Learn: biochem notes

What are the three life forms?

Bacteria, Eukarya, Archaea

E. coli, salmonella, bacillus, escherichia is an example of what life form?

an example of a bacteria, prokaryotic

homo, zea, saccharomyces, animals, plants, fungi are an example of what life form?

an example of eukaryotes with a nucleus

methanococcus, archaeoglobus, halobacterium, thermophiles are an example of what life form?

an example of archaea known for living in EXTREME environments

Prokaryotic cells: unicellular

-DNA

-Cell membrane

-Cytoplasm

-Ribosomes

-Cell Wall

Eukaryotic cells: multicellular

-Nucleus

-DNA

-Cell membrane

-Cytoplasm

-Ribosomes

-Mitochondria

-ER

-Golgi A

-MEMBRANE BOUND ORGANELLES

-some have a cell wall

Prokaryotes and Eukaryotes both have?

DNA, ribosomes, cytoplasm, plasma membrane

Bacteria and Archaea are?

Prokaryotic

Eukarya are?

Eukaryotic

What are the classes of biological monomers? ANML

Amino acids, nucleotides, monosaccharides, lipids

what is the biological POLYMER of amino acid?

polypeptides

what is the biological POLYMER of nucleotides?

nucleic acids

what is the biological POLYMER monosaccharides?

polysaccharides

what is the biological POLYMER lipids?

lipids form aggregates therefore have no true polymer

Monosaccharides or sugars have a ratio of what?

they have a 1:1 ratio of carbon to oxygen

ex: C6H12O6

-they can also have deviations such as nitrogen (rare)

ex: C6H13NO5

A nucleoTIDE is made of?

ribose + phosphate + nitrogenous base

A nucleoSIDE is made of?

ribose + nitrogenous base

Lipids structure consists of?

-they have a significant hydrophobic (nonpolar) region (chain)

ex: palmitate or cholesterol

How do you identify a lipid in terms of its ratio?

Lipids have a HIGH ratio of Carbon/Hydrogen : oxygen, nitrogen, phosphorus

ex: C16 H31 O2

ex: C27 H46 O

Monomers are covalently linked to form?

macromolecules

Monomers form what when bonded together?

they form polymers, and once they have been linked it is called a residue

Polypeptide is a polymer of amino acids that is?

a chain of amino acids connected via peptides bonds

A protein is?

a functional unit consisting of one or more polypeptides that is folded into a specific 3d structure

what does endothelin do, and how many residues does it have?

it increases vasoconstriction, and is 21 residues long

What kind of bond do polysaccharides use?

they use glycosidic bonds

glucose can form starch

glucose can form cellulose

Nucleic acids are connected via?

phosphodiester bonds

Deoxyribose has what on the 2'

2' H

Ribose has what on the 2'

2' OH

Roles of proteins?

carry out metabolic reactions, support cellular structures, and can sometimes store energy

Roles of nucleic acids?

encode info, sometimes carry out metabolic reactions, sometimes supports cellular structure

Roles of polysaccharides?

sometimes encode info, store energy, support cellular structures

When Delta G <0, the reaction is

its NEGATIVE, spontaneous, favorable and EXERgonic

work is being done

When Delta G >0, the reaction is

its POSITIVE, nonspontaneous, unfavorable ENDERgonic

loss of potential energy

catabolism is what?

the process of BREAKING down large macromolecules and involves oxidation which is favorable

Anabolism is what?

is the process of building complex molecules at the EXPENSE of energy

What happens when an unfavorable rxn is coupled with a favorable one?

this can make the overall process spontaneous

What is Pi?

inorganic phosphate

ex:

PO4-3

HPO4-2

H2PO4-

the oxidation of oxygen is considered what?

this is favorable, and can drive the synthesis of monomers and macromolecules

the less H's present mean?

the molecule is the least reduced, thus the most oxidized

when something is oxidized what happens?

if carbons gain oxygen but are losing hydrogen, or if they go from a single to a double bond

when something is reduced what happens

if carbons lose an oxygen and are gaining a hydrogen, or if they go from a single to double bond

how to calculate the oxidation number?

(#bonds to en EN element)-(#bonds to less EN element like hydrogen)-(#lone pairs of electrons)

when a nonpolar molecule is placed in water it will?

get constrained by a layer or water molecules.

hydrophobic effect is what?

where a nonpolar regions cluster together to maximize the entropy of surrounding water molecules

relative strength of biological molecules: strongest to least

covalent bonds --> ionic interactions --> hydrogen bonds --> van der waals

the melting point is determined by?

the strongest intermolecular forces

KW is what at 25 degrees Celsius

1x10^-14

Keq formula?

[products]/[reactants]

pOH=

-log[OH-]

pH=

-log[H+]

pH+pOH=

14 always

To find concentration of [H+]

10^-pH

To find concentration of [OH-]

10^-pOH

Ka=

[H+][A-]/[HA]

pka is =

pH when [HA]=[A-]

The larger the Ka, the _____________________ the acid.

stronger

The smaller the pKa, the ____ the acid

stronger

What is the Henderson-Hasselbalch ratio we can use?

[A-]/[HA]=10^(pH-pKa)

When pH < pKa, what does that tell us?

that [HA] dominates

When pH > pKa, what does that tell us?

that [A-] dominates

Kidney and lung function maintain the blood pH at?

7.4

What happens to blood CO2 levels during hyperventilation?

Hyperventilation causes you to breathe out more CO₂, so blood CO₂ decreases.

What happens to the bicarbonate equilibrium when CO₂ is removed from the blood?

H+ +HCO3− ⇌ H2CO3 ⇌H2O+CO2

The equilibrium shifts right to replace the lost CO₂.

Why does hyperventilation increase blood pH?

CO₂ decreases → equilibrium shifts right → H⁺ is consumed → [H+][H^+] decreases → pH increases.

Does hyperventilation make the blood more acidic or more basic?

More basic because CO₂ and H⁺ decrease and pH increases.

What happens to blood CO₂ during hypoventilation?

You don't breathe out enough CO₂, so blood CO₂ increases.

What happens to the bicarbonate equilibrium when CO₂ builds up?

The equilibrium shifts left to consume some of the excess CO₂.

Why does hypoventilation decrease blood pH?

CO₂ increases → equilibrium shifts left → H⁺ is produced → [H+][H^+] increases → pH decreases.

Does hypoventilation make blood more acidic or more basic?

More acidic because CO₂ and H⁺ increase and pH decreases.

Le Châtelier rule, if something is removed the equilibrium shifts?

TOWARD IT

Le Châtelier rule, if something is added the equilibrium shifts?

AWAY FROM IT

Purines in DNA are?

Adenine (A) and Guanine (G)

Purines are?

bicyclic

The pyrimidines in DNA and RNA are

DNA: Thymine (T) and Cytosine

RNA: (C) Uracil (U)

adenine + ribose =

Adenosine (nucleoside)

adenine + deoxyribose =

deoxyadenosine

guanine and ribose =

guanosine (nucleoside)

cytosine + ribose =

cytidine

uracil + ribose =

uridine

Thymine + ribose =

thymidine

Chargaff's Rule, in DOUBLE stranded DNA

%A=%T and %G=%C

DNA has a double helix structure, so if it has 100 nucleotide pairs and 25 are adenine how many of them are guanine?

(100 x 2) = 200 total

200 - (25 x 2) = 150 G and C left

150 / 2 = 75, therefore 75 Guanine

What is the structure of DNA?

dna strands are antiparallel, which results in the dna being right handed

what is the size of dna?

20 Å wide, and 34 Å tall

Major and Minor grooves of dna are shown by?

distance between backbones

How is DNA separated in vitro?

DNA can be denatured by heating it up. The complementary strands can then be rennealed, and come back into a double helix when cooled

How does the G-C content in DNA affect the melting temp?

the melting temp (Tm) of DNA can is sequence and length dependent. However, G-C base pairs contribute to base stacking and hydrogen bonding more A-T pairs, where the higher % of G-C pairs does have a higher melting point

Central Dogma

DNA-transcription-RNA-translation-protein

How do errors in genes lead to diseases such as sickle cell anemia?

Sickle cell anemia is caused by an gene error where an A pair turns into a T, a mutation in the DNA that alters the amino acid sequence

Which amino-acid enantiomer is normally used in proteins?

L-amino acids. Proteins use L-amino acids rather than D-amino acids.

Where are hydrophobic amino-acid residues usually found in a soluble protein?

Mostly in the interior of the protein, away from water.

Where are polar and charged amino-acid residues usually found in a soluble protein?

Mostly on the surface, where they can interact with water.

What happens to an ionizable group when pH < pKa?

The protonated form dominates; it tends to keep H⁺.

What happens to an ionizable group when pH > pKa?

The deprotonated form dominates; it tends to lose H⁺.

How are amino acids linked together?

By peptide bonds, with H₂O lost when the bond forms.

In what direction are polypeptides synthesized?

N-terminus→C-terminus

What is the N-terminus of a polypeptide?

The end containing the free amino group.

What is the C-terminus of a polypeptide?

The end containing the free carboxyl group.

lose H+

decreased pKa

keep H+

increases pKa