cell bio exam 1

significance of cell bio in the 1950s

it became a discipline/class and a premiere discipline of study

1 major challenge with cell bio

their small size

what is the size of a cell

less than 100 micrometers (mm) (or .1 millimeter (mm))

whats bigger micrometer or nanometer

micrometer > nanometer 1 mm=1000 nm

what is the size of a double helix

2 nm

why aren’t cells larger if it makes it easier to study?

b/c of surface area vs. volume

some basic fundamental actions depends on diffusion. The larger the cell is the more surface area you have, but volume is much less

You want a small surface area to volume ratio due to diffusion

definition of a cell

smallest structural and functional unit of ay living organism

What happened in the mid 1600s

Robert Hooke tried to understand and laid the foundation for cell biology.

He also liked microscopes and used polished glass as a microscope.

3 basic tenants of cell biology early-mid 1800s

1. all organisms consist of 1 or more cells

2. cell is basic unit of structure

3. all cells arise from pre-existing (no such things as spontaneous cells)

when were all the basics of cell bio formulated

mid 1800s

true or false, cells could have many elements within cells

true

99% of cell mass is what 6 elements

carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur

whats the most prevalent element in the cell

oxygen

most abundant substance?

water

water makes up what % of mass in all living organisms

70

all protein chemistry and transciptomic chemistry takes place where?

in an aqueous medium surrounded by water

Why do we use H20 Instead of ethanol, DMSO, or Acetone

1. Most don’t have the same characteristics as water (water is polar and can interact with itself and other molecules, 104 degree bond angle

2. 100 degree (212 degree F) boiling point —> acetone cant do that

3. high surface tension

Is Na+ hydrophilic or hydrophobic and why

hydrophilic bc it can easily interact with water (and water can arrange itself structurally easily around a sodium ion and hydrate the compound)

is methyl hydrophobic or hydrophilic

hydrophobic bc water cannot structure around methyl groups and stays away from it… theres no good lattice network

all organic molecules are what based

carbon

18% of body =

carbon

only what % of carbon is found on earth’s surface

18 % (limited in world, but concentrated in humans).

why is carbon unique

1. small atom = valuable

2. 4 covalent bonds

   1. from up to 4 other bonds w/ diff materials or itself

   2. can make as big as you can get them

closest element to carbon

silica (3 bonds)

basic pairings/ groupings that are very reactive

CH3, OH (hydroxyl), COOH (Carboxyl), NH2 (amino)

small organic molecules

less than 1000 dolants, approx 1000 diff types, found primarily in cytoplasm

4 primary families that can build macromolecules

simple sugars (monosaccharides), fatty acids, amino acids, nucleotides

monosaccharide structure

(CH2O)n (n=3-7)

made of hydroxyl groups, aldehyde or ketone groups

can be linear of cyclic

at least 30 others like glucose

monosaccharides functions

1. can be oxidized to release energy (energy source) [primary function]

2. energy storage

3. can be combined to make cellulose

4. can make functional proteins like glycoproteins and glycolipids

Monosaccharide function #1: can be oxidized to release energy (energy source)

1. glucose = 686 kilocalorie per mole

2. can use monosaccharides to combine in linear array like links of chain to make bigger saccharides

   1. di→ lactose

   2. tri

   3. poly

3. oligosaccharides

4. can be linked or branched

oligosaccharides

group of monosaccharides b/t minimum of 3 & up to 15 or 20 monosaccharides together

oligosaccharide + lipid=

glycolipid

oligosaccharide + protein =

glycoprotein

fatty acids structure

primarily carboxyl group with fatty acid chain w/ methyl group on the terminal end

Omega 6

double bond at carbons 6 and 7

fatty acid functions

1. can be completely oxidized as energy source

2. beta oxidation cuts chains into 2 carbon units and oxidizes them and uses fat source as energu source

3. link fatty acids to glycerol (sugar alcohol)

amino acid function

1. energy (can be fully oxidized to CO2)

2. makes proteins by linking together each amino acid group

nucleotides are made up of

nitrogen-containing ring, 5 carbon sugars, and phosphate(s) attached to sugar

pyrimidine has 2 types

ribose and deoxyribose

(Uracil, Thymine, Cytosine)

difference between ribose and deoxyribose

ribose has OH at carbons 2 and 3 deoxyribose only has OH at carbon 3

purine and their 2 types

nucleotide and nucleoside

(A and G)

nucleoside vs. Nucleotide

nucleotide has a phosphate attached to it, nucleoside doesn’t

nucleotide function

1. can be oxidized completely to form energy

2. can add nucleotide to make nucleic acids (can be deoxyribose nucleic acids [DNA])

3. can make cyclic AMP

cyclic AMP

powerful signaling/ Communicating cell chemically; cell signal

2 macromolecule families

proteins and nucleotides

what do covalent bonds tie

small molecules

Ionic Bonds

1. b/t fully or partially charged groups

2. NaCl (weak attraction in water means its strong in absence of water)

Hydrogen Bonds

Shares hydrogen atoms b/t 2 electronegative bonds

ex; H2O

Van der waals

1. weakest

2. transient in appearance (very short time)

3. shows up in certain instances

   1. close proximity

   2. can occur and disappear again and again

hydrophobic

repulsion of water molecules & organize those molecules together

what makes up more in cell DNA or RNA?

RNA (about 3-5%)

DNA (about 1%)

linear arrays of nucleotides can make what?

unbranched polymers

where can RNA and DNA be found

RNA anywhere in cell or shipped out of cell

DNA found in nucleus or mitochondrial DNA in mitchondria but that’s it

chromatin

1. Where DNA exists

2. and also the Series of proteins that help wrap and protect a particular material (DNA in this case)

on DNA every helix turn is how many base pairs

10

for DNA what do you need

histones

histones

1. + Closed proteins that interact together to form bases of structure to stbilize DNA

2. makes up chromatin

3. 3 diff types of globular proteins

3 types of globular proteins

1. H2A/H2B

2. H3

3. H4(you would have 2 of each)

8 histones make what

nucleosome

H1 globular protein

non nucleosomal and wraps around DNA that’s found between nucleosomes (think of hot dog in a bun)

when DNA wraps itself around entire nucleosome, how many base pairs

about 146

why does DNA need to be wrapped around the nucleosome

to be protected from nucleases that will chew apart naked DNA

most cellular processes require what for action?

proteins

½ dry matter of cell is what?

proteins

why are proteins stable yet flexible?

must be stable for structural stability and flexible enough to be able to move and do work.

2 types of proteins

globular or fibrous

primary protein structure

held by covalent bonds, no weak bonds

secondary structure

protein becomes more fibrous or globular

1. beta sheets form

2. weak hydrogen bonds can form b/t H above and below each other

3. Alpha helix forms

beta sheets vs alpha helix

beta→ hydrophobic and caused by various R groups (looks like ribbon that doesn’t overlap)

Alpha→ hydrophobic (more squiggly and overlapping)

tertiary structure

1. peptide bonds help secure structure

2. hydrogen bending secures structure

3. R groups interact w/ each other; additional weak bonding secures tertiary structure

4. Can have multiple disulfide bonds

quaternary structure

1. 2 or more peptide interacting together

2. monomers; heterodimer (diff) and homodimer (same)

3. polymers

polymers

can keep building and growing withoug needing energy source (costs energetically nothing to make0

Domain

proteins get larger by forming into domains.

subset under monomers

internal vs external proteins

internal hydrophobic external hydrophilic and bonds with other structures

ligand

any structure that will bind to protein (you still need to define what the ligand is

binding site

where ligand will bind to protein

(about 6 amino acids or less)

(most of the time there’s a specific site for ligands)

cofactor

can bind to enhance abilities to work better (nonpeptide)

explain + and - charges and hydrophobic and hydrophlic with amino acid at binding site and ligand

if amino acid at binding site is hydrophobic then ligand will have some sort of hydrophobicity as well and it’ll match up well

OR

+ amino acid charge and - ligand charge helps electrostatic interaction

enzyme

lower activation energy required for substrate to be converted to some product

how does enzyme work so efficiently?

1. holds substrate in appropriate orientation

2. binding requires energy; some of that energy reduces overall energy required to break it

think of Dr. Watts example with marker

typical enzyme can bind to substrate ligand about how many times per second

1000x

when looking at chart of substrate concentration how do you know if it’s saturated

line stops increasing

regulatory binding site

binds to regulatory ligand and can alter how substrate binds to active site for better or worse

if active site bind is better or worse after regulatory binding site what happens

better, positive moderator and graph shifts left

worse, negative moderator, shifts right

michaelis constant

km = [s] at1/2 Vmax

high affinity vs low affinity

high= quick and efficient

low= takes every now and then

high Km and low km in terms of affinity

low km = high affinity

high km= low affinity

vmax is what

fastest the enzyme will go

how to regulate enzymes

1. alter [s] (takes mins or seconds)

2. alter km (takes seconds, VERY fast)

3. 3. alter E (VERY slow)

energy for cells comes from where

the sun

1. derived from electromagnetic radiation

2. done by oxidation meaning energy will be released

bioenergetics have the same what for generating energy

procedure

1. worms and humans have same procedure for generating energy (mostly)

2. slight deviation depending on environment