Biochemistry Introduction

Flashcards created for key vocabulary and concepts in biochemistry based on lecture notes.

Biochemistry

The study of chemical processes within and relating to living organisms.

Endocytosis

Transport of substances into a cell.

Exocytosis

Transport of substances out of a cell.

Phototrophs

Organisms that obtain energy from light.

Chemotrophs

Organisms that obtain energy from chemical compounds.

Aerobic

Processes that require oxygen.

Anaerobic

Processes that do not require oxygen.

Cellular Foundations

Basic building blocks of life, including structures like plasma membrane, cytoplasm, and organelles.

Primary Alcohol

An alcohol in which the hydroxyl group is attached to a primary carbon.

Secondary Alcohol

An alcohol in which the hydroxyl group is attached to a secondary carbon.

Tertiary Alcohol

An alcohol in which the hydroxyl group is attached to a tertiary carbon.

Hydrocarbons

Compounds consisting only of hydrogen and carbon.

Functional Groups

Specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.

Structural Isomers

Compounds with the same chemical formula, but different order of attachment

Stereoisomers

Compounds with the same formula and same order of attachment, but different arrangements of atoms in space.

Geometric Isomers

Stereoisomers that differ in the spatial arrangement of groups around a double bond.

Cis Isomers

Isomers where similar groups are on the same side of a double bond.

Trans Isomers

Isomers where similar groups are on opposite sides of a double bond.

Epimers

A type of diastereomer that differs at only one specific stereogenic center.

Redox Reactions

Reactions involving the transfer of electrons between two species.

Dehydration

The removal of water. H2O is a product

Hydration

Addition of water across a double bond. H2O is a reactant

Hydrolysis

A chemical reaction in which water breaks down another compound.

Methylation

Addition of a Methyl (CH3) group

Phosphorylation

The addition of a phosphate group to a molecule.

Endergonic Reactions

Reactions that require energy to proceed.

Exergonic Reactions

Reactions that release energy.

Metabolic Pathways

Series of chemical reactions occurring within a cell.

Catabolic Pathways

Pathways that break down molecules to produce energy.

Anabolic Pathways

Pathways that construct molecules from smaller units.

In Vitro

Experiments performed in glass

In Vivo

Experiments done in whole, living organisms

Chemical foundations of life

99% of mass of cell is made of hydrogen, oxygen, nitrogen, and carbon

Alkanes

Carbon-Carbon single bond

Alkenes

Carbon-Carbon double bond

Alkynes

Carbon-Carbon triple bonds

Aldehyde

Ketone

Carboxylic Acid

Ester

Acid + Alcohol

Ether

Two alcohols

Amine

Amide

Thiol

Thioester

Homeostasis

Maintenance of condition in the body necessary to maintain life within the body’s internal environment

Dynamic steady state

Rate of intake or synthesis occurs at the same rate that it is being used up

Equilibrium

Reaction where the forward and reverse reaction are occurring at the same rate resulting in no net change in amounts of reactants and products

Water

the most abundant substance in living systems

Nonpolar covalent bonds

Between 2 nonmetals, electronegativity of 0-0.4

Polar covalent bonds

Between metals and nonmetals, electronegativity of 0.41-1.8

Ionic bonds

electrons transferred from metal to nonmetal, electronegativity of 1.8 or above

easily

Polar molecules dissolve blank in water

Cannot readily

Polar molecules blank dissolve in water

Polar covalent bonds

Bond found in water

Polar bonds

can dissolve in water, like dissolves like

Nonpolar bonds

cannot dissolve in water

Hydrogen donor and hydrogen acceptor

what is required for hydrogen bonds to occur

hydrogen donor

These can be a hydroxyl or amine

hydrogen acceptor

these are usually O or N

hydrogen bonds

weak attraction between hydrogen atom and a highly electronegative atom in another

Electrostatic interactions

forces between cation and anions or dipoles

London dispersion forces

The weakest of all attractive forces; caused by short lived dipole moments

Dipole-Dipole interaction

an attraction between two polar molecules, positive and negative dipoles

Ion-dipole

ions attract or repel dipoles

hydrophobic interactions

molecules that cluster together in a polar solution

passive diffusion

movement of a molecule from high to low concentration gradient

facilitated diffusion

movement of a molecule from high to low concentration with the help of a transport protein

osmosis

diffusion of water molecules from high to low water concentration

hypotonic

solutions with high water and low solute concentration

lysis

water flows into cells and cause them to burst

hypertonic

solutions with low water and high solute concentration

cremation

water flows out of cell and causes it to shrink

isotonic

equal solute concentration, water flows in and out at the same rate

lower ph

an increase in H+ causes

higher ph

decrease in H+ causes

H+ is still attached

The ph is below the PK

H+ is lost

The ph is above the PK

Biochemical acids

substances that can donate H+ to lower the ph

Biochemical Bases

Substances that can accept H+ to increase ph

Acidosis

Accumulation of acid or loss of base

Alkalosis

Accumulation of base or loss of acid

intracellular buffers

protein buffer system and phosphate buffers are what

extracellular buffers

Bicarbonate-carbonic acid buffer system are what

Respiratory buffers

control concentration of carbon dioxide

Metabolic buffers

Controls concentration of metabolic process concentration

Respiratory Acidosis

Causes increase in breathing rate to control pH

Respiratory Alkalosis

Causes decrease in breathing rate to control pH

Metabolic Acidosis

Caused by any other mechanism other than increased co2; usually due to loss of bicarbonate or excessive nonvolatile acids

Metabolic alkalosis

Excessive bicarbonate production; can be due to fluid imbalance or other mechanisms

Cohort Studies, Randomized control studies, Systematic Reviews, Meta-analysis

Types of Study designs that are better than opinions and case studies

Absolute risk

true incidence of disease; also called risk difference

Relative risk

measure of probability of risk, only used in cohort studies, (risk ratio)

Odds ratio

measure of odds of risk, can be used to calculate risk in cohort, case-
control and meta-analyses

OR and RR is not significant

If the confidence interval crosses the referent number (1)

OR and RR is significant

If the confidence interval stays on 1 side of the referent number (1)

Absolute Risk: Interpretation

risk in control minus risk in treatment, divide by 100 to get %

OR=1

exposure is not related to disease; no association

OR>1

exposure is positively related to disease; positive association (increased
risk)

OR<1

exposure is negatively related to disease; negative association
(decreased risk)