Mol Bio Exam 1 - D.J

Semwal

Define cell theory and key points

It is a fundamental theory of biology

1) All organisms consist of one or more cells

2) The cell is the basic unit of structure for all organisms

3) All cells arise from pre- existing cells

3 Main branches of biology and how they are connected to each other

1) Cytology - structure and function of plant cells

2) Genetics - the study of genes, genetic variation and heredity there of

3) Biochemistry - he chemical processes and substances that occur within living organisms

Cytology explores the cellular structures that house genetic material, while genetics examines how these materials dictate biochemical processes.

Cytology Tools

Microscopes (dyes, electron microscopy)

Immunohistochemistry

Biochemistry Tools

Centrifuges

Chromatography

Electrophoresis

Mass Spectrometry

Centrifuges

Biochemistry tool that spins around to separate by mass

solution based on size

Chromatography

Biochemistry tool used liquid or gas to separate by size/charge/or affinity

can be more specific

using liquid or gas to separate components

Electrophoresis

Biochemistry tool that uses electric current to separate DNA/RNA or proteins by size and charge

Genetrics Tools

Microarrays and Quantitative PCR to determine DNA sequencing

Robert Hooke

first described cells

Antonie van Leeuwenhoek

Made lenses / first to observe cells

Robert brown

Identification of the nucleus

Matthias Schleiden

All PLANTS made of cells

Theodor Schwann

All ANIMALS made of cells

Anselme Payen and Louis Pasteur and Wilhelm Kuhne

Discovered first enzymes

Gregor Mendel

DNA is genetic material

Importance of carbon and properties

Carbon is the fundamental building block for all biological structures serving as the backbone of lipids, carbohydrates, DNA, and proteins

Needs 4 more electrons

Carbon is versatile and can interact easily with others

Can do single, double, or triple covalent bonds

Stable (hard to break)

Compatible with functional groups

Importance of water and properties

Water is a universal solvent, which is crucial in the transport of nutrients and chemicals in our body

Polar covalent

Electronegativity of oxygen

As a whole, neutral

nonpolar does not dissolve

Extensive H bonding (high surface tension/boiling point/specific heat/vaporization)

How would the properties of water change if the water molecule were linear rather than bent?

Water would be considered a non-polar molecule and will no longer be a universal solvent for polar and ionic molecules. As well as no hydrogen bond. It would also loose its high boiling point

Ways atoms interact

covalent, hydrogen, ionic, van der waals and hydrophobic interactions

Properties of cellular membrane

Semi-permeable

Amphipathic ( both hydrophilic + hydrophobic )

double layer of phospholipids

formed by hydrophobic interactions

Moves ions with transport proteins

Steps of Polymerization

1) Monomer activation uses ATP

2). Release of water (condensation reaction)

3) Repeat (further polymerization)

Self-Assembly

Process where molecules organize themselves into larger macromolecules that they were meant to be, sometimes with the help of chaperones. Mainly uses van der waal forces to form

Proteins types

enzymes (catalysts)

structural (hair)

motility (flagella)

regulatory '

transport (channels)

signaling (neurons)

receptor

defensive (antibodies)

storage

What can disrupt protein formation

Heat, pH, chemicals, and salt concentration

Primary structure

Linear amino acids linked with PEPTIDE bonds. determined by gene sequence and dictates higher levels

Secondary structure

local folding with HYDROGEN bonds

a-helix(spiral and one polypeptide)

beta sheet (strands and 1 or more polypeptides)

Helix or sheet?

Depends on amino acids

Tertiary Structure

INTERACTION with R group. and Ionic

3D folding of polypeptide

Goal is to be as stable as possible

fibrous and globular

Tools to know tertiary structure

Computer program and X-ray

Fibrous vs globular

Both tertiary proteins

Fibrous: long, coiled, extensible, insoluble in water (muscle and hair)

Globular: Compact, folded in on each other, random loops, soluble in water (hemoglobin)

Quaternary structure

Combinatinon of 2 or more polypeptides to form final protein

Uses chaperones

Many type of bonds (hydrogen, ionic, disulfide, hydrophobic, covalent)

Why protein folding?

To form a specific 3-D shape that is essential to complete its function

peptide vs polypeptide

polypeptide is a long peptide chain

Domain

Tertiary structure unit with a specific function

Motifs

Secondary Structure specific arangment of alpha helix and beta sheets

X ray crystallography

Used to determine 3D structure of proteins. Crystalize the molecule and shine x rays through to create a diffraction pattern

Nucleic acid types

DNA (storage) and RNA (expression)

Types of bonds in nucleic acid

Phosphodiester (phosphate to sugar)

also hydrogen

Components of a nucleotide

Sugar (deo/ribose)

DEO - DNA

Ribose - RNA

phosphate group

nitrogen base

Carbohydrates functions

energy storage, structure, cell signaling

Carbohydrate definition

long chains of sugar, can be branched

monosaccharides

glucose and fructose

disaccharides

sucrose (Gluc and fruc) and lactose

polysaccharides

cellulose - plant cell wall

chitin - insect cytoskeleton

peptide glycan - bacteria cell wall

Lipids properties

hydrophobic (some ampipathic)

high molecular weight

condensation synthesis

important in cell structure

NOT LINEAR POLYMERIZATION

Lipids exception to rule / differences

Not made with linear polymerization (there is no monomer that makes lipids, they just are lipids)

Hydrophobic (sometimes amphipathic)

Function of lipids

energy storage

membrane structure

signaling

Lipids similarities to other macromolecules

Made with condensation synthesis and important to life functions

6 classes of lipids

fatty acids

triacylglycerol

phospholipids

glycolipids

steroids

terpenes

Fatty acids

long unbranched hydrocarbons with a carboxyl on the end

amphipathic

Storage of energy when oxidized

Triacylglycerols

Glycerol + 3 fatty acids

Store energy

Insulation

Phospholipids

membranes

different R groups

Amphipathic

length and degree of saturation affects the fluidity of membrane

Glycolipids

Membrane bio recognition

Plant cells and nervous system

Amphipathic

Steroids

4 ring hydrocarbons

Nonpolar

sex hormones, glucocoticoids/ mineral corticoids

Types of light microscopy

Brightfield (stained or unstained)

Phase contrast

Differential interference contrast

Fluorescence

Confocal

electron microscopy

Brightfield microscopy

Light directly on specimen, can be dyed to add more contrast

Phase contrast

similar to brightfield but doesn’t need dye because it highlights contrast by amplifying variations in refractive index

Differential interference contrast

Like phase contrast but created a 3D surface of the specimen by detecting phase gradients

Fluorescence

Shows location of specific molecules in cell, can use dyes on the molecule

Confocal

uses lasers to illuminate a single plane within the specimen

Electron microscopy

extremley high resolution

2 types:

Scanning (surface of cell)

Transmission (internal view)

Why are cells small ?

1. surface area to volume ratio - as cells increase in size , their volume grows faster than their surface area

2. diffusion rate - allows for more efficient diffusion of nutrients , gases , and waste products in and put of the cell

3. efficient transport and communication - small cells can more effectively transport materials within the cells bc the distance are shorter

4. DNA and Protein synthesis limits

5. energy efficiency

6. cell division and growth control

7. adequate concentrations of reactants and catalysts

Ancestral cell

1. bacteria

2. archaea ( 1 st arrived on earth )

3. eukarya

Prokaryotes vs Eukaryotes

pro : no nucleus, dna = circular , no membrane - bound organelle , smaller (1-10)

euk : nucleus , dna = linear , membrane - bound organelle , larger (10-100)

Archaea vs Eubacteria

a - cell wall is based on protein

e- cell wall is based on peptidoglycan ( sugar and protein)

Pili

hairs on the surface (cell-cell interaction, motility,
DNA uptake)

allows bacteria to stick to a surface
Mating: Can share information –
increases diversity

Flagella

motility

Cell attempts to solve 3 problems

1. Specificity problem
• Functional groups give specificity
• Atoms
2 Containment problem
• Bilipid layer (phospholipids)
• Gives rise to plasma membrane and organelles
3. Information problem
• Nucleic acids- DNA and RNA
• “storage” of data and is heritable

Differences between Cell types

1. Membrane-bound nucleus:
eukaryote→ (yes),
bacteria/archae → no
1. Organelles: internal, membrane-
bound with a specific function
• Exception: Caulobacter crescentus,
cyanobacteria
2. Exocytosis & endocytosis—
exchange material between
compartments in eukaryote

4. Organization of DNA: histones in euk, circular vs
Linear DNA
5. Segregation of DNA
• Binary fission (prok) vs. mitosis (euk)
6. Expression of DNA
• Prokaryotic: 1 mRNA→several proteins (operon)
• Eukaryotic: 1 mRNA→1 protein (usually)

Plant vs Animal differences

Plant - cell wall , central vacuole , chloroplasts

Animal - small or no vacuole , centrioles and centrosomes , flagella

Plants vs animals - similarities

ribosomes , endoplasmic reticulum , plasma membrane , golgi apparatus , mitochondria , nucleus

Where did cells come from?

Abiotic synthesis of simple compounds->Abiotic polymerization-
>encapsulated in lipid membranes

Plasma membrane

Lipid bilayer + proteins → fluid mosaic model.

Functions: selective permeability, structural support, signaling

A cell = p.m w membrane proteins = lipid bilayer with glycoprotein

Nucleus

Control center: DNA storage, transcription.
Components: nuclear envelope, chromatin, nucleolus (rRNA synthesis). Nuclear pores regulate transport.
Nuclear lamina = structural support

Mitochondria

Double membrane, dynamic movement in cells.
• Site of aerobic respiration:
o Glucose + O₂ → CO₂ + H₂O + ATP.
• Own DNA (circular, maternally inherited).
• 70S ribosomes.
• Endosymbiont origin

Chloroplasts (plants)

Photosynthesis: solar energy + CO₂ → sugars + O₂.
• Double membrane, own DNA + 70S ribosomes.
• Endosymbiont origin

Endosymbiont Theory for Chloroplasts and Mitochondria

The endosymbiont theory proposes that mitochondria and chloroplasts originated as
free-living prokaryotes that were engulfed by ancestral eukaryotic cells. Instead of being
digested, these prokaryotes formed a mutualistic relationship: the host cell provided
protection and nutrients, while the symbionts contributed energy production
(mitochondria: ATP via aerobic respiration; chloroplasts: sugars via photosynthesis).

Over time, most of their genes were transferred to the host nucleus, leaving them semi-
autonomous. Evidence includes their double membranes, circular DNA, 70S ribosomes,
maternal inheritance, and independent division similar to bacteria

Endomembrane system

1. endoplasmic reticulum

2. golgi apparatus

3. lysosomes

endoplasmic reticulum (ER)

Tubular membranes with
flattened sacs
• Outer membrane continuous
with nuclear envelope
• Rough: Associated with ribosomes to make
intermembrane proteins, secreted
proteins
• Smooth: Synthesis of lipid and steroids,
detoxification of drugs

Golgi Apparatus

Stacks of flattened vesicles
• Processing and packaging
secretory proteins
• Synthesizes complex
polysaccharides
• Vesicles

Lysosomes

stores enzymes to digest other molecules , autophagy

Peroxisomes

Several functions
• Generating/degrading H2O2
• Catalase
• Also degrade methanol,
ethanol, formate,
formaldehyde
• Breakdown of large fatty
acids
• High concentration in liver and kidney

Vacuole

• Animals
• Temporary storage and
transport
• Protozoa
• Feed by endocytosis, merge
with lysosome
• Plants
• Turgor pressure- maintains structure

Cytoskeleton

Highly structured (proteins)
• Dynamic
• Cell shape, movement, division,
moving organelles

cytoskeleton - 3 types

Microtubules (biggest)
• Intermediate filaments
• Microfilaments (actin, smallest)

Extracellular Matrix

Support outside plasma membrane.
• Animals: collagen-rich, flexible.
• Plants: rigid cellulose cell wall.
• Functions: support, adhesion, communication.