrane bound organelles

Genus

First part of the scientific name. Homo sapiens, genus is Homo

Species

Second part of scientific name, Homo sapiens, sapiens is species

5 Characteristics of Living Organisms

Cells, Replication, Information, Energy (acquire and use), Evolution (CRIEE)

The Central Dogma of Biology

DNA → RNA → Protein

Phylogenetic Tree

Diagram that shows evolutionary relationships

Dalton

unit of measurement (1Da = 1amu)

isotopes

Forms of an element with different amounts of neutrons

Covalent Bonds

two atoms share a pair of valence electrons

Electronegativity

How strongly an atom pulls shared electrons

Ionic Bonds

Electromagnetic attraction between oppositely charged ions (ex NaCl)

Hydrophobic Interactions

Clustering of nonpolar molecules in water

Hydrogen Bonds

The attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge

Van der Waals Interactions

weak electrostatic forces of attraction or repulsion between neutral atoms or molecules that are close to each other

Polar

electrons are not shared equally

Nonpolar

Equal electron sharing

Solution

Solute + Solvent

Solute

A substance that gets dissolved

Solvent

What does the dissolving

Dissolve

when a substance (the solute) breaks down into individual molecules or ions and spreads evenly through a liquid (the solvent) to form a clear, uniform mixture called a solution

Cohesion

Water sticks to itself

Adhesion

Water sticks to other things

Surface Tension

Cohesive force caused by the attraction of surface molecules

Acid

A molecule that gives up a proton (H+) during a chemical rxn

Base

A molecule that acquires a proton (H+) during a chem rxn

Buffer

Reduces the impact of adding acids or bases to the overall pH

Potential Energy

Stored energy

Kinetic Energy

energy of motion

Chemical energy

potential energy “stored in bonds”

Thermal Energy

kinetic energy of molecular motion

Entropy

A measurement of the disorder/randomness of a system

Condensation Reaction

A reaction where water is given off as a product when two molecules bond together

Hydrolysis reaction

Water is used to break bonds

Catalysis

Increasing the speed of a rxn by adding a catalyst

Amino Acid

monomer of proteins. Amino grouup + alpha carbon + carboxyl group + R group + H

R Group/Side Chain

A unique set of atoms connected to the base of a molecule. Amino Acids are differentiated by their R Groups

Peptide Bonds

The C-N bond that holds amino acids together. Electron sharing between the N and C gives the peptide bond properties of a double bond

Polypeptide

Chain of Amino Acid residues

Primary Protein Structure

Order of amino acids

H-terminus

The end of the polypeptide with the Amino Group

N-terminus

The end of the polypeptide with the Carboxyl group

Secondary Protein Structure

alpha helices and beta pleated sheets. Formed by hydrogen bonds between the backbone atoms

Tertiary Protein Structure

The secondary structure gets twisty and folds. Caused by interactions between R groups. This is where disulfide bonds happen

Quaternary Protein Structure

Multiple polypeptides come together. Not all proteins have this

Denatureation

a process where proteins or nucleic acids lose their native three-dimensional structure and biological activity due to external stress. Common denaturants are heat, pH, high salt, and reducing agents that break structural bonds.

Residue

The term for an amino acid that is in a chain. Also used for carbohydrates and other structures

Enyzme

Special proteins that act as catalysts

Active Site

Where catalysis occurs

Substrates

Reactants in a catalyzed reaction

Nucleotide

Monomer of nucleic acids. Phosphate group, 5 carbon sugar, nitrogenous base

5 Nitrogenous Bases

Adenine + Guanine (Purines) and Cytosine + Uracil(RNA)/Thymine(DNA) (Pyrimidines)

Ribose

5 carbon sugar with an OH on the 2’ carbon

Deoxyribose

5 carbon sugar with H on the 2’ carbon

DNA

Nucleic acid with deoxyribose and thymine

RNA

nucleic acid with ribose and uracil

Phosphodiester Linkage

Polymerization of nucleic acids. 3’ carbon attaches to phosphate group of next nucleic acid. Condensation rxn

Nucleic Acid ‘Polarity’

Always write from the 5’ → 3’. Nucleic Acids form from the 5’ → 3’ end

Complimentary Base Pairing (aka Watson-Crick Pairing)

C→G, A→T/U

Secondary DNA Structure

Base Pairing + Double Helix

Primary DNA Structure

Order of Amino Acids

Activated Nucleotide

Nucleotide with extra phosphate groups. higher potential energy, good for energy storage (think ATP)

3 main types of RNA

Ribosomal RNA (rRNA)

Transfer RNA (tRNA)

Messenger RNA (mRNA)

Ribozyme

RNA enzyme. Catalyzes chemical rxns

RNA structure

Single strand. Versatile structure (loops, stems, etc) makes for extremely diverse functions

Complimentary Strand

A matching strand of RNA or DNA that forms with the original strand during replication.

3 Functions of Carbohydrates

Energy, Structure, Cell Identity

Monosaccharide

Monomer of a carbohydrate. lots of Cs and Hs with a Carbonyl Group

Aldose vs Ketose Monosaccharide

Depends on the placement of the Carbonyl group. Aldose is on the end, Ketose is in the middle

Isomer

Same chemical formula but different structure and therefore different function

Alpha vs Beta Monosaccharide Structure

Depends on the placement of the OH on the 1’ Carbon. Alpha = below, Beta = above

Glycosidic Linkage

Condensation Reaction, bonding of monosaccharides. Can form between a variety of Carbon locations. (ex a1-4, b1-6, etc)

Alpha vs Beta Glycosidic Linkages

Orientation of the simple sugars. Flipped = beta, same direction = alpha

Starch

Energy storage in plants a1-4 linkages. Can be Amylose (unbranched) or Amylopectin (branched every 30 residues w/ a1-6 linkage).