BioChem Exam #1

What is biochemistry?

how biomolecules interact to maintain life

What are the universal structural features shared by all cells?

• Plasma membrane

• Cytoplasm

• Ribosomes and Proteasomes

• Cytosol

• Genome

Function of Cytoplasm?

Space enclosed in plasma membrane

Function of Cytosol?

Fluid in cell (aqueous solution in the cell.)

small organic molecules + inorganic ions are here

Function of Proteasomes?

degrades proteins

Function of Ribosomes?

protein synthesis

(make proteins)

Function of Genome?

Nucleus in Eukarya

Nucleoid in Archaea + Bacteria

What is the function of the plasma membrane?

• Separates cell contents from the surroundings

• Made of lipids and proteins

• Thin, flexible and hydrophobic

• Blocks and limits the movement of inorganic ions, charged, or polar molecules

• Lipds + proteins interact can Change size and shape of cell

What are Transport Proteins?

allow specfic polar + charged molecules in

embedded in the plasma membrane

What are Receptor Proteins?

recives signal + transmit signals into the cell

embedded in the plasma membrane

What are Membrane Enzymes?

help with chemical reactions (GTP to GDP)

embedded in the plasma membrane

What do Enzymes do?

proteins that catalyze reactions

What do Plasmids do?

circular DNA in bacteria

What are Cell dimensions?

Why do animal cells have more folds?

They have folds on surface for more surface area and to compensate for volume also uptake nutrients

What is Bacteria?

• Unicellular - prokaryote

• inhabit soils, surface waters, and the tissues of other living or decaying organisms

• Gram + Gram -

What is differnce between Gram + and Gram -?

Gram +: has the peptidoglycan layer as the outer layer

Gram -: as an outer membrane surrounding the peptidoglycan layer

What is Archaea?

• Unicellular - prokaryote

• inhabit extreme environments

What is Eukarya?

• unicellular - yeast

• multicellular - eukaryote

Which is eukarya more related?

Archea

What is phototrophs?

Energy from sunlight?

What is heterotrophs?

carbon from organic nutrients

What is chemotrophs?

energy from breakdown of chemicals

What is autotrophs?

Carbon from CO₂

What is Mitochondria?

Energy (ATP) production of cell

in Eukaryotic Cells

What is Rough Endoplasmic Reticulum?

Protein synthesis, ribosomes in ER

in Eukaryotic Cells

What is Golgi Complex?

Packages protein for exports

in Eukaryotic Cells

What is Peroxisomes?

Oxidizes (breaks down) fatty acids

in Eukaryotic Cells

What is Lysosomes?

Degrades intracellular debris (waste)

in Eukaryotic Cells

What is Vacuoles

Breaks down + recycles macromolecules, stores metabolites

in Plant Eukaryotic Cells

What are Metabolites?

Small organic molecules made or used by the body.

What is Smooth Endoplasmic Reticulum?

Lipid synthesis + drug metabolism

What is Transport vesicle?

Transports lipids and proteins

What is a nuclear envelope?

Separate chromatin from cytoplasm

What is Chloroplasts?

Harvests light to make ATP and carbohydrates

in Plant Eukaryotic Cells

Know what each orgenelle looks like

What is Differential Centrifugation?

Used to separate organelles

1. gently disrupt cells or tissues by physical force to break plasma membrane

2. centrifuge the homogenate (mix of cell parts)

3. Smaller parts settle at bottom as speed increases

What is cytoskeleton?

3D network of protein filaments in eukaryotic cells

Filaments aren’t permanent and move

What are actin filaments?

they are for cell shape + movement

What are microtubules?

They are for organization + movement of material

What are intermediate filaments?

They are for strength + stability

What is the endomembrane system?

modifies, packages + transport proteins and lipids

What is exocytosis?

cellular fission

cells move stuff OUT of cell

What is endocytosis?

cellular fission

creates vesicle to bring stuff IN cell

What are Non-Covalent interactions

hydrogen bonds- Attraction to partial + H

ionic interactions- attraction to + charge and - charge

van der Waals- weak interactions that come and go, very short-lived

hydrophobic effect- nonpolar molecules cluster together to avoid water

What are in vitro?

in glass, outside a living system

What in in vivo?

in the living, studying inside living organisms

Why can in vitro studies overlook important interactions?

Becuase they are taken out from from the living organism where they are interacting with differnt biomolecules which cant be seen in vitro

What is Biochemical Unity?

Organisms are differnet but the chemical and processes are the same

What are the four elements that make up 99% of the cell?

C, N, O, H

What are trace elements ?

Existing in small quantities, they are essential for the function of specific proteins

Which element of the four major elements is the most versatile?

Carbon

Why is carbon highly versatile?

Carbon can make 4 bonds

• Tetrahedral 109.5⁰

• Planar(3 bonds) (flat) 120⁰

• Linear 180⁰

Functional Groups

What is the concentration of organic molecules in the cytosol?

nanomolar to > 10mM

What is a Metabolome?

collection of small molecules (metabolites) in the cell

What is Metabolomics?

study and characterization of metabolome in certain conditions

• used for drug expirments

What is a Macromolecule?

Polymers with molecular weights above 5,000 made from small molecules

What is a monomer?

building block or unit of polymer

What is a polymer?

strand of monomers

What is Oligomer?

short polymer

What is monomer of Proteins?

amino acids

What is a Proteome?

all proteins of the cell

what is Proteomics?

characterization of proteome (all proteins) of cell

What is the monomers of Nucleic acids?

nucleotides

What is a Genome?

sequence of cell’s DNA

What is Genomics?

characterization of structure, function, evolution, and mapping of genomes

(study of genetic information)

What is monomer of Polysaccharides

Simple sugars

What is a Glycome?

all carbohydrate containing molecules

What do oligosaccharides attach to in order to serve as cellular signals at the cell surface

Proteins and Lipids

What are the 3 main functions of polysaccharides?

1. store energy in cell

2. Rigid and structural components

3. Extracellular recognition (signals)

What are Lipids?

water-insoluble hydrocarbons

Technically not a macromolecule

What is a Lipidome?

all lipid containing molecules in the cell

What are the 3 functions of lipids?

structural component of membranes

Energy-rich fuel stores

Intracellular signals

Why are lipds technically not a macromolecule?

they are to small and do not form polymers.

What are the two major “informational macromolecules”?

proteins

nucleic acids

What are Stereoisomers?

same molecule formula, same atoms, connect different 3-D arrangment

What are Geometric Isomers?

atoms arranged differently around double bond or ring

Cis + Trans

Cis more stable

What is Chirality?

4 different atoms, mirror image molecules

What are Enantiomers?

mirror image (D,L)

What are Diastereomers?

not mirror image

What is configuration?

how atoms are arranged in molecule

What is conformation?

how atoms rotate in a molecule

Which conformation is more stable Staggered v. Eclipsed?

Staggered, can not isolate these forms they change and move constantly

What limits the conformations?

Steric hinderence

What is sterospecfic?

Correct 3-D shape to interact with another molecule

Which form do Amino acids in proteins exist as?

L-isomers

Which form does Glucose exists as?

D-isomers

Do living cells produce one possible chiral form or both forms?

Living cells only produce one chiral form of a biomolecule because the enzymes that synthesize that molecule are also chiral

What is Stereospecificity?

the ability to a molecule/ biological system to distinguish between stereoisomers

Why do organisms eat?

Organisms need energy to fuel chemical reactions and stay orderly

Does nature prefer order or disorder?

Disorder

What processes in humans that require energy?

Storage expression of information

Synthetic chemical rxns : make molecules

What are coupling reactions used for?

coupling reactions are reactions paired together one gives energy (-G) and the other uses energy (+G)

What is an open system?

An open system is something that takes in and gives out matter and energy to its surroundings.

What is steady state?

Being maintained at constant level (homeostasis)

Ex. Body temp

What is Equilibrium?

No net change because system naturally settles into balance

ex. A hot cup of tea will release heat until it is the same temperature as the surroundings.

What is the first law of thermodynamics?

Energy is neither created nor destroyed

Why are cells excellent transducers?

they can easily convert one form of energy into a different form of energy.