chapter 1 principles of biochemistry

what is biochemistry

• explains biological processes at the molecular and cellular level

• relies heavily on the quantitative analysis of data

• often studies in vitro (outside a living cell) systems

fermentation

the conversion of rotting fruit or grain into alcohol solutions through the action of yeast (yeast enzymes act as a catalyst)

what type of process is alcohol fermentation?

anaerobic

Buchner’s experiment

• Buchner showed that carbon dioxide and ethanol were produced in vitro from sugar using brewer’s yeast in 1897

• credited with proposing that enzymes helped speed up the reaction

alcoholic fermentation reaction

• pyruvate decarboxylase converts pyruvate into acetaldehyde and carbon dioxide

• alcohol dehydrogenase reduces acetaldehyde to ethanol

• the second part involving alcohol dehydrogenase is a redox reaction

catalysts like proteins or RNA are

biomolecules that increase the rate of biochemical reactions by lowering the activation energy the reactants need

catalysts are found in

all living cells

catalysts are responsible for which reactions?

• aerobic respiration

• fermentation (anaerobic)

• nitrogen metabolism

• energy conversion

• programmed cell death

applied biochemistry is used in the following fields

• environmental science

• biotechnology

• agriculture

• pharmaceuticals

• clinical diagnostics

• commercial products

organizational hierarchy of biochemistry

elements and functional groups → biomolecules → macromolecules → metabolism → cells → organisms → ecosystems

trace elements are used as what in proteins?

cofactors

cofactors

non-protein chemical compounds that are required for an enzyme’s role as a catalyst

coenzymes

cofactors derived from vitamins and nutrients

trace elements

manganese, iron, cobalt, copper, zinc

essential ions that play a role in cell signaling

calcium, chloride, magnesium, potassium, sodium

97% of the weight of most organisms consists of

C, H, O, N, P, S

six most abundant functional groups in biomolecules

amino, hydroxyl, sulfhydryl, phosphoryl, methyl

which functional group only has one protonation state?

methyl

four major types of biomolecules

amino acids, nucleotides, simple sugars (mono and disaccharides), fatty acids

amino acids primary cellular functions

• protein function

• neurotransmission

• nitrogen metabolism

• energy conversion

amino acids are

nitrogen containing molecules that are the building blocks of proteins

the bond that links amino acid chains

peptide bonds

how do amino acids differ from each other?

the side chain

anything over 60 amino acids is a ?

protein

nucleotides primary cellular function

• nucleic acid function

• energy conversion

• signal transduction

• enzyme catalysis

nucleotides consist of

• nitrogenous base

• pentose sugar

• 1-3 phosphate groups

nucleosides consist of

• nitrogenous base

• pentose sugar

examples of nucleotides

• ATP

• cAMP

• NAD+

simple sugar primary cellular functions

• energy conversion

• cell wall structure

• cell recognition

• nucleotide structure

simple sugars are

monosaccharides and disaccharides

carbohydrates contain only

C, H, and O atoms

in carbohydrates the hydrogen to oxygen ratio is

2:1

fatty acids primary cellular functions

• cell membranes

• energy conversion

• cell signaling

• energy storage

fatty acids are

amphipathic molecules

amphipathic molecules

hydrophobic and hydrophilic chemical properties in one molecule

fatty acids consist of

• carboxyl group

• hydrocarbon chain

saturated fatty acid

solid at room temp, no double bonds (animal fats)

unsaturated fatty acid

liquid at room temp, double bonds (oils)

most abundant macromolecules

• proteins

• nucleic acids (RNA/ DNA)

• polysaccharides (starch, cellulose, amylose, glycogen)

macromolecules are

chemical polymers of biomolecules

nucleic acids are covalently linked by

3’, 5’-Phosphodiester bond

proteins always start from which terminal and ends at which terminal?

amino to carboxyl

the chemical properties of proteins are determined by

different side chains in the amino acid

polysaccharides are

mixtures of different simple sugars or just repeating glucose molecules linked by glycosidic bonds

glycosidic bonds are either

• α(1→4)

• β(1→4)

amylose (starch, glucose polymer) contains a

α(1→4) glycosidic bond

cellulose (glucose polymer) contains a

β(1→4) glycosidic bond

chitin contains a β(1→4) glycosidic bond linking

N-acetylglucosamine units

which enzyme do we lack, and which bond can humans not hydrolyze

we lack cellulase needed to hydrolyze β(1→4) glycosidic bonds

metabolite

small biomolecules that serve as reactants and products in biochemical reactions within cells

metabolic pathways

enable cells to coordinate and control complex biochemical processes in response to available energy

examples of metabolic pathways

• glycolysis and gluconeogenesis (glucose metabolism)

• citrate cycle (energy conversion)

• fatty acid oxidation and biosynthesis (fatty acid metabolism)

metabolic flux

the rate at which reactants and products are interconverted in a metabolic pathway

metabolic pathway formats

• linear (generates a single product used for next reaction)

• forked (generates two products that undergo separate reaction)

• cyclic (generates several products that regenerate during each turn of the cycle)

anabolic pathway

assembling macromolecules from monomers, requires energy

catabolic pathway

disassembling macromolecules into monomers, releases energy

form of energy needed to assemble many macromolecules

ATP

when ATP levels in the cell are high

anabolic pathways are favored

when ATP levels in the cell are low

catabolic pathways are favored

the flux of metabolites through a pathway depends on

• activity of the enzyme in the pathway

• intracellular concentrations of reactants and products (le chatelier’s principle)

reactions in metabolic pathways can be either

reversible or irreversible

living cells are highly what and surrounded by what?

ordered structures surrounded by a lipid membrane

in order to support metabolic processes cells either

obtain energy from the sun or from oxidation-reduction reactions

nucleolus

site of ribosome assembly

ribosomes

RNA-protein complexes that mediate protein synthesis

mitochondria

responsible for many of the metabolic reactions involved in energy conversion and production of ATP

peroxisomes

containing enzymes for forming or destroying peroxides

lysosomes

involved in the degradation and detoxification of macromolecules

endoplasmic reticulum

highly invaginated membrane structures that sequester ribosomes for protein synthesis

golgi apparatus

membranous structure involved in protein translocation within the cell and facilitating protein secretion at the plasma membrane

individual cells communicate with one another in response to environmental changes using

signal transduction

ligand

a small molecule that is often a metabolite, hormone, or peptide and which binds to target proteins (receptors) and alters their structure and function to control biochemical processes

transmembrane receptor proteins are able to transduce extracellular signals across the membrane upon ligand binding through

changes in shape (conformational changes) which activates the receptor and affects intracellular activity (increases enzyme activity)

the circulatory system allow

• biomolecules to travel throughout an organism

• transports signaling molecules

• distributes metabolic fuel (carbohydrates, and lipids)

primary tissues and organs involved in controlling metabolic function in humans

• brain (nerve center)

• liver (metabolic control center)

• skeletal muscle (mechanical work and glucose homeostasis)

• intestines (nutrient absorption)

• adipose tissue (energy storage and hormonal signaling)

• kidneys (water, nitrogen, and electrolyte balance)

• heart (pumps blood throughout the circulatory system)

• lungs (exchange oxygen and carbon dioxide gases with the atmosphere to keep tissues and organs alive)

primary tissues and organs involved in controlling metabolic function in humans are coordinated by

signal transduction mechanisms

multicellular organisms depend what to distribute metabolites between specialized tissues and organs

a circulatory system

ecosystems are the

highest level of hierarchical organization

ecosystems include

cohabitation of different organisms in the same environmental niche and involve a shared use of resources and waste management

in 1952 it was reported that DNA from a bacterial virus was sufficient enough to promote

viral replication

Rosalind Franklin collected

x-ray diffraction data to determine the structure of DNA

in 1953 Watson and Crick determined that DNA is a

double helix

the DNA double helix allows

for DNA replication and for genetic information to be passed onto daughter cells

genetic information is stored in DNA as

nucleotide base pairs

deoxyribonucleotides are monomeric units of DNA that

lack an -OH group on the C-2’ of the deoxyribose sugar (have an -H)

ribonucleotides are monomeric units of RNA that

contain an -OH on the C-2’ of the ribose sugar

strands of DNA are noncovalently associated through

hydrogen bonds

base pairs of DNA and RNA

• in DNA (A-T, 2 hydrogen bonds), (G-C, 3 hydrogen bonds)

• in RNA (A-U, 2 hydrogen bonds), (G-C, 3 hydrogen bonds)

purines

adenine and guanine

pyrimidines

cytosine and thymine (uracil is a pyrimidine derivative)

how is genetic information passed down through genetic inheritance

the complementary nucleotide base pairs allows for replication of exact DNA

DNA replication is

semi-conservative

central dogma

DNA (genes/ transcription) → RNA (translation) → protein

reverse transcription

conditions in which RNA molecules can be converted back to DNA (often related to virus replication)

genome

collection of genes

transcriptome

collection of DNA transcripts (RNA products) generated by DNA transcription; can refer to all possible RNA products present in an organism or cell type or to just those generated under defined conditions

proteome

collection of proteins produced by mRNA translation, either in the entire organism or under special conditions

structure determines

function

a gene is maintained through natural selection if

the DNA change leads to a beneficial change in function and structure

if a single nucleotide changes in a wild-type protein coding sequence then

the encoded protein may be functionally defective