Part 1 Flashcards by Haley Thompson

A molecular description of the structures, mechanisms, and processes of living things.

Definition of biochemistry

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primary function: chemical reactions and structural components
Monomer: amino acid
polymer/macromolecule: protein or peptide/polypeptide

protein

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-primary function: genetic information
- monomer: nucleotide
- polymer/ macromolecule: RNA/ DNA

nucleic acids

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-primary function: energy storage/membranes
- monomer: lipids

lipids

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-primary function: energy
- monomer: monosaccharide
- polymer/macromolecule: polysaccharide

carbohydrates

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maintaining a steady-state with the environment, even when faced with external challenges.

homeostasis

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an organic molecule that includes carbohydrates, protein, lipids, and nucleic acids.

biomolecules

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defines the periphery of the cell
composed of lipid and protein molecules
thin, flexible, hydrophobic barrier around the cell
contains embedded transport proteins, receptor proteins, and membrane enzymes

Plasma Membrane

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internal volume enclosed by the plasma membrane; composed of cytosol and organelles

cytoplasm

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(an aqueous solution) highly concentrated solution: contains enzymes RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions

cytosol

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the site of protein synthesis

ribosomes

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organic compounds required by many enzymes for catalytic activity

coenzymes

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small molecules that are intermediate products of biochemical processes that take place in living organisms
-(such as amino acids, lipids, peptides, nucleic acids, carbohydrates, vitamins, and minerals)

metabolites

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contains all of the cell’s chromosomes, which encode the genetic material.

nucleus

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complete set of genes, composed of DNA

genomes

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organisms whose cells contain a nucleus and other membrane-bound organelles.

eukaryotes

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a microscopic single-celled organism that has neither a distinct nucleus with a membrane nor other specialized organelles

Prokaryotes

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plentiful supply of O2; organisms transfer electrons from fuel to O2 for energy

Aerobic

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devoid of O2; organisms transfer electrons to nitrate, sulfate, or CO2 for energy

Anaerobic

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Mitochondria

the site of most of the energy-extracting reactions of the cell

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polymers that are assembled from relatively simple precursors: proteins, nucleic acids, polysaccharides

macromolecules

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long polymers of amino acids; can function as enzymes, structural elements, signal receptors, transporters

Proteins

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polymers of nucleotides; store and transmit genetic information
- DNA and RNA

nucleic acids

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polymers of simples sugars:
- energy-rich fuel stores
- rigid structural components of cell walls
- extracellular recognition elements that bind to proteins on other cells

polysaccharides

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stereoisomers that are mirror images of each other

enantiomers

system exchanges both energy and matter with its surroundings

open system

one reactant is oxidized (loses electrons) as another is reduced (gains electrons)

oxidation-reduction

represents the randomness or disorder of the components of a chemical system

entropy

negative is spontaneous/ exergonic, positive is non-spontaneous/ endergonic

Gibbs Free energy

a state in which opposing forces or influences are balanced.

equilibrium

proteins that help speed up metabolism, or the chemical reactions in our bodies.

enzymes

greatly enhance reaction rates of specific chemical reactions without being consumed in the process

catalyst

The breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy

catabolism

synthetic pathways that require the input of energy

anabolism

Is most often single-stranded and has a backbone made of alternating phosphate groups and the sugar ribose,

RNA

the molecule that carries genetic information for the development and functioning of an organism.

DNA

unmutated cells

Wild Type

changes in the nucleotide sequence of DNA - changes the instructions for a cellular component - can be beneficial

mutation

members of the same protein family

homologs

Why don't nonpolar compounds dissolve in water?

Nonpolar compounds do not dissolve in water due to thermodynamically unfavorable conditions (enthalpic and entropic problems)

biomolecule containing both hydrophobic and hydrophilic regions

amphipathic molecules

water flowing to areas of high concentration from areas of low concentration (not the size the quantity)

osmosis

not net water movement

isotonic

Cell in solution: water moves out and cell shrinks

hypertonic

Cell in solution: water moves in creating outward pressure; cell swells, may burst

hypotonic

What happens when a molecule ionizes?

gains or loses electrons; usually and equilibrium process but sometimes all or nothing with strong acids/ bases

any process by which electrically neutral atoms or molecules are converted to electrically charged atoms or molecules (ions) through gaining or losing electrons.

ionization

Strength of a chemical bond A-B the energy required—an endothermic process—to break a bond and form two atomic or molecular fragments, each with one electron of the original shared pair

bond dissociation energy

electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another

hydrogen bond

water loving; describe compounds that dissolve easily in water; generally charged or polar compounds

hydrophilic

water fearing; non polar molecules such as lipids and waxes

hydrophobic

contain regions that are polar (or charged) and regions that are non-polar

amphipathic

distance-dependent weak attractions and repulsions between transient dipoles

Van der Waals / London dipersion forces

gives the position of equilibrium for the generalized reaction - defined in terms of the concentrations of reactants and products at equilibrium

equilibrium constant / Keq

figure expressing the acidity or alkalinity of a solution on a logarithmic scale on which 7 is neutral, lower values are more acidic and higher values are more alkaline. - Defined by the expression: -log[H+]

used to differentiate between strong and weak acids. The acid dissociates more as the Ka increases. Strong acids must therefore dissociate more in water. A weak acid, on the other hand, is less likely to ionise and release a hydrogen ion, leading to a less acidic solution.

acid dissociation constant

- analogous to pH and defined by the equation: =log 1/Ka or =-logKa - the stronger the tendency to dissociate a proton, the stronger the acid and the lower its ___

pKa

aqueous systems that tend to resist changes in pH when small amounts of acid or base are added - consists of a weak acid (proton donor) and its conjugate base (proton acceptor) or vice versa

buffer

describes the shape of the titration curve of any weak acid

Henderson-Hasselbach

What are some functions of a protein?

transport, structure, channels, enzymes, signaling

Which amino acid is achiral?

glycine

Which amino acids are non polar and have aliphatic R groups?

glycine, alanin, proline, valine, leucine, isoleucine, methionine

Which amino acids are aromatic?

phenylalanine, tyrosine, tryptophan

Which amino acids are non charged polar (polar, uncharged R groups)

Serine, threonine, asparagine, glutamine, cysteine

Which amino acids positively charged?

Histidine, arginine, lysine

Which amino acids are negatively charged?

aspartate, glutamate

What are the two ionizable groups on every amino acid and what is the possible third?

the amino group and carboxylic acid group and possibly the side chain

a dipolar ion that has equal number of negative and positive charges

zwitterion

the pH when the overall charge is 0 (less soluble, proteins and amino acids alike have a pI

Isoelectric Point

water is released when we form a peptide bond between amino acids from the OH on the carboxy acid and the hydrogen connected to the nitrogen of the next amino acid

condensation reaction

homologs within an organism

paralogs

homologs among species

orthologs

What is the resonance imply in a peptide bond?

implies rigidity for the backbone

a collection of proteins that share >25% identical sequence (share common structure and function)

protein families

What is the blood buffering system?

bicarbonate system

When an amino acid is part of a polypeptide that amino acid is called a _____

residue

naturally occurring variation in an aa sequence in a population or organism

polymorphism