biol 2100 exam 1

element

 A distinct type of substance or matter. Each element has atoms that contain a unique number of protons in the nucleus.

atom

The fundamental unit of an element, made of protons, neutrons, and electrons.

ion

An atom or molecule that carries a full charge—positive if it contains more protons than electrons, and negative if it contains more electrons than protons. 

molecule

A structure made of two or more atoms held together by covalent bonds.

covalent bond

An attraction between two atoms based on shared electron

• require enzymes

• enzyme activity is regulated

• cells expend/harvest energy in many of these reactions

• not disrupted by temperature or pH changes (strong and stable)

electronegativity

The tendency for an atom's nucleus to attract the shared electrons in a covalent bond.

polar covalent bond

An asymmetry in the position of shared electrons, due to differences in the electronegativities of the atoms involved, that creates a partial positive charge on one atom and a partial negative charge on the second atom.

nonpolar covalent bond

Equal sharing of electrons, due to equal or roughly equal electronegativities of the atoms involved.

hydrogen bond

An attraction between a partial positive charge on a hydrogen atom and a partial negative charge on another atom.

hydrophilic molecule

a molecule that can readily interact with the partial charges on water

hydrophobic molecule

a molecule that contains mostly nonpolar covalent bonds and cannot readily interact with the partial charges on water.

acid

an ion or molecule that releases a proton (H⁺). 

base

an ion or molecule that acquires a proton (H+).

pH scale

 method for expressing the concentration of protons in a solution—specifically, the negative of the base 10 logarithm of the proton concentration. 

nucleotide

A molecule made up of a phosphate group and a nitrogenous base bonded to a 5-carbon sugar.

nucleic acid

A molecule made up of nucleotides linked to form a chain or strand.

phosphodiester bond

Covalent bonds between the phosphate group on the 5′ carbon of one nucleotide and the -OH group on the 3′ carbon of a second nucleotide.

complementary base pairing

Hydrogen bonding between A-T or A-U and G-C pairs in a nucleic acid.

primary structure

The sequence of nucleotides in a nucleic acid, read 5′ to 3′.

secondary structure

Formation of a double helix in DNA or a stem-and-loop structure in RNA, based on complementary base pairing.

sugar-phosphate backbone

The "spine" of 5-carbon sugars and phosphate groups in a nucleic acid (the nitrogenous bases project from this backbone).

antiparallel strands

Strands of DNA or RNA that align in opposite 5′ to 3′ orientation.

monomer

A small "subunit" molecule that can be linked to another, via a covalent bond, to form a larger molecule called a polymer.

polymer

A large molecule made up of strings of covalently bonded small molecules (monomers).

enzyme

a specific protein that accelerates chemical reactions, required for covalent bonds

relative electronegativities

O > N > C = H

non-covalent interactions

• not chemical reactions, they are independent of enzymes

• greatly influenced by molecule’s concentrations

• sensitive to temperature and pH changes

• ionic, hydrogen, hydrophobia, van der waals

ionic bonds

attraction of opposite chages

-weaker associations, they dissolve readily in physiological conditions (water is polar)

hydrogen bonds

sharing of H atoms, weak interaction between partial charges

-being hydrophilic requires participation in hydrogen bonds

-forming hydrogen bonds requires presence of polar covalent bonds

hydrophobic interactions

interactions of non-polar molecules in polar environment

van der Waals interactions

interaction of electrons of non-polar substance

amino acids

the building blocks that connect together via covalent bonds to form proteins

amino group

a group of NH₂ atoms; can pick up a proton to form NH₃⁺

carboxyl group

group of COOH atoms; can lose a proton to form COO^-

r group

a highly variable group of atoms bonded to the central carbon of an amino acid

purines

adenine and guanine, nitrogenous bases, have 2 rings

pyrimidines

cytosine, uracil + thymine (thymine has an extra methyl group), nitrgenous bases, 1 ring

2’ carbon on nucleotide

OH (RNA) ir H (DNA)

3’ carbon on nucleotide

OH and link to next molecule

5’ carbon on nucleotide

link to phosphate group and previous nucletide

ribose

sugar in RNA, has OH on 2’ carbon, more reactive, more functions, less stable

deoxyribose

sugar in DNA, has H on 2’ carbon, less reactive, less functions, more stable

nucleoside

base + sugar, no phosphate group

why is all nucleic acid synthesis always in the same direction?

the nucleotides arrive for synthesis as dNTP, the phosphate groups are what provide the energy for the synthesis, 2/3 phosphates are lost in the formation of the bond

strand widths

each pair ( A + T/U) or (G + C) contains one pyrimidine and one purine, making DNA a consistent width
RNA molecules are often single-stranded

bonds between G-C and A-T pairs

hydrogen bonds

antiparallel

the opposite orientations of the two strands of a DNA double helix; the 5' end of one strand aligns with the 3' end of the other strand.

A-T

2 H bonds

G-C

3 H bonds

DNA function

stores genetic information

RNA function

information transfer, catalyzes reactions, influences gene expression

DNA vs RNA location

both within cells, often in nucleus of eukaryotic cells
DNA: in mitochondria and chloroplasts
RNA: also outside nucleus and in cytoplasm