How do I make my bullet prefab do damage to the enemy?

Create a tag for your enemy, let's say "Enemy", and make sure you assign this tag to the Enemy. Then in your bullet script add this method:

 private void OnCollisionEnter(Collision collision)
     {
         if (collision.transform.tag == "Enemy")
         {
             // do damage here, for example:
             collision.gameObject.GetComponent<Enemy>().TakeDamage(5);
         }
     }

And in your Enemy Script, create the function:

 public void TakeDamage(int damageAmount)
         {
             health -= damageAmount;
             // other stuff you want to happen when enemy takes damage
         }

But in order to detect the collisions better, both of these objects should probably have a Rigidbody attached to them (The Enemy and the Bullet).

The answer from @pete94za will work and is the most direct answer to OP's question. But for future reference, it can help to implement an interface for anything that can take damage. In most games, there are multiple things that can take damage, not just a single "enemy" class. If you're searching for a class like Enemy in GetComponent, then the only way to have a bullet be able to damage multiple kinds of things is to do different checks for every kind of potential object, eg. GetComponent<Crate>(), GetComponent<Window>(), etc. (it can be a tad simpler using inheritance, but you get the point and interfaces are still better)

Instead, such interface could look like:

  public interface IDamageable 
 {
      void TakeDamage(float damage);
 }

Then, any class that should be damageable by the bullet (or anything else that does damage) can implement IDamageable, and have a method like TakeDamage(float damage). Each class like Enemy, Window, Crate, etc. can write that method differently, but implementing that interface guarantees that the method exists. It could look like:

 public class Enemy : MonoBehaviour, IDamageable
  {
      float hp = 10;
      void IDamageable.TakeDamage(float damage)
      {
          hp -= damage;
          Debug.Log(gameObject.name + " took " + damage + " damage.");
          if(hp <= 0)
          {
               Destroy(gameObject);
          }
      }
  }

Then in your bullet, you do:

  IDamageable damageable = collision.gameObject.GetComponent();
  
  if(damageable != null)
  {
      damageable.TakeDamage(5);
  }

That will work on any class that implements IDamageable, regardless of its actual type.

If the enemy is in a gameobject then do: gameObject.GetComponentInParent(typeof(Enemy)) as Enemy; or you can use my script here: using System.Collections; using System.Collections.Generic; using UnityEngine;

public class Bullet : MonoBehaviour {

 public float speed = 20f;
 public int damage = 10;
 public Rigidbody2D rb;
 public GameObject Enemy;
 public GameObject impactEffect;

 // Use this for initialization
 void Start () {
     rb.velocity = transform.right * speed;
 }

 void OnTriggerEnter2D (Collider2D hitInfo)
 {
     if(hitInfo.CompareTag("Enemy")){
     Enemy enemy = hitInfo.transform.gameObject.GetComponentInParent(typeof(Enemy)) as Enemy;
     if (enemy != null)
     {
         enemy.TakeDamage(damage);
     }

     Instantiate(impactEffect, transform.position, transform.rotation);

     Destroy(gameObject);
     }
 }

}