BIOL 161 - Exam 2 Study Guide

amino acids

protein monomers

amino acids include:

• central carbon

• amine group (NH2) (acts as base in water)

• carboxyl group (COOH) (acts as acid in water)

• R-group (variable region)

Different R-group categories

A. Charged

B. Polar

C. Nonpolar (Hydrophobic)

Disulfide bridge

when two sulfur atoms bond from two sulfoxyl groups (SH —> cysteine)

peptide bonds

covalent bonds that connect amino acids together via dehydration reactions (N-C-C)

hydrolysis

breaking covalent bonds by adding water

Primary protein structure

sequence of amino acids

Secondary protein structure

hydrogen bonds between non-variable parts of non-adjacent amino acids

1. alpha helix - H-bonding between elements on the same strand

2. B pleated sheet - H-bonding between adjacent strands

Tertiary protein structure

interactions between R-groups on one polypeptide

Quaternary protein structure

interactions between R-groups on different polypeptides

enzymes

proteins that catalyze reactions

induced fit

slight change in the enzyme or protein structure when a substrate binds

Orientation (enzymes)

enzymes can orient substrates next to each other so they can interact

Strain (enzymes)

enzymes can put strain on substrate to break bonds

Chemical change (enzymes)

enzymes can induce a chemical change in substrate to form products

monosaccharides

carbohydrate monomers

glycosidic linkage

covalent bonds that connect monosaccharides together via dehydration reactions

nucleotides

nucleic acid monomers

nucleotides are made up of 3 components:

1. Phosphate group

2. Pentose sugar

3. Nitrogenous base (A, T, C, G, U)

pentose - ribose

found in RNA nucleotides (A, U, C, G)

pentose - deoxyribose

found in DNA nucleotides and missing oxygen at C2 position (A, T, C, G)

phosphodiester bond

covalent bonds that connect nucleotides together via dehydration reactions

______ end has a free _______ on the ___ carbon of the sugar

5’, phosphate group, 5’

______ end has a free _______ on the ____ carbon of the sugar

3’, hydroxyl group (OH), 3’

lipids are made up of:

hydrophilic heads and hydrophobic (fatty acid) tails

fats

long fatty acid tail (mainly hydrocarbons)

amphipathic

molecule containing both hydrophilic AND hydrophobic components

steroids

4 fused hydrocarbon rings

triglyceride

glycerol + 3 fatty acids

phospholipid

glycerol + 2 fatty acids + phosphate group

ester linkages

covalent bonds that connect glycerol and fatty acids together via dehydration reactions

Central Dogma

DNA —> RNA —> Protein

Transcription

DNA —> pre-mRNA (nucleus)

Any process that creates new nucleic acid strands must follow _____ and _________.

structure (antiparallel), base pairing rules

polymerase

enzymes that synthesize new nucleic acid strands. Can only add to 3’ end

template strand

where we get info for new strand

Nucleotide triphosphate (NTP)

nucleotide that has 3 phosphate groups. Cleaves off two to bind to nucleotide strand

In transcription, DNA is read in the ________ direction, and RNA is built in the ______ direction

3’—> 5’, 5’ —> 3’

genome

all DNA of an organism

chromosome

long DNA molecule coiled around around proteins and compacted

gene

segment of DNA

mRNA

serve function of coding for a protein

non-coding RNA

serve RNA function (no proteins)

Promoter

DNA where RNA polymerase initially binds (NOT copied into RNA)

Initiation site

first DNA nucleotide transcribed into RNA

Transcribed region

DNA region with nucleotides that are copied into RNA

Termination site

tells RNA polymerase to stop (NOT copied into RNA)

Helicase

breaks H-bonds between DNA strands to separate non-template and template strands (in transcription, helicase is apart of RNA polymerase)

5’ cap

directs the ribosome to mRNA to initiate translation

Poly-A tail

added to 3’ end during RNA processing (lots of adenine)

Exons, during RNA processing, are ______

joined together

What do RNA processing modifications do?

1. Stabilizes mRNA

2. Helps with transporting mRNA to cytoplasm

3. 5’ cap directs the ribosome to mRNA

RNA splicing

process of cutting out introns

spliceosomes

protein complexes made up of ribosomes (coded by snRNA and snRNPs) that cut out introns

Ligation

process of putting exons back together by spliceosomes

5’UTR and 3’UTR

transcribed regions on mRNA but doesn’t get translated (untranslated regions)

codon

3 mRNA nucleotides that code for an amino acid

start codon

AUG

ribosome has ___ reading frames (one for each letter) to _______

3, find AUG and then start coding according to that reading frame

Genetic code - Universality

all living organisms use DNA the same way

Genetic code - Punctuation

start and stop (codons) that aren’t translated

Genetic code - Redundancy

multiple codons code for singular amino acid

tRNA

carries an amino acid at 3’ end (longer) and binds to mRNA and the other end with anti-codons (base-pairing)

rRNA

made up of a large and small subunit that attach to mRNA and has three sites for translation

Translation - Initiation

• small ribosomal subunit attaches to 5’ cap of mRNA

• small subunit scans for AUG

• once tRNA and mRNA base-pair, large subunit binds and sets reading frame

Translation - Elongation

• peptide bonds form between amino acids on tRNA (peptidyl transferase)

• when A site is left open after tRNAs shift, they accept another tRNA, keeps binding until stop codon

Translation - Termination

• stop codons don’t encode amino acids

• release factor binds and rRNA subunits separate

Post-translational modification to polypeptide formed after translation

• Phosphorylation - add phosphate groups

• Glycosylation - add sugars

• Proteolysis - cleaves polypeptide to form different shapes

Each carbon’s significance on pentose sugar in nucleotide

C₁ - nitrogenous base attached

C₂ - RNA vs. DNA (OH vs. H)

C₃ - where next nucleotide binds to

C₄ - close ring

C₅ - phosphate group